CA2989326A1 - Methods of diagnosing and treating autism - Google Patents
Methods of diagnosing and treating autismInfo
- Publication number
- CA2989326A1 CA2989326A1 CA2989326A CA2989326A CA2989326A1 CA 2989326 A1 CA2989326 A1 CA 2989326A1 CA 2989326 A CA2989326 A CA 2989326A CA 2989326 A CA2989326 A CA 2989326A CA 2989326 A1 CA2989326 A1 CA 2989326A1
- Authority
- CA
- Canada
- Prior art keywords
- subject
- autism
- mglur network
- gene
- disorder
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Abandoned
Links
- 208000020706 Autistic disease Diseases 0.000 title claims abstract description 162
- 206010003805 Autism Diseases 0.000 title claims abstract description 154
- 238000000034 method Methods 0.000 title claims abstract description 114
- 108090000623 proteins and genes Proteins 0.000 claims abstract description 309
- 108010010914 Metabotropic glutamate receptors Proteins 0.000 claims abstract description 245
- 102000016193 Metabotropic glutamate receptors Human genes 0.000 claims abstract description 238
- GOWRRBABHQUJMX-MRVPVSSYSA-N Fasoracetam Chemical compound C1CCCCN1C(=O)[C@H]1CCC(=O)N1 GOWRRBABHQUJMX-MRVPVSSYSA-N 0.000 claims abstract description 55
- 229950010008 fasoracetam Drugs 0.000 claims abstract description 43
- 208000029560 autism spectrum disease Diseases 0.000 claims description 172
- 150000007523 nucleic acids Chemical class 0.000 claims description 81
- 102000039446 nucleic acids Human genes 0.000 claims description 75
- 108020004707 nucleic acids Proteins 0.000 claims description 75
- 230000004077 genetic alteration Effects 0.000 claims description 53
- 231100000118 genetic alteration Toxicity 0.000 claims description 53
- 208000006096 Attention Deficit Disorder with Hyperactivity Diseases 0.000 claims description 45
- 208000036864 Attention deficit/hyperactivity disease Diseases 0.000 claims description 45
- -1 MGC11082 Proteins 0.000 claims description 36
- 238000012217 deletion Methods 0.000 claims description 34
- 230000037430 deletion Effects 0.000 claims description 34
- 238000003745 diagnosis Methods 0.000 claims description 33
- 230000002068 genetic effect Effects 0.000 claims description 30
- 102100038357 Metabotropic glutamate receptor 5 Human genes 0.000 claims description 27
- 208000027691 Conduct disease Diseases 0.000 claims description 24
- 206010034912 Phobia Diseases 0.000 claims description 24
- 208000019899 phobic disease Diseases 0.000 claims description 24
- 239000012190 activator Substances 0.000 claims description 23
- 238000009396 hybridization Methods 0.000 claims description 23
- 208000019901 Anxiety disease Diseases 0.000 claims description 21
- 102100036834 Metabotropic glutamate receptor 1 Human genes 0.000 claims description 20
- 102100037636 Metabotropic glutamate receptor 8 Human genes 0.000 claims description 20
- 239000002773 nucleotide Substances 0.000 claims description 20
- 125000003729 nucleotide group Chemical group 0.000 claims description 20
- 102100025580 Calmodulin-1 Human genes 0.000 claims description 19
- 102100038352 Metabotropic glutamate receptor 3 Human genes 0.000 claims description 19
- 101001032845 Homo sapiens Metabotropic glutamate receptor 5 Proteins 0.000 claims description 18
- 102100038294 Metabotropic glutamate receptor 7 Human genes 0.000 claims description 18
- 108010038449 metabotropic glutamate receptor 7 Proteins 0.000 claims description 18
- 101001071437 Homo sapiens Metabotropic glutamate receptor 1 Proteins 0.000 claims description 17
- 101001027295 Homo sapiens Metabotropic glutamate receptor 8 Proteins 0.000 claims description 17
- 208000011580 syndromic disease Diseases 0.000 claims description 17
- 101001032848 Homo sapiens Metabotropic glutamate receptor 3 Proteins 0.000 claims description 16
- 102100038354 Metabotropic glutamate receptor 4 Human genes 0.000 claims description 15
- 102100038300 Metabotropic glutamate receptor 6 Human genes 0.000 claims description 15
- 108010038422 metabotropic glutamate receptor 4 Proteins 0.000 claims description 15
- 102100036837 Metabotropic glutamate receptor 2 Human genes 0.000 claims description 14
- 101710179353 Ran-specific GTPase-activating protein Proteins 0.000 claims description 14
- 206010071249 thalidomide embryopathy Diseases 0.000 claims description 14
- 102100039790 Ran-specific GTPase-activating protein Human genes 0.000 claims description 13
- 101710180752 Ran-specific GTPase-activating protein 1 Proteins 0.000 claims description 13
- 102100040973 26S proteasome non-ATPase regulatory subunit 1 Human genes 0.000 claims description 12
- 208000036395 Fetal valproate spectrum disease Diseases 0.000 claims description 12
- 206010066485 Foetal anticonvulsant syndrome Diseases 0.000 claims description 12
- 101000612655 Homo sapiens 26S proteasome non-ATPase regulatory subunit 1 Proteins 0.000 claims description 12
- 101001032837 Homo sapiens Metabotropic glutamate receptor 6 Proteins 0.000 claims description 12
- 101001116937 Homo sapiens Protocadherin alpha-4 Proteins 0.000 claims description 12
- 102100024261 Protocadherin alpha-4 Human genes 0.000 claims description 12
- 201000004291 fetal valproate syndrome Diseases 0.000 claims description 12
- 101001071429 Homo sapiens Metabotropic glutamate receptor 2 Proteins 0.000 claims description 11
- 208000024891 symptom Diseases 0.000 claims description 11
- 208000012202 Pervasive developmental disease Diseases 0.000 claims description 10
- YUBYMONBCDIKAB-DDWIOCJRSA-N (5r)-5-(piperidine-1-carbonyl)pyrrolidin-2-one;hydrate Chemical group O.C1CCCCN1C(=O)[C@H]1CCC(=O)N1 YUBYMONBCDIKAB-DDWIOCJRSA-N 0.000 claims description 9
- 238000004458 analytical method Methods 0.000 claims description 9
- 208000036640 Asperger disease Diseases 0.000 claims description 8
- 201000006062 Asperger syndrome Diseases 0.000 claims description 8
- 208000024825 childhood disintegrative disease Diseases 0.000 claims description 8
- 208000030251 communication disease Diseases 0.000 claims description 8
- 238000005516 engineering process Methods 0.000 claims description 8
- 102100022197 Glutamate receptor ionotropic, kainate 1 Human genes 0.000 claims description 7
- 101000900515 Homo sapiens Glutamate receptor ionotropic, kainate 1 Proteins 0.000 claims description 7
- 101000735360 Homo sapiens Poly(rC)-binding protein 3 Proteins 0.000 claims description 7
- 101001012157 Homo sapiens Receptor tyrosine-protein kinase erbB-2 Proteins 0.000 claims description 7
- 102100034955 Poly(rC)-binding protein 3 Human genes 0.000 claims description 7
- 102100030086 Receptor tyrosine-protein kinase erbB-2 Human genes 0.000 claims description 7
- 238000002493 microarray Methods 0.000 claims description 7
- 238000012163 sequencing technique Methods 0.000 claims description 7
- HONKEGXLWUDTCF-YFKPBYRVSA-N (2s)-2-amino-2-methyl-4-phosphonobutanoic acid Chemical compound OC(=O)[C@](N)(C)CCP(O)(O)=O HONKEGXLWUDTCF-YFKPBYRVSA-N 0.000 claims description 6
- 102100030390 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 Human genes 0.000 claims description 6
- 102100040962 26S proteasome non-ATPase regulatory subunit 13 Human genes 0.000 claims description 6
- 102100022644 26S proteasome regulatory subunit 4 Human genes 0.000 claims description 6
- 102100036512 7-dehydrocholesterol reductase Human genes 0.000 claims description 6
- 102100022910 ADP-ribosylation factor-like protein 15 Human genes 0.000 claims description 6
- 102000017904 ADRA2C Human genes 0.000 claims description 6
- 102100023989 Actin-related protein 2 Human genes 0.000 claims description 6
- 108090000963 Actin-related protein 2 Proteins 0.000 claims description 6
- 102100022734 Acyl carrier protein, mitochondrial Human genes 0.000 claims description 6
- 102100039677 Adenylate cyclase type 1 Human genes 0.000 claims description 6
- 102100034033 Alpha-adducin Human genes 0.000 claims description 6
- 102100033307 Ankyrin repeat domain-containing protein 37 Human genes 0.000 claims description 6
- 102100024044 Aprataxin Human genes 0.000 claims description 6
- 102100036781 Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2 Human genes 0.000 claims description 6
- 102000017916 BDKRB1 Human genes 0.000 claims description 6
- 108060003359 BDKRB1 Proteins 0.000 claims description 6
- 102000017915 BDKRB2 Human genes 0.000 claims description 6
- 102100021738 Beta-adrenergic receptor kinase 1 Human genes 0.000 claims description 6
- 102000014819 CACNA1B Human genes 0.000 claims description 6
- 102000017925 CHRM3 Human genes 0.000 claims description 6
- 102100024317 Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C Human genes 0.000 claims description 6
- 102100025232 Calcium/calmodulin-dependent protein kinase type II subunit beta Human genes 0.000 claims description 6
- 102100021849 Calretinin Human genes 0.000 claims description 6
- 102100036375 Carbonic anhydrase-related protein Human genes 0.000 claims description 6
- 102100023473 Cell growth-regulating nucleolar protein Human genes 0.000 claims description 6
- 102100022589 Coatomer subunit beta' Human genes 0.000 claims description 6
- 102100036943 Cytoplasmic protein NCK1 Human genes 0.000 claims description 6
- 102100027700 DNA-directed RNA polymerase I subunit RPA2 Human genes 0.000 claims description 6
- 102100035784 Decorin Human genes 0.000 claims description 6
- 102000003668 Destrin Human genes 0.000 claims description 6
- 108090000082 Destrin Proteins 0.000 claims description 6
- 108010044266 Dopamine Plasma Membrane Transport Proteins Proteins 0.000 claims description 6
- 102100031853 Endoplasmic reticulum resident protein 44 Human genes 0.000 claims description 6
- 102100021822 Enoyl-CoA hydratase, mitochondrial Human genes 0.000 claims description 6
- 101710180035 Enoyl-CoA hydratase, mitochondrial Proteins 0.000 claims description 6
- 102100025413 Formyltetrahydrofolate synthetase Human genes 0.000 claims description 6
- 102100022277 Fructose-bisphosphate aldolase A Human genes 0.000 claims description 6
- 102100035233 Furin Human genes 0.000 claims description 6
- 101150111025 Furin gene Proteins 0.000 claims description 6
- 108700031843 GRB7 Adaptor Proteins 0.000 claims description 6
- 101150052409 GRB7 gene Proteins 0.000 claims description 6
- 102100028953 Gelsolin Human genes 0.000 claims description 6
- 108010086246 Glucagon-Like Peptide-1 Receptor Proteins 0.000 claims description 6
- 108010024044 Glucagon-Like Peptide-2 Receptor Proteins 0.000 claims description 6
- 102100032882 Glucagon-like peptide 1 receptor Human genes 0.000 claims description 6
- 102100032879 Glucagon-like peptide 2 receptor Human genes 0.000 claims description 6
- 102100033067 Growth factor receptor-bound protein 2 Human genes 0.000 claims description 6
- 102100033107 Growth factor receptor-bound protein 7 Human genes 0.000 claims description 6
- 102100034155 Guanine nucleotide-binding protein G(i) subunit alpha-1 Human genes 0.000 claims description 6
- 102100034154 Guanine nucleotide-binding protein G(i) subunit alpha-2 Human genes 0.000 claims description 6
- 102100034264 Guanine nucleotide-binding protein G(i) subunit alpha-3 Human genes 0.000 claims description 6
- 102100025334 Guanine nucleotide-binding protein G(q) subunit alpha Human genes 0.000 claims description 6
- 102100023954 Guanine nucleotide-binding protein subunit alpha-15 Human genes 0.000 claims description 6
- 102100035669 Heterogeneous nuclear ribonucleoprotein A3 Human genes 0.000 claims description 6
- 102100023607 Homer protein homolog 1 Human genes 0.000 claims description 6
- 102100023603 Homer protein homolog 3 Human genes 0.000 claims description 6
- 101000583063 Homo sapiens 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1 Proteins 0.000 claims description 6
- 101000612536 Homo sapiens 26S proteasome non-ATPase regulatory subunit 13 Proteins 0.000 claims description 6
- 101000619137 Homo sapiens 26S proteasome regulatory subunit 4 Proteins 0.000 claims description 6
- 101000928720 Homo sapiens 7-dehydrocholesterol reductase Proteins 0.000 claims description 6
- 101000974504 Homo sapiens ADP-ribosylation factor-like protein 15 Proteins 0.000 claims description 6
- 101000837584 Homo sapiens Acetyl-CoA acetyltransferase, cytosolic Proteins 0.000 claims description 6
- 101000598552 Homo sapiens Acetyl-CoA acetyltransferase, mitochondrial Proteins 0.000 claims description 6
- 101000678845 Homo sapiens Acyl carrier protein, mitochondrial Proteins 0.000 claims description 6
- 101000959343 Homo sapiens Adenylate cyclase type 1 Proteins 0.000 claims description 6
- 101000720032 Homo sapiens Alpha-2C adrenergic receptor Proteins 0.000 claims description 6
- 101000799076 Homo sapiens Alpha-adducin Proteins 0.000 claims description 6
- 101000732539 Homo sapiens Ankyrin repeat domain-containing protein 37 Proteins 0.000 claims description 6
- 101000757586 Homo sapiens Aprataxin Proteins 0.000 claims description 6
- 101000928215 Homo sapiens Arf-GAP with GTPase, ANK repeat and PH domain-containing protein 2 Proteins 0.000 claims description 6
- 101000695703 Homo sapiens B2 bradykinin receptor Proteins 0.000 claims description 6
- 101000751445 Homo sapiens Beta-adrenergic receptor kinase 1 Proteins 0.000 claims description 6
- 101001117094 Homo sapiens Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C Proteins 0.000 claims description 6
- 101001077352 Homo sapiens Calcium/calmodulin-dependent protein kinase type II subunit beta Proteins 0.000 claims description 6
- 101000898072 Homo sapiens Calretinin Proteins 0.000 claims description 6
- 101000710899 Homo sapiens Cannabinoid receptor 1 Proteins 0.000 claims description 6
- 101000714515 Homo sapiens Carbonic anhydrase-related protein Proteins 0.000 claims description 6
- 101000622133 Homo sapiens Cell growth-regulating nucleolar protein Proteins 0.000 claims description 6
- 101000899916 Homo sapiens Coatomer subunit beta' Proteins 0.000 claims description 6
- 101001024707 Homo sapiens Cytoplasmic protein NCK1 Proteins 0.000 claims description 6
- 101000650600 Homo sapiens DNA-directed RNA polymerase I subunit RPA2 Proteins 0.000 claims description 6
- 101001000206 Homo sapiens Decorin Proteins 0.000 claims description 6
- 101000670093 Homo sapiens Dolichyl-diphosphooligosaccharide-protein glycosyltransferase subunit 2 Proteins 0.000 claims description 6
- 101000755879 Homo sapiens Fructose-bisphosphate aldolase A Proteins 0.000 claims description 6
- 101001059150 Homo sapiens Gelsolin Proteins 0.000 claims description 6
- 101000871017 Homo sapiens Growth factor receptor-bound protein 2 Proteins 0.000 claims description 6
- 101001070526 Homo sapiens Guanine nucleotide-binding protein G(i) subunit alpha-1 Proteins 0.000 claims description 6
- 101001070508 Homo sapiens Guanine nucleotide-binding protein G(i) subunit alpha-2 Proteins 0.000 claims description 6
- 101000997034 Homo sapiens Guanine nucleotide-binding protein G(i) subunit alpha-3 Proteins 0.000 claims description 6
- 101000857888 Homo sapiens Guanine nucleotide-binding protein G(q) subunit alpha Proteins 0.000 claims description 6
- 101000904080 Homo sapiens Guanine nucleotide-binding protein subunit alpha-15 Proteins 0.000 claims description 6
- 101000854041 Homo sapiens Heterogeneous nuclear ribonucleoprotein A3 Proteins 0.000 claims description 6
- 101001048469 Homo sapiens Homer protein homolog 1 Proteins 0.000 claims description 6
- 101001048461 Homo sapiens Homer protein homolog 3 Proteins 0.000 claims description 6
- 101001076642 Homo sapiens Inosine-5'-monophosphate dehydrogenase 2 Proteins 0.000 claims description 6
- 101000975428 Homo sapiens Inositol 1,4,5-trisphosphate receptor type 1 Proteins 0.000 claims description 6
- 101001015037 Homo sapiens Integrin beta-7 Proteins 0.000 claims description 6
- 101001128393 Homo sapiens Interferon-induced GTP-binding protein Mx1 Proteins 0.000 claims description 6
- 101000967589 Homo sapiens LRP2-binding protein Proteins 0.000 claims description 6
- 101000972488 Homo sapiens Laminin subunit alpha-4 Proteins 0.000 claims description 6
- 101000611240 Homo sapiens Low molecular weight phosphotyrosine protein phosphatase Proteins 0.000 claims description 6
- 101001116368 Homo sapiens Melatonin receptor type 1A Proteins 0.000 claims description 6
- 101000616438 Homo sapiens Microtubule-associated protein 4 Proteins 0.000 claims description 6
- 101001052493 Homo sapiens Mitogen-activated protein kinase 1 Proteins 0.000 claims description 6
- 101000928919 Homo sapiens Muscarinic acetylcholine receptor M3 Proteins 0.000 claims description 6
- 101000982000 Homo sapiens N-alpha-acetyltransferase 15, NatA auxiliary subunit Proteins 0.000 claims description 6
- 101000603245 Homo sapiens Neuropeptide Y receptor type 2 Proteins 0.000 claims description 6
- 101000604540 Homo sapiens PRKCA-binding protein Proteins 0.000 claims description 6
- 101001098517 Homo sapiens Paxillin Proteins 0.000 claims description 6
- 101000827313 Homo sapiens Peptidyl-prolyl cis-trans isomerase FKBP3 Proteins 0.000 claims description 6
- 101001131990 Homo sapiens Peroxidasin homolog Proteins 0.000 claims description 6
- 101001124867 Homo sapiens Peroxiredoxin-1 Proteins 0.000 claims description 6
- 101000605639 Homo sapiens Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform Proteins 0.000 claims description 6
- 101001045704 Homo sapiens Phosphoribosyl pyrophosphate synthase-associated protein 1 Proteins 0.000 claims description 6
- 101001097889 Homo sapiens Platelet-activating factor acetylhydrolase Proteins 0.000 claims description 6
- 101000735354 Homo sapiens Poly(rC)-binding protein 1 Proteins 0.000 claims description 6
- 101000705756 Homo sapiens Proteasome activator complex subunit 1 Proteins 0.000 claims description 6
- 101000900789 Homo sapiens Protein canopy homolog 2 Proteins 0.000 claims description 6
- 101001051777 Homo sapiens Protein kinase C alpha type Proteins 0.000 claims description 6
- 101001098557 Homo sapiens Proteinase-activated receptor 3 Proteins 0.000 claims description 6
- 101000994790 Homo sapiens Ras GTPase-activating-like protein IQGAP2 Proteins 0.000 claims description 6
- 101001130441 Homo sapiens Ras-related protein Rap-2a Proteins 0.000 claims description 6
- 101000668416 Homo sapiens Regulator of chromosome condensation Proteins 0.000 claims description 6
- 101001092206 Homo sapiens Replication protein A 32 kDa subunit Proteins 0.000 claims description 6
- 101001091990 Homo sapiens Rho GTPase-activating protein 24 Proteins 0.000 claims description 6
- 101000694338 Homo sapiens RuvB-like 2 Proteins 0.000 claims description 6
- 101000641122 Homo sapiens Sacsin Proteins 0.000 claims description 6
- 101000642661 Homo sapiens Serine-threonine kinase receptor-associated protein Proteins 0.000 claims description 6
- 101000836075 Homo sapiens Serpin B9 Proteins 0.000 claims description 6
- 101000700752 Homo sapiens Serum response factor-binding protein 1 Proteins 0.000 claims description 6
- 101000617830 Homo sapiens Sterol O-acyltransferase 1 Proteins 0.000 claims description 6
- 101000642613 Homo sapiens Sterol O-acyltransferase 2 Proteins 0.000 claims description 6
- 101000692107 Homo sapiens Syndecan-3 Proteins 0.000 claims description 6
- 101000706152 Homo sapiens Syntaxin-12 Proteins 0.000 claims description 6
- 101000666730 Homo sapiens T-complex protein 1 subunit alpha Proteins 0.000 claims description 6
- 101000852559 Homo sapiens Thioredoxin Proteins 0.000 claims description 6
- 101000802356 Homo sapiens Tight junction protein ZO-1 Proteins 0.000 claims description 6
- 101000835023 Homo sapiens Transcription factor A, mitochondrial Proteins 0.000 claims description 6
- 101000597043 Homo sapiens Transcriptional enhancer factor TEF-5 Proteins 0.000 claims description 6
- 101000838463 Homo sapiens Tubulin alpha-1A chain Proteins 0.000 claims description 6
- 101000788607 Homo sapiens Tubulin alpha-3C chain Proteins 0.000 claims description 6
- 101001054878 Homo sapiens Tyrosine-protein kinase Lyn Proteins 0.000 claims description 6
- 101000604583 Homo sapiens Tyrosine-protein kinase SYK Proteins 0.000 claims description 6
- 101000639802 Homo sapiens U2 small nuclear ribonucleoprotein B'' Proteins 0.000 claims description 6
- 101000710040 Homo sapiens UPF0415 protein C7orf25 Proteins 0.000 claims description 6
- 101000607645 Homo sapiens Ubiquilin-4 Proteins 0.000 claims description 6
- 101000935123 Homo sapiens Voltage-dependent N-type calcium channel subunit alpha-1B Proteins 0.000 claims description 6
- 102100025891 Inosine-5'-monophosphate dehydrogenase 2 Human genes 0.000 claims description 6
- 102100024039 Inositol 1,4,5-trisphosphate receptor type 1 Human genes 0.000 claims description 6
- 102100033016 Integrin beta-7 Human genes 0.000 claims description 6
- 102100031802 Interferon-induced GTP-binding protein Mx1 Human genes 0.000 claims description 6
- 102100022743 Laminin subunit alpha-4 Human genes 0.000 claims description 6
- 102100024930 Melatonin receptor type 1A Human genes 0.000 claims description 6
- 102100021794 Microtubule-associated protein 4 Human genes 0.000 claims description 6
- 102100024193 Mitogen-activated protein kinase 1 Human genes 0.000 claims description 6
- 101001033610 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) Inosine-5'-monophosphate dehydrogenase Proteins 0.000 claims description 6
- 102100026781 N-alpha-acetyltransferase 15, NatA auxiliary subunit Human genes 0.000 claims description 6
- 102100038991 Neuropeptide Y receptor type 2 Human genes 0.000 claims description 6
- 102100038730 PRKCA-binding protein Human genes 0.000 claims description 6
- 102100023846 Peptidyl-prolyl cis-trans isomerase FKBP3 Human genes 0.000 claims description 6
- 102100034601 Peroxidasin homolog Human genes 0.000 claims description 6
- 102100029139 Peroxiredoxin-1 Human genes 0.000 claims description 6
- 102100038332 Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform Human genes 0.000 claims description 6
- 102100022063 Phosphoribosyl pyrophosphate synthase-associated protein 1 Human genes 0.000 claims description 6
- 102100037518 Platelet-activating factor acetylhydrolase Human genes 0.000 claims description 6
- 102100034960 Poly(rC)-binding protein 1 Human genes 0.000 claims description 6
- 102100031300 Proteasome activator complex subunit 1 Human genes 0.000 claims description 6
- 102100022050 Protein canopy homolog 2 Human genes 0.000 claims description 6
- 102100024924 Protein kinase C alpha type Human genes 0.000 claims description 6
- 102100037133 Proteinase-activated receptor 3 Human genes 0.000 claims description 6
- 102000004912 RYR2 Human genes 0.000 claims description 6
- 108060007241 RYR2 Proteins 0.000 claims description 6
- 102100034418 Ras GTPase-activating-like protein IQGAP2 Human genes 0.000 claims description 6
- 102100034485 Ras-related protein Rab-2A Human genes 0.000 claims description 6
- 102100031420 Ras-related protein Rap-2a Human genes 0.000 claims description 6
- 101000629598 Rattus norvegicus Sterol regulatory element-binding protein 1 Proteins 0.000 claims description 6
- 102100025234 Receptor of activated protein C kinase 1 Human genes 0.000 claims description 6
- 108010044157 Receptors for Activated C Kinase Proteins 0.000 claims description 6
- 102100035772 Regulator of G-protein signaling 12 Human genes 0.000 claims description 6
- 101710148337 Regulator of G-protein signaling 12 Proteins 0.000 claims description 6
- 102100039977 Regulator of chromosome condensation Human genes 0.000 claims description 6
- 208000006289 Rett Syndrome Diseases 0.000 claims description 6
- 208000036353 Rett disease Diseases 0.000 claims description 6
- 102100035741 Rho GTPase-activating protein 24 Human genes 0.000 claims description 6
- 102100027092 RuvB-like 2 Human genes 0.000 claims description 6
- 102000005029 SLC6A3 Human genes 0.000 claims description 6
- 102000001332 SRC Human genes 0.000 claims description 6
- 108060006706 SRC Proteins 0.000 claims description 6
- 101000857460 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) RuvB-like protein 2 Proteins 0.000 claims description 6
- 102100034272 Sacsin Human genes 0.000 claims description 6
- 102100025517 Serpin B9 Human genes 0.000 claims description 6
- 102100029282 Serum response factor-binding protein 1 Human genes 0.000 claims description 6
- 102100021993 Sterol O-acyltransferase 1 Human genes 0.000 claims description 6
- 102100036673 Sterol O-acyltransferase 2 Human genes 0.000 claims description 6
- 102100030529 Suppressor of cytokine signaling 7 Human genes 0.000 claims description 6
- 102100026084 Syndecan-3 Human genes 0.000 claims description 6
- 102100031117 Syntaxin-12 Human genes 0.000 claims description 6
- 102100038410 T-complex protein 1 subunit alpha Human genes 0.000 claims description 6
- 108090000925 TNF receptor-associated factor 2 Proteins 0.000 claims description 6
- 102100034779 TRAF family member-associated NF-kappa-B activator Human genes 0.000 claims description 6
- 102100036407 Thioredoxin Human genes 0.000 claims description 6
- 102100034686 Tight junction protein ZO-1 Human genes 0.000 claims description 6
- 102100026155 Transcription factor A, mitochondrial Human genes 0.000 claims description 6
- 102100035147 Transcriptional enhancer factor TEF-5 Human genes 0.000 claims description 6
- 102100028968 Tubulin alpha-1A chain Human genes 0.000 claims description 6
- 102100025235 Tubulin alpha-3C chain Human genes 0.000 claims description 6
- 102100026857 Tyrosine-protein kinase Lyn Human genes 0.000 claims description 6
- 102100038183 Tyrosine-protein kinase SYK Human genes 0.000 claims description 6
- 102100034461 U2 small nuclear ribonucleoprotein B'' Human genes 0.000 claims description 6
- 102100034623 UPF0415 protein C7orf25 Human genes 0.000 claims description 6
- 102100039932 Ubiquilin-4 Human genes 0.000 claims description 6
- ZUPXXZAVUHFCNV-UHFFFAOYSA-N [[5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [5-(3-carbamoyl-4h-pyridin-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl hydrogen phosphate;potassium Chemical compound [K].C1=CCC(C(=O)N)=CN1C1C(O)C(O)C(COP(O)(=O)OP(O)(=O)OCC2C(C(O)C(O2)N2C3=NC=NC(N)=C3N=C2)O)O1 ZUPXXZAVUHFCNV-UHFFFAOYSA-N 0.000 claims description 6
- 102000052116 epidermal growth factor receptor activity proteins Human genes 0.000 claims description 6
- 108700015053 epidermal growth factor receptor activity proteins Proteins 0.000 claims description 6
- 108010022790 formyl-methenyl-methylenetetrahydrofolate synthetase Proteins 0.000 claims description 6
- YOHYSYJDKVYCJI-UHFFFAOYSA-N n-[3-[[6-[3-(trifluoromethyl)anilino]pyrimidin-4-yl]amino]phenyl]cyclopropanecarboxamide Chemical compound FC(F)(F)C1=CC=CC(NC=2N=CN=C(NC=3C=C(NC(=O)C4CC4)C=CC=3)C=2)=C1 YOHYSYJDKVYCJI-UHFFFAOYSA-N 0.000 claims description 6
- 108010041801 2',3'-Cyclic Nucleotide 3'-Phosphodiesterase Proteins 0.000 claims description 5
- 101001084266 Homo sapiens Parathyroid hormone 2 receptor Proteins 0.000 claims description 5
- 101000650667 Homo sapiens SET domain-containing protein 4 Proteins 0.000 claims description 5
- 102100030869 Parathyroid hormone 2 receptor Human genes 0.000 claims description 5
- 102100027707 SET domain-containing protein 4 Human genes 0.000 claims description 5
- 230000000052 comparative effect Effects 0.000 claims description 5
- 238000007482 whole exome sequencing Methods 0.000 claims description 5
- 238000012070 whole genome sequencing analysis Methods 0.000 claims description 5
- SVJQCVOKYJWUBC-OWOJBTEDSA-N (e)-3-(2,3,4,5-tetrabromophenyl)prop-2-enoic acid Chemical compound OC(=O)\C=C\C1=CC(Br)=C(Br)C(Br)=C1Br SVJQCVOKYJWUBC-OWOJBTEDSA-N 0.000 claims description 4
- 102100030388 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 Human genes 0.000 claims description 4
- 102100026210 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2 Human genes 0.000 claims description 4
- 102100040964 26S proteasome non-ATPase regulatory subunit 11 Human genes 0.000 claims description 4
- 102100033097 26S proteasome non-ATPase regulatory subunit 6 Human genes 0.000 claims description 4
- 102100030877 28S ribosomal protein S16, mitochondrial Human genes 0.000 claims description 4
- 102100026433 39S ribosomal protein L14, mitochondrial Human genes 0.000 claims description 4
- 102100036321 5-hydroxytryptamine receptor 2A Human genes 0.000 claims description 4
- 102100026112 60S acidic ribosomal protein P2 Human genes 0.000 claims description 4
- BSFODEXXVBBYOC-UHFFFAOYSA-N 8-[4-(dimethylamino)butan-2-ylamino]quinolin-6-ol Chemical compound C1=CN=C2C(NC(CCN(C)C)C)=CC(O)=CC2=C1 BSFODEXXVBBYOC-UHFFFAOYSA-N 0.000 claims description 4
- 102000017908 ADRA1B Human genes 0.000 claims description 4
- 102000017906 ADRA2A Human genes 0.000 claims description 4
- 102000017919 ADRB2 Human genes 0.000 claims description 4
- 102100021624 Acid-sensing ion channel 1 Human genes 0.000 claims description 4
- 102100022094 Acid-sensing ion channel 2 Human genes 0.000 claims description 4
- 102100036664 Adenosine deaminase Human genes 0.000 claims description 4
- 102100033346 Adenosine receptor A1 Human genes 0.000 claims description 4
- 102100026882 Alpha-synuclein Human genes 0.000 claims description 4
- 102100034613 Annexin A2 Human genes 0.000 claims description 4
- 102000004888 Aquaporin 1 Human genes 0.000 claims description 4
- 108090001004 Aquaporin 1 Proteins 0.000 claims description 4
- 102100024630 Asc-type amino acid transporter 1 Human genes 0.000 claims description 4
- 102100023025 Ataxin-7-like protein 3 Human genes 0.000 claims description 4
- 102100024272 BTB/POZ domain-containing protein 2 Human genes 0.000 claims description 4
- 102100024348 Beta-adducin Human genes 0.000 claims description 4
- 102100029649 Beta-arrestin-1 Human genes 0.000 claims description 4
- 102100029648 Beta-arrestin-2 Human genes 0.000 claims description 4
- 102100028989 C-X-C chemokine receptor type 2 Human genes 0.000 claims description 4
- 101150006869 CACYBP gene Proteins 0.000 claims description 4
- 102000017926 CHRM2 Human genes 0.000 claims description 4
- 108091005471 CRHR1 Proteins 0.000 claims description 4
- 102100024318 Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B Human genes 0.000 claims description 4
- 102100033086 Calcium/calmodulin-dependent protein kinase type 1 Human genes 0.000 claims description 4
- 102100022789 Calcium/calmodulin-dependent protein kinase type IV Human genes 0.000 claims description 4
- 102100039901 Calcyclin-binding protein Human genes 0.000 claims description 4
- 102100025579 Calmodulin-2 Human genes 0.000 claims description 4
- 102100025926 Calmodulin-3 Human genes 0.000 claims description 4
- 102100028002 Catenin alpha-2 Human genes 0.000 claims description 4
- 102000011068 Cdc42 Human genes 0.000 claims description 4
- 102100024340 Contactin-4 Human genes 0.000 claims description 4
- 102100038018 Corticotropin-releasing factor receptor 1 Human genes 0.000 claims description 4
