WO2023233148A1 - Cancérothérapie - Google Patents

Cancérothérapie Download PDF

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WO2023233148A1
WO2023233148A1 PCT/GB2023/051429 GB2023051429W WO2023233148A1 WO 2023233148 A1 WO2023233148 A1 WO 2023233148A1 GB 2023051429 W GB2023051429 W GB 2023051429W WO 2023233148 A1 WO2023233148 A1 WO 2023233148A1
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methyl
phenyl
methoxy
pyrimidin
pyrido
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PCT/GB2023/051429
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Karen Annette LANE
Jessica Anne Downs
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The Institute Of Cancer Research: Royal Cancer Hospital,
Cancer Research Technology Limited
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Publication of WO2023233148A1 publication Critical patent/WO2023233148A1/fr

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    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57484—Immunoassay; Biospecific binding assay; Materials therefor for cancer involving compounds serving as markers for tumor, cancer, neoplasia, e.g. cellular determinants, receptors, heat shock/stress proteins, A-protein, oligosaccharides, metabolites
    • 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
    • A61K31/4353—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 ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/4375—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 ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a six-membered ring having nitrogen as a ring heteroatom, e.g. quinolizines, naphthyridines, berberine, vincamine
    • 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
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/50—Pyridazines; Hydrogenated pyridazines
    • A61K31/5025—Pyridazines; Hydrogenated pyridazines ortho- or peri-condensed with heterocyclic ring systems
    • 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
    • A61K31/495—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with two or more nitrogen atoms as the only ring heteroatoms, e.g. piperazine or tetrazines
    • A61K31/505—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim
    • A61K31/519—Pyrimidines; Hydrogenated pyrimidines, e.g. trimethoprim ortho- or peri-condensed with heterocyclic rings
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the present invention provides a method of stratifying an individual suffering from a cancer for treatment with a compound for inhibiting monopolar spindle 1 (Mps1).
  • the invention further provides medical uses, biomarker panels and kits thereof.
  • Background Chromatin structure and accessibility are regulated by multiple pathways, including through the activity of chromatin remodelling complexes.
  • the SWI/SNF complexes are one of four families of remodelling complexes, alongside CHD, ISW, and INO80 (Clapier et al. 2017).
  • SWI/SNF can be further subdivided into three categories based on subunit composition: BAF, PBAF (polybromo-associated BAF (PBAF) complex) and ncBAF (Harrod et al.2020).
  • All three complexes contain either SMARCA4 or SMARCA2 as the catalytic ATPase, and a number of additional subunits are shared between them.
  • the defining subunits of PBAF include PBRM1, BRD7 and ARID2.
  • the genes encoding subunits of all three SWI/SNF categories are commonly mutated in cancer (Harrod et al.2020), suggesting that these complexes play an important role in cancer biology.
  • the PBAF specific subunit PBRM1 is among the most frequently mutated SWI/SNF subunits. This is particularly evident in clear cell renal cell carcinoma (ccRCC) where PBRM1 mutations are present in approximately 40% of patient samples (Harrod et al.2020).
  • the main target of the SAC is the anaphase promoting complex/cyclosome (APC/C), which is inhibited by a network of regulatory mechanisms in response to unattached kinetochores.
  • This network includes the activity of the mitotic Cyclin B1-CDK1 kinase (Jackman et al.2020) and the MPS1 kinase (monopolar spindle 1 also known as TTK) (Lara-Gonzalez et al.2021). Impaired SAC activity will result in chromosome missegregation and aneuploidy in the daughter cells (Lara-Gonzalez et al.2021), which can lead to a loss of fitness (Stingele et al.
  • PBRM1 is one of the most frequently altered genes in cancer.
  • PBRM1 Polybromo 1
  • PBAF1 a tumor suppressor gene encoding the BAF180 protein
  • SWItch/sucrose non- fermentable (SWI/SNF) chromatin remodeling complexes is a specific subunit of the PBAF complex, which is one of the three classes of SWItch/sucrose non- fermentable (SWI/SNF) chromatin remodeling complexes.