- 102100030497 Cytochrome c Human genes 0.000 claims description 4
- 102100020756 D(2) dopamine receptor Human genes 0.000 claims description 4
- 102100029808 D(3) dopamine receptor Human genes 0.000 claims description 4
- 102100031817 Delta-type opioid receptor Human genes 0.000 claims description 4
- 101001046554 Dictyostelium discoideum Thymidine kinase 1 Proteins 0.000 claims description 4
- 102100031920 Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial Human genes 0.000 claims description 4
- 102100036966 Dipeptidyl aminopeptidase-like protein 6 Human genes 0.000 claims description 4
- 102100028027 Double-stranded RNA-binding protein Staufen homolog 1 Human genes 0.000 claims description 4
- 102100040565 Dynein light chain 1, cytoplasmic Human genes 0.000 claims description 4
- 102100023471 E-selectin Human genes 0.000 claims description 4
- 102100021838 E3 ubiquitin-protein ligase SIAH1 Human genes 0.000 claims description 4
- 102100021650 ER membrane protein complex subunit 1 Human genes 0.000 claims description 4
- 101000944251 Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) Calcium/calmodulin-dependent protein kinase cmkA Proteins 0.000 claims description 4
- 102100029777 Eukaryotic translation initiation factor 3 subunit M Human genes 0.000 claims description 4
- 102100036089 Fascin Human genes 0.000 claims description 4
- 102100036931 G-protein coupled receptor 26 Human genes 0.000 claims description 4
- 102100032340 G2/mitotic-specific cyclin-B1 Human genes 0.000 claims description 4
- 102000058063 Glucose Transporter Type 1 Human genes 0.000 claims description 4
- 102100030652 Glutamate receptor 1 Human genes 0.000 claims description 4
- 102100022767 Glutamate receptor ionotropic, kainate 3 Human genes 0.000 claims description 4
- 102100027978 Glutamine-rich protein 2 Human genes 0.000 claims description 4
- 102100036424 Glutaredoxin-3 Human genes 0.000 claims description 4
- 102100031181 Glyceraldehyde-3-phosphate dehydrogenase Human genes 0.000 claims description 4
- 102100029481 Glycogen phosphorylase, liver form Human genes 0.000 claims description 4
- 102100029492 Glycogen phosphorylase, muscle form Human genes 0.000 claims description 4
- 102100032510 Heat shock protein HSP 90-beta Human genes 0.000 claims description 4
- 101000583069 Homo sapiens 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3 Proteins 0.000 claims description 4
- 101000691589 Homo sapiens 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2 Proteins 0.000 claims description 4
- 101000612519 Homo sapiens 26S proteasome non-ATPase regulatory subunit 11 Proteins 0.000 claims description 4
- 101001135306 Homo sapiens 26S proteasome non-ATPase regulatory subunit 6 Proteins 0.000 claims description 4
- 101000635698 Homo sapiens 28S ribosomal protein S16, mitochondrial Proteins 0.000 claims description 4
- 101000692875 Homo sapiens 39S ribosomal protein L14, mitochondrial Proteins 0.000 claims description 4
- 101000783617 Homo sapiens 5-hydroxytryptamine receptor 2A Proteins 0.000 claims description 4
- 101000691878 Homo sapiens 60S acidic ribosomal protein P2 Proteins 0.000 claims description 4
- 101000754290 Homo sapiens Acid-sensing ion channel 1 Proteins 0.000 claims description 4
- 101000901079 Homo sapiens Acid-sensing ion channel 2 Proteins 0.000 claims description 4
- 101000756632 Homo sapiens Actin, cytoplasmic 1 Proteins 0.000 claims description 4
- 101000929495 Homo sapiens Adenosine deaminase Proteins 0.000 claims description 4
- 101000799712 Homo sapiens Adenosine receptor A1 Proteins 0.000 claims description 4
- 101000689698 Homo sapiens Alpha-1B adrenergic receptor Proteins 0.000 claims description 4
- 101000756842 Homo sapiens Alpha-2A adrenergic receptor Proteins 0.000 claims description 4
- 101000834898 Homo sapiens Alpha-synuclein Proteins 0.000 claims description 4
- 101000924474 Homo sapiens Annexin A2 Proteins 0.000 claims description 4
- 101000929698 Homo sapiens Aspartate aminotransferase, cytoplasmic Proteins 0.000 claims description 4
- 101000974945 Homo sapiens Ataxin-7-like protein 3 Proteins 0.000 claims description 4
- 101000761884 Homo sapiens BTB/POZ domain-containing protein 2 Proteins 0.000 claims description 4
- 101000959437 Homo sapiens Beta-2 adrenergic receptor Proteins 0.000 claims description 4
- 101000689619 Homo sapiens Beta-adducin Proteins 0.000 claims description 4
- 101000916059 Homo sapiens C-X-C chemokine receptor type 2 Proteins 0.000 claims description 4
- 101001117099 Homo sapiens Calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1B Proteins 0.000 claims description 4
- 101000944250 Homo sapiens Calcium/calmodulin-dependent protein kinase type 1 Proteins 0.000 claims description 4
- 101000974816 Homo sapiens Calcium/calmodulin-dependent protein kinase type IV Proteins 0.000 claims description 4
- 101000984150 Homo sapiens Calmodulin-2 Proteins 0.000 claims description 4
- 101000933777 Homo sapiens Calmodulin-3 Proteins 0.000 claims description 4
- 101000859073 Homo sapiens Catenin alpha-2 Proteins 0.000 claims description 4
- 101000909504 Homo sapiens Contactin-4 Proteins 0.000 claims description 4
- 101000726355 Homo sapiens Cytochrome c Proteins 0.000 claims description 4
- 101000931901 Homo sapiens D(2) dopamine receptor Proteins 0.000 claims description 4
- 101000865224 Homo sapiens D(3) dopamine receptor Proteins 0.000 claims description 4
- 101000992305 Homo sapiens Delta-type opioid receptor Proteins 0.000 claims description 4
- 101000992065 Homo sapiens Dihydrolipoyllysine-residue succinyltransferase component of 2-oxoglutarate dehydrogenase complex, mitochondrial Proteins 0.000 claims description 4
- 101000804935 Homo sapiens Dipeptidyl aminopeptidase-like protein 6 Proteins 0.000 claims description 4
- 101000697574 Homo sapiens Double-stranded RNA-binding protein Staufen homolog 1 Proteins 0.000 claims description 4
- 101000966403 Homo sapiens Dynein light chain 1, cytoplasmic Proteins 0.000 claims description 4
- 101000622123 Homo sapiens E-selectin Proteins 0.000 claims description 4
- 101000616722 Homo sapiens E3 ubiquitin-protein ligase SIAH1 Proteins 0.000 claims description 4
- 101000896333 Homo sapiens ER membrane protein complex subunit 1 Proteins 0.000 claims description 4
- 101000920799 Homo sapiens Endoplasmic reticulum resident protein 44 Proteins 0.000 claims description 4
- 101001012700 Homo sapiens Eukaryotic translation initiation factor 3 subunit M Proteins 0.000 claims description 4
- 101001021925 Homo sapiens Fascin Proteins 0.000 claims description 4
- 101001071346 Homo sapiens G-protein coupled receptor 26 Proteins 0.000 claims description 4
- 101000868643 Homo sapiens G2/mitotic-specific cyclin-B1 Proteins 0.000 claims description 4
- 101001010445 Homo sapiens Glutamate receptor 1 Proteins 0.000 claims description 4
- 101000903337 Homo sapiens Glutamate receptor ionotropic, kainate 3 Proteins 0.000 claims description 4
- 101001060579 Homo sapiens Glutamine-rich protein 2 Proteins 0.000 claims description 4
- 101001071851 Homo sapiens Glutaredoxin-3 Proteins 0.000 claims description 4
- 101000700616 Homo sapiens Glycogen phosphorylase, liver form Proteins 0.000 claims description 4
- 101000700475 Homo sapiens Glycogen phosphorylase, muscle form Proteins 0.000 claims description 4
- 101001016856 Homo sapiens Heat shock protein HSP 90-beta Proteins 0.000 claims description 4
- 101001053564 Homo sapiens IQ domain-containing protein N Proteins 0.000 claims description 4
- 101000998810 Homo sapiens Insulin-like peptide INSL6 Proteins 0.000 claims description 4
- 101000935043 Homo sapiens Integrin beta-1 Proteins 0.000 claims description 4
- 101001008442 Homo sapiens La-related protein 7 Proteins 0.000 claims description 4
- 101000579789 Homo sapiens Leucine-rich repeat-containing protein 59 Proteins 0.000 claims description 4
- 101000619643 Homo sapiens Ligand-dependent nuclear receptor-interacting factor 1 Proteins 0.000 claims description 4
- 101000764535 Homo sapiens Lymphotoxin-alpha Proteins 0.000 claims description 4
- 101001059427 Homo sapiens MAP/microtubule affinity-regulating kinase 4 Proteins 0.000 claims description 4
- 101000978418 Homo sapiens Melanocortin receptor 4 Proteins 0.000 claims description 4
- 101001116395 Homo sapiens Melatonin receptor type 1B Proteins 0.000 claims description 4
- 101000891579 Homo sapiens Microtubule-associated protein tau Proteins 0.000 claims description 4
- 101000798124 Homo sapiens Multifunctional methyltransferase subunit TRM112-like protein Proteins 0.000 claims description 4
- 101000928929 Homo sapiens Muscarinic acetylcholine receptor M2 Proteins 0.000 claims description 4
- 101001030211 Homo sapiens Myc proto-oncogene protein Proteins 0.000 claims description 4
- 101000961071 Homo sapiens NF-kappa-B inhibitor alpha Proteins 0.000 claims description 4
- 101000979259 Homo sapiens Neurolysin, mitochondrial Proteins 0.000 claims description 4
- 101000598100 Homo sapiens Nuclear migration protein nudC Proteins 0.000 claims description 4
- 101000945735 Homo sapiens Parafibromin Proteins 0.000 claims description 4
- 101000741800 Homo sapiens Peptidyl-prolyl cis-trans isomerase H Proteins 0.000 claims description 4
- 101001120056 Homo sapiens Phosphatidylinositol 3-kinase regulatory subunit alpha Proteins 0.000 claims description 4
- 101000583553 Homo sapiens Phosphoglucomutase-1 Proteins 0.000 claims description 4
- 101000731078 Homo sapiens Phosphorylase b kinase gamma catalytic chain, liver/testis isoform Proteins 0.000 claims description 4
- 101001137939 Homo sapiens Phosphorylase b kinase regulatory subunit beta Proteins 0.000 claims description 4
- 101000615933 Homo sapiens Phosphoserine aminotransferase Proteins 0.000 claims description 4
- 101001070790 Homo sapiens Platelet glycoprotein Ib alpha chain Proteins 0.000 claims description 4
- 101000609363 Homo sapiens Platelet-activating factor acetylhydrolase IB subunit alpha1 Proteins 0.000 claims description 4
- 101000617536 Homo sapiens Presenilin-1 Proteins 0.000 claims description 4
- 101000734643 Homo sapiens Programmed cell death protein 5 Proteins 0.000 claims description 4
- 101001123492 Homo sapiens Prolactin-releasing peptide receptor Proteins 0.000 claims description 4
- 101000736929 Homo sapiens Proteasome subunit alpha type-1 Proteins 0.000 claims description 4
- 101000933604 Homo sapiens Protein BTG2 Proteins 0.000 claims description 4
- 101000668432 Homo sapiens Protein RCC2 Proteins 0.000 claims description 4
- 101000757216 Homo sapiens Protein arginine N-methyltransferase 1 Proteins 0.000 claims description 4
- 101001129833 Homo sapiens Protein-L-isoaspartate(D-aspartate) O-methyltransferase Proteins 0.000 claims description 4
- 101000666171 Homo sapiens Protein-glutamine gamma-glutamyltransferase 2 Proteins 0.000 claims description 4
- 101001098529 Homo sapiens Proteinase-activated receptor 1 Proteins 0.000 claims description 4
- 101001017961 Homo sapiens Ragulator complex protein LAMTOR5 Proteins 0.000 claims description 4
- 101001130465 Homo sapiens Ras-related protein Ral-A Proteins 0.000 claims description 4
- 101000945390 Homo sapiens Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma Proteins 0.000 claims description 4
- 101001074727 Homo sapiens Ribonucleoside-diphosphate reductase large subunit Proteins 0.000 claims description 4
- 101000631701 Homo sapiens Secretin receptor Proteins 0.000 claims description 4
- 101000716809 Homo sapiens Secretogranin-1 Proteins 0.000 claims description 4
- 101000674278 Homo sapiens Serine-tRNA ligase, cytoplasmic Proteins 0.000 claims description 4
- 101000674040 Homo sapiens Serine-tRNA ligase, mitochondrial Proteins 0.000 claims description 4
- 101000783404 Homo sapiens Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform Proteins 0.000 claims description 4
- 101000863858 Homo sapiens Sialic acid synthase Proteins 0.000 claims description 4
- 101000650857 Homo sapiens Small glutamine-rich tetratricopeptide repeat-containing protein beta Proteins 0.000 claims description 4
- 101000662997 Homo sapiens TRAF2 and NCK-interacting protein kinase Proteins 0.000 claims description 4
- 101001095487 Homo sapiens Telomere-associated protein RIF1 Proteins 0.000 claims description 4
- 101000715050 Homo sapiens Thromboxane A2 receptor Proteins 0.000 claims description 4
- 101000945477 Homo sapiens Thymidine kinase, cytosolic Proteins 0.000 claims description 4
- 101000809797 Homo sapiens Thymidylate synthase Proteins 0.000 claims description 4
- 101000763537 Homo sapiens Toll-like receptor 10 Proteins 0.000 claims description 4
- 101000801742 Homo sapiens Triosephosphate isomerase Proteins 0.000 claims description 4
- 101000838456 Homo sapiens Tubulin alpha-1B chain Proteins 0.000 claims description 4
- 101000788548 Homo sapiens Tubulin alpha-4A chain Proteins 0.000 claims description 4
- 101000625727 Homo sapiens Tubulin beta chain Proteins 0.000 claims description 4
- 101000788517 Homo sapiens Tubulin beta-2A chain Proteins 0.000 claims description 4
- 101000838301 Homo sapiens Tubulin gamma-1 chain Proteins 0.000 claims description 4
- 101000835622 Homo sapiens Tubulin-specific chaperone A Proteins 0.000 claims description 4
- 101001022129 Homo sapiens Tyrosine-protein kinase Fyn Proteins 0.000 claims description 4
- 101000818543 Homo sapiens Tyrosine-protein kinase ZAP-70 Proteins 0.000 claims description 4
- 101001138544 Homo sapiens UMP-CMP kinase Proteins 0.000 claims description 4
- 101000982023 Homo sapiens Unconventional myosin-Ic Proteins 0.000 claims description 4
- 101000904228 Homo sapiens Vesicle transport protein GOT1A Proteins 0.000 claims description 4
- 101000904204 Homo sapiens Vesicle transport protein GOT1B Proteins 0.000 claims description 4
- 101000818522 Homo sapiens fMet-Leu-Phe receptor Proteins 0.000 claims description 4
- 102100024427 IQ domain-containing protein N Human genes 0.000 claims description 4
- 102100025304 Integrin beta-1 Human genes 0.000 claims description 4
- 102100027436 La-related protein 7 Human genes 0.000 claims description 4
- 102100028206 Leucine-rich repeat-containing protein 59 Human genes 0.000 claims description 4
- 102100022172 Ligand-dependent nuclear receptor-interacting factor 1 Human genes 0.000 claims description 4
- 101001089108 Lotus tetragonolobus Anti-H(O) lectin Proteins 0.000 claims description 4
- 102100026238 Lymphotoxin-alpha Human genes 0.000 claims description 4
- 102100028913 MAP/microtubule affinity-regulating kinase 4 Human genes 0.000 claims description 4
- 102100023724 Melanocortin receptor 4 Human genes 0.000 claims description 4
- 102100024970 Melatonin receptor type 1B Human genes 0.000 claims description 4
- 102100040243 Microtubule-associated protein tau Human genes 0.000 claims description 4
- 102100032242 Multifunctional methyltransferase subunit TRM112-like protein Human genes 0.000 claims description 4
- 102100038895 Myc proto-oncogene protein Human genes 0.000 claims description 4
- 102100039337 NF-kappa-B inhibitor alpha Human genes 0.000 claims description 4
- 102100023072 Neurolysin, mitochondrial Human genes 0.000 claims description 4
- 102100036965 Nuclear migration protein nudC Human genes 0.000 claims description 4
- 102100034743 Parafibromin Human genes 0.000 claims description 4
- 102100038827 Peptidyl-prolyl cis-trans isomerase H Human genes 0.000 claims description 4
- 102100026169 Phosphatidylinositol 3-kinase regulatory subunit alpha Human genes 0.000 claims description 4
- 102100030999 Phosphoglucomutase-1 Human genes 0.000 claims description 4
- 102100032391 Phosphorylase b kinase gamma catalytic chain, liver/testis isoform Human genes 0.000 claims description 4
- 102100020854 Phosphorylase b kinase regulatory subunit beta Human genes 0.000 claims description 4
- 102100021768 Phosphoserine aminotransferase Human genes 0.000 claims description 4
- 102100034173 Platelet glycoprotein Ib alpha chain Human genes 0.000 claims description 4
- 102100039446 Platelet-activating factor acetylhydrolase IB subunit alpha1 Human genes 0.000 claims description 4
- 102100022033 Presenilin-1 Human genes 0.000 claims description 4
- 102100034807 Programmed cell death protein 5 Human genes 0.000 claims description 4
- 102100029002 Prolactin-releasing peptide receptor Human genes 0.000 claims description 4
- 102000004885 Protease-activated receptor 4 Human genes 0.000 claims description 4
- 108090001010 Protease-activated receptor 4 Proteins 0.000 claims description 4
- 102100036042 Proteasome subunit alpha type-1 Human genes 0.000 claims description 4
- 102100026034 Protein BTG2 Human genes 0.000 claims description 4
- 102100039972 Protein RCC2 Human genes 0.000 claims description 4
- 102100032421 Protein S100-A6 Human genes 0.000 claims description 4
- 102100022985 Protein arginine N-methyltransferase 1 Human genes 0.000 claims description 4
- 102100031674 Protein-L-isoaspartate(D-aspartate) O-methyltransferase Human genes 0.000 claims description 4
- 102100038095 Protein-glutamine gamma-glutamyltransferase 2 Human genes 0.000 claims description 4
- 102100037136 Proteinase-activated receptor 1 Human genes 0.000 claims description 4
- 101150111584 RHOA gene Proteins 0.000 claims description 4
- 102000004913 RYR1 Human genes 0.000 claims description 4
- 108060007240 RYR1 Proteins 0.000 claims description 4
- 102100033373 Ragulator complex protein LAMTOR5 Human genes 0.000 claims description 4
- 102100031424 Ras-related protein Ral-A Human genes 0.000 claims description 4
- 102100021258 Regulator of G-protein signaling 2 Human genes 0.000 claims description 4
- 101710140412 Regulator of G-protein signaling 2 Proteins 0.000 claims description 4
- 102100033597 Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma Human genes 0.000 claims description 4
- 102100036320 Ribonucleoside-diphosphate reductase large subunit Human genes 0.000 claims description 4
- 108010005260 S100 Calcium Binding Protein A6 Proteins 0.000 claims description 4
- 102100032735 SH3 and multiple ankyrin repeat domains protein 1 Human genes 0.000 claims description 4
- 101710101742 SH3 and multiple ankyrin repeat domains protein 1 Proteins 0.000 claims description 4
- 108091006296 SLC2A1 Proteins 0.000 claims description 4
- 108091006242 SLC7A10 Proteins 0.000 claims description 4
- 102100028927 Secretin receptor Human genes 0.000 claims description 4
- 102100020867 Secretogranin-1 Human genes 0.000 claims description 4
- 102100040516 Serine-tRNA ligase, cytoplasmic Human genes 0.000 claims description 4
- 102100036122 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform Human genes 0.000 claims description 4
- 108010089417 Sex Hormone-Binding Globulin Proteins 0.000 claims description 4
- 102100030758 Sex hormone-binding globulin Human genes 0.000 claims description 4
- 102100029954 Sialic acid synthase Human genes 0.000 claims description 4
- 102100027721 Small glutamine-rich tetratricopeptide repeat-containing protein beta Human genes 0.000 claims description 4
- 102100026974 Sorbitol dehydrogenase Human genes 0.000 claims description 4
- 101710184713 Sorbitol dehydrogenase Proteins 0.000 claims description 4
- 102100037671 TRAF2 and NCK-interacting protein kinase Human genes 0.000 claims description 4
- 102100036704 Thromboxane A2 receptor Human genes 0.000 claims description 4
- 102100034838 Thymidine kinase, cytosolic Human genes 0.000 claims description 4
- 102100038618 Thymidylate synthase Human genes 0.000 claims description 4
- 102100027009 Toll-like receptor 10 Human genes 0.000 claims description 4
- 102100022387 Transforming protein RhoA Human genes 0.000 claims description 4
- 102100033598 Triosephosphate isomerase Human genes 0.000 claims description 4
- 102100028969 Tubulin alpha-1B chain Human genes 0.000 claims description 4
- 102100025239 Tubulin alpha-4A chain Human genes 0.000 claims description 4
- 102100024717 Tubulin beta chain Human genes 0.000 claims description 4
- 102100028979 Tubulin gamma-1 chain Human genes 0.000 claims description 4
- 102100026477 Tubulin-specific chaperone A Human genes 0.000 claims description 4
- 102100035221 Tyrosine-protein kinase Fyn Human genes 0.000 claims description 4
- 102100021125 Tyrosine-protein kinase ZAP-70 Human genes 0.000 claims description 4
- 102100020797 UMP-CMP kinase Human genes 0.000 claims description 4
- 108010005656 Ubiquitin Thiolesterase Proteins 0.000 claims description 4
- 102100026785 Unconventional myosin-Ic Human genes 0.000 claims description 4
- 102100038388 Vasoactive intestinal polypeptide receptor 1 Human genes 0.000 claims description 4
- 101710137655 Vasoactive intestinal polypeptide receptor 1 Proteins 0.000 claims description 4
- 102100024010 Vesicle transport protein GOT1A Human genes 0.000 claims description 4
- 108010032969 beta-Arrestin 1 Proteins 0.000 claims description 4
- 108010032967 beta-Arrestin 2 Proteins 0.000 claims description 4
- 108010051348 cdc42 GTP-Binding Protein Proteins 0.000 claims description 4
- 102100021145 fMet-Leu-Phe receptor Human genes 0.000 claims description 4
- 108020004445 glyceraldehyde-3-phosphate dehydrogenase Proteins 0.000 claims description 4
- 238000013507 mapping Methods 0.000 claims description 4
- 238000007481 next generation sequencing Methods 0.000 claims description 4
- 108010067765 rab2 GTP Binding protein Proteins 0.000 claims description 4
- 108090000850 ribosomal protein S14 Proteins 0.000 claims description 4
- 102000004314 ribosomal protein S14 Human genes 0.000 claims description 4
- 238000007480 sanger sequencing Methods 0.000 claims description 4
- 102100022273 Disrupted in schizophrenia 1 protein Human genes 0.000 claims description 3
- 101000902072 Homo sapiens Disrupted in schizophrenia 1 protein Proteins 0.000 claims description 3
- 101000652220 Homo sapiens Suppressor of cytokine signaling 4 Proteins 0.000 claims description 3
- 101000652226 Homo sapiens Suppressor of cytokine signaling 6 Proteins 0.000 claims description 3
- 101000652229 Homo sapiens Suppressor of cytokine signaling 7 Proteins 0.000 claims description 3
- 101000807541 Homo sapiens Ubiquitin carboxyl-terminal hydrolase 24 Proteins 0.000 claims description 3
- 102100037176 Ubiquitin carboxyl-terminal hydrolase 24 Human genes 0.000 claims description 3
- 238000002560 therapeutic procedure Methods 0.000 claims description 3
- 108010089790 Eukaryotic Initiation Factor-3 Proteins 0.000 claims description 2
- 102100037115 Eukaryotic translation initiation factor 3 subunit H Human genes 0.000 claims description 2
- 201000000980 schizophrenia Diseases 0.000 claims description 2
- 102100027831 14-3-3 protein theta Human genes 0.000 claims 2
- 102100031478 C-type natriuretic peptide Human genes 0.000 claims 2
- 101000723543 Homo sapiens 14-3-3 protein theta Proteins 0.000 claims 2
- 101000984164 Homo sapiens Calmodulin-1 Proteins 0.000 claims 2
- 101000973623 Homo sapiens Neuronal growth regulator 1 Proteins 0.000 claims 2
- 101000883014 Homo sapiens Protein capicua homolog Proteins 0.000 claims 2
- 101100203078 Homo sapiens SF3B6 gene Proteins 0.000 claims 2
- 102100022223 Neuronal growth regulator 1 Human genes 0.000 claims 2
- 102100038777 Protein capicua homolog Human genes 0.000 claims 2
- 102100021817 Splicing factor 3B subunit 6 Human genes 0.000 claims 2
- 102100025038 Ubiquitin carboxyl-terminal hydrolase isozyme L1 Human genes 0.000 claims 2
- 102100031834 Unconventional myosin-VI Human genes 0.000 claims 2
- 108010049787 myosin VI Proteins 0.000 claims 2
- 102100025296 Guanine nucleotide-binding protein G(o) subunit alpha Human genes 0.000 claims 1
- 101000857837 Homo sapiens Guanine nucleotide-binding protein G(o) subunit alpha Proteins 0.000 claims 1
- 101001074571 Homo sapiens PIN2/TERF1-interacting telomerase inhibitor 1 Proteins 0.000 claims 1
- 102100036257 PIN2/TERF1-interacting telomerase inhibitor 1 Human genes 0.000 claims 1
- 208000037265 diseases, disorders, signs and symptoms Diseases 0.000 abstract description 24
- 150000004682 monohydrates Chemical class 0.000 abstract description 4
- 230000003595 spectral effect Effects 0.000 abstract 2
- 239000013610 patient sample Substances 0.000 abstract 1
- 239000000523 sample Substances 0.000 description 56
- 108020004414 DNA Proteins 0.000 description 38
- 208000000323 Tourette Syndrome Diseases 0.000 description 28
- 208000016620 Tourette disease Diseases 0.000 description 28
- 230000007547 defect Effects 0.000 description 27
- 230000003993 interaction Effects 0.000 description 25
- 101150081424 grm gene Proteins 0.000 description 24
- 208000027448 Attention Deficit and Disruptive Behavior disease Diseases 0.000 description 22
- 208000024196 oppositional defiant disease Diseases 0.000 description 22
- 238000011282 treatment Methods 0.000 description 22
- 230000000295 complement effect Effects 0.000 description 19
- 101710164735 Calmodulin-1 Proteins 0.000 description 17
- 238000012360 testing method Methods 0.000 description 17
- 108091032973 (ribonucleotides)n+m Proteins 0.000 description 16
- 208000000398 DiGeorge Syndrome Diseases 0.000 description 16
- 108091034117 Oligonucleotide Proteins 0.000 description 14
- 230000037361 pathway Effects 0.000 description 14
- 210000004027 cell Anatomy 0.000 description 13
- 239000003550 marker Substances 0.000 description 13
- UEJJHQNACJXSKW-UHFFFAOYSA-N 2-(2,6-dioxopiperidin-3-yl)-1H-isoindole-1,3(2H)-dione Chemical compound O=C1C2=CC=CC=C2C(=O)N1C1CCC(=O)NC1=O UEJJHQNACJXSKW-UHFFFAOYSA-N 0.000 description 12
- 208000035475 disorder Diseases 0.000 description 12
- 230000014509 gene expression Effects 0.000 description 12
- 102000004169 proteins and genes Human genes 0.000 description 12
- 230000011664 signaling Effects 0.000 description 12
- 229960003433 thalidomide Drugs 0.000 description 12
- 239000002299 complementary DNA Substances 0.000 description 11
- 230000002950 deficient Effects 0.000 description 11
- 239000003814 drug Substances 0.000 description 11
- 201000010099 disease Diseases 0.000 description 10
- 230000004044 response Effects 0.000 description 10
- 239000013598 vector Substances 0.000 description 10
- 208000001914 Fragile X syndrome Diseases 0.000 description 9
- 108010065028 Metabotropic Glutamate 5 Receptor Proteins 0.000 description 9
- 108091028043 Nucleic acid sequence Proteins 0.000 description 9
- 239000008186 active pharmaceutical agent Substances 0.000 description 9
- NIJJYAXOARWZEE-UHFFFAOYSA-N di-n-propyl-acetic acid Natural products CCCC(C(O)=O)CCC NIJJYAXOARWZEE-UHFFFAOYSA-N 0.000 description 9
- 229940079593 drug Drugs 0.000 description 9
- 238000003752 polymerase chain reaction Methods 0.000 description 9
- 238000012552 review Methods 0.000 description 9
- MSRILKIQRXUYCT-UHFFFAOYSA-M valproate semisodium Chemical compound [Na+].CCCC(C(O)=O)CCC.CCCC(C([O-])=O)CCC MSRILKIQRXUYCT-UHFFFAOYSA-M 0.000 description 9
- 229960000604 valproic acid Drugs 0.000 description 9
- 208000010543 22q11.2 deletion syndrome Diseases 0.000 description 8
- 208000032170 Congenital Abnormalities Diseases 0.000 description 8
- 230000007698 birth defect Effects 0.000 description 8
- OPTASPLRGRRNAP-UHFFFAOYSA-N cytosine Chemical compound NC=1C=CNC(=O)N=1 OPTASPLRGRRNAP-UHFFFAOYSA-N 0.000 description 8
- 230000000694 effects Effects 0.000 description 8
- 238000011156 evaluation Methods 0.000 description 8
- UYTPUPDQBNUYGX-UHFFFAOYSA-N guanine Chemical compound O=C1NC(N)=NC2=C1N=CN2 UYTPUPDQBNUYGX-UHFFFAOYSA-N 0.000 description 8
- 230000036541 health Effects 0.000 description 8
- RWQNBRDOKXIBIV-UHFFFAOYSA-N thymine Chemical compound CC1=CNC(=O)NC1=O RWQNBRDOKXIBIV-UHFFFAOYSA-N 0.000 description 8
- 206010010356 Congenital anomaly Diseases 0.000 description 7
- 238000000729 Fisher's exact test Methods 0.000 description 7
- 208000026911 Tuberous sclerosis complex Diseases 0.000 description 7
- 230000004075 alteration Effects 0.000 description 7
- 239000003795 chemical substances by application Substances 0.000 description 7
- 210000000349 chromosome Anatomy 0.000 description 7
- 238000012790 confirmation Methods 0.000 description 7
- 230000007614 genetic variation Effects 0.000 description 7
- 238000003780 insertion Methods 0.000 description 7
- 230000037431 insertion Effects 0.000 description 7
- 208000009999 tuberous sclerosis Diseases 0.000 description 7
- 201000010374 Down Syndrome Diseases 0.000 description 6
- 206010028980 Neoplasm Diseases 0.000 description 6
- 238000003491 array Methods 0.000 description 6
- 150000001875 compounds Chemical class 0.000 description 6
- 230000006870 function Effects 0.000 description 6
- 238000003205 genotyping method Methods 0.000 description 6
- 230000007246 mechanism Effects 0.000 description 6
- 238000002360 preparation method Methods 0.000 description 6
- 102000005962 receptors Human genes 0.000 description 6
- 108020003175 receptors Proteins 0.000 description 6
- 230000001105 regulatory effect Effects 0.000 description 6
- 108091008146 restriction endonucleases Proteins 0.000 description 6
- 210000001519 tissue Anatomy 0.000 description 6
- 102000004190 Enzymes Human genes 0.000 description 5
- 108090000790 Enzymes Proteins 0.000 description 5
- 206010044688 Trisomy 21 Diseases 0.000 description 5
- 230000002159 abnormal effect Effects 0.000 description 5
- 239000002775 capsule Substances 0.000 description 5
- 230000008859 change Effects 0.000 description 5
- 238000011161 development Methods 0.000 description 5
- 230000018109 developmental process Effects 0.000 description 5
- 230000037433 frameshift Effects 0.000 description 5
- 108020004999 messenger RNA Proteins 0.000 description 5
- 239000002664 nootropic agent Substances 0.000 description 5
- 238000001558 permutation test Methods 0.000 description 5
- 108091033319 polynucleotide Proteins 0.000 description 5
- 102000040430 polynucleotide Human genes 0.000 description 5
- 239000002157 polynucleotide Substances 0.000 description 5
- 230000010076 replication Effects 0.000 description 5
- 238000006467 substitution reaction Methods 0.000 description 5
- 230000003390 teratogenic effect Effects 0.000 description 5
- GFFGJBXGBJISGV-UHFFFAOYSA-N Adenine Chemical compound NC1=NC=NC2=C1N=CN2 GFFGJBXGBJISGV-UHFFFAOYSA-N 0.000 description 4
- 229930024421 Adenine Natural products 0.000 description 4
- 102000053602 DNA Human genes 0.000 description 4
- 241000282412 Homo Species 0.000 description 4
- 101000685990 Homo sapiens Specifically androgen-regulated gene protein Proteins 0.000 description 4
- GMZVRMREEHBGGF-UHFFFAOYSA-N Piracetam Chemical compound NC(=O)CN1CCCC1=O GMZVRMREEHBGGF-UHFFFAOYSA-N 0.000 description 4
- 108700008625 Reporter Genes Proteins 0.000 description 4
- 102100023355 Specifically androgen-regulated gene protein Human genes 0.000 description 4
- 229960000643 adenine Drugs 0.000 description 4
- 230000006399 behavior Effects 0.000 description 4
- 230000003542 behavioural effect Effects 0.000 description 4
- 239000012472 biological sample Substances 0.000 description 4
- 239000000090 biomarker Substances 0.000 description 4
- 230000015572 biosynthetic process Effects 0.000 description 4
- 210000004369 blood Anatomy 0.000 description 4
- 239000008280 blood Substances 0.000 description 4
- 201000011510 cancer Diseases 0.000 description 4
- 229940104302 cytosine Drugs 0.000 description 4
- 238000013461 design Methods 0.000 description 4
- 230000002964 excitative effect Effects 0.000 description 4
- 230000007717 exclusion Effects 0.000 description 4
- 239000012634 fragment Substances 0.000 description 4
- 231100000221 frame shift mutation induction Toxicity 0.000 description 4
- 239000000203 mixture Substances 0.000 description 4
- 229960004526 piracetam Drugs 0.000 description 4
- 238000003908 quality control method Methods 0.000 description 4
- 238000011160 research Methods 0.000 description 4
- 230000035945 sensitivity Effects 0.000 description 4
- 230000003997 social interaction Effects 0.000 description 4
- 238000003786 synthesis reaction Methods 0.000 description 4
- 229940113082 thymine Drugs 0.000 description 4
- WGOIHPRRFBCVBZ-VKHMYHEASA-N (2s)-5-oxopyrrolidine-2-carboxamide Chemical group NC(=O)[C@@H]1CCC(=O)N1 WGOIHPRRFBCVBZ-VKHMYHEASA-N 0.000 description 3
- 101150028074 2 gene Proteins 0.000 description 3
- 102100040458 2',3'-cyclic-nucleotide 3'-phosphodiesterase Human genes 0.000 description 3
- 208000033902 22q11.2 duplication syndrome Diseases 0.000 description 3
- 101150090724 3 gene Proteins 0.000 description 3
- 241000972773 Aulopiformes Species 0.000 description 3
- 102100037152 BAG family molecular chaperone regulator 1 Human genes 0.000 description 3
- 108020004635 Complementary DNA Proteins 0.000 description 3
- 206010012289 Dementia Diseases 0.000 description 3
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 3
- 102000018899 Glutamate Receptors Human genes 0.000 description 3
- 108010027915 Glutamate Receptors Proteins 0.000 description 3
- 241001465754 Metazoa Species 0.000 description 3
- 101001024425 Mus musculus Ig gamma-2A chain C region secreted form Proteins 0.000 description 3
- 241000699670 Mus sp. Species 0.000 description 3
- JLCPHMBAVCMARE-UHFFFAOYSA-N [3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[3-[[3-[[3-[[3-[[3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-[[5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(6-aminopurin-9-yl)oxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-5-(4-amino-2-oxopyrimidin-1-yl)oxolan-2-yl]methyl [5-(6-aminopurin-9-yl)-2-(hydroxymethyl)oxolan-3-yl] hydrogen phosphate Polymers Cc1cn(C2CC(OP(O)(=O)OCC3OC(CC3OP(O)(=O)OCC3OC(CC3O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c3nc(N)[nH]c4=O)C(COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3COP(O)(=O)OC3CC(OC3CO)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3ccc(N)nc3=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cc(C)c(=O)[nH]c3=O)n3cc(C)c(=O)[nH]c3=O)n3ccc(N)nc3=O)n3cc(C)c(=O)[nH]c3=O)n3cnc4c3nc(N)[nH]c4=O)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)n3cnc4c(N)ncnc34)O2)c(=O)[nH]c1=O JLCPHMBAVCMARE-UHFFFAOYSA-N 0.000 description 3
- 238000013459 approach Methods 0.000 description 3
- 238000003556 assay Methods 0.000 description 3
- 230000008901 benefit Effects 0.000 description 3
- 210000001124 body fluid Anatomy 0.000 description 3
- 239000010839 body fluid Substances 0.000 description 3
- 230000002759 chromosomal effect Effects 0.000 description 3
- 239000003086 colorant Substances 0.000 description 3
- 230000007423 decrease Effects 0.000 description 3
- 230000006735 deficit Effects 0.000 description 3
- 230000001419 dependent effect Effects 0.000 description 3
- 238000009826 distribution Methods 0.000 description 3
- 229940000406 drug candidate Drugs 0.000 description 3
- 230000013020 embryo development Effects 0.000 description 3
- 230000007613 environmental effect Effects 0.000 description 3
- 235000019688 fish Nutrition 0.000 description 3
- ZHNUHDYFZUAESO-UHFFFAOYSA-N formamide Substances NC=O ZHNUHDYFZUAESO-UHFFFAOYSA-N 0.000 description 3
- 238000009472 formulation Methods 0.000 description 3
- 230000013016 learning Effects 0.000 description 3
- 230000001404 mediated effect Effects 0.000 description 3
- 238000002483 medication Methods 0.000 description 3
- 108010038421 metabotropic glutamate receptor 2 Proteins 0.000 description 3
- 108010038445 metabotropic glutamate receptor 3 Proteins 0.000 description 3
- 108010038450 metabotropic glutamate receptor 6 Proteins 0.000 description 3
- 108010038448 metabotropic glutamate receptor 8 Proteins 0.000 description 3
- 108010014719 metabotropic glutamate receptor type 1 Proteins 0.000 description 3
- 230000035772 mutation Effects 0.000 description 3
- 230000001537 neural effect Effects 0.000 description 3
- 230000036403 neuro physiology Effects 0.000 description 3
- 230000003557 neuropsychological effect Effects 0.000 description 3
- 230000036961 partial effect Effects 0.000 description 3
- 239000000902 placebo Substances 0.000 description 3
- 229940068196 placebo Drugs 0.000 description 3
- 102000054765 polymorphisms of proteins Human genes 0.000 description 3
- 230000008569 process Effects 0.000 description 3
- 108090000765 processed proteins & peptides Proteins 0.000 description 3
- 230000004850 protein–protein interaction Effects 0.000 description 3
- 238000000746 purification Methods 0.000 description 3
- 235000019515 salmon Nutrition 0.000 description 3
- 210000002966 serum Anatomy 0.000 description 3
- 230000019491 signal transduction Effects 0.000 description 3
- 239000007787 solid Substances 0.000 description 3
- 230000007847 structural defect Effects 0.000 description 3
- 239000000126 substance Substances 0.000 description 3
- 231100000378 teratogenic Toxicity 0.000 description 3
- 230000001225 therapeutic effect Effects 0.000 description 3
- 210000002700 urine Anatomy 0.000 description 3
- YBJHBAHKTGYVGT-ZKWXMUAHSA-N (+)-Biotin Chemical compound N1C(=O)N[C@@H]2[C@H](CCCCC(=O)O)SC[C@@H]21 YBJHBAHKTGYVGT-ZKWXMUAHSA-N 0.000 description 2
- 101150084750 1 gene Proteins 0.000 description 2
- WVAKRQOMAINQPU-UHFFFAOYSA-N 2-[4-[2-[5-(2,2-dimethylbutyl)-1h-imidazol-2-yl]ethyl]phenyl]pyridine Chemical compound N1C(CC(C)(C)CC)=CN=C1CCC1=CC=C(C=2N=CC=CC=2)C=C1 WVAKRQOMAINQPU-UHFFFAOYSA-N 0.000 description 2
- 108700028369 Alleles Proteins 0.000 description 2
- 208000009575 Angelman syndrome Diseases 0.000 description 2
- 102000000584 Calmodulin Human genes 0.000 description 2
- 108010041952 Calmodulin Proteins 0.000 description 2
- 108010077544 Chromatin Proteins 0.000 description 2
- 101100505657 Drosophila melanogaster grim gene Proteins 0.000 description 2
- 101150017533 ERP44 gene Proteins 0.000 description 2
- 108700024394 Exon Proteins 0.000 description 2
- 102000007338 Fragile X Mental Retardation Protein Human genes 0.000 description 2
- 108010032606 Fragile X Mental Retardation Protein Proteins 0.000 description 2
- 102100037410 Gigaxonin Human genes 0.000 description 2
- 101000740062 Homo sapiens BAG family molecular chaperone regulator 1 Proteins 0.000 description 2
- 101001025761 Homo sapiens Gigaxonin Proteins 0.000 description 2
- 101000974340 Homo sapiens Nuclear receptor corepressor 1 Proteins 0.000 description 2
- 101001132279 Homo sapiens Ras-related protein Rab-2A Proteins 0.000 description 2
- 101000772888 Homo sapiens Ubiquitin-protein ligase E3A Proteins 0.000 description 2
- 101000777650 Homo sapiens Uncharacterized protein C4orf3 Proteins 0.000 description 2
- 102000004310 Ion Channels Human genes 0.000 description 2
- 108090000862 Ion Channels Proteins 0.000 description 2
- 208000035781 Non-specific syndromic intellectual disability Diseases 0.000 description 2
- 102100022935 Nuclear receptor corepressor 1 Human genes 0.000 description 2
- 238000012408 PCR amplification Methods 0.000 description 2
- 208000028017 Psychotic disease Diseases 0.000 description 2
- 238000011529 RT qPCR Methods 0.000 description 2
- 238000002105 Southern blotting Methods 0.000 description 2
- 108091023040 Transcription factor Proteins 0.000 description 2
- 102000040945 Transcription factor Human genes 0.000 description 2
- 102000005918 Ubiquitin Thiolesterase Human genes 0.000 description 2
- 102100030434 Ubiquitin-protein ligase E3A Human genes 0.000 description 2
- 102100031588 Uncharacterized protein C4orf3 Human genes 0.000 description 2
- 241000700605 Viruses Species 0.000 description 2
- 230000009471 action Effects 0.000 description 2
- 108060000200 adenylate cyclase Proteins 0.000 description 2
- 102000030621 adenylate cyclase Human genes 0.000 description 2
- 150000001413 amino acids Chemical class 0.000 description 2
- 238000000137 annealing Methods 0.000 description 2
- 239000005557 antagonist Substances 0.000 description 2
- 210000004958 brain cell Anatomy 0.000 description 2
- 238000006243 chemical reaction Methods 0.000 description 2
- 210000003483 chromatin Anatomy 0.000 description 2
- 208000013407 communication difficulty Diseases 0.000 description 2
- 208000013577 complex neurodevelopmental disease Diseases 0.000 description 2
- 238000010276 construction Methods 0.000 description 2
- 230000001276 controlling effect Effects 0.000 description 2
- 238000012937 correction Methods 0.000 description 2
- 230000002596 correlated effect Effects 0.000 description 2
- 230000002559 cytogenic effect Effects 0.000 description 2
- 238000001514 detection method Methods 0.000 description 2
- 239000010432 diamond Substances 0.000 description 2
- 238000006471 dimerization reaction Methods 0.000 description 2
- 230000003828 downregulation Effects 0.000 description 2
- 230000008482 dysregulation Effects 0.000 description 2
- 230000002496 gastric effect Effects 0.000 description 2
- 230000009395 genetic defect Effects 0.000 description 2
- 230000009206 glutamatergic signaling Effects 0.000 description 2
- 229910052739 hydrogen Inorganic materials 0.000 description 2
- 239000001257 hydrogen Substances 0.000 description 2
- 230000006872 improvement Effects 0.000 description 2
- 230000005764 inhibitory process Effects 0.000 description 2
- 108091008042 inhibitory receptors Proteins 0.000 description 2
- 230000000977 initiatory effect Effects 0.000 description 2
- 230000001057 ionotropic effect Effects 0.000 description 2
- 210000000265 leukocyte Anatomy 0.000 description 2
- 101150094104 mGluR gene Proteins 0.000 description 2
- 238000004519 manufacturing process Methods 0.000 description 2
- 210000005087 mononuclear cell Anatomy 0.000 description 2
- 238000010172 mouse model Methods 0.000 description 2
- 230000001717 pathogenic effect Effects 0.000 description 2
- 239000013612 plasmid Substances 0.000 description 2
- 229920001184 polypeptide Polymers 0.000 description 2
- 230000035935 pregnancy Effects 0.000 description 2
- 102000004196 processed proteins & peptides Human genes 0.000 description 2
- 230000006916 protein interaction Effects 0.000 description 2
- 230000003989 repetitive behavior Effects 0.000 description 2
- 208000013406 repetitive behavior Diseases 0.000 description 2
- 230000003252 repetitive effect Effects 0.000 description 2
- 238000001209 resonance light scattering Methods 0.000 description 2
- 150000003839 salts Chemical class 0.000 description 2
- 238000012216 screening Methods 0.000 description 2
- 238000001228 spectrum Methods 0.000 description 2
- 230000000946 synaptic effect Effects 0.000 description 2
- 230000002103 transcriptional effect Effects 0.000 description 2
- VLZBRVJVCCNPRJ-KPHUOKFYSA-N (1S,2S)-2-[(1S)-1-amino-1-carboxy-2-(9H-xanthen-9-yl)ethyl]-1-cyclopropanecarboxylic acid Chemical compound C([C@@H]1[C@](CC2C3=CC=CC=C3OC3=CC=CC=C32)(N)C(O)=O)[C@@H]1C(O)=O VLZBRVJVCCNPRJ-KPHUOKFYSA-N 0.000 description 1
- HYOGJHCDLQSAHX-UHFFFAOYSA-N 1-butyl-3-chloro-4-(4-phenylpiperidin-1-yl)pyridin-2-one Chemical compound O=C1N(CCCC)C=CC(N2CCC(CC2)C=2C=CC=CC=2)=C1Cl HYOGJHCDLQSAHX-UHFFFAOYSA-N 0.000 description 1
- 208000004675 22q11 Deletion Syndrome Diseases 0.000 description 1
- YRQCDCNQANSUPB-UHFFFAOYSA-N AMN082 dihydrochloride Chemical compound Cl.Cl.C=1C=CC=CC=1C(C=1C=CC=CC=1)NCCNC(C=1C=CC=CC=1)C1=CC=CC=C1 YRQCDCNQANSUPB-UHFFFAOYSA-N 0.000 description 1
- 108091006112 ATPases Proteins 0.000 description 1
- 206010000117 Abnormal behaviour Diseases 0.000 description 1
- 240000005020 Acaciella glauca Species 0.000 description 1
- 108010085238 Actins Proteins 0.000 description 1
- 102000007469 Actins Human genes 0.000 description 1
- 102000057290 Adenosine Triphosphatases Human genes 0.000 description 1
- 208000024827 Alzheimer disease Diseases 0.000 description 1
- 102100021569 Apoptosis regulator Bcl-2 Human genes 0.000 description 1
- 101710089792 BAG family molecular chaperone regulator 1 Proteins 0.000 description 1
- 101150033765 BAG1 gene Proteins 0.000 description 1
- 108091012583 BCL2 Proteins 0.000 description 1
- 241000894006 Bacteria Species 0.000 description 1
- 206010006187 Breast cancer Diseases 0.000 description 1
- 208000026310 Breast neoplasm Diseases 0.000 description 1
- OYPRJOBELJOOCE-UHFFFAOYSA-N Calcium Chemical compound [Ca] OYPRJOBELJOOCE-UHFFFAOYSA-N 0.000 description 1
- 102000005701 Calcium-Binding Proteins Human genes 0.000 description 1
- 108010045403 Calcium-Binding Proteins Proteins 0.000 description 1
- 206010009269 Cleft palate Diseases 0.000 description 1
- 108010060434 Co-Repressor Proteins Proteins 0.000 description 1
- 102000008169 Co-Repressor Proteins Human genes 0.000 description 1
- 208000028698 Cognitive impairment Diseases 0.000 description 1
- 208000020401 Depressive disease Diseases 0.000 description 1
- 206010013654 Drug abuse Diseases 0.000 description 1
- 206010059866 Drug resistance Diseases 0.000 description 1
- 208000006586 Ectromelia Diseases 0.000 description 1
- 241000206602 Eukaryota Species 0.000 description 1
- 206010073513 Exposure during pregnancy Diseases 0.000 description 1
- 102000003688 G-Protein-Coupled Receptors Human genes 0.000 description 1
- 108090000045 G-Protein-Coupled Receptors Proteins 0.000 description 1
- 108700039691 Genetic Promoter Regions Proteins 0.000 description 1
- 108010009202 Growth Factor Receptors Proteins 0.000 description 1
- 102000009465 Growth Factor Receptors Human genes 0.000 description 1
- 102000003964 Histone deacetylase Human genes 0.000 description 1
- 108090000353 Histone deacetylase Proteins 0.000 description 1
- 102000009331 Homeodomain Proteins Human genes 0.000 description 1
- 108010048671 Homeodomain Proteins Proteins 0.000 description 1
- 101000996111 Homo sapiens Neuroligin-4, X-linked Proteins 0.000 description 1
- 101001125071 Homo sapiens Neuromedin-K receptor Proteins 0.000 description 1
- 101000613614 Homo sapiens Protein mono-ADP-ribosyltransferase PARP10 Proteins 0.000 description 1
- 208000026350 Inborn Genetic disease Diseases 0.000 description 1
- ROHFNLRQFUQHCH-YFKPBYRVSA-N L-leucine Chemical compound CC(C)C[C@H](N)C(O)=O ROHFNLRQFUQHCH-YFKPBYRVSA-N 0.000 description 1
- 241001487991 Lettuce chlorosis virus Species 0.000 description 1
- ROHFNLRQFUQHCH-UHFFFAOYSA-N Leucine Natural products CC(C)CC(N)C(O)=O ROHFNLRQFUQHCH-UHFFFAOYSA-N 0.000 description 1
- 206010024503 Limb reduction defect Diseases 0.000 description 1
- 102000018697 Membrane Proteins Human genes 0.000 description 1
- 108010052285 Membrane Proteins Proteins 0.000 description 1
- 208000024556 Mendelian disease Diseases 0.000 description 1
- 108060004795 Methyltransferase Proteins 0.000 description 1
- 208000019695 Migraine disease Diseases 0.000 description 1
- 206010027603 Migraine headaches Diseases 0.000 description 1
- 241000699666 Mus <mouse, genus> Species 0.000 description 1
- 208000029726 Neurodevelopmental disease Diseases 0.000 description 1
- NHXYSAFTNPANFK-HDMCBQFHSA-N Neurokinin B Chemical compound C([C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](CCSC)C(N)=O)C(C)C)NC(=O)[C@H](CC=1C=CC=CC=1)NC(=O)[C@H](CC(O)=O)NC(=O)[C@H](CC=1N=CNC=1)NC(=O)[C@H](CCSC)NC(=O)[C@@H](N)CC(O)=O)C1=CC=CC=C1 NHXYSAFTNPANFK-HDMCBQFHSA-N 0.000 description 1
- 102000009493 Neurokinin receptors Human genes 0.000 description 1
- 108050000302 Neurokinin receptors Proteins 0.000 description 1
- 102100034441 Neuroligin-4, X-linked Human genes 0.000 description 1
- 102100029409 Neuromedin-K receptor Human genes 0.000 description 1
- 238000000636 Northern blotting Methods 0.000 description 1
- 108020005497 Nuclear hormone receptor Proteins 0.000 description 1
- 108020005187 Oligonucleotide Probes Proteins 0.000 description 1
- 108700020796 Oncogene Proteins 0.000 description 1
- 241000531743 Pelargonium trifidum Species 0.000 description 1
- 108090000608 Phosphoric Monoester Hydrolases Proteins 0.000 description 1
- 102000004160 Phosphoric Monoester Hydrolases Human genes 0.000 description 1
- 108091000080 Phosphotransferase Proteins 0.000 description 1
- 108010061844 Poly(ADP-ribose) Polymerases Proteins 0.000 description 1
- 102000012338 Poly(ADP-ribose) Polymerases Human genes 0.000 description 1
- 229920000776 Poly(Adenosine diphosphate-ribose) polymerase Polymers 0.000 description 1
- 102100040847 Protein mono-ADP-ribosyltransferase PARP10 Human genes 0.000 description 1
- 206010037180 Psychiatric symptoms Diseases 0.000 description 1
- 101150018472 RANBP1 gene Proteins 0.000 description 1
- 241000700159 Rattus Species 0.000 description 1
- 108020004682 Single-Stranded DNA Proteins 0.000 description 1
- 108091027568 Single-stranded nucleotide Proteins 0.000 description 1
- 108700025695 Suppressor Genes Proteins 0.000 description 1
- 102100033009 Tachykinin-3 Human genes 0.000 description 1
- 101710149429 Tachykinin-3 Proteins 0.000 description 1
- 206010043275 Teratogenicity Diseases 0.000 description 1
- 230000005856 abnormality Effects 0.000 description 1
- 230000036982 action potential Effects 0.000 description 1
- 230000004913 activation Effects 0.000 description 1
- 239000004480 active ingredient Substances 0.000 description 1
- 239000000556 agonist Substances 0.000 description 1
- 235000013334 alcoholic beverage Nutrition 0.000 description 1
- 230000001668 ameliorated effect Effects 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 230000002424 anti-apoptotic effect Effects 0.000 description 1
- 230000001745 anti-biotin effect Effects 0.000 description 1
- 230000001773 anti-convulsant effect Effects 0.000 description 1
- 230000000692 anti-sense effect Effects 0.000 description 1
- 239000001961 anticonvulsive agent Substances 0.000 description 1
- 229960003965 antiepileptics Drugs 0.000 description 1
- 239000002246 antineoplastic agent Substances 0.000 description 1
- 230000005775 apoptotic pathway Effects 0.000 description 1
- 230000006907 apoptotic process Effects 0.000 description 1
- VHGCDTVCOLNTBX-QGZVFWFLSA-N atomoxetine Chemical compound O([C@H](CCNC)C=1C=CC=CC=1)C1=CC=CC=C1C VHGCDTVCOLNTBX-QGZVFWFLSA-N 0.000 description 1
- 229960002430 atomoxetine Drugs 0.000 description 1
- 208000022379 autosomal dominant Opitz G/BBB syndrome Diseases 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- 238000004166 bioassay Methods 0.000 description 1
- 230000004071 biological effect Effects 0.000 description 1
- 230000008236 biological pathway Effects 0.000 description 1
- 230000033228 biological regulation Effects 0.000 description 1
- 229960002685 biotin Drugs 0.000 description 1
- 235000020958 biotin Nutrition 0.000 description 1
- 239000011616 biotin Substances 0.000 description 1
- 210000004556 brain Anatomy 0.000 description 1
- 238000009395 breeding Methods 0.000 description 1
- 230000001488 breeding effect Effects 0.000 description 1
- 229910052791 calcium Inorganic materials 0.000 description 1
- 239000011575 calcium Substances 0.000 description 1
- 229910052799 carbon Inorganic materials 0.000 description 1
- 230000024245 cell differentiation Effects 0.000 description 1
- 230000004663 cell proliferation Effects 0.000 description 1
- 206010008118 cerebral infarction Diseases 0.000 description 1
- 210000001175 cerebrospinal fluid Anatomy 0.000 description 1
- 208000026106 cerebrovascular disease Diseases 0.000 description 1
- 208000009890 chromosome 22q11.2 microduplication syndrome Diseases 0.000 description 1
- 238000004140 cleaning Methods 0.000 description 1
- 238000010367 cloning Methods 0.000 description 1
- 208000010877 cognitive disease Diseases 0.000 description 1
- 230000001149 cognitive effect Effects 0.000 description 1
- 230000037411 cognitive enhancing Effects 0.000 description 1
- 238000013264 cohort analysis Methods 0.000 description 1
- 238000002648 combination therapy Methods 0.000 description 1
- 230000006854 communication Effects 0.000 description 1
- 238000004891 communication Methods 0.000 description 1
- 208000029404 congenital absence of upper arm and forearm with hand present Diseases 0.000 description 1
- 230000000875 corresponding effect Effects 0.000 description 1
- 230000001186 cumulative effect Effects 0.000 description 1
- 238000005520 cutting process Methods 0.000 description 1
- 230000003247 decreasing effect Effects 0.000 description 1
- 239000005547 deoxyribonucleotide Substances 0.000 description 1
- 125000002637 deoxyribonucleotide group Chemical group 0.000 description 1
- 238000010586 diagram Methods 0.000 description 1
- LZXMUJCJAWVHPZ-UHFFFAOYSA-N dipraglurant Chemical compound C=1N2C=C(F)C=CC2=NC=1CCC#CC1=CC=CC=N1 LZXMUJCJAWVHPZ-UHFFFAOYSA-N 0.000 description 1
- 239000003937 drug carrier Substances 0.000 description 1
- 210000001671 embryonic stem cell Anatomy 0.000 description 1
- 239000003623 enhancer Substances 0.000 description 1
- 238000001976 enzyme digestion Methods 0.000 description 1
- 229960004756 ethanol Drugs 0.000 description 1
- 238000013213 extrapolation Methods 0.000 description 1
- 230000002349 favourable effect Effects 0.000 description 1
- 239000012530 fluid Substances 0.000 description 1
- 230000005714 functional activity Effects 0.000 description 1
- 208000016361 genetic disease Diseases 0.000 description 1
- 238000000732 glass refractive index measurement Methods 0.000 description 1
- 229940121372 histone deacetylase inhibitor Drugs 0.000 description 1
- 239000003276 histone deacetylase inhibitor Substances 0.000 description 1
- 210000005260 human cell Anatomy 0.000 description 1
- 150000004677 hydrates Chemical class 0.000 description 1
- 125000002887 hydroxy group Chemical group [H]O* 0.000 description 1
- 239000002117 illicit drug Substances 0.000 description 1
- 238000003018 immunoassay Methods 0.000 description 1
- 101150030475 impact gene Proteins 0.000 description 1
- 238000007901 in situ hybridization Methods 0.000 description 1
- 238000000338 in vitro Methods 0.000 description 1
- 230000002401 inhibitory effect Effects 0.000 description 1
- 239000003999 initiator Substances 0.000 description 1
- 238000007689 inspection Methods 0.000 description 1
- 150000002500 ions Chemical class 0.000 description 1
- 238000002955 isolation Methods 0.000 description 1
- 238000005304 joining Methods 0.000 description 1
- 238000002372 labelling Methods 0.000 description 1
- 230000004807 localization Effects 0.000 description 1
- 229940124807 mGLUR antagonist Drugs 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 230000008774 maternal effect Effects 0.000 description 1
- 239000011159 matrix material Substances 0.000 description 1
- 238000005259 measurement Methods 0.000 description 1
- 230000003340 mental effect Effects 0.000 description 1
- 230000002503 metabolic effect Effects 0.000 description 1
- OJLOPKGSLYJEMD-URPKTTJQSA-N methyl 7-[(1r,2r,3r)-3-hydroxy-2-[(1e)-4-hydroxy-4-methyloct-1-en-1-yl]-5-oxocyclopentyl]heptanoate Chemical compound CCCCC(C)(O)C\C=C\[C@H]1[C@H](O)CC(=O)[C@@H]1CCCCCCC(=O)OC OJLOPKGSLYJEMD-URPKTTJQSA-N 0.000 description 1
- 229960005249 misoprostol Drugs 0.000 description 1
- 238000010369 molecular cloning Methods 0.000 description 1
- 238000012544 monitoring process Methods 0.000 description 1
- 229940127237 mood stabilizer Drugs 0.000 description 1
- 239000004050 mood stabilizer Substances 0.000 description 1
- 229940126662 negative allosteric modulator Drugs 0.000 description 1
- 230000003988 neural development Effects 0.000 description 1
- 210000001178 neural stem cell Anatomy 0.000 description 1
- 230000004770 neurodegeneration Effects 0.000 description 1
- 208000015122 neurodegenerative disease Diseases 0.000 description 1
- 230000007472 neurodevelopment Effects 0.000 description 1
- 230000001123 neurodevelopmental effect Effects 0.000 description 1
- 239000002858 neurotransmitter agent Substances 0.000 description 1
- 230000001777 nootropic effect Effects 0.000 description 1
- 230000002474 noradrenergic effect Effects 0.000 description 1
- 238000010606 normalization Methods 0.000 description 1
- 102000006255 nuclear receptors Human genes 0.000 description 1
- 108020004017 nuclear receptors Proteins 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 238000001668 nucleic acid synthesis Methods 0.000 description 1
- 239000002777 nucleoside Substances 0.000 description 1
- 230000000474 nursing effect Effects 0.000 description 1
- 239000002751 oligonucleotide probe Substances 0.000 description 1
- 230000008506 pathogenesis Effects 0.000 description 1
- 230000007310 pathophysiology Effects 0.000 description 1
- 238000003068 pathway analysis Methods 0.000 description 1
- 238000011458 pharmacological treatment Methods 0.000 description 1
- 102000020233 phosphotransferase Human genes 0.000 description 1
- 210000002381 plasma Anatomy 0.000 description 1
- 210000004910 pleural fluid Anatomy 0.000 description 1
- 229940126027 positive allosteric modulator Drugs 0.000 description 1
- 230000000270 postfertilization Effects 0.000 description 1
- 239000002243 precursor Substances 0.000 description 1
- 238000000513 principal component analysis Methods 0.000 description 1
- 208000020016 psychiatric disease Diseases 0.000 description 1
- 238000003127 radioimmunoassay Methods 0.000 description 1
- 230000007115 recruitment Effects 0.000 description 1
- 230000009467 reduction Effects 0.000 description 1
- 235000003499 redwood Nutrition 0.000 description 1
- 230000022983 regulation of cell cycle Effects 0.000 description 1
- 230000026267 regulation of growth Effects 0.000 description 1
- 230000004043 responsiveness Effects 0.000 description 1
- 238000007894 restriction fragment length polymorphism technique Methods 0.000 description 1
- 210000003705 ribosome Anatomy 0.000 description 1
- 238000011808 rodent model Methods 0.000 description 1
- 201000005404 rubella Diseases 0.000 description 1
- 210000003296 saliva Anatomy 0.000 description 1
- 239000004576 sand Substances 0.000 description 1
- 230000028327 secretion Effects 0.000 description 1
- CJUDSKIRZCSXJA-UHFFFAOYSA-M sodium;3-(n-ethyl-3-methoxyanilino)-2-hydroxypropane-1-sulfonate Chemical compound [Na+].[O-]S(=O)(=O)CC(O)CN(CC)C1=CC=CC(OC)=C1 CJUDSKIRZCSXJA-UHFFFAOYSA-M 0.000 description 1
- 241000894007 species Species 0.000 description 1
- 239000000021 stimulant Substances 0.000 description 1
- 230000004936 stimulating effect Effects 0.000 description 1
- 230000000638 stimulation Effects 0.000 description 1
- 208000011117 substance-related disease Diseases 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- 210000000225 synapse Anatomy 0.000 description 1
- 230000024587 synaptic transmission, glutamatergic Effects 0.000 description 1
- 238000010189 synthetic method Methods 0.000 description 1
- 230000008685 targeting Effects 0.000 description 1
- 210000001138 tear Anatomy 0.000 description 1
- 231100000211 teratogenicity Toxicity 0.000 description 1
- 238000012549 training Methods 0.000 description 1
- 238000013518 transcription Methods 0.000 description 1
- 230000035897 transcription Effects 0.000 description 1
- 229960000575 trastuzumab Drugs 0.000 description 1
- 150000005691 triesters Chemical class 0.000 description 1
- 239000001226 triphosphate Substances 0.000 description 1
- 235000011178 triphosphate Nutrition 0.000 description 1
- 230000003827 upregulation Effects 0.000 description 1
- 210000004291 uterus Anatomy 0.000 description 1
- 238000010200 validation analysis Methods 0.000 description 1
- 201000000866 velocardiofacial syndrome Diseases 0.000 description 1
- 238000001086 yeast two-hybrid system Methods 0.000 description 1
Classifications
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
- A61K31/00—Medicinal preparations containing organic active ingredients
- A61K31/33—Heterocyclic compounds
- A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
- A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
- A61K31/44—Non condensed pyridines; Hydrogenated derivatives thereof
- A61K31/445—Non condensed piperidines, e.g. piperocaine
- A61K31/4523—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems
- A61K31/454—Non condensed piperidines, e.g. piperocaine containing further heterocyclic ring systems containing a five-membered ring with nitrogen as a ring hetero atom, e.g. pimozide, domperidone
-
- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P25/00—Drugs for disorders of the nervous system
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6813—Hybridisation assays
- C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
-
- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/156—Polymorphic or mutational markers
-
- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2800/00—Detection or diagnosis of diseases
- G01N2800/28—Neurological disorders
Landscapes
- Health & Medical Sciences (AREA)
- Chemical & Material Sciences (AREA)
- Life Sciences & Earth Sciences (AREA)
- Organic Chemistry (AREA)
- General Health & Medical Sciences (AREA)
- Engineering & Computer Science (AREA)
- Proteomics, Peptides & Aminoacids (AREA)
- Public Health (AREA)
- Genetics & Genomics (AREA)
- Analytical Chemistry (AREA)
- Animal Behavior & Ethology (AREA)
- Pharmacology & Pharmacy (AREA)
- Medicinal Chemistry (AREA)
- Veterinary Medicine (AREA)
- Bioinformatics & Cheminformatics (AREA)
- Wood Science & Technology (AREA)
- Zoology (AREA)
- Biophysics (AREA)
- Biochemistry (AREA)
- General Engineering & Computer Science (AREA)
- Molecular Biology (AREA)
- Biomedical Technology (AREA)
- Neurology (AREA)
- Neurosurgery (AREA)
- Chemical Kinetics & Catalysis (AREA)
- General Chemical & Material Sciences (AREA)
- Microbiology (AREA)
- Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
- Immunology (AREA)
- Biotechnology (AREA)
- Physics & Mathematics (AREA)
- Pathology (AREA)
- Epidemiology (AREA)
- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
Methods for diagnosing and treating autism spectral disorders are encompassed. In one embodiment, a patient is diagnosed as having autism spectral disorder if at least one CNV in an mGluR network gene is found in a patient sample. Patients with at least one mGluR network gene CNV are effectively treated with (+) - 5-oxo-Dprolinepiperidinamide monohydrate (NS-105) (also known as NFC-1 or fasoracetam).