  • PBRM1 contains six bromodomains, which recognize acetylated lysine histone residues, and is involved in preserving genome and chromosomal stability by maintaining centromeric cohesion during mitosis (Brownlee et al, 2014).
  • PBRM1 influences the antitumor immune response, notably by mediating resistance to T-cell-dependent killing in preclinical cancer models
  • Deleterious PBRM1 mutations are found in 28% to 55% of clear cell renal cell carcinomas (ccRCC), where they are an early, driver event.
  • ccRCC clear cell renal cell carcinomas
  • Several other aggressive malignancies also harbor PBRM1 defects, including 11% to 59% of chordomas, 12% to 23% of cholangiocarcinomas, 7% to 20% of mesotheliomas, 12% of endometrial carcinomas, and 3% of non–small cell lung cancers.
  • PBRM1 mutations were associated with higher TMB in diverse cancer types and significant associations were observed in LUAD and BLCA.
  • the expression of PBRM1 was found to positively correlate with immune infiltrates in diverse cancer types.
  • PBRM1 is thus an attractive target for cancer treatment.
  • the invention is based on the surprising finding that PBRM1 shows synthetic lethality with Cyclin B1, and PBRM1 deficient cells are sensitive to CDK1 inhibition.
  • PBRM1 deficient cells show elevated levels of mitotic defects when compared with the parental cells. In addition, this is accompanied by increased centromere fragility in the absence of PBRM1. Together these data show a model in which PBRM1 deficient cells have centromere defects that create a dependency on SAC activity for viability. Consistent with this model, PBRM1 deficient cells were observed to be sensitive to MPS1 (monopolar spindle 1) inhibitors, showing that MPS1 inhibitors have efficacy when used on patients with PBRM1 deficient tumours.
  • MPS1 monopolar spindle 1
  • the inventors thus have addressed a problem in the field by establishing a method of stratifying an individual suffering from a cancer for treatment with a compound for inhibiting monopolar spindle 1 (Mps1). No previous relationship between MPS1 and PBRM1-defective cancers has been reported. This therefore represents a major advance in the field.
  • Mps1 monopolar spindle 1
  • a method of stratifying an individual suffering from a cancer for treatment with a compound for inhibiting monopolar spindle 1 (Mps1) comprising the steps of: (i) providing a sample from the individual; (ii) determining the presence of defective PBRM1 in the sample compared to a control; wherein the presence of defective PBRM1 identifies the individual as having a PBRM1- defective cancer; (iii) stratifying the individual based on the presence or absence of defective PBRM1; wherein the presence of defective PBRM1 is indicative of an increased likelihood of efficacy of treatment with the compound for inhibiting Mps1; and wherein the absence of defective PBRM1 is indicative of a decreased likelihood of efficacy of treatment with the compound for inhibiting Mps1.
  • Mps1 monopolar spindle 1
  • a compound for inhibiting Mps1 for use in a method of treating a PBRM1-defective cancer in an individual in need thereof, the method comprising administering an effective amount of the compound to the individual, wherein the individual has been stratified as having an increased likelihood of efficacy of treatment with the compound for inhibiting Mps1 by a method according to claim 1.
  • the control is a level of expression of PBRM1 and defective PBRM1 comprises a reduced level of expression of PBRM1 in comparison to the control;
  • the control comprises an activity of a reference PBRM1 protein and defective PBRM1 comprises a reduced activity of a PBRM1 protein in comparison to the reference PBRM1 protein;
  • the control comprises an activity of a reference PBRM1 gene and defective PBRM1 comprises a reduced activity of a PBRM1 gene in comparison to the reference PBRM1 gene;
  • the control comprises a reference PBRM1 protein and defective PBRM1 comprises a variant PBRM1 protein comprising one or more mutations compared to the reference PBRM1 protein; and/or the control comprises a reference PBRM1 gene and defective PBRM1 comprises a variant PBRM1 gene comprising one or more mutations compared to the reference PBRM1 gene.