Description
METHODS OF DIAGNOSING AND TREATING AUTISM
CROSS-REFERENCE TO RELATED APPLICATIONS
[001] This application claims priority to United States Nonprovisional Patent Application No. 14/740, 230, filed June 15, 2015, as well as to United States Provisional Patent Applications 62/215,628, 62/215,633, 62/215,636, and 62/215,673, all of which were filed September 8, 2015. All of the above-listed applications are incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
CROSS-REFERENCE TO RELATED APPLICATIONS
[001] This application claims priority to United States Nonprovisional Patent Application No. 14/740, 230, filed June 15, 2015, as well as to United States Provisional Patent Applications 62/215,628, 62/215,633, 62/215,636, and 62/215,673, all of which were filed September 8, 2015. All of the above-listed applications are incorporated herein by reference in their entirety.
FIELD OF THE INVENTION
[002] Methods for diagnosing and treating autism spectrum disorders are provided.
BACKGROUND OF THE INVENTION
BACKGROUND OF THE INVENTION
[003] Autism spectrum disorder (ASD) is a range of complex neurodevelopmental disorders characterized by mild to severe social impairments, communication difficulties, and restrictive or repetitive behaviors. ASD, previously known as pervasive developmental disorders (PDD), is an umbrella term that includes various conditions that used to be diagnosed separately such as autistic disorder (or classic autism), Asperger's syndrome, childhood disintegrative disorder, Retf s disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD). (Vieux et al., "Autism Spectrum Disorder: DSM-5 Changes, Epidemiology & Outcomes," The Car/at Report, Vol. 11, Issue 6, June 2013.)
[004] ASD occurs in all racial, ethnic, and socioeconomic groups. (Durkin et al., "Socioeconomic inequality in the prevalence of autism spectrum disorder:
evidence from a U.S. cross-sectional study," PLOS One, 5(7), July 2010.) In 2013, ASD was estimated to occur in 2% of children between the ages of 6 and 17, a significant increase from the estimate of 1.16% in 2007. (see, e.g., Blumberg et. al., National Health Statistics Reports, No. 65, March 20, 2013) While it is not known how many adults suffer from ASD, a British study reported that 1.8% adult men and 0.2%
adult women have ASD. (Brugha et al., "Epidemiology of autism spectrum disorders in adults in the community in England," Arch. Gen. Psych. 68: 459-66, 2011.)
evidence from a U.S. cross-sectional study," PLOS One, 5(7), July 2010.) In 2013, ASD was estimated to occur in 2% of children between the ages of 6 and 17, a significant increase from the estimate of 1.16% in 2007. (see, e.g., Blumberg et. al., National Health Statistics Reports, No. 65, March 20, 2013) While it is not known how many adults suffer from ASD, a British study reported that 1.8% adult men and 0.2%
adult women have ASD. (Brugha et al., "Epidemiology of autism spectrum disorders in adults in the community in England," Arch. Gen. Psych. 68: 459-66, 2011.)
[005] With the increased incidence of ASD comes increased costs to society.
The CDC estimates that it costs between $17,000 -$21,000 more per year to care for a child diagnosed with ASD as compared to a child not diagnosed with ASD.
Medical costs alone for children diagnosed with ASD can be elevated by $4,100-$6,200 per year, with behavioral interventions for children diagnosed with ASD costing $40,000 -$60,000 per year. It is estimated that total societal costs of caring for children diagnosed with ASD were over $9 billion in 2011.
The CDC estimates that it costs between $17,000 -$21,000 more per year to care for a child diagnosed with ASD as compared to a child not diagnosed with ASD.
Medical costs alone for children diagnosed with ASD can be elevated by $4,100-$6,200 per year, with behavioral interventions for children diagnosed with ASD costing $40,000 -$60,000 per year. It is estimated that total societal costs of caring for children diagnosed with ASD were over $9 billion in 2011.
[006] Some risk factors and patterns have emerged to assist in diagnosing ASD, and various treatment regimes are often used on a trial and error basis.
While there have been improvements in diagnosis and treatment of ASD, there remains a need for consistent diagnosis and treatment of ASD using a genetic approach.
SUMMARY OF THE INVENTION
While there have been improvements in diagnosis and treatment of ASD, there remains a need for consistent diagnosis and treatment of ASD using a genetic approach.
SUMMARY OF THE INVENTION
[007] In accordance with the description, a method for treating autism spectrum disorder (ASD) in patients having at least one CNV in a GRM/mGluR
network gene, as shown in Figures 15A-D, comprising administering a therapeutically effective amount of fasoracetam (NS-105 or NFC-1), or member of the piracetam family of nootropic agents, is encompassed. CNVs in GRM/mGluR network genes are sensitive and specific biomarkers for diagnosing ASD. The inventors have identified drug candidates that specifically activate mGluRs, restoring normal neurophysiology in ASD patients having at least one CNV in any of the GRM/mGluR network genes shown in Figures 15A-D.
network gene, as shown in Figures 15A-D, comprising administering a therapeutically effective amount of fasoracetam (NS-105 or NFC-1), or member of the piracetam family of nootropic agents, is encompassed. CNVs in GRM/mGluR network genes are sensitive and specific biomarkers for diagnosing ASD. The inventors have identified drug candidates that specifically activate mGluRs, restoring normal neurophysiology in ASD patients having at least one CNV in any of the GRM/mGluR network genes shown in Figures 15A-D.
[008] In some embodiments, a CNV in at least one of the GRM/mGluR
network genes recited in Tables 16-18 indicates a diagnosis of ASD. These genes include ACAT1, ACAT2, ACCN1, ACCN2, ACP1, ACTB, ACTR2, ADA, ADCY1, ADD1, ADD2, ADORA1, ADRA1B, ADRA2A, ADRA2C, ADRB2, ADRBK1, ALDOA, ANXA2, APP, APTX, AQP1, ARHGAP24, ARL15, ARRB1, ARRB2, ATXN7L3, BDKRB1, BDKRB2, BTBD2, BTG2, C17orf44, C1orf116, C7orf25, CA8, CACNA1B, CACYBP, CALB2, CALM1, CALM2, CALM3, CAMK1, CAMK2B, CAMK4, CCNB1, CDC42, CENTG1, CHGB, CHP, CHRM2, CHRM3, GIG, CMPK, CNP, CNR1, CNTN4, COPB2, CRHR1, CTNNA2, CYCS, DCN, DHCR7, DISC1, DLST, DPP6, DRD2, DRD3, DSTN, DYNLL1, ECHS1, EGFR, EIF3S3, ERBB2, F2R, F2RL2, F2RL3, F3, FKBP3, FPR1, FSCN1, FURIN, FYN, GAPDH, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNA01, GNAQ, GNB2L1, GOT1, GP1BA, GPR26, GRB2, GRB7, GRIA1, GRIK1, GRIK3, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GSN, HBXIP, HD, HNRPA3, HOMER1, HOMER3, HRPT2, HSP90AB1, HTR2A, IL8RB, IMPDH2, IQGAP2, ITGB1, ITGB7, ITPR1, KIAA0090, KIAA1683, LAMA4, LARP7, LRP2BP, LRRC59, LTA, LYAR, LYN, MAP4, MAPK1, MAPT, MARK4, MC4R, MGC11082, MRPL14, MRPS16, MTHFD1, MTNR1A, MTNR1B, MX1, MYC, MY06, NANS, NARG1, NCK1, NEGRI., NFKBIA, NLN, NMI, NPY2R, NUDC, OPRD1, PAFAH1B3, PCBP1, PCBP3, PCDHA4, PCID1, PCMT1, PDCD5, PDE1B, PDE1C, PDE6G, PGM1, PHKB, PHKG2, PICK1, PIK3CA, PIK3R1, PLA2G7, PLCB1, PLCB3, PLCG2, PPIH, PPP2R1A, PRDX1, PRKCA, PRLHR, PRMT1, PRPSAP1, PSAT1, PSEN1, PSMA1, PSMC1, PSMD1, PSMD11, PSMD13, PSMD6, PSME1, PTHR2, PXN, PYGL, PYGM, QRICH2, RAB2, RALA, RANBP1, RAP2A, RCC1, RCC2, RGS12, RGS2, RHOA, RIF1, RPA2, RPLP2, RPN2, RPS14, RRM1, RUVBL2, RYR1, RYR2, S100A6, SACS, SARS, SCTR, SDC3, SELE, SERPINB9, SET, SETD4, 5F3B14, SGTB, SHANK1, SHBG, SIAH1, SLC2A1, SLC6A3, SLC7A10, SNCA, SNRPB2, 50056, 50057, SORD, SRC, STAU1, STRAP, STX12, SYK, TBCA, TBXA2R, TCP1, TEAD3, TFAM, TGM2, TJP1, TK1, TLR10, TMEM4, TNIK, TPI1, TRAF2, TRMT112, TUBA1, TUBA1A, TUBA1B, TUBA2, TUBB, TUBG1, TXN, TXNDC4, TXNL2, TYMS, UBQLN4, UCHL1, U5P24, VHL, VIPR1, WHAQ, and ZAP70.
network genes recited in Tables 16-18 indicates a diagnosis of ASD. These genes include ACAT1, ACAT2, ACCN1, ACCN2, ACP1, ACTB, ACTR2, ADA, ADCY1, ADD1, ADD2, ADORA1, ADRA1B, ADRA2A, ADRA2C, ADRB2, ADRBK1, ALDOA, ANXA2, APP, APTX, AQP1, ARHGAP24, ARL15, ARRB1, ARRB2, ATXN7L3, BDKRB1, BDKRB2, BTBD2, BTG2, C17orf44, C1orf116, C7orf25, CA8, CACNA1B, CACYBP, CALB2, CALM1, CALM2, CALM3, CAMK1, CAMK2B, CAMK4, CCNB1, CDC42, CENTG1, CHGB, CHP, CHRM2, CHRM3, GIG, CMPK, CNP, CNR1, CNTN4, COPB2, CRHR1, CTNNA2, CYCS, DCN, DHCR7, DISC1, DLST, DPP6, DRD2, DRD3, DSTN, DYNLL1, ECHS1, EGFR, EIF3S3, ERBB2, F2R, F2RL2, F2RL3, F3, FKBP3, FPR1, FSCN1, FURIN, FYN, GAPDH, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNA01, GNAQ, GNB2L1, GOT1, GP1BA, GPR26, GRB2, GRB7, GRIA1, GRIK1, GRIK3, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GSN, HBXIP, HD, HNRPA3, HOMER1, HOMER3, HRPT2, HSP90AB1, HTR2A, IL8RB, IMPDH2, IQGAP2, ITGB1, ITGB7, ITPR1, KIAA0090, KIAA1683, LAMA4, LARP7, LRP2BP, LRRC59, LTA, LYAR, LYN, MAP4, MAPK1, MAPT, MARK4, MC4R, MGC11082, MRPL14, MRPS16, MTHFD1, MTNR1A, MTNR1B, MX1, MYC, MY06, NANS, NARG1, NCK1, NEGRI., NFKBIA, NLN, NMI, NPY2R, NUDC, OPRD1, PAFAH1B3, PCBP1, PCBP3, PCDHA4, PCID1, PCMT1, PDCD5, PDE1B, PDE1C, PDE6G, PGM1, PHKB, PHKG2, PICK1, PIK3CA, PIK3R1, PLA2G7, PLCB1, PLCB3, PLCG2, PPIH, PPP2R1A, PRDX1, PRKCA, PRLHR, PRMT1, PRPSAP1, PSAT1, PSEN1, PSMA1, PSMC1, PSMD1, PSMD11, PSMD13, PSMD6, PSME1, PTHR2, PXN, PYGL, PYGM, QRICH2, RAB2, RALA, RANBP1, RAP2A, RCC1, RCC2, RGS12, RGS2, RHOA, RIF1, RPA2, RPLP2, RPN2, RPS14, RRM1, RUVBL2, RYR1, RYR2, S100A6, SACS, SARS, SCTR, SDC3, SELE, SERPINB9, SET, SETD4, 5F3B14, SGTB, SHANK1, SHBG, SIAH1, SLC2A1, SLC6A3, SLC7A10, SNCA, SNRPB2, 50056, 50057, SORD, SRC, STAU1, STRAP, STX12, SYK, TBCA, TBXA2R, TCP1, TEAD3, TFAM, TGM2, TJP1, TK1, TLR10, TMEM4, TNIK, TPI1, TRAF2, TRMT112, TUBA1, TUBA1A, TUBA1B, TUBA2, TUBB, TUBG1, TXN, TXNDC4, TXNL2, TYMS, UBQLN4, UCHL1, U5P24, VHL, VIPR1, WHAQ, and ZAP70.
[009] Moreover, patients with at least one CNV in a GRM/mGluR network gene will see improvement in ASD upon administration of a therapeutically effective amount of a member of the piracetam family of nootropic agents, as described in F.
Gualtieri et al., Curr. Phann. Des., 8: 125-38 (2002). In one embodiment, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al. In one embodiment the nootropic agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (fasoracetam; NS-105).
Gualtieri et al., Curr. Phann. Des., 8: 125-38 (2002). In one embodiment, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al. In one embodiment the nootropic agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (fasoracetam; NS-105).
[0010] In one embodiment, the patient has been diagnosed as having pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Retf s disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), or social (pragmatic) communication disorder (SCD).
[0011] The CNV may be a duplication or deletion.
[0012] The ASD may be syndromic or non-syndromic.
[0013] In one embodiment, the ASD may be in a patient having 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy.
[0014] In one embodiment, the patient has at least two CNVs in a gene selected from the group consisting of ACAT1, ACAT2, ACCN1, ACCN2, ACP1, ACTB, ACTR2, ADA, ADCY1, ADD1, ADD2, ADORA1, ADRA1B, ADRA2A, ADRA2C, ADRB2, ADRBK1, ALDOA, ANXA2, APP, APTX, AQP1, ARHGAP24, ARL15, ARRB1, ARRB2, ATXN7L3, BDKRB1, BDKRB2, BTBD2, BTG2, C17orf44, C1orf116, C7orf25, CA8, CACNA1B, CACYBP, CALB2, CALM1, CALM2, CALM3, CAMK1, CAMK2B, CAMK4, CCNB1, CDC42, CENTG1, CHGB, CHP, CHRM2, CHRM3, GIG, CMPK, CNP, CNR1, CNTN4, COPB2, CRHR1, CTNNA2, CYCS, DCN, DHCR7, DISCI, DLST, DPP6, DRD2, DRD3, DSTN, DYNLL1, ECHS1, EGFR, EIF353, ERBB2, F2R, F2RL2, F2RL3, F3, FKBP3, FPR1, FSCN1, FURIN, FYN, GAPDH, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNA01, GNAQ, GNB2L1, GOT1, GP1BA, GPR26, GRB2, GRB7, GRIA1, GRIK1, GRIK3, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GSN, HBXIP, HD, HNRPA3, HOMER1, HOMER3, HRPT2, HSP90AB1, HTR2A, IL8RB, IMPDH2, IQGAP2, ITGB1, ITGB7, ITPR1, KIAA0090, KIAA1683, LAMA4, LARP7, LRP2BP, LRRC59, LTA, LYAR, LYN, MAP4, MAPK1, MAPT, MARK4, MC4R, MGC11082, MRPL14, MRPS16, MTHFD1, MTNR1A, MTNR1B, MX1, MYC, MY06, NANS, NARG1, NCK1, NEGRI, NFKBIA, NLN, NMI, NPY2R, NUDC, OPRD1, PAFAH1B3, PCBP1, PCBP3, PCDHA4, PCID1, PCMT1, PDCD5, PDE1B, PDE1C, PDE6G, PGM1, PHKB, PHKG2, PICK1, PIK3CA, PIK3R1, PLA2G7, PLCB1, PLCB3, PLCG2, PPIH, PPP2R1A, PRDX1, PRKCA, PRLHR, PRMT1, PRPSAP1, PSAT1, PSEN1, PSMA1, PSMC1, PSMD1, PSMD11, PSMD13, PSMD6, PSME1, PTHR2, PXN, PYGL, PYGM, QRICH2, RAB2, RALA, RANBP1, RAP2A, RCC1, RCC2, RGS12, RGS2, RHOA, RIF1, RPA2, RPLP2, RPN2, RPS14, RRM1, RUVBL2, RYR1, RYR2, 5100A6, SACS, SARS, SCTR, SDC3, SELE, SERPINB9, SET, SETD4, 5F3B14, SGTB, SHANK1, SHBG, SIAH1, SLC2A1, SLC6A3, SLC7A10, SNCA, SNRPB2, SOCS6, SOCS7, SORD, SRC, STAU1, STRAP, STX12, SYK, TBCA, TBXA2R, TCP1, TEAD3, TFAM, TGM2, TJP1, TK1, TLR10, TMEM4, TNIK, TPI1, TRAF2, TRMT112, TUBA1, TUBA1A, TUBA1B, TUBA2, TUBB, TUBG1, TXN, TXNDC4, TXNL2, TYMS, UBQLN4, UCHL1, USP24, VHL, VIPR1, WHAQ, and ZAP70.
[0015] In one embodiment, the CNVs are detected in any type of biological sample taken from a human patient, including but not limited to, body fluids (including blood, urine, serum, gastric lavage), any type of cell (such as brain cells, white blood cells, mononuclear cells) or body tissue.
[0016] Methods for determining whether a patient has a GRM/mGluR
network gene CNV include, for example, analyzing the biological sample on a SNP-array, taking into account both LOG-R ratio (intensity data) and BAF (B allele frequency), which assesses allele states. SNP array platforms are commercially available from, for example, Illumina, Affymetrix, and Agilent.
network gene CNV include, for example, analyzing the biological sample on a SNP-array, taking into account both LOG-R ratio (intensity data) and BAF (B allele frequency), which assesses allele states. SNP array platforms are commercially available from, for example, Illumina, Affymetrix, and Agilent.
[0017] Other methods for determining whether a patient has a GRM/mGluR
network gene CNV include, for example, CGH (comparative genomic hybridization), which utilizes intensity data for evaluation of CNVs; whole exome or whole genome sequencing (or targeted sequencing); utilizing specific FISH probes; qPCR;
droplet PCR; and taqman probes. Alternatively, certain companies that use proprietary methods for determining the presence or absence of CNVs may be provided samples to be tested for presence of CNVs in GRM/mGluR network genes in accordance with the methods of the invention.
network gene CNV include, for example, CGH (comparative genomic hybridization), which utilizes intensity data for evaluation of CNVs; whole exome or whole genome sequencing (or targeted sequencing); utilizing specific FISH probes; qPCR;
droplet PCR; and taqman probes. Alternatively, certain companies that use proprietary methods for determining the presence or absence of CNVs may be provided samples to be tested for presence of CNVs in GRM/mGluR network genes in accordance with the methods of the invention.
[0018] Some embodiments include methods of treating autism in a subject comprising administering an effective amount of a nonselective activator of metabotropic glutamate receptors (mGluRs) to a subject, thereby improving at least one symptom of autism. Some embodiments include treating autism in a subject comprising administering an effective amount of a nonselective activator of metabotropic glutamate receptors (mGluRs) to a subject that has at least one genetic alteration in an mGluR network gene (e.g. as shown in Figures 16-18), thereby improving at least one symptom of autism. Some embodiments include methods of treating autism in a subject comprising obtaining results from a genetic screen that determines whether a subject has a genetic alteration in an mGluR network gene, and, if the results show that the subject has at least one genetic alteration in an mGluR network gene, treating the subject by administering an effective amount of a nonselective activator of mGluRs. In some such embodiments, the genetic alteration is a copy number variation (CNV) or single nucleotide variation (SNV). In some such embodiments, the nonselective activator of mGluRs is fasoracetam, such as fasoracetam monohydrate (NS-105 or NFC-1).
[0019] In methods comprising fasoracetam administration, the fasoracetam may be administered at a dose of 50 mg, 100mg, 150 mg, 200 mg, 250 mg, 300 mg, mg, or 400 mg, wherein the dose is administered once, twice, or three times daily. For example, fasoracetam may be administered at a dose of 50-400 mg, 100-400 mg, or 200-400 mg, wherein the dose is administered once, twice, or three times daily. For example, the fasoracetam is administered at a dose of 200-400 mg, such as 200 mg, 300 mg, or 400 mg, wherein the dose is administered twice daily.
[0020] In some of the above embodiments, the subject has a CNV in at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 mGluR network genes. For example, the subject may have a CNV in an mGluR network gene, which is found by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes. In other cases, the subject may have a CNV in an mGluR
network gene that is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes. In yet other cases the subject may have a CNV in an mGluR network gene that is determined by obtaining a nucleic acid sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes. In some embodiments, the screen does not assess CNVs in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, or GRM8. In some embodiments, the subject does not have a CNV in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRA47, or GRA48.
network gene that is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes. In yet other cases the subject may have a CNV in an mGluR network gene that is determined by obtaining a nucleic acid sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes. In some embodiments, the screen does not assess CNVs in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, or GRM8. In some embodiments, the subject does not have a CNV in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRA47, or GRA48.
[0021] In some of the above embodiments, the subject is a pediatric subject, for instance between the ages of 5 and 17, 5 and 8, 8 and 17, 8 and 12, or 12 and 17. In other embodiments the subject is an adult.
[0022] In some embodiments above, the nonselective activator of mGluRs is administered in combination with another pharmaceutical or non-pharmaceutical therapy.
[0023] In some of the above embodiments, the subject has been diagnosed with autism spectrum disorder, pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD). In some cases, the autism is syndromic ASD. In some cases, the patient has ASD and 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy. In some embodiments, the patient does not have any of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In other cases, the autism patient also has one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression.
[0024] Also encompassed herein are methods for diagnosing autism in a subject comprising isolating a nucleic acid comprising sample from a subject, analyzing the sample for the presence or absence of a genetic alteration in at least one mGluR
network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene. Further encompassed are methods for diagnosing autism in a subject comprising isolating a nucleic acid comprising sample from a subject, isolating nucleic acid from the sample, analyzing the nucleic acid for the presence or absence of a genetic alteration in at least one mGluR network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene.
Additional embodiments include methods for identifying a subject as having autism comprising obtaining a sample from a patient, optionally isolating nucleic acid from the sample, optionally amplifying the nucleic acid, and analyzing the nucleic acid in the sample for the presence or absence of a genetic alteration, such as a CNV, in at least one mGluR
network gene, wherein the subject is identified as having autism if at least one genetic alteration, such as a CNV, in an mGluR network gene is detected. Further encompassed are methods for diagnosing autism in a subject comprising analyzing genetic information about one or more mGluR network genes, comparing the subject's information to a control subject that does not have autism, and diagnosing autism if the genetic information suggests that the subject has at least one genetic alteration in a mGluRne twork gene. Also encompassed are methods of confirming a diagnosis of autism in a subject comprising: obtaining a nucleic acid-comprising sample from a subject diagnosed with autism by a method that comprises detecting or analyzing genetic alterations in mGluR network genes; optionally amplifying the nucleic acid in the sample; and determining whether the subject has at least one genetic alteration, such as a CNV, in an mGluR network gene; and confirming a diagnosis of autism if the subject has at least one genetic alteration in an mGluR network gene. In any of those methods, the analysis for the presence or absence of at least one genetic alteration in an mGluR
network gene can comprise microarrays, whole genome sequencing, exome sequencing, targeted sequencing, FISH, comparative genomic hybridization, genome mapping, or other methods using next-generation sequencing, Sanger sequencing, PCR, or TaqMan technologies.
network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene. Further encompassed are methods for diagnosing autism in a subject comprising isolating a nucleic acid comprising sample from a subject, isolating nucleic acid from the sample, analyzing the nucleic acid for the presence or absence of a genetic alteration in at least one mGluR network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene.
Additional embodiments include methods for identifying a subject as having autism comprising obtaining a sample from a patient, optionally isolating nucleic acid from the sample, optionally amplifying the nucleic acid, and analyzing the nucleic acid in the sample for the presence or absence of a genetic alteration, such as a CNV, in at least one mGluR
network gene, wherein the subject is identified as having autism if at least one genetic alteration, such as a CNV, in an mGluR network gene is detected. Further encompassed are methods for diagnosing autism in a subject comprising analyzing genetic information about one or more mGluR network genes, comparing the subject's information to a control subject that does not have autism, and diagnosing autism if the genetic information suggests that the subject has at least one genetic alteration in a mGluRne twork gene. Also encompassed are methods of confirming a diagnosis of autism in a subject comprising: obtaining a nucleic acid-comprising sample from a subject diagnosed with autism by a method that comprises detecting or analyzing genetic alterations in mGluR network genes; optionally amplifying the nucleic acid in the sample; and determining whether the subject has at least one genetic alteration, such as a CNV, in an mGluR network gene; and confirming a diagnosis of autism if the subject has at least one genetic alteration in an mGluR network gene. In any of those methods, the analysis for the presence or absence of at least one genetic alteration in an mGluR
network gene can comprise microarrays, whole genome sequencing, exome sequencing, targeted sequencing, FISH, comparative genomic hybridization, genome mapping, or other methods using next-generation sequencing, Sanger sequencing, PCR, or TaqMan technologies.
[0025] In some embodiments, the subject has CNVs in at least two mGluR
network genes. In some embodiments, the method comprises detecting CNVs in mGluR network genes by subjecting the sample to a screen that assesses CNVs in at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes.
network genes. In some embodiments, the method comprises detecting CNVs in mGluR network genes by subjecting the sample to a screen that assesses CNVs in at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes. In some embodiments, CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes.
[0026] In some of the above embodiments, the subject is a pediatric subject, such as a subject between the ages of Sand 17,5 and 8, 8 and 17, 8 and 12, or 12 and 17.
In other embodiments, the subject is an adult subject.
In other embodiments, the subject is an adult subject.
[0027] In some embodiments, the subject is not assessed for genetic alterations or CNVs in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, and GRM8.
[0028] In some embodiments, the method for determining the presence or absence of at least one mGluR network gene genetic alteration comprises microarrays, whole genome sequencing, exome sequencing, targeted sequencing, FISH, comparative genomic hybridization, genome mapping, or other methods using next-generation sequencing, Sanger sequencing, PCR, or TaqMan technologies.
[0029] In some of the above embodiments, the subject has been diagnosed with autism spectrum disorder, pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD). In some cases, the autism is syndromic ASD. In some cases, the patient has ASD and 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy. In some embodiments, the patient does not have any of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In other cases, the autism patient also has one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In some cases, the patient has both autism and ADHD.
[0030] Additional objects and advantages will be set forth in part in the description which follows, and in part will be obvious from the description, or may be learned by practice. The objects and advantages will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims.
[0031] It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the claims.
[0032] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several embodiments and together with the description, serve to explain the principles described herein.
BRIEF DESCRIPTION OF THE DRAWINGS
BRIEF DESCRIPTION OF THE DRAWINGS
[0033] Figure 1 provides the design of a clinical study. In this two-stage design, 2076 cases vs 4754 controls were used in the discovery cohort (Stage 1), and 1159 cases vs 2546 controls were used for a replication cohort (Stage 2). All samples used passed minimal quality control metrics, but the default quality calls of PennCNV
were used to discriminate the discovery cohort (best quality) from the replication cohort (lesser quality.)
were used to discriminate the discovery cohort (best quality) from the replication cohort (lesser quality.)
[0034] Figure 2 is a graph showing certain classes of gene pathways, which are disrupted by the ASD-related CNVRs disclosed herein. All genes with exons disrupted by replicated CNVRs were submitted to Ingenuity to ascertain significance of pathway enrichment.
[0035] Figures 3A-F are a schematic of a first-degree interactome of the GABAR-A family highlighting copy number defects enriched in cases vs controls.
[0036] Figure 4 shows a test and treat model for targeting therapeutics to specific pathways defective in disease. The generic test and treat model is shown in black where a molecular diagnostic is used to genetically define a population with defective pathways that are likely to benefit from a targeted intervention.
Examples of tras tuzumab as a targeted intervention for HER2 specific breast cancer is shown as well as an extrapolation of behavioral programs and novel therapeutics that are being developed to target ASDs due to defective GABAR-A pathways.
Examples of tras tuzumab as a targeted intervention for HER2 specific breast cancer is shown as well as an extrapolation of behavioral programs and novel therapeutics that are being developed to target ASDs due to defective GABAR-A pathways.
[0037] Figure 5 shows certain identified genetic marker CNVRs by GWAS
predictive of ASDs in European-derived or African-derived populations. The Manhattan plots show the -log 10 transformed P value of association for each CNVR
along the genome. Adjacent chromosomes are shown. The regions discovered in Europeans (P 0.0001) that replicated in Africans (P<=0.001) are highlighted with black arrows labeled by chromosome band. GWAS of 4,634 cases vs 4,726 controls in Europeans is shown on top and GWAS of 312 cases vs 4,173 controls in Africans is shown below.
predictive of ASDs in European-derived or African-derived populations. The Manhattan plots show the -log 10 transformed P value of association for each CNVR
along the genome. Adjacent chromosomes are shown. The regions discovered in Europeans (P 0.0001) that replicated in Africans (P<=0.001) are highlighted with black arrows labeled by chromosome band. GWAS of 4,634 cases vs 4,726 controls in Europeans is shown on top and GWAS of 312 cases vs 4,173 controls in Africans is shown below.
[0038] Figures 6A-D show a representative enrichment of certain CNVRs across mGluR network of genes. Nodes of the network are labeled with their gene names, with red and green representing deletions and duplications respectively, while grey nodes lack CNV data. Dark and light colors represent enrichment in cases and controls respectively. The genes defining the network are showed as diamonds, while all other genes are shown as circles. Blue lines indicate evidence of interaction.
[0039] Figure 7 shows a representative graph of enrichment of optimal CNVRs across the CALM1 network. The first degree directed interaction network defined by CALM1 is shown.
[0040] Figure 8 shows a diagram of representative study design. Results from this study show that children with ASD and gene changes in mGluR network (mGluR+ASD) were more likely to have Syndromic ASD as compared to children with ASD without abnormalities of mGluR network genes (mGluR-ASD). P<0.0001.
See US Patent application no. 14/292,480 incorporated herein by reference as though set forth in full.
See US Patent application no. 14/292,480 incorporated herein by reference as though set forth in full.
[0041] Figure 9 shows significant CNVRs in the mGluR network. The table shows the 10 most significant CNVRs for 189 genes with data in the GFIN for the GRM gene family across a European-derived population, as well as the most significant CNVRs harbored by the GRM mGluR receptors themselves.
[0042] Figure 10 shows significant CNVRs across genes in the MXD network in European-derived populations. Where large CNVs span multiple genes, the component gene implicated within the MXD gene family interaction network is bolded.
[0043] Figure 11 shows significant CNVRs across genes in the CALM1 network in European-derived populations.
[0044] Figure 12 shows CNVRs distinguishing cases from controls significant across both European-derived populations (I3 0.0001 by Fisher's exact test) and African-derived populations (P 0.001). CNVR=copy-number variable region;
OR=odds ratio. For each CNVR, the table lists the type (del or dup), the closest gene impacted, the chromosomal band, the approximate size of the defect (Kb), the number of contributing SNPs, the numbers of affected cases and controls, as well as P-value and odds ratio (OR) from Fisher's exact test for across all populations, and subsets of European-derived and African-derived populations. *Genes with an asterisk (*) harbor CNVRs that disrupt their exons of directly, while those without the asterisk are located in the genomic region around the intergenic CNVRs.
OR=odds ratio. For each CNVR, the table lists the type (del or dup), the closest gene impacted, the chromosomal band, the approximate size of the defect (Kb), the number of contributing SNPs, the numbers of affected cases and controls, as well as P-value and odds ratio (OR) from Fisher's exact test for across all populations, and subsets of European-derived and African-derived populations. *Genes with an asterisk (*) harbor CNVRs that disrupt their exons of directly, while those without the asterisk are located in the genomic region around the intergenic CNVRs.
[0045] Figures 13A-B show significant gene family interaction networks (GFINs) by network permutation testing (Pperm0.05) enriched for CNV defects across at least 5% of cases. The table lists the name and size of gene family tested, the number and frequency of network genes enriched in the second degree gene interaction network, the number and frequency of cases harboring defects across the network, the number and frequency of controls harboring defects across the network, the significance of association by Fisher's exact test, the enrichment of CNV
defects in cases, and the significance of that enrichment by 1,000 random network permutations.
defects in cases, and the significance of that enrichment by 1,000 random network permutations.
[0046] Figure 14 shows significant individual gene interaction networks ranked by permutation testing. Figure 14 lists the name and gene family member tested, the number and frequency of network genes enriched, the number and frequency of cases harbouring defects, the number and frequency of controls harbouring defects, and the significance of association by Fisher's exact test, the odds ratio of the effect size, and the significance of association by random permutation of network while controlling for number of genes tested. Among other highly ranked first degree gene interaction networks were the nuclear receptor co-repressor (NCOR1; Pfisher 1.11E-06, enrichment=13.37, Pperm 0.004) and BCL2-associated athanogene 1 (BAG1; Pfisher 2.18E-04, enrichment=15.40, Pperm 0.014) networks. NCOR1 is a transcriptional co-regulatory protein that appears to assist nuclear receptors in the downregulation of DNA expression through recruitment of histone deacetylases to DNA promoter regions; it is a principal regulator in neural stem cells. The oncogene BCL2 is a membrane protein that blocks the apoptosis pathway, and BAG1 forms a BCL2-associated athanogene and represents a link between growth factor receptors and antiapoptotic mechanisms. The BAG1 gene has been implicated in age-related neurodegenerative diseases, including Alzheimer's disease.
[0047] Figures 15A-D show the raw data described in Examples 1-4. Column A lists the GRNI/mGluR network genes that are enriched in patients with ASD.
Column B indicates whether the CNV is a duplication or deletion and the genetic start and stop locus. The odds ratio recited in column J recites "none" for any gene where no CNV was found in the control group. In column K, enrichment, the word "case" is indicative of enrichment in CNVs in the associated gene in ASD
patients as compared to controls. Finding at least one CNV in any of the genes listed in Figures 15A-D, Column A, indicates a diagnosis of ASD and implicates treatment with NS-105.
Column B indicates whether the CNV is a duplication or deletion and the genetic start and stop locus. The odds ratio recited in column J recites "none" for any gene where no CNV was found in the control group. In column K, enrichment, the word "case" is indicative of enrichment in CNVs in the associated gene in ASD
patients as compared to controls. Finding at least one CNV in any of the genes listed in Figures 15A-D, Column A, indicates a diagnosis of ASD and implicates treatment with NS-105.
[0048] Figures 16A-D show the mGluR network genes included in the Tier 1 gene set. These genes have 2 degrees of protein-protein interaction with mGluR
genes (GRA41-8) based on the Cytoscape Human Interactome, which is software for integrating biomolecular interaction networks with high-throughput data (as described in Shannon P (2003) Genome Research 13:2498-2 304). The Tier 1 gene set includes 76 genes. The exact location for each gene in Tier 1 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from 500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19. The start single nucleotide polymorphism (StartSNP) (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) are also listed. Genes of the mGluRs themselves are noted as "GRIM."
The expanded regions (i.e., 500kg up and down stream) frequently harbor regulatory elements and if impacted by a CNV, can have the same impact on the gene expression and function as a CNV residing in the gene sequence itself.
genes (GRA41-8) based on the Cytoscape Human Interactome, which is software for integrating biomolecular interaction networks with high-throughput data (as described in Shannon P (2003) Genome Research 13:2498-2 304). The Tier 1 gene set includes 76 genes. The exact location for each gene in Tier 1 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from 500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19. The start single nucleotide polymorphism (StartSNP) (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) are also listed. Genes of the mGluRs themselves are noted as "GRIM."
The expanded regions (i.e., 500kg up and down stream) frequently harbor regulatory elements and if impacted by a CNV, can have the same impact on the gene expression and function as a CNV residing in the gene sequence itself.
[0049] Figures 17A-I show the mGluR network genes included in the Tier 2 gene set. These genes have 2 degrees of protein-protein interaction with mGluR
genes (GRM1-8) based on the Cytoscape Human Interactome but exclude genes from Tier 1. The Tier 2 gene set includes 197 genes. The exact location for each gene in Tier 2 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19.
The start single nucleotide polymorphism (StartSNP) (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) in hg19 are also listed.
genes (GRM1-8) based on the Cytoscape Human Interactome but exclude genes from Tier 1. The Tier 2 gene set includes 197 genes. The exact location for each gene in Tier 2 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19.
The start single nucleotide polymorphism (StartSNP) (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) in hg19 are also listed.
[0050] Figures 18A-Y shows genes within the Tier 3 gene set. Genes with reciprocal gene querying with 2 degrees of protein-protein interaction with mGluR
genes based on Cytoscape Human Interactome are included. Genes contained within Tiers 1 and 2 are excluded from Tier 3. The Tier 3 gene set includes 599 genes. The exact location for each gene in Tier 3 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from 500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19. The StartSNP (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) in hg19 are also listed.
DESCRIPTION OF PARTICULAR EMBODIMENTS
Definitions
genes based on Cytoscape Human Interactome are included. Genes contained within Tiers 1 and 2 are excluded from Tier 3. The Tier 3 gene set includes 599 genes. The exact location for each gene in Tier 3 is listed in both the Human Genome version 18 (hg18) and Human Genome version 19 (hg19). In addition, the exact gene location plus 500 kilobase (i.e., the range from 500 kilobase before and 500 kilobase after the gene of interest) is listed for hg19. The StartSNP (i.e., the SNP located 500 kilobases before the gene of interest) and the EndSNP (i.e., the SNP located 500 kilobases after the gene of interest) in hg19 are also listed.
DESCRIPTION OF PARTICULAR EMBODIMENTS
Definitions
[0051] In this invention, "a" or "an" means "at least one" or "one or more,"
etc., unless clearly indicated otherwise by context. The term "or" means "and/or"
unless stated otherwise. In the case of a multiple-dependent claim, however, use of the term "or" refers back to more than one preceding claim in the alternative only.
etc., unless clearly indicated otherwise by context. The term "or" means "and/or"
unless stated otherwise. In the case of a multiple-dependent claim, however, use of the term "or" refers back to more than one preceding claim in the alternative only.
[0052] "Autism" and "Autism Spectrum Disorder" (ASD) are used interchangeably herein. As noted earlier, autism or ASD comprises a range of complex neurodevelopmental disorders characterized by symptoms such as mild to severe social impairments, communication difficulties, and restrictive or repetitive behaviors. ASD, previously known as pervasive developmental disorders (PDD), is an umbrella term that includes various conditions that used to be diagnosed separately such as autistic disorder (or classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD).
[0053] An "mGluR" or metabotropic glutamate receptor refers to one of eight glutamate receptors expressed in neural tissue named mGluR1, mGluR2, mGluR3, mGluR4, mGluR5, mGluR6, mGluR7, and mGluR8. Their genes are abbreviated GRM1 to GRM8. The mGluR proteins are G-protein-coupled receptors. They are typically placed into three sub-groups, Group I receptors including mGluR1 and mGluR5 are classed as slow excitatory receptors. Group II includes mGluR2 and mGluR3. Group III includes mGluR4, mGluR6, mGluR7, and mGluR8. Groups II
and III are classed as slow inhibitory receptors. The mGluRs are distinguished from the ionotropic GluRs or iGluRs, which are ion channel-associated glutamate receptors and are classed as fast excitatory receptors.
and III are classed as slow inhibitory receptors. The mGluRs are distinguished from the ionotropic GluRs or iGluRs, which are ion channel-associated glutamate receptors and are classed as fast excitatory receptors.
[0054] An "mGluR network gene," for purposes of this invention, comprises not only the mGluR genes GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, and GRM8, but also each of the other genes listed herein in Figs. 16-18 as well as the regions of DNA that regulate the genes listed in Figs 16-18. In addition, "mGluR
network proteins" are the proteins encoded by the mGluR network genes.
network proteins" are the proteins encoded by the mGluR network genes.
[0055] The mGluR network genes are grouped into three subsets: Tier 1, Tier2, and Tier 3. (See Figs. 16-18.) Tier 1 mGluR network genes, shown in Figs.
16A-D, comprise 76 genes, including some GRM genes themselves as well as a number of other genes. The Tier 2 mGluR network genes, shown in Figs. 17A-I, comprise 197 genes, and exclude the Tier 1 genes.
16A-D, comprise 76 genes, including some GRM genes themselves as well as a number of other genes. The Tier 2 mGluR network genes, shown in Figs. 17A-I, comprise 197 genes, and exclude the Tier 1 genes.
[0056] Tiers 1 and 2 together are included in the "primary mGluR network."
The "primary network" of mGluR genes also includes the genes 4-Sep, L00642393, and L00653098, for a total of 276 genes. There are presently technical difficulties in assessing the 4-Sep, L00642393, and L00653098 genes. Thus, they are not included in the genes of Tiers 1 and 2, although they are included in the primary network of genes of the present invention. The genes of Tier 1 and Tier 2 differ in that alterations in Tier 1 genes had been documented in previous geno typing studies of subjects suffering from mental disorders.
The "primary network" of mGluR genes also includes the genes 4-Sep, L00642393, and L00653098, for a total of 276 genes. There are presently technical difficulties in assessing the 4-Sep, L00642393, and L00653098 genes. Thus, they are not included in the genes of Tiers 1 and 2, although they are included in the primary network of genes of the present invention. The genes of Tier 1 and Tier 2 differ in that alterations in Tier 1 genes had been documented in previous geno typing studies of subjects suffering from mental disorders.
[0057] Tier 3 mGluR network genes, shown in Figs. 18A-Y, comprise 599 genes that are in the distal part of the mGluR network based on the merged human interactome provided by the Cytoscape Software (Shannon P et al. (2003) Genorne Research 13:2498- 2304), and exclude the Tier 1 and Tier 2 genes. The Tier 3 genes are thus part of the "distal mGluR network." In addition to the Tier 3 genes, the genes LOC285147, LOC147004, and L0C93444 are included in the "distal mGluR
network," although they were not assessed in the present study and are not included in Tier 3 due to technical difficulties in assessing genetic alterations in these genes.
network," although they were not assessed in the present study and are not included in Tier 3 due to technical difficulties in assessing genetic alterations in these genes.
[0058] A "genetic alteration" as used herein means any alteration in the DNA
of a gene, or in the DNA regulating a gene, that results in a gene product that is functionally changed as compared to a gene product produced from a non-altered DNA. A functional change may be differing expression levels (up-regulation or down-regulation) or loss or change in one or more biological activities, for example. A genetic alteration includes without limitation, copy number variations (CNVs), single nucleotide variants (SNVs), also called single nucleotide polymorphisms (SNPs) herein, frame shift mutations, or any other base pair subs titutions, insertions, and deletions or duplications.
of a gene, or in the DNA regulating a gene, that results in a gene product that is functionally changed as compared to a gene product produced from a non-altered DNA. A functional change may be differing expression levels (up-regulation or down-regulation) or loss or change in one or more biological activities, for example. A genetic alteration includes without limitation, copy number variations (CNVs), single nucleotide variants (SNVs), also called single nucleotide polymorphisms (SNPs) herein, frame shift mutations, or any other base pair subs titutions, insertions, and deletions or duplications.
[0059] A "copy number variation (CNV)" refers to the number of copies of a particular gene in the genotype of an individual. CNVs represent a major genetic component of human phenotypic diversity. Susceptibility to genetic disorders is known to be associated not only with single nucleotide polymorphisms (SNP), but also with structural and other genetic variations, including CNVs. A CNV
represents a copy number change involving a DNA fragment that is -1 kilobases (kb) or larger (Feuk et al. 2006a). CNVs described herein do not include those variants that arise from the insertion/deletion of transposable elements (e.g., .about.6-kb KpnI
repeats) to minimize the complexity of future CNV analyses. The term CNV therefore encompasses previously introduced terms such as large-scale copy number variants (LCVs; Iafrate et al. 2004), copy number polymorphisms (CNPs; Sebat et al.
2004), and intermediate-sized variants (ISVs; Tuzun et al. 2005), but not retroposon insertions.
represents a copy number change involving a DNA fragment that is -1 kilobases (kb) or larger (Feuk et al. 2006a). CNVs described herein do not include those variants that arise from the insertion/deletion of transposable elements (e.g., .about.6-kb KpnI
repeats) to minimize the complexity of future CNV analyses. The term CNV therefore encompasses previously introduced terms such as large-scale copy number variants (LCVs; Iafrate et al. 2004), copy number polymorphisms (CNPs; Sebat et al.
2004), and intermediate-sized variants (ISVs; Tuzun et al. 2005), but not retroposon insertions.
[0060] A "CNV deletion" or "deletion CNV" or similar terms refer to a CNV in which a gene, DNA segment regulating a gene, or gene segment is deleted. A
"CNV
duplication" or "duplication CNV" or similar terms refer to a CNV in which a gene, DNA segment regulating a gene, or gene segment is present in at least two, and possibly more than two, copies in comparison with the single copy found in a normal reference genome.
"CNV
duplication" or "duplication CNV" or similar terms refer to a CNV in which a gene, DNA segment regulating a gene, or gene segment is present in at least two, and possibly more than two, copies in comparison with the single copy found in a normal reference genome.
[0061] A "single nucleotide polymorphism (SNP)" refers to a change in which a single base in the DNA differs from the usual base at that position. These single base changes are called SNPs or "snips." Millions of SNP's have been cataloged in the human genome. Some SNPs such as that which causes sickle cell are responsible for disease. Other SNPs are normal variations in the genome.
[0062] A "sample" refers to a sample from a subject that may be tested, for example, for presence of a CNV in one or more mGluR network proteins, as described herein. The sample may comprise cells, and it may comprise body fluids, such as blood, serum, plasma, cerebral spinal fluid, urine, saliva, tears, pleural fluid, and the like.
[0063] The terms "subject" and "patient" are used interchangeably to refer to a human. The terms "pediatric subject" or "pediatric patient" are used interchangeably to refer to a human less than 18 years of age. An "adult patient" refers to a human 18 years of age or older.
[0064] "Target nucleic acid" as used herein refers to a previously defined region of a nucleic acid present in a complex nucleic acid mixture wherein the defined wild-type region contains at least one known nucleotide variation, which may or may not be associated with autism. The nucleic acid molecule may be isolated from a natural source by cDNA cloning or subtractive hybridization or synthesized manually. The nucleic acid molecule may be synthesized manually by the triester synthetic method or by using an automated DNA synthesizer.
[0065] With regard to nucleic acids used in the invention, the term "isolated nucleic acid" is sometimes employed. This term, when applied to DNA, refers to a DNA molecule that is separated from sequences with which it is immediately contiguous (in the 5' and 3' directions) in the naturally occurring genome of the organism from which it was derived. For example, the "isolated nucleic acid"
may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a prokaryote or eukaryote. An "isolated nucleic acid molecule" may also comprise a cDNA molecule. An isolated nucleic acid molecule inserted into a vector is also sometimes referred to herein as a recombinant nucleic acid molecule.
may comprise a DNA molecule inserted into a vector, such as a plasmid or virus vector, or integrated into the genomic DNA of a prokaryote or eukaryote. An "isolated nucleic acid molecule" may also comprise a cDNA molecule. An isolated nucleic acid molecule inserted into a vector is also sometimes referred to herein as a recombinant nucleic acid molecule.
[0066] With respect to RNA molecules, the term "isolated nucleic acid"
primarily refers to an RNA molecule encoded by an isolated DNA molecule as defined above. Alternatively, the term may refer to an RNA molecule that has been sufficiently separated from RNA molecules with which it would be associated in its natural state (i.e., in cells or tissues), such that it exists in a "substantially pure" form.
primarily refers to an RNA molecule encoded by an isolated DNA molecule as defined above. Alternatively, the term may refer to an RNA molecule that has been sufficiently separated from RNA molecules with which it would be associated in its natural state (i.e., in cells or tissues), such that it exists in a "substantially pure" form.
[0067] By the use of the term "enriched" in reference to nucleic acid it is meant that the specific DNA or RNA sequence constitutes a significantly higher fraction (2-5 fold) of the total DNA or RNA present in the cells or solution of interest than in normal cells or in the cells from which the sequence was taken. This could be caused by a person by preferential reduction in the amount of other DNA
or RNA present, or by a preferential increase in the amount of the specific DNA or RNA sequence, or by a combination of the two. However, it should be noted that "enriched" does not imply that there are no other DNA or RNA sequences present, just that the relative amount of the sequence of interest has been significantly increased.
or RNA present, or by a preferential increase in the amount of the specific DNA or RNA sequence, or by a combination of the two. However, it should be noted that "enriched" does not imply that there are no other DNA or RNA sequences present, just that the relative amount of the sequence of interest has been significantly increased.
[0068] It is also advantageous for some purposes that a nucleotide sequence be in purified form. The term "purified" in reference to nucleic acid does not require absolute purity (such as a homogeneous preparation); instead, it represents an indication that the sequence is relatively purer than in the natural environment (compared to the natural level, this level should be at least 2-5 fold greater, e.g., in terms of mg/ml). Individual clones isolated from a cDNA library may be purified to electrophore tic homogeneity. The claimed DNA molecules obtained from these clones can be obtained directly from total DNA or from total RNA. The cDNA
clones are not naturally occurring, but rather are preferably obtained via manipulation of a partially purified naturally occurring substance (messenger RNA). The construction of a cDNA library from mRNA involves the creation of a synthetic substance (cDNA) and pure individual cDNA clones can be isolated from the synthetic library by clonal selection of the cells carrying the cDNA library.
Thus, the process which includes the construction of a cDNA library from mRNA and isolation of distinct cDNA clones yields an approximately 10-6-fold purification of the native message. Thus, purification of at least one order of magnitude, preferably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated.
clones are not naturally occurring, but rather are preferably obtained via manipulation of a partially purified naturally occurring substance (messenger RNA). The construction of a cDNA library from mRNA involves the creation of a synthetic substance (cDNA) and pure individual cDNA clones can be isolated from the synthetic library by clonal selection of the cells carrying the cDNA library.
Thus, the process which includes the construction of a cDNA library from mRNA and isolation of distinct cDNA clones yields an approximately 10-6-fold purification of the native message. Thus, purification of at least one order of magnitude, preferably two or three orders, and more preferably four or five orders of magnitude is expressly contemplated.
[0069] The term "substantially pure" refers to a preparation comprising at least 50-60% by weight the compound of interest (e.g., nucleic acid, oligonucleotide, etc.). More preferably, the preparation comprises at least 75% by weight, and most preferably 90-99% by weight, the compound of interest. Purity is measured by methods appropriate for the compound of interest.
[0070] The term "complementary" describes two nucleotides that can form multiple favorable interactions with one another. For example, adenine is complementary to thymine as they can form two hydrogen bonds. Similarly, guanine and cytosine are complementary since they can form three hydrogen bonds. Thus if a nucleic acid sequence contains the following sequence of bases, thymine, adenine, guanine and cytosine, a "complement" of this nucleic acid molecule would be a molecule containing adenine in the place of thymine, thymine in the place of adenine, cytosine in the place of guanine, and guanine in the place of cytosine.
Because the complement can contain a nucleic acid sequence that forms optimal interactions with the parent nucleic acid molecule, such a complement can bind with high affinity to its parent molecule.
Because the complement can contain a nucleic acid sequence that forms optimal interactions with the parent nucleic acid molecule, such a complement can bind with high affinity to its parent molecule.
[0071] With respect to single stranded nucleic acids, particularly oligonucleotides, the term "specifically hybridizing" refers to the association between two single-stranded nucleotide molecules of sufficiently complementary sequence to permit such hybridization under pre-determined conditions generally used in the art (sometimes termed "substantially complementary"). In particular, the term refers to hybridization of an oligonucleotide with a substantially complementary sequence contained within a single-stranded DNA or RNA molecule of the invention, to the substantial exclusion of hybridization of the oligonucleotide with single-stranded nucleic acids of non-complementary sequence. For example, specific hybridization can refer to a sequence which hybridizes to any autism specific marker gene or nucleic acid, but does not hybridize to other nucleotides. Also polynucleo tide which "specifically hybridizes" may hybridize only to a neurospecific specific marker, such an autism-specific marker shown in the Table contained herein. Appropriate conditions enabling specific hybridization of single stranded nucleic acid molecules of varying complementarity are well known in the art.
[0072] For instance, one common formula for calculating the stringency conditions required to achieve hybridization between nucleic acid molecules of a specified sequence homology is set forth below (Sambrook et al., Molecular Cloning, Cold Spring Harbor Laboratory (1989):
Tm=81.5 degrees C+16.6 Log [Nal +0.41( /o G+C)-0.63(% formamide)-600/#bp in duplex
Tm=81.5 degrees C+16.6 Log [Nal +0.41( /o G+C)-0.63(% formamide)-600/#bp in duplex
[0073] As an illustration of the above formula, using [Nal = [0.368] and 50%
formamide, with GC content of 42% and an average probe size of 200 bases, the Tm is 57 degrees C. The Tm of a DNA duplex decreases by 1-1.5 degrees C with every 1% decrease in homology. Thus, targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42 degrees C.
formamide, with GC content of 42% and an average probe size of 200 bases, the Tm is 57 degrees C. The Tm of a DNA duplex decreases by 1-1.5 degrees C with every 1% decrease in homology. Thus, targets with greater than about 75% sequence identity would be observed using a hybridization temperature of 42 degrees C.
[0074] The stringency of the hybridization and wash depend primarily on the salt concentration and temperature of the solutions. In general, to maximize the rate of annealing of the probe with its target, the hybridization is usually carried out at salt and temperature conditions that are 20-25 degrees C below the calculated Tm of the hybrid.
[0075] Wash conditions should be as stringent as possible for the degree of identity of the probe for the target. In general, wash conditions are selected to be approximately 12-20 degrees C below the Tm of the hybrid. In regards to the nucleic acids of the current invention, a moderate stringency hybridization is defined as hybridization in 6xSSC, 5xDenhardt's solution, 0.5% SDS and 100 micro-gram/ml denatured salmon sperm DNA at 42 degree C, and washed in 2xSSC and 0.5% SDS
at 55 degree C for 15 minutes. A high stringency hybridization is defined as hybridization in 6xSSC, 5x Denhardt's solution, 0.5% SDS and 100 micro-gram/ml denatured salmon sperm DNA at 42 degree C, and washed in 1xSSC and 0.5% SDS
at 65 degree C for 15 minutes. A very high stringency hybridization is defined as hybridization in 6xSSC, 5x Denhardt's solution, 0.5% SDS and 100 micro-gram/ml denatured salmon sperm DNA at 42 degree C, and washed in 0.1xSSC and 0.5% SDS
at 65 degrees C for 15 minutes.
at 55 degree C for 15 minutes. A high stringency hybridization is defined as hybridization in 6xSSC, 5x Denhardt's solution, 0.5% SDS and 100 micro-gram/ml denatured salmon sperm DNA at 42 degree C, and washed in 1xSSC and 0.5% SDS
at 65 degree C for 15 minutes. A very high stringency hybridization is defined as hybridization in 6xSSC, 5x Denhardt's solution, 0.5% SDS and 100 micro-gram/ml denatured salmon sperm DNA at 42 degree C, and washed in 0.1xSSC and 0.5% SDS
at 65 degrees C for 15 minutes.
[0076] The term "oligonucleotide," as used herein is defined as a nucleic acid molecule comprised of two or more ribo- or deoxyribonucleotides, preferably more than three. The exact size of the oligonucleotide will depend on various factors and on the particular application and use of the oligonucleotide.
Oligonucleotides, which include probes and primers, can be any length from 3 nucleotides to the full length of the nucleic acid molecule, and explicitly include every possible number of contiguous nucleic acids from 3 through the full length of the polynucleotide.
Preferably, oligonucleotides are at least about 10 nucleotides in length, more preferably at least 15 nucleotides in length, more preferably at least about 20 nucleotides in length.
Oligonucleotides, which include probes and primers, can be any length from 3 nucleotides to the full length of the nucleic acid molecule, and explicitly include every possible number of contiguous nucleic acids from 3 through the full length of the polynucleotide.
Preferably, oligonucleotides are at least about 10 nucleotides in length, more preferably at least 15 nucleotides in length, more preferably at least about 20 nucleotides in length.
[0077] The term "probe" as used herein refers to an oligonucleotide, polynucleotide or nucleic acid, either RNA or DNA, whether occurring naturally as in a purified restriction enzyme digest or produced synthetically, which is capable of annealing with or specifically hybridizing to a nucleic acid with sequences complementary to the probe. A probe may be either single-stranded or double-stranded. The exact length of the probe will depend upon many factors, including temperature, source of probe and use of the method. For example, for diagnostic applications, depending on the complexity of the target sequence, the oligonucleotide probe typically contains 15-25 or more nucleotides, although it may contain fewer nucleotides. The probes herein are selected to be complementary to different strands of a particular target nucleic acid sequence. This means that the probes must be sufficiently complementary so as to be able to "specifically hybridize" or anneal with their respective target strands under a set of pre-determined conditions.
Therefore, the probe sequence need not reflect the exact complementary sequence of the target.
For example, a non-complementary nucleotide fragment may be attached to the 5' or 3' end of the probe, with the remainder of the probe sequence being complementary to the target strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the sequence of the target nucleic acid to anneal therewith specifically.
Therefore, the probe sequence need not reflect the exact complementary sequence of the target.
For example, a non-complementary nucleotide fragment may be attached to the 5' or 3' end of the probe, with the remainder of the probe sequence being complementary to the target strand. Alternatively, non-complementary bases or longer sequences can be interspersed into the probe, provided that the probe sequence has sufficient complementarity with the sequence of the target nucleic acid to anneal therewith specifically.
[0078] The term "primer" as used herein refers to an oligonucleotide, either RNA or DNA, either single-stranded or double-stranded, either derived from a biological system, generated by restriction enzyme digestion, or produced synthetically which, when placed in the proper environment, is able to functionally act as an initiator of template-dependent nucleic acid synthesis. When presented with an appropriate nucleic acid template, suitable nucleoside triphosphate precursors of nucleic acids, a polymerase enzyme, suitable cofactors and conditions such as a suitable temperature and pH, the primer may be extended at its 3' terminus by the addition of nucleotides by the action of a polymerase or similar activity to yield a primer extension product. The primer may vary in length depending on the particular conditions and requirement of the application. For example, in diagnostic applications, the oligonucleotide primer is typically 15-25 or more nucleotides in length. The primer must be of sufficient complementarity to the desired template to prime the synthesis of the desired extension product, that is, to be able anneal with the desired template strand in a manner sufficient to provide the 3' hydroxyl moiety of the primer in appropriate juxtaposition for use in the initiation of synthesis by a polymerase or similar enzyme. It is not required that the primer sequence represent an exact complement of the desired template. For example, a non-complementary nucleotide sequence may be attached to the 5' end of an otherwise complementary primer. Alternatively, non-complementary bases may be interspersed within the oligonucleotide primer sequence, provided that the primer sequence has sufficient complementarity with the sequence of the desired template strand to functionally provide a template-primer complex for the synthesis of the extension product.
Probes and primers having the appropriate sequence homology which specifically hybridized to CNV containing nucleic acids are useful in the detecting the presence of such nucleic acids in biological samples.
Probes and primers having the appropriate sequence homology which specifically hybridized to CNV containing nucleic acids are useful in the detecting the presence of such nucleic acids in biological samples.
[0079] Polymerase chain reaction (PCR) has been described in U.S. Pat. Nos.
4,683,195, 4,800,195, and 4,965,188, the entire disclosures of which are incorporated by reference herein.
4,683,195, 4,800,195, and 4,965,188, the entire disclosures of which are incorporated by reference herein.
[0080] The term "vector" relates to a single or double stranded circular nucleic acid molecule that can be infected, transfected or transformed into cells and replicate independently or within the host cell genome. A circular double stranded nucleic acid molecule can be cut and thereby linearized upon treatment with restriction enzymes.
An assortment of vectors, restriction enzymes, and the knowledge of the nucleotide sequences that are targeted by restriction enzymes are readily available to those skilled in the art, and include any replicon, such as a plasmid, cosmid, bacmid, phage or virus, to which another genetic sequence or element (either DNA or RNA) may be attached so as to bring about the replication of the attached sequence or element. A
nucleic acid molecule of the invention can be inserted into a vector by cutting the vector with restriction enzymes and ligating the two pieces together.
An assortment of vectors, restriction enzymes, and the knowledge of the nucleotide sequences that are targeted by restriction enzymes are readily available to those skilled in the art, and include any replicon, such as a plasmid, cosmid, bacmid, phage or virus, to which another genetic sequence or element (either DNA or RNA) may be attached so as to bring about the replication of the attached sequence or element. A
nucleic acid molecule of the invention can be inserted into a vector by cutting the vector with restriction enzymes and ligating the two pieces together.
[0081] Those skilled in the art will recognize that a nucleic acid vector can contain nucleic acid elements other than the promoter element and the autism specific marker gene nucleic acid molecule. These other nucleic acid elements include, but are not limited to, origins of replication, ribosomal binding sites, nucleic acid sequences encoding drug resistance enzymes or amino acid metabolic enzymes, and nucleic acid sequences encoding secretion signals, localization signals, or signals useful for polypeptide purification.
[0082] As used herein, the terms "reporter," "reporter system", "reporter gene," or "reporter gene product" shall mean an operative genetic system in which a nucleic acid comprises a gene that encodes a product that when expressed produces a reporter signal that is a readily measurable, e.g., by biological assay, immunoassay, radio immunoassay, or by colorimetric, fluorogenic, chemiluminescent or other methods. The nucleic acid may be either RNA or DNA, linear or circular, single or double stranded, antisense or sense polarity, and is operatively linked to the necessary control elements for the expression of the reporter gene product. The required control elements will vary according to the nature of the reporter system and whether the reporter gene is in the form of DNA or RNA, but may include, but not be limited to, such elements as promoters, enhancers, translational control sequences, poly A
addition signals, transcriptional termination signals and the like.
Methods of Using Autism-Associated CNVs for Diagnosing a Propensity for the Development of Autism and Autistic Spectrum Disorders
addition signals, transcriptional termination signals and the like.
Methods of Using Autism-Associated CNVs for Diagnosing a Propensity for the Development of Autism and Autistic Spectrum Disorders
[0083] Autism-related-CNV containing nucleic acids, including but not limited to those listed in the Tables and Figures provided herein, for example in Figures 15-18, may be used for a variety of purposes in accordance with the present invention.
Autism-associated CNV/SNP containing DNA, RNA, or fragments thereof may be used as probes to detect the presence of and/or expression of autism specific markers. Methods in which autism specific marker nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR).
Autism-associated CNV/SNP containing DNA, RNA, or fragments thereof may be used as probes to detect the presence of and/or expression of autism specific markers. Methods in which autism specific marker nucleic acids may be utilized as probes for such assays include, but are not limited to: (1) in situ hybridization; (2) Southern hybridization (3) northern hybridization; and (4) assorted amplification reactions such as polymerase chain reactions (PCR).
[0084] Further, assays for detecting autism-associated CNVs/SNPs may be conducted on any type of biological sample, including but not limited to body fluids (including blood, urine, serum, gastric lavage), any type of cell (such as brain cells, white blood cells, mononuclear cells) or body tissue. Such detection methods can include for example, southern and northern blotting, RFLP, direct sequencing and PCR amplification followed by hybridization of amplified products to a microarray comprising reference nucleic acid sequences.
[0085] Autism-associated CNV/SNP containing nucleic acids, vectors expressing the same, autism CNV/SNP containing marker proteins and anti-Autism specific marker antibodies of the invention can be used to detect autism associated CNVs/SNPs in body tissue, cells, or fluid, and alter autism SNP containing marker protein expression for purposes of assessing the genetic and protein interactions involved in the development of autism.
[0086] In some embodiments for screening for autism-associated CNVs, the autism-associated CNV containing nucleic acid in the sample will initially be amplified, e.g. using PCR, to increase the amount of the templates as compared to other sequences present in the sample. This allows the target sequences to be detected with a high degree of sensitivity if they are present in the sample.
This initial step may be avoided by using highly sensitive array techniques that are becoming increasingly important in the art. Alternatively, new detection technologies can overcome this limitation and enable analysis of small samples containing as little as 1 microgram of total RNA. Using Resonance Light Scattering (RLS) technology, as opposed to traditional fluorescence techniques, multiple reads can detect low quantities of mRNAs using biotin labeled hybridized targets and anti-biotin antibodies. Another alternative to PCR amplification involves planar wave guide technology (PWG) to increase signal-to-noise ratios and reduce background interference. Both techniques are commercially available from Qiagen Inc.
(USA).
This initial step may be avoided by using highly sensitive array techniques that are becoming increasingly important in the art. Alternatively, new detection technologies can overcome this limitation and enable analysis of small samples containing as little as 1 microgram of total RNA. Using Resonance Light Scattering (RLS) technology, as opposed to traditional fluorescence techniques, multiple reads can detect low quantities of mRNAs using biotin labeled hybridized targets and anti-biotin antibodies. Another alternative to PCR amplification involves planar wave guide technology (PWG) to increase signal-to-noise ratios and reduce background interference. Both techniques are commercially available from Qiagen Inc.
(USA).
[0087] Thus any of the aforementioned techniques may be used to detect or quantify autism-associated CNV marker expression and accordingly, diagnose autism or an autism spectrum disorder.
Methods of Diagnosing Autism
Methods of Diagnosing Autism
[0088] In some embodiments, the invention comprises a method of diagnosing autism (including autism spectrum disorder) in a subject comprising analyzing the genetic information of the subject to determine whether the subject has a genetic variation in at least one mGluR network gene, and diagnosing the subject as having autism if a genetic variation is found. In some embodiments, the subject has autism but does not have ADHD, oppositional defiant disorder (ODD), conduct disorder, Tourette's syndrome (TS), anxiety disorder, phobia, or depression.
In some embodiments, the subject has autism and also one or more of ADHD, conduct disorder, TS, anxiety disorder, phobia, and depression. In some embodiments, the subject has both autism and ADHD.
In some embodiments, the subject has autism and also one or more of ADHD, conduct disorder, TS, anxiety disorder, phobia, and depression. In some embodiments, the subject has both autism and ADHD.
[0089] In other embodiments, the invention encompasses confirming a diagnosis of autism in a subject. As used herein, "confirming a diagnosis of autism"
means diagnosing a subject who has already been diagnosed with autism. In some embodiments, the method of confirming a diagnosis of autism comprises analyzing the genetic information of a subject that has been diagnosed as having autism by a method that does not comprise analyzing mGluR network genes, to determine whether the subject has a genetic variation in at least one mGluR network gene, and confirming the diagnosis of autism if a genetic variation in at least one mGluR network gene is found.
In some embodiments, a screen for the presence of mGluR network gene variations is one of two or more tests or evaluations that are performed to confirm a diagnosis in a subject. In some embodiments, the subject has autism but does not have ADHD, ODD, conduct disorder, TS,anxie ty disorder, phobia, or depression. In some embodiments, the subject has autism and also one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression. In some embodiments the subject has both autism and ADHD.
means diagnosing a subject who has already been diagnosed with autism. In some embodiments, the method of confirming a diagnosis of autism comprises analyzing the genetic information of a subject that has been diagnosed as having autism by a method that does not comprise analyzing mGluR network genes, to determine whether the subject has a genetic variation in at least one mGluR network gene, and confirming the diagnosis of autism if a genetic variation in at least one mGluR network gene is found.
In some embodiments, a screen for the presence of mGluR network gene variations is one of two or more tests or evaluations that are performed to confirm a diagnosis in a subject. In some embodiments, the subject has autism but does not have ADHD, ODD, conduct disorder, TS,anxie ty disorder, phobia, or depression. In some embodiments, the subject has autism and also one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression. In some embodiments the subject has both autism and ADHD.
[0090] In other embodiments, the invention comprises confirming a diagnosis of autism in a subject who does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression, comprising analyzing the genetic information of a subject that has been diagnosed as having autism by a method that does not comprise analyzing mGluR network genes, to determine whether the subject has a genetic variation in at least one mGluR network gene, and confirming the diagnosis of autism if a genetic variation in at least one mGluR network gene is found.
[0091] In one embodiment, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, deletion or duplication in an mGluR network gene is detected. In other embodiments, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, or deletion in a Tier 1 mGluR
network gene is detected. In another embodiment, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, or deletion in a Tier 2 mGluR network gene is detected. In still other embodiments, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, or deletion in a Tier 3 mGluR network gene is detected.
network gene is detected. In another embodiment, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, or deletion in a Tier 2 mGluR network gene is detected. In still other embodiments, autism is diagnosed and/or confirmed if at least one CNV, SNV, frameshift mutation, or any other base pair substitution, insertion, or deletion in a Tier 3 mGluR network gene is detected.
[0092] A diagnosis or confirmation of diagnosis of autism may be based or confirmed on finding a genetic alteration in a Tier 1, Tier 2, and/or Tier 3 mGluR
network gene. The genetic alteration may be a CNV. The CNV may be a duplication or deletion of a region of DNA that contains some or all of the DNA encoding and controlling/regulating an mGluR network gene. In another embodiment, the diagnosis or confirmation of diagnosis of autism is made in a patient who does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In some embodiments, the diagnosis or confirmation of diagnosis of autism is made in a patient who has autism as well as one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression.
network gene. The genetic alteration may be a CNV. The CNV may be a duplication or deletion of a region of DNA that contains some or all of the DNA encoding and controlling/regulating an mGluR network gene. In another embodiment, the diagnosis or confirmation of diagnosis of autism is made in a patient who does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In some embodiments, the diagnosis or confirmation of diagnosis of autism is made in a patient who has autism as well as one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression.
[0093] In some embodiments, the diagnosis or confirmation of diagnosis of autism is based on a finding that the copy number of an mGluR network gene deviates from the normal diploid state. In some embodiments, the diagnosis or confirmation of diagnosis of autism is based on a copy number of zero or one, which indicates a CNV deletion. In some embodiments, the diagnosis or confirmation of diagnosis of autism is based on a copy number of three or greater, which indicates a CNV duplication. In another embodiment, the diagnosis or confirmation of diagnosis of autism is made in a patient who does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression by the presence of a copy number of zero or one, by a copy number of three or greater, or by any deviation from the diploid state.
[0094] In one embodiment, a more severe form of autism is diagnosed if at least two CNVs in mGluR network genes are detected. In one embodiment, a more severe form of autism in a patient who does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression is diagnosed if at least two CNVs in mGluR network genes are detected.
[0095] In one embodiment, a method of diagnosing and/or confirming autism comprises: obtaining a nucleic acid-containing sample from a subject;
optionally amplifying the nucleic acid; optionally labeling the nucleic acid sample;
applying the nucleic acid to a solid support that comprises one or more nucleic acids of mGluR
network genes, wherein the nucleic acids optionally comprise SNVs of mGluR
network genes; removing any unbound nucleic acid sample; and detecting any nucleic acid that has bound to the nucleic acid on the solid support, wherein the subject is diagnosed or confirmed as having autism if bound nucleic acids are detected.
In one embodiment the method further comprises comparing any bound nucleic acids to a standard or control and diagnosing or confirming autism if the analysis finds that the test sample is different from the control or standard. In another embodiment of this method, the patient with autism does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In another embodiment, the autism patient also has one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression.
optionally amplifying the nucleic acid; optionally labeling the nucleic acid sample;
applying the nucleic acid to a solid support that comprises one or more nucleic acids of mGluR
network genes, wherein the nucleic acids optionally comprise SNVs of mGluR
network genes; removing any unbound nucleic acid sample; and detecting any nucleic acid that has bound to the nucleic acid on the solid support, wherein the subject is diagnosed or confirmed as having autism if bound nucleic acids are detected.
In one embodiment the method further comprises comparing any bound nucleic acids to a standard or control and diagnosing or confirming autism if the analysis finds that the test sample is different from the control or standard. In another embodiment of this method, the patient with autism does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In another embodiment, the autism patient also has one or more of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression.
[0096] In some diagnostic, confirming, and treatment method of the invention, the subject may have autism but not any of ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In other diagnostic, confirming, and treatment methods of the invention, the subject may have autism and one or more additional disorders such as ADHD, conduct disorder, TS, anxiety disorder, phobia, or depression.
In some methods, the subject has both autism and ADHD.
Methods of Treating Autism
In some methods, the subject has both autism and ADHD.
Methods of Treating Autism
[0097] Encompassed herein are methods of treating autism in a subject comprising administering an effective amount of a nonselective mGluR
activator.
The term "treatment," as used herein, includes any administration or application of a therapeutic for a disease or disorder in a subject, and includes inhibiting the disease, arresting its development, relieving the symptoms of the disease, or preventing occurrence or reoccurrence of the disease or symptoms of the disease.
activator.
The term "treatment," as used herein, includes any administration or application of a therapeutic for a disease or disorder in a subject, and includes inhibiting the disease, arresting its development, relieving the symptoms of the disease, or preventing occurrence or reoccurrence of the disease or symptoms of the disease.
[0098] The mGluR proteins are typically placed into three sub-groups, group I
receptors including mGluR1 and mGluR5 are classed as slow excitatory receptors.
receptors including mGluR1 and mGluR5 are classed as slow excitatory receptors.
[0099] Group II includes mGluR2 and mGluR3. Group III includes mGluR4, mGluR6, mGluR7, and mGluR8. Groups II and III are classed as slow inhibitory receptors.
[00100] The mGluRs are distinguished from the ionotropic GluRs or iGluRs, which are ion channel-as s ociated glutamate receptors and are classed as fast excitatory receptors.
[00101] A "nonselective activator of mGluRs" refers to a molecule that activates mGluRs from more than one of the group I, II, and III categories.
Thus, a nonselective activator of mGluRs may provide for a general stimulation of the mGluR
networks. This is in contrast to specific mGluR activators that may only significantly activate a single mGluR, such as mGluR5, for example. Nonselective mGluRactivators include, for example, nonselective mGluRagonists.
Thus, a nonselective activator of mGluRs may provide for a general stimulation of the mGluR
networks. This is in contrast to specific mGluR activators that may only significantly activate a single mGluR, such as mGluR5, for example. Nonselective mGluRactivators include, for example, nonselective mGluRagonists.
[00102] In some embodiments, the nonselective mGluR activator is fasoracetam. Fasoracetam is a nootropic (i.e., cognitive-enhancing) drug that can stimulate both group I and group II/III mGluRs in in vitro studies. (See Hirouchi M, et al. (2000) European Journal of Pharmacology 387:9-17.) Fasoracetam may stimulate adenylate cyclase activity through activation of group I mGluRs, while it may also inhibit adenylate cyclase activity by stimulating group II and III mGluRs.
(Oka M, et al (1997) Brain Research 734:121-130.) Fasoracetam has been observed to be highly bioavailable (79%-97%) with a half-life of 5-6.5 hours in prior human studies (see Malykh AG, etal. (2010) Drugs 70(3).287-312). Fasoracetam is a member of the racetam family of chemicals that share a five-carbon oxopyrrolidone ring. The structure of fasoracetam is:
(Oka M, et al (1997) Brain Research 734:121-130.) Fasoracetam has been observed to be highly bioavailable (79%-97%) with a half-life of 5-6.5 hours in prior human studies (see Malykh AG, etal. (2010) Drugs 70(3).287-312). Fasoracetam is a member of the racetam family of chemicals that share a five-carbon oxopyrrolidone ring. The structure of fasoracetam is:
[00103] The term "fasoracetam" as used herein encompasses pharmaceutically acceptable hydrates and any solid state, amorphous, or crystalline forms of the fasoracetam molecule. For example, the term fasoracetam herein includes forms such as NFC-1: fasoracetam monohydrate. In addition to NFC-1, fasoracetam is also known as C-NS-105,NS105,and LAM-105.
[00104] NFC-1 has been previously studied in Phase I-III clinical trials in dementia-related cognitive impairment but did not show sufficient efficacy in dementia in Phase III trials. These trials demonstrated that NFC-1 was generally safe and well tolerated for those indications. Phase III data indicated that NFC-1 showed beneficial effects on psychiatric symptoms in cerebral infarct patients and adult dementia patients with cerebrovascular diseases.
[00105] In each of the method of treatment embodiments, a metabotropic glutamate receptor positive allosteric modulator, a metabotropic glutamate receptor negative allosteric modulator, or a tachykinin-3/neurokinin-receptor (TACR- 3/NK3R) antagonist may be administered alone or in combination with a nonselective activator of mGluRs to a subject, for example, having an alteration in an mGluR network gene. In some embodiments, the treatment agent comprises ADX63365, ADX50938, ADX71149, AMN082, a 1-(hetero)ary1-3-amino-pyrrolidine derivative, LY341495, ADX48621, GSK1144814, or SB223412.
[00106] Also encompassed herein are methods of treating autism comprising administering fasoracetam to a subject that has a genetic alteration in at least one mGluR network gene. In some embodiments, this subject has autism but does not have ADHD, ODD, conduct disorder, TS, anxie ty disorder, phobia, or depression, while in other embodiments, the subject has autism as well as at least one of ADHD, ODD, conduct disorder, TS,anxie ty disorder, phobia, or depression. In some embodiments, the subject has both autism and ADHD.
[00107] In some embodiments, the treatment methods comprise identifying or diagnosing a subject as having a genetic alteration in at least one mGluR network gene, and administering a nonselective mGluR activator such as fasoracetam to the identified or diagnosed subject. In some of the embodiments, the subject has autism, but does not have ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression. In other embodiments, the subject has autism, as well as one or more neuropsychological disorders such as ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression.
[00108] In one embodiment, the nonselective mGluR activator, such as fasoracetam, is administered to a subject that has autism and has been confirmed as having at least one genetic alteration in an mGluR network gene. The genetic alteration may be in a Tier 1 mGluR network gene. The genetic alteration may be in a Tier 2 mGluR network gene. The genetic alteration may be in a Tier 3 mGluR
network gene. The genetic alteration may be more than one genetic alteration, and the more than one alteration may be in one of Tiers 1,2, or 3, or in any combination of Tiers.
network gene. The genetic alteration may be more than one genetic alteration, and the more than one alteration may be in one of Tiers 1,2, or 3, or in any combination of Tiers.
[00109] Some embodiments include a method of treating autism comprising obtaining genetic information about a subject's mGluR network genes, and administering a nonselective mGluR activator, such as fasoracetam, if the subject has at least one genetic alteration, such as a CNV, in an mGluR network gene. Other embodiments encompass a method of treating autism comprising obtaining genetic information about a subject's mGluR network genes, and administering a nonselective mGluR activator, such as fasoracetam, if the subject has least one genetic alteration, such as a CNV, in a Tier 1 mGluR network gene. Other embodiments include a method of treating autism comprising obtaining genetic information about a subject's mGluR network genes, and administering a nonselective mGluR activator, such as fasoracetam, if the subject has at least one genetic alteration, such as a CNV, in a Tier 2 mGluR network gene. Still other embodiments encompass a method of treating autism comprising obtaining genetic information about a subject's mGluR network genes, and administering a nonselective mGluR activator, such as fasoracetam, if the subject has at least one genetic alteration, such as a CNV, in a Tier 3 mGluR network gene.
Subjects having more than one CNV in any one Tier, or in a combination of any of the three Tiers, may be treated by administering a nonselective mGluR activator, such as fasoracetam. In some embodiments, subjects having autism, but not having ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression, may be treated. In other method of treatment embodiments of the invention, the subject has one or more neuropsychological disorders such as ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression in addition to autism.
Dosing
Subjects having more than one CNV in any one Tier, or in a combination of any of the three Tiers, may be treated by administering a nonselective mGluR activator, such as fasoracetam. In some embodiments, subjects having autism, but not having ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, or depression, may be treated. In other method of treatment embodiments of the invention, the subject has one or more neuropsychological disorders such as ADHD, ODD, conduct disorder, TS, anxiety disorder, phobia, and depression in addition to autism.
Dosing
[00110] In some embodiments, fasoracetam may be administered as fasoracetam monohydrate (NFC-1). In some embodiments, fasoracetam may be administered by mouth (i.e., per os). In some embodiments, fasoracetam may be administered as capsules. In some embodiments, fasoracetam capsules may contain 50, 60, 70, 80, 90, 100, 110, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, or 200 mg of fasoracetam monohydrate. In some embodiments, fasoracetam may be dosed once daily or twice daily. In some embodiments, the daily dose of fasoracetam maybe 50 mg once-daily, 100 mg once-daily, 200 mg once-daily, 400 mg once-daily, 50 mg twic e-daily,100 mg twic e-daily, 200 mg twice-daily, or 400 mg twice-daily. In some embodiments, fasoracetam dosing may be adjusted using a series of dose escalations. In some embodiments, pharmacokine tic data on drug level or clinical response is used to determine changes in dosing. In some embodiments, dose escalation of fasoracetam is not used. In some embodiments, subjects are treated at a dose of fasoracetam expected to be clinically efficacious without a dose-escalation protocol.
Combination Therapies
Combination Therapies
[00111] In some embodiments, fasoracetam is used in combination with other agents for the treatment of autism.
Kits and Articles of Manufacture
Kits and Articles of Manufacture
[00112] Any of the aforementioned products can be incorporated into a kit which may contain a autism-associated CNV/SNP specific marker polynucleo tide or one or more such markers immobilized on a Gene Chip, an oligonucleotide, a polypeptide, a peptide, an antibody, a label, marker, or reporter, a pharmaceutically acceptable carrier, a physiologically acceptable carrier, instructions for use, a container, a vessel for administration, an assay substrate, or any combination thereof.
[00113] Vectors and probes comprising any of the autism-associated CNV/SNP specific marker polynucleotides or the Tier 1, 2, and/or 3 genes described in Figures 15-18 are encompassed.
[00114] Host cells expressing the autism-associated CNVs/SNPs of the present invention or functional fragments thereof are encompassed.
[00115] The following examples are provided to illustrate certain embodiments of the invention. They are not intended to limit the invention in any way.
EXA M PI, ES
Example 1
EXA M PI, ES
Example 1
[00116] A large genome-wide association study (GWAS) of structural variants that disrupt gene family protein interaction networks in patients with autism was performed. Multiple defective networks in the ASDs were found, most notably rare copy-number variants (CNVs) in the metabotropic glutamate receptor (mGluR) signaling pathway in 5.8% of patients with the ASDs. Defective mGluR signaling was found in both ADHD and schizophrenia, two common neuropsychiatric disorders that are highly coincident with the ASDs. Furthermore, other attractive candidates were found such as the MAX dimerization protein (MXD) network that is implicated in cancer, and a Calmodulin 1 (CALM1) gene interaction network that is active in neuronal tissues. The numerous defective gene family interactions found to underlie autism present many novel translational opportunities to explore for therapeutic interventions.
[00117] To identify and comprehensively characterize defective genetic networks underlying the ASDs, a large-scale genome association study for copy-number variation (CNVs) enriched in patients with autism was performed. By combining the affected cases from previously published large ASD studies with more recently recruited cases from the Children's Hospital of Philadelphia, one of the largest searches for rare pathogenic CNVs in ASDs to date was executed. In sum, 6,742 geno typed samples from patients with the ASDs were compared with those from 12,544 neurologically normal controls recruited at The Children's Hospital of Philadelphia (CHOP).
[00118] These cases were each screened by neurodevelopmental specialists to exclude patients with known syndromic causes for autism. Geno typing was performed for the vast majority of the ASD cases as well as all the controls. After cleaning the data to remove sample duplicates and performing standard QC for CNVs, the continental ancestry of 5,627 affected cases and 9,644 disease-free controls was inferred using a training set defined by populations from HapMap 3 and the Human Genome Diversity Panel (Table 1). Using this QC criteria, it was estimated that the sensitivity and specificity of calling CNVs is ¨70% and 100%, respectively, across 121 different genomic regions assayed by PCR. Across all ethnicities, there was an increased burden of CNVs in cases versus controls, a statistically significantly difference (P 0.001) in the larger European (63.3 versus 54.5 Kb, respectively) and African-derived (70.4 versus 48.0 Kb, respectively) populations.
[00119] Table 1: Distribution of CNVs across samples and estimated ancestry.
Continentai ancestry Case Control Total Europe Number of samples 4,602 4,722 9,324 :',CNIµ,/ burden (Kb) 63.3 54.5 Africa Number of samples 312 4,189 4,481 :',CNIµ,/ burden (Kb) 70.4 48.0 America Number of samples 485 276 761 CNV burden (Kb) 59.1 58.4 Asia Number of samples 201 350 551 CNV burden (Kb) 56.1 54.1 Other Number of samples 27 127 154 CNV burden (Kb) 51.5 49,4 All Ethnicities Number of samples 5,627 9,644 15,271 CNV burden (Kb) 63.0 51,7
Continentai ancestry Case Control Total Europe Number of samples 4,602 4,722 9,324 :',CNIµ,/ burden (Kb) 63.3 54.5 Africa Number of samples 312 4,189 4,481 :',CNIµ,/ burden (Kb) 70.4 48.0 America Number of samples 485 276 761 CNV burden (Kb) 59.1 58.4 Asia Number of samples 201 350 551 CNV burden (Kb) 56.1 54.1 Other Number of samples 27 127 154 CNV burden (Kb) 51.5 49,4 All Ethnicities Number of samples 5,627 9,644 15,271 CNV burden (Kb) 63.0 51,7
[00120] Referring to Table 1, CNV=copy-number variation. The table shows the distribution of cases, controls and CNV coverage across estimated continental ancestry. For groups of cases and controls across estimated ancestries, the table lists the numbers of subjects that passed quality control and their group-wise CNV burden, defined as the average span of CNVs in Kb for each group.
[00121] Referring to Table 1, *Statistically significant 0.01 by PLINK permutation test) differences in CNV burden are marked with an asterisk(*).
Example 2
Example 2
[00122] A search was performed for pan-ethnic CNV regions (CNVRs) discovered in the European-derived data set (4,602 cases versus 4,722 controls;
0.0001 by Fisher's exact test) and replicated in an independent ASD data set of African ancestry (312 cases versus 4,169 controls; P 0.001 by Fisher's exact test) with subsequent measurement of overall significance across the entire multi-ethnic discovery cohort (5,627 cases versus 9,644 controls) for maximal power (Fig.
5, Fig.
10).
0.0001 by Fisher's exact test) and replicated in an independent ASD data set of African ancestry (312 cases versus 4,169 controls; P 0.001 by Fisher's exact test) with subsequent measurement of overall significance across the entire multi-ethnic discovery cohort (5,627 cases versus 9,644 controls) for maximal power (Fig.
5, Fig.
10).
[00123] Figure 5 shows the significance of CNVRs by GWAS of ASDs in European-derived or African-derived populations. The Manhattan plots show the ¨log10 transformed P-value of association for each CNVR along the genome.
Adjacent chromosomes are shown in alternating red and blue colors. The regions discovered in Europeans (I3 0.0001) that replicated in Africans (I3 0.001) are highlighted with black arrows labeled by chromosome band. GWAS of 4,634 cases versus 4,726 controls in Europeans is shown on top and GWAS of 312 cases versus 4,173 controls in Africans is shown below.
Adjacent chromosomes are shown in alternating red and blue colors. The regions discovered in Europeans (I3 0.0001) that replicated in Africans (I3 0.001) are highlighted with black arrows labeled by chromosome band. GWAS of 4,634 cases versus 4,726 controls in Europeans is shown on top and GWAS of 312 cases versus 4,173 controls in Africans is shown below.
[00124] On the basis of these selection criteria, two large well-known ASD risk loci emerged that harbored multiple duplications in the Prader Willi/Angelman syndrome (15q11-13) critical region, and multiple deletions were detected in the DiGeorge syndrome (22q11) critical region, albeit notably smaller than the 22q11 deletion syndrome. A third locus harboring deletions in poly ADP-ribose polymerase family 8 (PARP8) on chromosome 5q11 was also discovered.
PARP8 has previously been identified as associated with the ASDs in a Dutch population but it has not previously been described for its pan ethnic distribution across European-derived and African-derived populations.
Example 3
PARP8 has previously been identified as associated with the ASDs in a Dutch population but it has not previously been described for its pan ethnic distribution across European-derived and African-derived populations.
Example 3
[00125] The genetic interaction networks derived from gene families with members localized to the Prader Willi/Angelman syndrome (15q11-13) critical region, the DiGeorge syndrome (22q11) critical region, and the novel PARP8 (5q11) region were examined using a method previously applied to ADHD; however, hardly any of the most significant genes harboring significant CNVRs clustered within gene families. Consequently, the search for gene family interaction networks (GFINs) was broadened to search the entire genome for GFINs with CNVs enriched in autism.
For every gene family, a GFIN was defined as the genetic interaction network spawned by its multiple duplicated members. Standard HUGO gene names were used to define 1,732 GFINs across which were searched for enrichment of network defects associated with the ASDs. However, because there is an a priori excess of CNV burden in ASD cases over disease-free controls (Table 1), larger GFINs are expected to display significant enrichment of case defects by virtue solely of their increased size and complexity. Therefore, for each GFIN, a network permutation test of case enrichment was used across 1,000 random sets of networked genes to control for the GFIN size and complexity. With this approach, network defects associated with the ASDs were identified by minimizing statistical artifact derived from any a priori excessive CNV burden in cases over controls, as well as other unknown biases that may be inherent in the human interactome data that were mined.
For every gene family, a GFIN was defined as the genetic interaction network spawned by its multiple duplicated members. Standard HUGO gene names were used to define 1,732 GFINs across which were searched for enrichment of network defects associated with the ASDs. However, because there is an a priori excess of CNV burden in ASD cases over disease-free controls (Table 1), larger GFINs are expected to display significant enrichment of case defects by virtue solely of their increased size and complexity. Therefore, for each GFIN, a network permutation test of case enrichment was used across 1,000 random sets of networked genes to control for the GFIN size and complexity. With this approach, network defects associated with the ASDs were identified by minimizing statistical artifact derived from any a priori excessive CNV burden in cases over controls, as well as other unknown biases that may be inherent in the human interactome data that were mined.
[00126] Out of 1,732 GFINs, the network permutation test was used to rank 1,557 GFINs with defined CNVs for enrichment of genetic defects in the ASDs. Among the top GFINs (Figures 13A-B) was the metabotropic glutamate receptor (mGluR) pathway defined by the GRM family of genes that impacts glutamatergic neurotransmission. The GRM family contains eight members, all of which were defined in the human interactome to cumulatively spawn a GFIN of genes (Figs. 6A-D). Across this GFIN for the GRM family of genes, we found CNV
defects in 5.8% of European-derived ASD cases (265/4,602) versus only 3% of ethnically matched controls (153/4,722), a 1.8-fold enrichment of frequency (PFisher 2.40E-09). By 1,000 random network permutations, we found this excess of enrichment across cases in the mGluR pathway to also be statistically significant (Pperm 0.05). In addition, 69.2% (124/181) of the informative genes within our mGluR network showed an excess of CNVs among cases. However, the component genes that harbor the most significant CNVRs contributing to this overall network significance reveal that the duplicated mGluR genes themselves (GRM1, GRM3, GRM4, GRM5, GRM6, GRM7 and GRM8) fail to achieve significance individually, although there is a trend for an excess of CNV defects across a specific subset of mGluR receptors (GRM1, GRM3, GRM5, GRM7, GRM8) that is unique to cases (Fig. 9).
defects in 5.8% of European-derived ASD cases (265/4,602) versus only 3% of ethnically matched controls (153/4,722), a 1.8-fold enrichment of frequency (PFisher 2.40E-09). By 1,000 random network permutations, we found this excess of enrichment across cases in the mGluR pathway to also be statistically significant (Pperm 0.05). In addition, 69.2% (124/181) of the informative genes within our mGluR network showed an excess of CNVs among cases. However, the component genes that harbor the most significant CNVRs contributing to this overall network significance reveal that the duplicated mGluR genes themselves (GRM1, GRM3, GRM4, GRM5, GRM6, GRM7 and GRM8) fail to achieve significance individually, although there is a trend for an excess of CNV defects across a specific subset of mGluR receptors (GRM1, GRM3, GRM5, GRM7, GRM8) that is unique to cases (Fig. 9).
[00127] Figures 6A-D shows enrichment of optimal CNVRs across mGluR network of genes. Nodes of the network are labeled with their gene names, with red and green representing deletions and duplications, respectively, while grey nodes lack CNV data. Dark and light colors represent enrichment in cases and controls, respectively. The genes defining the network are shown as diamonds, while all other genes are shown as circles. Blue lines indicate evidence of interaction.
Example 4
Example 4
[00128] Many large studies of CNVs implicate genes within the glutamatergic signaling pathway in the etiology of the ASDs, and SNP and CNV
duplications of GRM8 have been reported in association with the ASDs before in humans. Moreover, a recent functional study demonstrated that in mouse models of tuberous sclerosis and fragile X, two different forms of syndromic autism, the autistic phenotype was ameliorated by modulation of GRM5 in opposite directions for each syndrome, which suggests that GRM5 functional activity is central in defining the axis of synaptopathophysiology in syndromic autism. The GRM network findings herein implicate rare defects in mGluR signalling also contribute to the ASDs outside of fragile X and tuberous sclerosis, and functional mGluR synaptopathophysiology may be initiated from many dozens if not hundreds of defective genes within the mGluR
pathway that may account for as much as 6% of the endophenotypes of the ASDs (Figures 13A-B).
duplications of GRM8 have been reported in association with the ASDs before in humans. Moreover, a recent functional study demonstrated that in mouse models of tuberous sclerosis and fragile X, two different forms of syndromic autism, the autistic phenotype was ameliorated by modulation of GRM5 in opposite directions for each syndrome, which suggests that GRM5 functional activity is central in defining the axis of synaptopathophysiology in syndromic autism. The GRM network findings herein implicate rare defects in mGluR signalling also contribute to the ASDs outside of fragile X and tuberous sclerosis, and functional mGluR synaptopathophysiology may be initiated from many dozens if not hundreds of defective genes within the mGluR
pathway that may account for as much as 6% of the endophenotypes of the ASDs (Figures 13A-B).
[00129] In addition, the importance of mGluRs in ADHD, a highly co-incident neuropsychiatric disorder within the autism spectrum, has been demonstrated. However, in contrast to ADHD where defects within the mGluR
receptors themselves (GRMs) were among the most significant copy-number defects contributing to the overall network significance, it was found that in the ASDs defects of component GRMs contributed only modestly to the overall significance of the mGluR pathway. Nonetheless, the defects within GRM1, GRM3, GRM5, GRM7 and GRM8 that were identified as unique to cases and thus enriched are the same GRMs that were identified as being pathogenic in ADHD and may impact glutamatergic signaling.
receptors themselves (GRMs) were among the most significant copy-number defects contributing to the overall network significance, it was found that in the ASDs defects of component GRMs contributed only modestly to the overall significance of the mGluR pathway. Nonetheless, the defects within GRM1, GRM3, GRM5, GRM7 and GRM8 that were identified as unique to cases and thus enriched are the same GRMs that were identified as being pathogenic in ADHD and may impact glutamatergic signaling.
[00130] Among the most highly ranked GFINs by permutation testing, the MAX dimerization protein (MXD) GFIN (PFisher 3.83E-23, enrichment=2.53, Pperm 0.042) was the most enriched. The MXD family of genes encode proteins that interact with MYC/MAX network of basic helix-loop-helix leucine zipper (bHLHZ) transcription factors that regulate cell proliferation, differentiation and apoptosis (IN/JIM 600021); MXD genes are important candidate tumour suppressor genes as the MXD-MYC-MAX network is dysregulated in various types of cancer. Interestingly an epidemiological link between autism and specific types of cancer has been reported, and anticancer therapeutics were recently shown to modulate ASD phenotypes in the mouse through regulation of synaptic NLGN
protein levels. Within the component genes contributing to the MXD GFIN
significance, duplications in PARP10 (I34.06E-11, OR=2.04) and UBE3A
(1.50E-06, OR=inf) are the most significantly enriched (Figure 12). It is notable that PARP8 was found to be significant across ethnicities as described earlier (Figure 12), and the importance of structural defects in UBE3A in the ASDs was previously described.
protein levels. Within the component genes contributing to the MXD GFIN
significance, duplications in PARP10 (I34.06E-11, OR=2.04) and UBE3A
(1.50E-06, OR=inf) are the most significantly enriched (Figure 12). It is notable that PARP8 was found to be significant across ethnicities as described earlier (Figure 12), and the importance of structural defects in UBE3A in the ASDs was previously described.
[00131] Other notable significant GFINs uncovered were POU class 5 homeobox (POU5F) GIFN (PFisher2.96E-17, enrichment=2.3, Pperm 0.008, and the SWI/SNF related, matrix associated, actin-dependent regulator of chromatin, subfamily c (SMARCC) GFIN (PFisher 1.22E-09, enrichment=1.9, Pperm 0.035). The POU5F family of genes encodes for transcription factors containing a POU homeodomain, and their role has been demonstrated in embryonic development, especially during early embryogenesis, and it is necessary for embryonic stem cell pluripotency. Component genes of the SMARCC gene family are members of the SWI/SNF family of proteins, whose members display helicase and ATPase activities and which are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. Most interestingly, the KIAA
family of genes ranked among the top GFINs (PFisher 3.12E-23, enrichment=1.6, Pperm 0.040). KIAA genes have been identified in the Kazusa cDNA sequencing project and are predicted from novel large human cDNAs; however, they have no known function.
family of genes ranked among the top GFINs (PFisher 3.12E-23, enrichment=1.6, Pperm 0.040). KIAA genes have been identified in the Kazusa cDNA sequencing project and are predicted from novel large human cDNAs; however, they have no known function.
[00132] Some component members of gene families may contribute disproportionately to the significance of a GFIN because they are highly connected to interacting gene partners that are enriched for CNV defects in ASD.
Therefore, the 1,732 gene families were decomposed into their 15,352 component duplicated genes of which 1,218 had defined networks with data to test for significance by genome-wide network permutation. The calmodulin 1 (CALM1) gene interaction network ranked highest by network permutation testing of case enrichment for CNV
defects across 1,000 random gene networks (Figure 7, Figure 14) and represents a novel and attractive candidate gene for the ASDs. Across the CALM1 network, CNV
defects were found in 14/4,618 cases versus only 1/4726 controls (Pfisher 4.16E-04, enrichment=14.37, Pperm 0.002), and these defects were distributed such that 90% (9/10) of genes that harbored CNVs in the CALM1 interactome were enriched in cases. Closer inspection of the most significant CNVR contributing to the CALM1 network significance (Figure 11) revealed that no single gene was significant on its own; instead, with the exception of only one gene (PTH2R), each contributing CNVR tagged highly penetrant rare defects unique to cases. Calmodulin is the archetype of the family of calcium-modulated proteins of which nearly 20 members have been found. Calmodulin contains 149 amino acids that define four calcium-binding domains used for Ca2+-mediated coordination of a large number of enzymes, ion channels and other proteins including kinases and phosphatases;
its functions include roles in growth and cell cycle regulation as well as in signal transduction and the synthesis and release of neurotransmitters [MIM 1141801.
Therefore, the 1,732 gene families were decomposed into their 15,352 component duplicated genes of which 1,218 had defined networks with data to test for significance by genome-wide network permutation. The calmodulin 1 (CALM1) gene interaction network ranked highest by network permutation testing of case enrichment for CNV
defects across 1,000 random gene networks (Figure 7, Figure 14) and represents a novel and attractive candidate gene for the ASDs. Across the CALM1 network, CNV
defects were found in 14/4,618 cases versus only 1/4726 controls (Pfisher 4.16E-04, enrichment=14.37, Pperm 0.002), and these defects were distributed such that 90% (9/10) of genes that harbored CNVs in the CALM1 interactome were enriched in cases. Closer inspection of the most significant CNVR contributing to the CALM1 network significance (Figure 11) revealed that no single gene was significant on its own; instead, with the exception of only one gene (PTH2R), each contributing CNVR tagged highly penetrant rare defects unique to cases. Calmodulin is the archetype of the family of calcium-modulated proteins of which nearly 20 members have been found. Calmodulin contains 149 amino acids that define four calcium-binding domains used for Ca2+-mediated coordination of a large number of enzymes, ion channels and other proteins including kinases and phosphatases;
its functions include roles in growth and cell cycle regulation as well as in signal transduction and the synthesis and release of neurotransmitters [MIM 1141801.
[00133] Figure 7 shows the enrichment of optimal CNVRs across CALM1 network. The first degree-directed interaction network defined by CALM1 is shown.
[00134] The comprehensive, unbiased analytical approach described herein has identified a diverse set of specific defective biological pathways that contribute to the underlying aetiology of the ASDs. Among GFINs robustly enriched for structural defects, the most enriched was that of the MXD family of genes that has been implicated in cancer pathogenesis, thereby providing concrete genetic defects to explore the reported coincidence of specific cancers with the ASDs.
The most highly ranked component duplicated gene interaction network involves defects in CALM1 and its multiple interacting partners that are important in regulating voltage-independent calcium-activated action potentials at the neuronal synapse.
Moreover, there was significant enrichment for defects within the GFIN for GRM
that defines the mGluR pathway. While specific mGluR gene family members have been shown to underlie syndromic ASDs, these findings suggest that rare defects in mGluR signaling also contribute to idiopathic autism across the entire GFIN
for GRM genes.
The most highly ranked component duplicated gene interaction network involves defects in CALM1 and its multiple interacting partners that are important in regulating voltage-independent calcium-activated action potentials at the neuronal synapse.
Moreover, there was significant enrichment for defects within the GFIN for GRM
that defines the mGluR pathway. While specific mGluR gene family members have been shown to underlie syndromic ASDs, these findings suggest that rare defects in mGluR signaling also contribute to idiopathic autism across the entire GFIN
for GRM genes.
[00135] Given the unmet need for better treatment for neurodevelopmental diseases, the functionally diverse set of defective genetic interaction networks reported herein presents attractive genetic biomarkers to consider for targeted therapeutic intervention in ASDs and across the neuropsychiatric disease spectrum.
Methods applicable to Examples 1-4
Methods applicable to Examples 1-4
[00136] The majority of cases (5,049 of 6,742) and all controls (12,544) were genotyped with genome-wide coverage using the Infinium II platform across various iterations of the HumanHap BeadChip with 550 K, 610 K, 660 K and 1 M
markers by the Center for Applied Genomics at The Children's Hospital of Philadelphia (CHOP). There were 1,693 cases geno typed by the AGP consortium.
All cases and ¨ \n50% of controls were re-used from previously published large ASD
studies. All cases were diagnosed by ADI-R/ADOS and fulfilled standard criteria for ASDs. Duplicate samples were removed by selecting unique samples with the best quality (based on genotyping statistics used to QC samples) from clusters defined by single linkage clustering of all pairs of samples with high pairwise identity by state measures (IBS ?0.9) across 140 K non-correlated SNPs. Ethnicity of samples was inferred by a supervised k-means classification (k=3) of the first 10 eigenvectors estimated by principal component analysis across the same subset of 140 K non-correlated SNPs. We used HapMap 3 and the Human Genome Diversity Panel samples with known continental ancestry to train the k-means classifier implemented by the R Language for Statistical Computing.
CNV inference and association
markers by the Center for Applied Genomics at The Children's Hospital of Philadelphia (CHOP). There were 1,693 cases geno typed by the AGP consortium.
All cases and ¨ \n50% of controls were re-used from previously published large ASD
studies. All cases were diagnosed by ADI-R/ADOS and fulfilled standard criteria for ASDs. Duplicate samples were removed by selecting unique samples with the best quality (based on genotyping statistics used to QC samples) from clusters defined by single linkage clustering of all pairs of samples with high pairwise identity by state measures (IBS ?0.9) across 140 K non-correlated SNPs. Ethnicity of samples was inferred by a supervised k-means classification (k=3) of the first 10 eigenvectors estimated by principal component analysis across the same subset of 140 K non-correlated SNPs. We used HapMap 3 and the Human Genome Diversity Panel samples with known continental ancestry to train the k-means classifier implemented by the R Language for Statistical Computing.
CNV inference and association
[00137] CNVs with the PennCNV algorithm, which combines multiple values, including geno typing fluorescence intensity (Log R Ratio), population frequency of SNP minor alleles (B-allele frequency) and SNP spacing were called into a hidden Markov model. The term `CNV' represents individual CNV calls, whereas `CNVR' refers to population-level variation shared across subjects. Quality control thresholds for sample inclusion in CNV analysis included a high call rate (call rate ?95 /0) across SNPs, low s.d. of normalized intensity (s.d. 0.3), low absolute genomic wave artifacts (IGCWF1 0.02) and low numbers of CNVs called (#CNVs 100). Genome-wide differences in CNV burden, defined as the average span of CNVs, between cases and controls and estimates of significance were computed using PLINK. CNVRs were defined based on the genomic boundaries of individual CNVs, and the significance of the difference in CNVR frequency between cases and controls was evaluated at each CNVR using Fisher's exact test.
Gene family interaction networks definition and association
Gene family interaction networks definition and association
[00138] Previous work on ADHD was extended here to rank all GFINs by a network permutation test. Specifically, using merged human interactome data from three different yeast two hybrid generated data sets accessed through the Human Interactome Database, the directed second-degree gene interaction network was defined for all gene families just as was done for the sole metabotropic glutamate receptor gene family network in ADHD. Specifically, GFIN was used to refer to these gene family-derived interaction networks. In sum, 2,611 gene families were found with at least two members based on official HUGO gene nomenclature, and generated 1,732 GFINs using. For 1,557 GFINs with defined CNVs an odds ratio was calculated of cumulative network enrichment over all genes harboring CNVs within the network. Moreover, for each GFIN, its enrichment was quantified by a permutation test of 1,000 second-degree gene interaction networks derived from a random set of N genes, where N is the number of members of a given gene family.
Because the CNVs focused on are so rare, there is relatively not enough power to achieve significance by permutation testing after correcting for multiple GFIN
tests.
However, all GFINs are reported in order of their nominal/marginal significance.
Experimental validation of CNVs
Because the CNVs focused on are so rare, there is relatively not enough power to achieve significance by permutation testing after correcting for multiple GFIN
tests.
However, all GFINs are reported in order of their nominal/marginal significance.
Experimental validation of CNVs
[00139] Significant CNVRs that were identified were validated using commercially available qPCR Taqman probes run on the ABI GeneAmp 9700 system from Life Technology. Figure 9 lists 251 reactions that were tested using 121 different genomic probes across 85 different samples for which DNA was available.
For deletions, sensitivity=0.65, specificity=1.00, NPV=1.00 and PPV=0.88. For duplications, sensitivity=0.68, specificity=0.99, NPV=0.94 and PPV=0.91.
Conclusions
For deletions, sensitivity=0.65, specificity=1.00, NPV=1.00 and PPV=0.88. For duplications, sensitivity=0.68, specificity=0.99, NPV=0.94 and PPV=0.91.
Conclusions
[00140] The data presented herein is evidence that ASD can be diagnosed after recognition of at least one CNV in an mGluR network gene selected from the group consisting of ACAT1, ACAT2, ACP1, ACTR2, ADCY1, ADD1, ADRA2C, ADRBK1, AGAP2, ALDOA, APTX, ARHGAP24, ARL15, BDKRB1, BDKRB2, C1orf116, C4orf3, C7orf25, CA8, CACNA1B, CALB2, CALM1, CAMK2B, CHP, CHRM3, CNPY2, CNR1, COPB2, DCN, DHCR7, DISC 1, DSTN, ECHS1, EGFR, ERBB2, ERP44, F2RL2, FKBP3, FURIN, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNA01, GNAQ, GNB2L1, GRB2, GRB7, GRIK1, GRM1, GRM3, GRM5, GRM7, GRM8, GSN, HNRNPA3, HOMER1, HOMER3, HTT, IMPDH2, IQGAP2, ITGB7, ITPR1, LAMA4, LRP2BP, LYAR, LYN, MAP4, MAPK1, MTHFD1, MTNR1A, MX1, MY06, NAA15, NCK1, NPY2R, PCBP1, PCBP3, PCDHA4, PDE1C, PICK1, PIK3CA, PLA2G7, PLCB1, PRDX1, PRKCA, PRPSAP1, PSMC1, PSMD1, PSMD13, PSME1, PXN, RAB2A, RANBP1, RAP2A, RCC1, RGS12, RPA2, RPN2, RUVBL2, RYR2, 5100A6, SACS, SDC3, SERPINB9, SLC6A3, SNRPB2, SRC, STRAP, STX12, SYK, TCP1, TEAD3, TFAM, TJP1, TRAF2, TUBA1A, TUBA3C, TXN, UBQLN4, VHL, and WHAQ
(also shown in Figures 15A-D).
(also shown in Figures 15A-D).
[00141] The CNVs in these genes are sensitive and specific biomarkers for selecting and treating ADHD due to defective mGluR pathways. Furthermore, the present inventors have identified drug candidates that specifically activate the mGluRs, potentially restoring normal neurophysiology in ASD patients with mutations in any of the mGluR network genes, as shown in Figures 15A-D.
[00142] For example, compounds which may be administered in implementing the test and treat paradigm described herein include the piracetam family of nootropic agents, as described in F. Gualtieri et al., Curr. Phann.
Des., 8:
125-38 (2002). More preferably, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al.
A particularly preferred agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (NS-105).
Example 5 The Role of mGluR Copy Number Variation in Genetic and Environmental Forms of Syndromic Autism Spectrum Disorder
Des., 8:
125-38 (2002). More preferably, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al.
A particularly preferred agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (NS-105).
Example 5 The Role of mGluR Copy Number Variation in Genetic and Environmental Forms of Syndromic Autism Spectrum Disorder
[00143] Abnormal signaling mediated through mGluR5 is involved in the pathophysiology of Autism Spectrum Disorder (ASD) in Fragile X Syndrome and Tuberous Sclerosis. However, the role of other mGluR associated network/signaling genes in syndromic ASD is unknown. To determine whether copy number variants (CNV'S) are enriched in syndromic ASD, microarrays were used to identify mGluR
network CNV's in children with ASD. We set out to determine 1) whether rate of syndromic features vary between children with ASD with and without CNV's in mGluR network genes; and 2) whether "second hits" in mGluR network genes occur more often in children with ASD in children with 22q11.2 Deletion Syndrome (who all have haplo insufficiency of RANBP1, an mGluR network gene in the 22q11.2 region.
network CNV's in children with ASD. We set out to determine 1) whether rate of syndromic features vary between children with ASD with and without CNV's in mGluR network genes; and 2) whether "second hits" in mGluR network genes occur more often in children with ASD in children with 22q11.2 Deletion Syndrome (who all have haplo insufficiency of RANBP1, an mGluR network gene in the 22q11.2 region.
[00144] Individuals in our biorepository with parental report of ASD
(n=6,452) were screened for parental consent to access clinical evaluations in the Electronic Health Record at the Children's Hospital of Philadelphia (n=539).
Our syndromic comparison cohort included children with 22q11.2 Deletion Syndrome with full access to past medical and neuropsychological evaluations (n=75), including those with diagnosis of ASD (n=25) and those with no concern for ASD (n=50).
(n=6,452) were screened for parental consent to access clinical evaluations in the Electronic Health Record at the Children's Hospital of Philadelphia (n=539).
Our syndromic comparison cohort included children with 22q11.2 Deletion Syndrome with full access to past medical and neuropsychological evaluations (n=75), including those with diagnosis of ASD (n=25) and those with no concern for ASD (n=50).
[00145] Patient categorization (syndromic vs nonsyndromic) was done via blinded medical chart review in all mGluR positive and 100 randomly selected mGluR negative cases.
[00146] Our results, explained further herein show that 11.5% of ASD
had mGluR CNV's vs. 3.2% in healthy controls (p<0.001). Syndromic ASD was more prevalent in children with mGluR CNVs (72% vs 16%, p<0.001). A
comparison cohort of children with 22q11.2 Deletion Syndrome (n=25 with ASD, n=50 without ASD), all haplo-insufficient for mGluR network gene RANBP1, was evaluated to determine whether "second hits" in mGluR network genes confer additional risk for ASD. 20% with 22q11.2D5+ASD had "second hits" in mGluR
signaling genes vs 2% in 22q11.2D5-ASD (p<0.014). Conclusions: We propose that altered RANBP1 expression may provide a mechanistic link between ASD in 22q11.2D5, Thalidomide Embryopathy and Fetal Valproate Syndrome, providing a link for seemingly unrelated genetic and environmental forms of ASD.
had mGluR CNV's vs. 3.2% in healthy controls (p<0.001). Syndromic ASD was more prevalent in children with mGluR CNVs (72% vs 16%, p<0.001). A
comparison cohort of children with 22q11.2 Deletion Syndrome (n=25 with ASD, n=50 without ASD), all haplo-insufficient for mGluR network gene RANBP1, was evaluated to determine whether "second hits" in mGluR network genes confer additional risk for ASD. 20% with 22q11.2D5+ASD had "second hits" in mGluR
signaling genes vs 2% in 22q11.2D5-ASD (p<0.014). Conclusions: We propose that altered RANBP1 expression may provide a mechanistic link between ASD in 22q11.2D5, Thalidomide Embryopathy and Fetal Valproate Syndrome, providing a link for seemingly unrelated genetic and environmental forms of ASD.
[00147] The results suggest that CNV's in mGluR network genes, previously implicated in altered neurological development in Fragile X
Syndrome and Tuberous Sclerosis, may link many other genetic and environmental forms of Autism Spectrum Disorder. As discussed in the previous examples, Autism Spectrum Disorder (ASD) occurs in approximately 1/88 individuals and is characterized by impairment in social communication and repetitive interests and activities.
Approximately 20% of cases occur in the context of an identifiable syndrome.
Genetic syndromes with ASD are heterogeneous, including cytogenetically visible chromosomal alterations (e.g. Trisomy 21), microdeletion and microduplication syndromes (e.g. 22q11.2 deletion syndrome [22q11.2DS]; 22q11.2 duplication syndrome [22q11.2DupS1), and monogenic disorders (e.g. Fragile X Syndrome [FXS], Tuberous Sclerosis [TS1). In addition, prenatal exposure to thalidomide, valproic acid, misoprostol, ethanol and maternal rubella infection, have been associated with an elevated risk of ASD.
Syndrome and Tuberous Sclerosis, may link many other genetic and environmental forms of Autism Spectrum Disorder. As discussed in the previous examples, Autism Spectrum Disorder (ASD) occurs in approximately 1/88 individuals and is characterized by impairment in social communication and repetitive interests and activities.
Approximately 20% of cases occur in the context of an identifiable syndrome.
Genetic syndromes with ASD are heterogeneous, including cytogenetically visible chromosomal alterations (e.g. Trisomy 21), microdeletion and microduplication syndromes (e.g. 22q11.2 deletion syndrome [22q11.2DS]; 22q11.2 duplication syndrome [22q11.2DupS1), and monogenic disorders (e.g. Fragile X Syndrome [FXS], Tuberous Sclerosis [TS1). In addition, prenatal exposure to thalidomide, valproic acid, misoprostol, ethanol and maternal rubella infection, have been associated with an elevated risk of ASD.
[00148] The mechanism for the development of ASD in most forms of idiopathic and syndromic forms of ASD remains elusive. Recently, signaling through metabotropic glutamate receptor 5 (mGluR5) has been implicated in the development of ASD in FXS and TS. In FXS, abnormal production of Fragile X Mental Retardation Protein (FMRP) removes normal inhibition of signaling through the mGluR pathway. Tuberous Sclerosis leads to over inhibition of signaling.
Auerbach and colleagues (2011) demonstrated abnormal synaptic learning and atypical behavior in mouse models of FXS and TS, and reversed these effects by breeding the two strains together--mice harboring both mutations had normal mGluR signaling, and learning and behavior that was indistinguishable from control mice. Other studies have demonstrated normalization of learning and behavior in Fragile X mice by administration of an mGluR5 antagonist. In addition to elucidating the mechanism for cognitive and behavioral differences in FXS and TS, these studies suggest a promising avenue for pharmacological treatment. To determine whether additional forms of syndromic ASD may share a similar mechanism (through disruption of the mGluR gene network), we analyzed DNA from 539 children with ASD (not filtered for comorbid genetic syndrome) followed at the Children's Hospital of Philadelphia.
Auerbach and colleagues (2011) demonstrated abnormal synaptic learning and atypical behavior in mouse models of FXS and TS, and reversed these effects by breeding the two strains together--mice harboring both mutations had normal mGluR signaling, and learning and behavior that was indistinguishable from control mice. Other studies have demonstrated normalization of learning and behavior in Fragile X mice by administration of an mGluR5 antagonist. In addition to elucidating the mechanism for cognitive and behavioral differences in FXS and TS, these studies suggest a promising avenue for pharmacological treatment. To determine whether additional forms of syndromic ASD may share a similar mechanism (through disruption of the mGluR gene network), we analyzed DNA from 539 children with ASD (not filtered for comorbid genetic syndrome) followed at the Children's Hospital of Philadelphia.
[00149] The following materials and methods are provided to facilitate the practice of Example 5.
[00150] Participants: Phenotypic data for patients with ASD as reported on parental health questionnaires from our biorepository (n=6,452) were evaluated to identify patients who received clinical assessment at the Children's Hospital of Philadelphia and agreed to Electronic Health Record chart review. DNA from these cases (n=539) were selected for further phenotypic and genotypic analysis.
Children were recruited for inclusion in the general Center for Applied Genomics biorepository when they were getting blood drawn for another purpose at The Children's Hospital of Philadelphia, so there is an overrepresentation of children with at least one medical problem in this patient cohort. The parents of all patients gave consent for participation in the study, which was approved by the Institutional Review Board at the Children's Hospital of Philadelphia (IRB 06-004886).
Children were recruited for inclusion in the general Center for Applied Genomics biorepository when they were getting blood drawn for another purpose at The Children's Hospital of Philadelphia, so there is an overrepresentation of children with at least one medical problem in this patient cohort. The parents of all patients gave consent for participation in the study, which was approved by the Institutional Review Board at the Children's Hospital of Philadelphia (IRB 06-004886).
[00151] Chart Review: Subject selection and randomization process:
All patients with an mGluR CNV (n=62) and 100 patients without mGluR CNV were randomly selected for chart review. This procedure was selected to ensure that all patients with mGluR CNV received detailed chart review with an adequately sized comparison cohort. A three-step process was done to ensure blinded chart review.
The selection of the 162 charts was done by a geneticist with access to CNV
data but without access to the Electronic Health Record (CK). Another author who had no access to CNV data nor the Electronic Health Record blinded and randomized the patient ID's (RTS). Finally, a physician with access to the Electronic Health Record but blinded to mGluR status (TLW) reviewed charts for documentation of ASD
diagnosis and presence of other medical comorbidities.
All patients with an mGluR CNV (n=62) and 100 patients without mGluR CNV were randomly selected for chart review. This procedure was selected to ensure that all patients with mGluR CNV received detailed chart review with an adequately sized comparison cohort. A three-step process was done to ensure blinded chart review.
The selection of the 162 charts was done by a geneticist with access to CNV
data but without access to the Electronic Health Record (CK). Another author who had no access to CNV data nor the Electronic Health Record blinded and randomized the patient ID's (RTS). Finally, a physician with access to the Electronic Health Record but blinded to mGluR status (TLW) reviewed charts for documentation of ASD
diagnosis and presence of other medical comorbidities.
[00152] ASD: Charts were reviewed to confirm a diagnosis of ASD and also to determine medical comorbidities for each patient. Diagnosis of ASD was confirmed in the chart, but as this was a retrospective chart review, gold-standard research instruments (e.g. Autism).
[00153] Medical Comorbidities: Structural birth defects, genetic testing and medical conditions were recorded for each patient. Cases were categorized as "Syndromic ASD" if they had ASD and presence of a medical condition or structural birth defect (e.g. cleft palate) that occurs in less than 1% of the general population.
This criteria was established to define a subset of patients whose ASD and other medical problems would be highly unlikely to occur coincidentally With a baseline rate of ASD at 1/88 and a medical condition that occurs in <1% of the general population, the compound likelihood of both occurring by chance would be approximately 0.001%. See FIG. 8.
This criteria was established to define a subset of patients whose ASD and other medical problems would be highly unlikely to occur coincidentally With a baseline rate of ASD at 1/88 and a medical condition that occurs in <1% of the general population, the compound likelihood of both occurring by chance would be approximately 0.001%. See FIG. 8.
[00154] Genotyping Arrays and CNV Calling: DNA from subjects with ASD were each geno typed on the Human610-Quad or HumanHap550 SNP arrays from Illumina. For 22q11 DS cohorts, subjects were typed either on Illumina SNP
arrays (Human610-Quad v1.0 or HumanHap550) or Affymetrix 6.0 SNP arrays.
Clustering and SNP calling was performed using GenomeStudio (Illumina) to generate normalized intensity (i.e. Log-R ratio, or LRR) and B-allele frequencies (BAF). CNV calling was performed using the PennCNV algorithm [PMID:
179213541 following waviness correction [PMID: 187841891. In brief, PennCNV
uses a hidden Markov model (HMM) that incorporates information from LRR, BAF, as well as features of the array (e.g. distance between neighboring SNPs) to detect CNVs.
arrays (Human610-Quad v1.0 or HumanHap550) or Affymetrix 6.0 SNP arrays.
Clustering and SNP calling was performed using GenomeStudio (Illumina) to generate normalized intensity (i.e. Log-R ratio, or LRR) and B-allele frequencies (BAF). CNV calling was performed using the PennCNV algorithm [PMID:
179213541 following waviness correction [PMID: 187841891. In brief, PennCNV
uses a hidden Markov model (HMM) that incorporates information from LRR, BAF, as well as features of the array (e.g. distance between neighboring SNPs) to detect CNVs.
[00155] CNV Quality Control: Samples with SNP arrays of poor quality were excluded from CNV calling, since typically the proportion of false positives increases considerably for these samples. Those samples where the genotyping call rate>96%, standard deviation of LRR (LRR sd)<0.4, GC-wave factor (GCWF) is between -0.2 and 0.2 after waviness correction, and total number of CNV calls for the sample <100 were included in analysis.
[00156] CNV Annotation: For syndromic ASD regions, genomic coordinates were those described by Betancur [PMID: 211293641. The GRM/mGluR
network generated by Cytoscape from the Human Interactome database was described by Elia et al. [PMID: 221386921 using UCSC Genome Browser definitions for gene coordinates (UCSC genes). This network from Cytoscape was used to define mGluR+ vs. mGluR-subsets. For 22q11 DS cohort analysis, additional GRM/mGluR network genes were identified based on 1st degree interaction network of the eight GRIM genes using the program Ingenuity Pathway Analysis (Ingenuity Systems Inc./Qiagen; Redwood City, Calif.) as well as the genes encoding the group I
mGluR signaling pathway described in Kelleher et al. [PMID: 225581071. CNV
calls were analyzed for overlap to known syndromic regions and GRM network genes.
All syndromic aberrations detected by clinical cytogenetic laboratory testing were confirmed on corresponding SNP arrays.
Results: mGluR Network Copy Number Variations (CNVs) are Prevalent in Syndromic ASD Compared to Nonsyndromic ASD
network generated by Cytoscape from the Human Interactome database was described by Elia et al. [PMID: 221386921 using UCSC Genome Browser definitions for gene coordinates (UCSC genes). This network from Cytoscape was used to define mGluR+ vs. mGluR-subsets. For 22q11 DS cohort analysis, additional GRM/mGluR network genes were identified based on 1st degree interaction network of the eight GRIM genes using the program Ingenuity Pathway Analysis (Ingenuity Systems Inc./Qiagen; Redwood City, Calif.) as well as the genes encoding the group I
mGluR signaling pathway described in Kelleher et al. [PMID: 225581071. CNV
calls were analyzed for overlap to known syndromic regions and GRM network genes.
All syndromic aberrations detected by clinical cytogenetic laboratory testing were confirmed on corresponding SNP arrays.
Results: mGluR Network Copy Number Variations (CNVs) are Prevalent in Syndromic ASD Compared to Nonsyndromic ASD
[00157] CNVs in the mGluR network genes were found in 74% of patients with syndromic ASD compared to 16% of patients with nonsyndromic ASD
(p<0.001). Most of the mGluR CNV's in patients with syndromic ASD (75%) were included in larger clinically significant CNV's. As mGluR network genes are present in the 22q11.2 region (RANBP1) and on chromosome 21 (APP GRIK1 MX1 PCBP3 SETD4), patients with ASD in the presence of 22q11.2DS, 22q11.2DupS or Trisomy 21 accounted for 15 (33%) of the patients with Syndromic ASD+mGluR network changes. The remainder of observed cytogenetic changes had individual non-overlapping deletions or duplications. The analysis was repeated after exclusion of children with Trisomy 21, 22q11.2DS and 22q11.2DupS, (the syndromes in children in this study which have previously been associated with ASD). After their exclusion, the effect remained significant (p<0.001).
Autism Spectrum Disorder in 22q11.2 Deletion Syndrome is Associated with "Second Hit" in mGluR Pathway
(p<0.001). Most of the mGluR CNV's in patients with syndromic ASD (75%) were included in larger clinically significant CNV's. As mGluR network genes are present in the 22q11.2 region (RANBP1) and on chromosome 21 (APP GRIK1 MX1 PCBP3 SETD4), patients with ASD in the presence of 22q11.2DS, 22q11.2DupS or Trisomy 21 accounted for 15 (33%) of the patients with Syndromic ASD+mGluR network changes. The remainder of observed cytogenetic changes had individual non-overlapping deletions or duplications. The analysis was repeated after exclusion of children with Trisomy 21, 22q11.2DS and 22q11.2DupS, (the syndromes in children in this study which have previously been associated with ASD). After their exclusion, the effect remained significant (p<0.001).
Autism Spectrum Disorder in 22q11.2 Deletion Syndrome is Associated with "Second Hit" in mGluR Pathway
[00158] As a comparison cohort, data from children with 22q11.2 DS
with ASD (n=25) and without ASD (n=50) who had completed high density microarray evaluation (either Affymetrix 6.0, Illumina 500K, and Illumina 610Q) and clinical developmental assessments (as enrolled through a parallel study, approved by the Children's Hospital of Philadelphia Institutional Review Board, IRB 07-005352) were examined for the presence of a second mGluR network hit outside of the 22q11.2 region. "Second hits", deletions of an mGluR network gene outside of the 22q11.2 region, were found in 20% (5/25) of patients with ASD and only 2%
(1/50) without ASD (p<0.014).
with ASD (n=25) and without ASD (n=50) who had completed high density microarray evaluation (either Affymetrix 6.0, Illumina 500K, and Illumina 610Q) and clinical developmental assessments (as enrolled through a parallel study, approved by the Children's Hospital of Philadelphia Institutional Review Board, IRB 07-005352) were examined for the presence of a second mGluR network hit outside of the 22q11.2 region. "Second hits", deletions of an mGluR network gene outside of the 22q11.2 region, were found in 20% (5/25) of patients with ASD and only 2%
(1/50) without ASD (p<0.014).
[00159] Prior studies have demonstrated that abnormal signaling (either too much or too little) through mGluR5 could be the basis for abnormal neural development (and possibly ASD) in FXS and TS. Our data suggest that derangement of the mGluR network may be responsible for increased rates of ASD seen in cytogenetically distinct forms of syndromic ASD. mGluR network genes are found in the 22q11.2 region as well as on Chromosome 21, which may be involved in the increased prevalence of ASD in both Down Syndrome and 22q11.2 DS. However, all patients with Trisomy 21 or 22q11.2 DS harbor the change in the mGluR network suggesting a second hit outside of the region may be necessary for expression of the ASD phenotype.
Autism Spectrum Disorder in 22q11.2 Deletion Syndrome, 22q11.2 Duplication Syndrome, Thalidomide Embryopathy and Fetal Valproate Syndrome
Autism Spectrum Disorder in 22q11.2 Deletion Syndrome, 22q11.2 Duplication Syndrome, Thalidomide Embryopathy and Fetal Valproate Syndrome
[00160] The 22q11.2 DS is the most common microdeletion syndrome in humans, occurring in 1 in 4,000 individuals. The typical deletion spans approximately 3 Mb and includes approximately 45 genes, causing a variety of medical and behavioral disorders. ASD occurs in approximately 20%, and psychosis in 25%. The 22q11.2DupS results in the same types of birth defects and medical comorbidities seen in 22q11.2 DS, but at a lower rate (among over 60 patients in our clinical cohort). There are no cases of psychosis in 22q11DupS in the literature29 or our cohort. Among our cases with documentation of developmental evaluation after the age of 4, the prevalence of ASD is 27%, which is slightly higher than the rate in children with 22q11.2DS.
[00161] Thalidomide exposure during pregnancy causes a variety of birth defects that have all been reported in 22q11.2DS, including some that are extremely rare (e.g. phocomelia, radial ray defects). Miller and Stromland reported an elevated risk of ASD following exposure to thalidomide during early embryogenesis.
This study included prospective evaluation by a psychiatrist was done for adults who had been exposed to thalidomide during pregnancy and evaluation by a physician to document birth defects and associated features. All cases of ASD following thalidomide exposure had ear anomalies, suggesting exposure between days 24-28 post-fertilization. Among individuals exposed at this time, there was a 27%
rate of ASD. Replications of this study in additional cohorts of children have not been possible because the use of thalidomide in pregnant women was widely restricted in the 1960's; therefore, additional cases are not available. Though several mechanisms for the cause of many of the birth defects in thalidomide embryopathy have been proposed, animal studies of the teratogenic effects of thalidomide have been limited due to significant species differences. One of the reasons thalidomide was used widely in the 1960's was because of a lack of teratogenicity in animals at levels that are highly teratogenic in humans. This has resulted in significant limitation in the ability of researchers to determine the teratogenic mechanism of thalidomide, as studies have taken place in animals for which thalidomide is not particularly teratogenic, or using dosages which are much higher than that used in humans. Recent changes in legislation have allowed for a study to be completed in human embryonic stem cells--the first of its kind to use human cells and dosages which would have been analogous to that experienced by women taking thalidomide in the 1950's and 1960's30.
This study, conducted by Meganathan and colleagues (2012) proposed that the teratogenic effects of thalidomide may be mediated through RANBP1. Valproic acid (VPA) is widely used as an anticonvulsant, mood stabilizer, and to prevent migraine headaches. Exposure to VPA during pregnancy causes an increased rate of several birth defects, all of which have been reported in 22q11.2DS, and most of which have been seen in Thalidomide Embryopathy. The comparison of all birth defects seen in 22q11.2 DS to the exposures syndromes was not made because 22q11.2 DS includes deletion of dozens of additional genes that we do not propose to be affected in Thalidomide Embryopathy or Fetal Valproate Syndrome. In addition to structural defects, children exposed to VPA in utero have an elevated risk of developing ASD.
Rodent models of autism have used prenatal exposure to VPA to reproduce some of the neuroanatomic features of autism and abnormal behavior. Due to its action as a Histone Deacetylase Inhibitor, VPA affects expression of many genes. Based on homology, decreased expression of RanBP1 mRNA is predicted in VPA-treated rats.
Moreover, a recent study showed reversal of atypical behaviors in VPA-exposed mice with treatment with an mGluR antagonist.
CONCLUSIONS
This study included prospective evaluation by a psychiatrist was done for adults who had been exposed to thalidomide during pregnancy and evaluation by a physician to document birth defects and associated features. All cases of ASD following thalidomide exposure had ear anomalies, suggesting exposure between days 24-28 post-fertilization. Among individuals exposed at this time, there was a 27%
rate of ASD. Replications of this study in additional cohorts of children have not been possible because the use of thalidomide in pregnant women was widely restricted in the 1960's; therefore, additional cases are not available. Though several mechanisms for the cause of many of the birth defects in thalidomide embryopathy have been proposed, animal studies of the teratogenic effects of thalidomide have been limited due to significant species differences. One of the reasons thalidomide was used widely in the 1960's was because of a lack of teratogenicity in animals at levels that are highly teratogenic in humans. This has resulted in significant limitation in the ability of researchers to determine the teratogenic mechanism of thalidomide, as studies have taken place in animals for which thalidomide is not particularly teratogenic, or using dosages which are much higher than that used in humans. Recent changes in legislation have allowed for a study to be completed in human embryonic stem cells--the first of its kind to use human cells and dosages which would have been analogous to that experienced by women taking thalidomide in the 1950's and 1960's30.
This study, conducted by Meganathan and colleagues (2012) proposed that the teratogenic effects of thalidomide may be mediated through RANBP1. Valproic acid (VPA) is widely used as an anticonvulsant, mood stabilizer, and to prevent migraine headaches. Exposure to VPA during pregnancy causes an increased rate of several birth defects, all of which have been reported in 22q11.2DS, and most of which have been seen in Thalidomide Embryopathy. The comparison of all birth defects seen in 22q11.2 DS to the exposures syndromes was not made because 22q11.2 DS includes deletion of dozens of additional genes that we do not propose to be affected in Thalidomide Embryopathy or Fetal Valproate Syndrome. In addition to structural defects, children exposed to VPA in utero have an elevated risk of developing ASD.
Rodent models of autism have used prenatal exposure to VPA to reproduce some of the neuroanatomic features of autism and abnormal behavior. Due to its action as a Histone Deacetylase Inhibitor, VPA affects expression of many genes. Based on homology, decreased expression of RanBP1 mRNA is predicted in VPA-treated rats.
Moreover, a recent study showed reversal of atypical behaviors in VPA-exposed mice with treatment with an mGluR antagonist.
CONCLUSIONS
[00162] Derangement of genes in the mGluR network are found at a high rate in patients with different forms of Syndromic ASD, including 22q11.2DS, 22q11.2DupS, Trisomy 21 and a large number of other seemingly-unrelated chromosomal alterations. Moreover, among children with 22q11.2DS, the presence of a "second hit" in the mGluR network was identified in 20% of children with ASD, and only 2% of those without ASD (p<0.014). Significantly, four children, all with autism phenotype, had a small deletion in the vicinity of the RANBP1 gene.
While the expression level of RANBP1 was not affected in one individual available for testing (data not shown), these atypical deletions could impact gene function with resulting dysregulation of the RANBP1 protein.
While the expression level of RANBP1 was not affected in one individual available for testing (data not shown), these atypical deletions could impact gene function with resulting dysregulation of the RANBP1 protein.
[00163] Taken together, these data implicate dysregulation of the mGluR network as a likely permissive factor that increases the propensity to develop an ASD, including syndromic ASD, and ASD in individuals with 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome and Thalidomide Embryopathy.
The striking increase in prevalence of ASD with a CNV affecting a second gene in the network suggests perturbations of mGluR signaling at multiple points is likely.
The striking increase in prevalence of ASD with a CNV affecting a second gene in the network suggests perturbations of mGluR signaling at multiple points is likely.
[00164] CNVs in the genes recited in Figures 15A-D are sensitive and specific biomarkers for selecting and treating ASD, syndromic ASD, and ASD in individuals with 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome and Thalidomide Embryopathy. Furthermore, the present inventors have identified drug candidates that specifically activate the mGluRs, potentially restoring normal neurophysiology in patients with mutations in any of the mGluR network genes, as shown in Figures 15A-D.
[00165] For example, compounds which may be administered in implementing the test and treat paradigm described herein include the piracetam family of nootropic agents, as described in F. Gualtieri et al., Curr. Phann.
Des., 8:
125-38 (2002). More preferably, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al.
A particularly preferred agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (NS-105).
Des., 8:
125-38 (2002). More preferably, the treating agent is a pyroglutamide. Details regarding the preparation and formulation of pyroglutamides, which may be used in the practice of this invention, are provided in U.S. Pat. No. 5,102,882 to Kimura et al.
A particularly preferred agent for the treatment of ASD in patients determined to have one or more of the CNVs indicative as set forth in Figures 15A-D, is (+)-5-oxo-Dprolinepiperidinamide monohydrate (NS-105).
[00166] Therefore, in one embodiment, methods for treating an ASD, syndromic ASD, and ASD in patients with 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy are encompassed comprising administering NS-105 to a patient having at least one CNV in an GRM/mGluR network gene selected from the group consisting of ACAT1, ACAT2, ACP1, ACTR2, ADCY1, ADD1, ADRA2C, ADRBK1, AGAP2, ALDOA, APTX, ARHGAP24, ARL15, BDKRB1, BDKRB2, C1orf116, C4orf3, C7orf25, CA8, CACNA1B, CALB2, CALM1, CAMK2B, CHP, CHRM3, CNPY2, CNR1, COPB2, DCN, DHCR7, DISC1, DSTN, ECHS1, EGFR, ERBB2, ERP44, F2RL2, FKBP3, FURIN, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNA01, GNAQ, GNB2L1, GRB2, GRB7, GRIK1, GRM1, GRM3, GRM5, GRM7, GRM8, GSN, HNRNPA3, HOMER1, HOMER3, HTT, IMPDH2, IQGAP2, ITGB7, ITPR1, LAMA4, LRP2BP, LYAR, LYN, MAP4, MAPK1, MTHFD1, MTNR1A, MX1, MY06, NAA15, NCK1, NPY2R, PCBP1, PCBP3, PCDHA4, PDE1C, PICK1, PIK3CA, PLA2G7, PLCB1, PRDX1, PRKCA, PRPSAP1, PSMC1, PSMD1, PSMD13, PSME1, PXN, RAB2A, RANBP1, RAP2A, RCC1, RGS12, RPA2, RPN2, RUVBL2, RYR2, S100A6, SACS, SDC3, SERPINB9, SLC6A3, SNRPB2, SRC, STRAP, STX12, SYK, TCP1, TEAD3, TFAM, TJP1, TRAF2, TUBA1A, TUBA3C, TXN, UBQLN4, VHL, and WHAQ.
Example 6 Treatment with Fasoracetam Monohydrate (NFC-1) of ADHD Patients with CNVs in mGluR Network Genes and Impact on Autism Symptoms
Example 6 Treatment with Fasoracetam Monohydrate (NFC-1) of ADHD Patients with CNVs in mGluR Network Genes and Impact on Autism Symptoms
[00167] An open-label Phase Ib clinical trial was conducted to investigate the safety, pharmacokinetics and efficacy of NFC-1 (fasoracetam monohydrate) in adolescent subjects between the ages of 12 and 17 previously diagnosed with ADHD
who also had at least one genetic alteration in an mGluR network gene.
who also had at least one genetic alteration in an mGluR network gene.
[00168] The study included 30 ADHD subjects who were between ages 12 and 17, of any ancestry or race, and of weight within the 5th to 95th percentile for their age, and otherwise judged to be in good medical health. Subjects were genotyped and included in the trial if they possess at least one genetic alteration in the form of at least one copy number variation (deletion or duplication) in an mGluR network gene that potentially disrupts the function of the gene. Seventeen of the 30 subjects have a CNV
in a tier 1 mGluR network gene, while 7 subjects have a CNV in a tier 2 gene and 6 in a tier 3 gene. At enrollment, several trial subjects showed evidence of co-morbid phenotypes, including a few subjects with symptoms related to autism.
in a tier 1 mGluR network gene, while 7 subjects have a CNV in a tier 2 gene and 6 in a tier 3 gene. At enrollment, several trial subjects showed evidence of co-morbid phenotypes, including a few subjects with symptoms related to autism.
[00169] Exclusion criteria comprised subjects suffering from a clinically significant illness, either mental or physical, that, in the investigator's opinion, might confound the results of the study or that might prevent them from completing the study, subjects that are pregnant or nursing, subjects that test positive for illicit drugs of that have a history of drug abuse, subjects that consume alcoholic beverages, or subjects for which the investigator is otherwise concerned regarding their compliance or suitability.
[00170] NFC-1 capsules of either 50 mg or 200 mg comprising fasoracetam monohydrate as active ingredient and placebo capsules comprising microcellulose were used for the study. The design of the trial was a phone screening (1 day), enrollment phase (1 to 2 days), a wash-out phase for subjects currently on ADHD
medications (1-14 days),pharmacokinetic (PK) assessment (2 days), followed by a dose-escalation phase (35 days) and a follow-up phone visit approximately four weeks after the last dose, for a maximum of 127 days. All ADHD medications were discontinued during the wash-out phase prior to the study. The wash-out period for stimulants was 2-3 days and that for atomoxetine or noradrenergic agonists was 10-12 days. No new ADHD medications were started during the study.
medications (1-14 days),pharmacokinetic (PK) assessment (2 days), followed by a dose-escalation phase (35 days) and a follow-up phone visit approximately four weeks after the last dose, for a maximum of 127 days. All ADHD medications were discontinued during the wash-out phase prior to the study. The wash-out period for stimulants was 2-3 days and that for atomoxetine or noradrenergic agonists was 10-12 days. No new ADHD medications were started during the study.
[00171] A dose-escalation phase of the trial ran over a 5-week period, after the initial wash-out period and the PK and initial safety assessments. During week 1, all subjects were administered placebo capsules twice daily. After one week of placebo treatment, patients were started on 50 mg bid NFC-1 for 1 week. If safety and responsiveness data from prior dose level of fasoracetam indicated it was appropriate, subjects were then escalated to the next higher dose (100, 200, or 400 mg).
Subjects who showed tolerance to the 50 mg bid dose as well as response to the drug were to be maintained at that level for the remaining 3 weeks of the trial.
Subjects who showed tolerance to the 50 mg bid dose as well as response to the drug were to be maintained at that level for the remaining 3 weeks of the trial.
[00172] Subjects who showed tolerance but lack of response or partial response to the 50 mg bid dose were to be moved up to the next higher dose of mg during the following week. Subjects who showed tolerance at 100 mg but lack of response or partial response were to be moved up to the 200 mg dose the following week while those who showed both tolerance and response at 100 mg were to be kept at 100 mg bid for the remainder of the trial. Similarly, subjects moved up to the 200 mg dose who showed both tolerance and response were to be kept at 200 mg for the final week of the trial while those showing tolerance but lack of response or partial response were moved to a 400 mg dose for the final week. Of the 30 trial subjects, 3 received a maximum dose of 100 mg, 9 received a maximum dose of 200 mg, and the remaining received a maximum dose of 400 mg.
[00173] While this study was not specifically directed at identifying autism sufferers or monitoring their symptoms, 7 of the 30 ADHD subjects showed certain signs of autism, particularly lack of social interactions or engagement, that appeared to improve from the therapy with NFC-1. For example, two subjects showed increased social interactions after treatment. One of these two subjects, who had not communicated with a close relative for a long time, initiated contact with the relative.
One subject went from not making eye contact to initiating conversation with clinicians. This same subject also had episodes of rapid repetitive movements, particularly when excited. These movements stopped while on the NFC-1 treatment and started again when the drug was discontinued. A teacher also commented during the trial that this subject also had increased social interactions. One subject went from not wanting to talk to peers to joining a school debating team. One subject was reported to be better able to relate to peers and to organize a peer get together. One subject was able to go to their locker at school without being fearful. And in a further subject, there was a decrease in self-talk. Thus, overall, in these seven subjects, social interactions appeared to improve while on NFC-1 medication.
EQUIVALENTS
One subject went from not making eye contact to initiating conversation with clinicians. This same subject also had episodes of rapid repetitive movements, particularly when excited. These movements stopped while on the NFC-1 treatment and started again when the drug was discontinued. A teacher also commented during the trial that this subject also had increased social interactions. One subject went from not wanting to talk to peers to joining a school debating team. One subject was reported to be better able to relate to peers and to organize a peer get together. One subject was able to go to their locker at school without being fearful. And in a further subject, there was a decrease in self-talk. Thus, overall, in these seven subjects, social interactions appeared to improve while on NFC-1 medication.
EQUIVALENTS
[00174] The foregoing written specification is considered to be sufficient to enable one skilled in the art to practice the embodiments. The foregoing description and Examples detail certain embodiments and describes the best mode contemplated by the inventors. It will be appreciated, however, that no matter how detailed the foregoing may appear in text, the embodiment may be practiced in many ways and should be construed in accordance with the appended claims and any equivalents thereof.
[00175] As used herein, the term about refers to a numeric value, including, for example, whole numbers, fractions, and percentages, whether or not explicitly indicated. The term about generally refers to a range of numerical values (e.g., +/-5-10% of the recited range) that one of ordinary skill in the art would consider equivalent to the recited value (e.g., having the same function or result).
When terms such as at least and about precede a list of numerical values or ranges, the terms modify all of the values or ranges provided in the list. In some instances, the term about may include numerical values that are rounded to the nearest significant figure.
When terms such as at least and about precede a list of numerical values or ranges, the terms modify all of the values or ranges provided in the list. In some instances, the term about may include numerical values that are rounded to the nearest significant figure.
Claims (48)
1. A method of treating autism in a human patient comprising administering a therapeutically effective amount of fasoracetam (NS-105 or NFC-1) to the patient, wherein the patient has at least one CNV in a gene selected from the group consisting of ACAT1, ACAT2, ACCN1, ACCN2, ACP1, ACTB, ACTR2, ADA, ADCY1, ADD1, ADD2, ADORA1, ADRA1B, ADRA2A, ADRA2C, ADRB2, ADRBK1, ALDOA, ANXA2, APP, APTX, AQP1, ARHGAP24, ARL15, ARRB1, ARRB2, ATXN7L3, BDKRB1, BDKRB2, BTBD2, BTG2, C17orf44, Clorf116, C7orf25, CA8, CACNA1B, CACYBP, CALB2, CALM1, CALM2, CALM3, CAMK1, CAMK2B, CAMK4, CCNB1, CDC42, CENTG1, CHGB, CHP, CHRM2, CHRM3, CIC, CMPK, CNP, CNR1, CNTN4, COPB2, CRHR1, CTNNA2, CYCS, DCN, DHCR7, DISC1, DLST, DPP6, DRD2, DRD3, DSTN, DYNLL1, ECHS1, EGFR, EIF3S3, ERBB2, F2R, F2RL2, F2RL3, F3, FKBP3, FPR1, FSCN1, FURIN, FYN, GAPDH, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNO1, GNAQ, GNB2L1, GOT1, GP1BA, GPR26, GRB2, GRB7, GRIA1, GRIK1, GRIK3, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GSN, HBXIP, HD, HNRPA3, HOMER1, HOMER3, HRPT2, HSP90AB1, HTR2A, IL8RB, IMPDH2, IQGAP2, ITGB1, ITGB7, ITPR1, KIAA0090, KIAA1683, LAMA4, LARP7, LRP2BP, LRRC59, LTA, LYAR, LYN, MAP4, MAPK1, MAPT, MARK4, MC4R, MGC11082, MRPL14, MRPS16, MTHFD1, MTNR1A, MTNR1B, MX1, MYC, MYO6, NANS, NARG1, NCK1, NEGR1, NFKBIA, NLN, NMI, NPY2R, NUDC, OPRD1, PAFAH1B3, PCBP1, PCBP3, PCDHA4, PCID1, PCMT1, PDCD5, PDE1B, PDE1C, PDE6G, PGM1, PHKB, PHKG2, PICK1, PIK3CA, PIK3R1, PLA2G7, PLCB1, PLCB3, PLCG2, PPIH, PPP2R1A, PRDX1, PRKCA, PRLHR, PRMT1, PRPSAP1, PSAT1, PSEN1, PSMA1, PSMC1, PSMD1, PSMD11, PSMD13, PSMD6, PSME1, PTHR2, PXN, PYGL, PYGM, QRICH2, RAB2, RALA, RANBP1, RAP2A, RCC1, RCC2, RGS12, RGS2, RHOA, RIF1, RPA2, RPLP2, RPN2, RPS14, RRM1, RUVBL2, RYR1, RYR2, S100A6, SACS, SARS, SCTR, SDC3, SELE, SERPINB9, SET, SETD4, SF3B14, SGTB, SHANK1, SHBG, SIAH1, SLC2A1, SLC6A3, SLC7A10, SNCA, SNRPB2, SOCS6, SOCS7, SORD, SRC, STAU1, STRAP, STX12, SYK, TBCA, TBXA2R, TCP1, TEAD3, TFAM, TGM2, TJP1, TK1, TLR10, TMEM4, TNIK, TPI1, TRAF2, TRMT112, TUBA1, TUBA1A, TUBA1B, TUBA2, TUBB, TUBG1, TXN, TXNDC4, TXNL2, TYMS, UBQLN4, UCHL1, USP24, VHL, VIPR1, YWHAQ, and ZAP70, thereby improving at least one symptom of autism in the patient.
2. The method of claim 1, wherein the patient has been diagnosed with autism spectrum disorder, pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD).
3. The method of claim 1 or claim 2, wherein the CNV is a duplication or deletion.
4. The method of claim 1 or 2, wherein the autism is syndromic ASD.
5. The method of claim 1 or 2, wherein the patient has ASD and 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy.
6. The method of claim 1 or 2, wherein the patient has at least two CNVs in a gene selected from the group consisting of ACAT1, ACAT2, ACCN1, ACCN2, ACP1, ACTB, ACTR2, ADA, ADCY1, ADD1, ADD2, ADORA1, ADRA1B, ADRA2A, ADRA2C, ADRB2, ADRBK1, ALDOA, ANXA2, APP, APTX, AQP1, ARHGAP24, ARL15, ARRB1, ARRB2, ATXN7L3, BDKRB1, BDKRB2, BTBD2, BTG2, C17orf44, Clorf116, C7orf25, CA8, CACNA1B, CACYBP, CALB2, CALM1, CALM2, CALM3, CAMK1, CAMK2B, CAMK4, CCNB1, CDC42, CENTG1, CHGB, CHP, CHRM2, CHRM3, CIC, CMPK, CNP, CNR1, CNTN4, COPB2, CRHR1, CTNNA2, CYCS, DCN, DHCR7, DISCI, DLST, DPP6, DRD2, DRD3, DSTN, DYNLL1, ECHS1, EGFR, EIF353, ERBB2, F2R, F2RL2, F2RL3, F3, FKBP3, FPR1, FSCN1, FURIN, FYN, GAPDH, GLP1R, GLP2R, GNA15, GNAI1, GNAI2, GNAI3, GNAO1, GNAQ, GNB2L1, GOT1, GP1BA, GPR26, GRB2, GRB7, GRIA1, GRIK1, GRIK3, GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, GRM8, GSN, HBXIP, HD, HNRPA3, HOMER1, HOMER3, HRPT2, HSP90AB1, HTR2A, IL8RB, IMPDH2, IQGAP2, ITGB1, ITGB7, ITPR1, KIAA0090, KIAA1683, LAMA4, LARP7, LRP2BP, LRRC59, LTA, LYAR, LYN, MAP4, MAPK1, MAPT, MARK4, MC4R, MGC11082, MRPL14, MRPS16, MTHFD1, MTNR1A, MTNR1B, MX1, MYC, MYO6, NANS, NARG1, NCK1, NEGR1, NFKBIA, NLN, NMI, NPY2R, NUDC, OPRD1, PAFAH1B3, PCBP1, PCBP3, PCDHA4, PCID1, PCMT1, PDCD5, PDE1B, PDE1C, PDE6G, PGM1, PHKB, PHKG2, PICK1, PIK3CA, PIK3R1, PLA2G7, PLCB1, PLCB3, PLCG2, PPIH, PPP2R1A, PRDX1, PRKCA, PRLHR, PRMT1, PRPSAP1, PSAT1, PSEN1, PSMA1, PSMC1, PSMD1, PSMD11, PSMD13, PSMD6, PSME1, PTHR2, PXN, PYGL, PYGM, QRICH2, RAB2, RALA, RANBP1, RAP2A, RCC1, RCC2, RGS12, RGS2, RHOA, RIF1, RPA2, RPLP2, RPN2, RPS14, RRM1, RUVBL2, RYR1, RYR2, S100A6, SACS, SARS, SCTR, SDC3, SELE, SERPINB9, SET, SETD4, SF3B14, SGTB, SHANK1, SHBG, SIAH1, SLC2A1, SLC6A3, SLC7A10, SNCA, SNRPB2, SOCS6, SOCS7, SORD, SRC, STAU1, STRAP, STX12, SYK, TBCA, TBXA2R, TCP1, TEAD3, TFAM, TGM2, TJP1, TK1, TLR10, TMEM4, TNIK, TPI1, TRAF2, TRMT112, TUBA1, TUBA1A, TUBA1B, TUBA2, TUBB, TUBG1, TXN, TXNDC4, TXNL2, TYMS, UBQLN4, UCHL1, USP24, VHL, VIPR1, YWHAQ, and ZAP70.
7. A method of treating autism in a subject comprising administering an effective amount of a nonselective activator of metabotropic glutamate receptors (mGluRs) to a subject, thereby improving at least one symptom of autism.
8. A method of treating autism in a subject comprising administering an effective amount of a nonselective activator of metabotropic glutamate receptors (mGluRs) to a subject that has at least one genetic alteration in an mGluR network gene, thereby improving at least one symptom of autism.
9. A method of treating autism in a subject comprising obtaining results from a genetic screen that determines whether a subject has a genetic alteration in an mGluR
network gene, and, if the results show that the subject has at least one genetic alteration in an mGluR network gene, treating the subject by administering an effective amount of a nonselective activator of mGluRs.
network gene, and, if the results show that the subject has at least one genetic alteration in an mGluR network gene, treating the subject by administering an effective amount of a nonselective activator of mGluRs.
10. The method of claim 8, wherein the genetic alteration is a copy number variation (CNV) or single nucleotide variation (SNV).
11. The method of any one of claims 7 to 10, wherein the nonselective activator of mGluRs is fasoracetam.
12. The method of claim 11, wherein fasoracetam is fasoracetam monohydrate (NS-105 or NFC-1).
13. The method of claim 11 or 12, wherein fasoracetam is administered at a dose of 50 mg, 100mg, 150 mg, 200 mg, 250 mg, 300 mg, 350 mg, or 400 mg, and wherein the dose is administered once, twice, or three times daily.
14. The method of claim 11 or 12, wherein fasoracetam is administered at a dose of 50-400 mg, 100-400 mg, or 200-400 mg, and wherein the dose is administered once, twice, or three times daily.
15. The method of claim 11 or 12, wherein the fasoracetam is administered at a dose of 200-400 mg, such as 200 mg, 300 mg, or 400 mg, and wherein the dose is administered twice daily.
16. The method of any one of claims 7-15, wherein the subject has a CNV in at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 mGluR network genes.
17. The method of any one of claims 10-16, wherein a CNV in an mGluR
network gene is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes.
network gene is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes.
18. The method of any one of claims 10-17, wherein a CNV in an mGluR
network gene is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes.
network gene is determined by obtaining a nucleic acid-comprising sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes.
19. The method of any one of claims 10-18, wherein a CNV in an mGluR
network gene is determined by obtaining a nucleic acid sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes.
network gene is determined by obtaining a nucleic acid sample from the subject and subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR network genes.
20. The method of claim 19, wherein the screen does not assess CNVs in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, or GRM8.
21. The method of any one of claims 1-20, wherein the subject does not have a CNV in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, or GRM8.
22. The method of any one of claims 1-21, wherein the subject is a pediatric subject.
23. The method of claim 22, wherein the pediatric subject is between the ages of 5 and 17, 5 and 8, 8 and 17, 8 and 12, or 12 and 17.
24. The method of any one of claims 1-21 wherein the subject is an adult.
25. The method of any one of claims 1-22, wherein the nonselective activator of mGluRs is administered in combination with another pharmaceutical or non-pharmaceutical therapy.
26. The method of any one of claims 7-25, wherein the patient has been diagnosed with autism spectrum disorder, pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD).
27. The method of claim 26, wherein the autism is syndromic ASD.
28. The method of claim 26 or 27, wherein the patient has ASD and 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy.
29. A method for diagnosing autism in a subject comprising isolating a nucleic acid comprising sample from a subject, analyzing the sample for the presence or absence of a genetic alteration in at least one mGluR network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene.
30. A method for diagnosing autism in a subject comprising isolating a nucleic acid comprising sample from a subject, isolating nucleic acid from the sample, analyzing the nucleic acid for the presence or absence of a genetic alteration in at least one mGluR
network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene.
network genes, and diagnosing autism if the subject has at least one genetic alteration in a mGluR network gene.
31. A method for identifying a subject as having autism comprising obtaining a sample from a patient, optionally isolating nucleic acid from the sample, optionally amplifying the nucleic acid, and analyzing the nucleic acid in the sample for the presence or absence of a genetic alteration, such as a CNV, in at least one mGluR
network gene, wherein the subject is identified as having autism if at least one genetic alteration, such as a CNV, in an mGluR network gene is detected.
network gene, wherein the subject is identified as having autism if at least one genetic alteration, such as a CNV, in an mGluR network gene is detected.
32. A method for diagnosing autism in a subject comprising analyzing genetic information about one or more mGluR network genes, comparing the subject's information to a control subject that does not have autism, and diagnosing autism if the genetic information suggests that the subject has at least one genetic alteration in a mGluR network gene.
33. A method of confirming a diagnosis of autism in a subject comprising:
obtaining a nucleic acid-comprising sample from a subject diagnosed with autism by a method that comprises detecting or analyzing genetic alterations in mGluR network genes;
optionally amplifying the nucleic acid in the sample; and determining whether the subject has at least one genetic alteration, such as a CNV, in an mGluR network gene;
and confirming a diagnosis of autism if the subject has at least one genetic alteration in an mGluR network gene.
obtaining a nucleic acid-comprising sample from a subject diagnosed with autism by a method that comprises detecting or analyzing genetic alterations in mGluR network genes;
optionally amplifying the nucleic acid in the sample; and determining whether the subject has at least one genetic alteration, such as a CNV, in an mGluR network gene;
and confirming a diagnosis of autism if the subject has at least one genetic alteration in an mGluR network gene.
34. The method of any one of claims 29-33, wherein the analysis for the presence or absence of at least one genetic alteration in an mGluR network gene comprises microarrays, whole genome sequencing, exome sequencing, targeted sequencing, FISH, comparative genomic hybridization, genome mapping, or other methods using next-generation sequencing, Sanger sequencing, PCR, or TaqMan technologies.
35. The method of any one of claims 29-34, wherein the subject has CNVs in at least two mGluR network genes.
36. The method of any one of claims 29-35, wherein the method comprises detecting CNVs in mGluR network genes by subjecting the sample to a screen that assesses CNVs in at least 2, 3, 4, 5, 6, 7, 8, 9, or 10 mGluR network genes.
37. The method of any one of claims 29-36, wherein CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, 60, 70, or all of Tier 1 mGluR network genes.
38. The method of any one of claims 29-37, wherein CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 150, at least 175, or all of Tier 2 mGluR network genes.
39. The method of any one of claims 29-38, wherein CNVs in mGluR network genes are determined by subjecting the sample to a screen that assesses CNVs in at least 50, at least 100, at least 200, at least 300, at least 400, at least 500, or all of Tier 3 mGluR
network genes.
network genes.
40. The method of any one of claims 29-40, wherein the subject is a pediatric subject, such as a subject between the ages of 5 and 17, 5 and 8, 8 and 17, 8 and 12, or 12 and 17.
41. The method of any one of claims 29-40, wherein the subject is an adult subject.
42. The method of any one of claims 29-41, wherein the subject is not assessed for genetic alterations or CNVs in one or more of GRM1, GRM2, GRM3, GRM4, GRM5, GRM6, GRM7, and GRM8.
43. The method of any one of claims 29-42, wherein the method for determining the presence or absence of at least one mGluR network gene genetic alteration comprises microarrays, whole genome sequencing, exome sequencing, targeted sequencing, FISH, comparative genomic hybridization, genome mapping, or other methods using next-generation sequencing, Sanger sequencing, PCR, or TaqMan technologies.
44. The method of any one of claims 1-43, wherein the subject has autism as well as ADHD.
45. The method of any one of claims 1-43, wherein the subject does not have one or more of ADHD, schizophrenia, conduct disorder, TS, anxiety disorder, phobia, or depression.
46. The method of any one of claims 29-45, wherein the patient has autism spectrum disorder, pervasive developmental disorder, or one or more conditions selected from autistic disorder (classic autism), Asperger's syndrome, childhood disintegrative disorder, Rett's disorder, pervasive developmental disorder not otherwise specified (PDD-NOS), and social (pragmatic) communication disorder (SCD).
47. The method of claim 46, wherein the patient has syndromic ASD.
48. The method of claim 46 or 48, wherein the patient has ASD and 22q11.2 Deletion or Duplication Syndrome, Fetal Valproate Syndrome or Thalidomide Embryopathy.
Applications Claiming Priority (11)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
US14/740,230 | 2015-06-15 | ||
US14/740,230 US11219617B2 (en) | 2014-05-30 | 2015-06-15 | Methods of diagnosing and treating autism |
US201562215636P | 2015-09-08 | 2015-09-08 | |
US201562215628P | 2015-09-08 | 2015-09-08 | |
US201562215633P | 2015-09-08 | 2015-09-08 | |
US201562215673P | 2015-09-08 | 2015-09-08 | |
US62/215,633 | 2015-09-08 | ||
US62/215,628 | 2015-09-08 | ||
US62/215,673 | 2015-09-08 | ||
US62/215,636 | 2015-09-08 | ||
PCT/US2016/037596 WO2016205348A1 (en) | 2015-06-15 | 2016-06-15 | Methods of diagnosing and treating autism |
Publications (1)
Publication Number | Publication Date |
---|---|
CA2989326A1 true CA2989326A1 (en) | 2016-12-22 |
Family
ID=57546224
Family Applications (1)
Application Number | Title | Priority Date | Filing Date |
---|---|---|---|
CA2989326A Abandoned CA2989326A1 (en) | 2015-06-15 | 2016-06-15 | Methods of diagnosing and treating autism |
Country Status (5)
Country | Link |
---|---|
EP (1) | EP3307913A4 (en) |
CN (1) | CN108474036A (en) |
AU (1) | AU2016278053A1 (en) |
CA (1) | CA2989326A1 (en) |
WO (1) | WO2016205348A1 (en) |
Families Citing this family (6)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
AU2011293363A1 (en) | 2010-08-24 | 2013-02-28 | The Children's Hospital Of Philadelphia | Association of rare recurrent genetic variations to attention-deficit, hyperactivity disorder (ADHD) and methods of use thereof for the diagnosis and treatment of the same |
CA2997191A1 (en) | 2015-09-08 | 2017-03-16 | The Children's Hospital Of Philadelphia | Methods of diagnosing and treating anxiety disorder |
WO2018195184A1 (en) * | 2017-04-19 | 2018-10-25 | Aevi Genomics Medicine, Inc. | Methods of diagnosing and treating adhd in biomarker positive subjects |
CN109813912B (en) * | 2019-01-04 | 2021-12-28 | 深圳大学 | Application of group of serum differential protein combinations in preparation of reagent for detecting autism |
CN113706458B (en) * | 2021-07-15 | 2023-03-28 | 电子科技大学 | Autism detection device based on Gossip model |
CN114446476B (en) * | 2022-01-28 | 2023-02-17 | 中南大学湘雅二医院 | Construction method, prediction method and device of autism treatment effect prediction model |
Family Cites Families (8)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CA1202962A (en) | 1982-10-19 | 1986-04-08 | David P. Clifford | Substituted n-phenyl-n'-benzoyl ureas and their use as insecticides and acaricides |
US4683195A (en) | 1986-01-30 | 1987-07-28 | Cetus Corporation | Process for amplifying, detecting, and/or-cloning nucleic acid sequences |
US4965188A (en) | 1986-08-22 | 1990-10-23 | Cetus Corporation | Process for amplifying, detecting, and/or cloning nucleic acid sequences using a thermostable enzyme |
FR2597100A1 (en) | 1986-01-21 | 1987-10-16 | Nippon Shinyaku Co Ltd | PYROGLUTAMIDE DERIVATIVES |
US20100216734A1 (en) * | 2006-03-08 | 2010-08-26 | Braincells, Inc. | Modulation of neurogenesis by nootropic agents |
US20140315992A1 (en) | 2011-07-07 | 2014-10-23 | The Children's Hospital Of Philadelphia | Genetic Alterations Associated with Autism and the Autistic Phenotype and Methods of Use Thereof for the Diagnosis and Treatment of Autism |
US20140216734A1 (en) * | 2013-02-05 | 2014-08-07 | Schlumberger Technology Corporation | Casing collar location using elecromagnetic wave phase shift measurement |
WO2014152965A2 (en) * | 2013-03-14 | 2014-09-25 | The Children's Hospital Of Philadelphia | Schizophrenia-associated genetic loci identified in genome wide association studies and use thereof as novel therapeutic targets |
-
2016
- 2016-06-15 CA CA2989326A patent/CA2989326A1/en not_active Abandoned
- 2016-06-15 CN CN201680048195.4A patent/CN108474036A/en active Pending
- 2016-06-15 EP EP16812321.4A patent/EP3307913A4/en not_active Withdrawn
- 2016-06-15 AU AU2016278053A patent/AU2016278053A1/en not_active Abandoned
- 2016-06-15 WO PCT/US2016/037596 patent/WO2016205348A1/en unknown
Also Published As
Publication number | Publication date |
---|---|
EP3307913A4 (en) | 2019-03-27 |
WO2016205348A1 (en) | 2016-12-22 |
AU2016278053A1 (en) | 2018-01-04 |
CN108474036A (en) | 2018-08-31 |
EP3307913A1 (en) | 2018-04-18 |
Similar Documents
Publication | Publication Date | Title |
---|---|---|
AU2017245271B2 (en) | Association of rare recurrent genetic variations to attention-deficit, hyperactivity disorder (adhd) and methods of use thereof for the diagnosis and treatment of the same | |
EP3347016B1 (en) | Diagnosing and treating anxiety disorder | |
Mill et al. | Epigenomic profiling reveals DNA-methylation changes associated with major psychosis | |
JP6078211B2 (en) | Genetic changes associated with autism and the phenotype of autism and its use for diagnosis and treatment of autism | |
CA2989326A1 (en) | Methods of diagnosing and treating autism | |
US20220033903A1 (en) | Genetic markers associated with asd and other childhood developmental delay disorders | |
US20160244831A9 (en) | Genetic Alterations Associated with Autism and the Autistic Phenotype and Methods of Use Thereof for the Diagnosis and Treatment of Autism | |
US20230304094A1 (en) | Genomic alterations associated with schizophrenia and methods of use thereof for the diagnosis and treatment of the same | |
Sala et al. | Neuronal and synaptic dysfunction in autism spectrum disorder and intellectual disability | |
US11219617B2 (en) | Methods of diagnosing and treating autism | |
AU2015298618A1 (en) | Genetic alterations associated with autism and autistic phenotype and methods of diagnosing and treating autism | |
Sun et al. | Genome-wide DNA methylation profiles of autism spectrum disorder | |
Kakinuma et al. | Copy-number variations associated with autism spectrum disorder | |
Kaufman | Identification of Non-Syndromic Intellectual Disability Genes and Their Overlap with Autism | |
Roohi | Identification of potential candidate genes in autism spectrum disorder |
Legal Events
Date | Code | Title | Description |
---|---|---|---|
EEER | Examination request |
Effective date: 20210514 |
|
EEER | Examination request |
Effective date: 20210514 |
|
EEER | Examination request |
Effective date: 20210514 |
|
EEER | Examination request |
Effective date: 20210514 |
|
FZDE | Discontinued |
Effective date: 20231010 |