  • the reference PBRM1 protein comprises an amino acid sequence comprising SEQ ID NO: 1; the reference PBRM1 gene comprises a nucleic acid sequence comprising SEQ ID NO: 2.
  • the variant PBRM1 protein comprises one or more deleterious mutations in comparison to SEQ ID NO: 1; the variant PBRM1 gene comprises one or more deleterious mutations in comparison to SEQ ID NO: 2; optionally wherein the one or more deleterious mutations comprises at least one loss of function mutation.
  • the variant PBRM1 protein comprises or the PBRM1 gene comprises a nucleic acid sequence encoding a PBRM1 protein comprising one or more mutations selected from the group consisting of: R710*; R1160*; R921*; G1324Afs*8; K485Sfs*14; I1170Sfs*23; Y387Lfs*5; X79_splice; Y963*; X216_splice; R710*; I279Yfs*4; N258Mfs*25; X989_splice; E707*; R1496Pfs*12; X272_splice; E1538*; X1016_splice; Y417Ifs*3; R710*; E1189R f s*6; E1538*; E846*; E457*; R1160*; S371*; Y697*; R1027
  • the variant PBRM1 protein comprises an amino acid sequence comprising a sequence at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to any one of: SEQ ID NOs: 1; or (ii) the variant PBRM1 gene comprises a nucleic acid sequence comprising a sequence at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to any one of: SEQ ID NOs: 2. 8.
  • R 1 is selected from: (i) a 5- or 6-membered heteroaryl optionally substituted with one or more substituents independently selected from halo, trifluoromethyl, difluoromethyl, trifluoromethoxy, difluoromethoxy, cyano, nitro, (1-4C)alkyl, NR a R b , OR a , C(O)R a , C(O)OR a , OC(O)R a , N(R b )OR a , C(O)N(R b )R a , N(R b )C(O)R a , S(O)pR a (where p is 0, 1 or 2), SO 2 N(R b )R a , or N(R b )SO 2 R a , wherein R a and R b are each independently selected from H or (1-4C)alkyl, and wherein any alkyl moiety present in the substituent group
  • the MPS1 inhibitor is selected from the group consisting of a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or pharmaceutically acceptable salts or solvates thereof. In certain embodiments, the MPS1 inhibitor is selected from the group consisting of a compound of formula I or a compound of formula II, or pharmaceutically acceptable salts or solvates thereof.
  • the MPS1 inhibitor is selected from the following: 5-(furan-2-yl)-N-(4-methoxyphenyl)isoquinolin-3-amine; N-(4-methoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine; N-(2-methoxy-4-((1-methylpiperidin-4-yl)oxy)phenyl)-5-(1-methyl-1H-pyrazol-4- yl)isoquinolin-3-amine; N-(2,4-dimethoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine; 3-chloro-N,N-dimethyl-4-((5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3- yl)amino)benzamide; 3-methoxy-N,N-dimethyl-4-((5-(1-methyl-1H-pyrazol
  • the MPS1 inhibitor is selected from the following: N-cyclopropyl-4-(6-(2,3-difluoro-4-methoxyphenoxy)-8-((3,3,3- trifluoropropyl)amino)imidazo[1,2-b]pyridazin-3-yl)-2-methylbenzamide; (R)-2-(4-fluorophenyl)-N-(4-(2-((2-methoxy-4-(methylsulfonyl)phenyl)amino)- [1,2,4]triazolo[1,5-a]pyridin-6-yl)phenyl)propanamide; N2-(4-(4,5-dimethyl-4H-1,2,4-triazol-3-yl)-2-ethoxyphenyl)-6-methyl-N8- neopentylpyrido[3,4-d]pyrimidine-2,8-diamine; (S)-N8-(3,3-dimethylbutan
  • the cancer or the PBRM1-defective cancer is selected from the group consisting of: clear cell renal cell carcinoma, chordoma, cholangiocarcinoma, mesothelioma, endometrial carcinoma, non–small cell lung cancer and skin cutaneous melanoma
  • the methods disclosed herein further comprise generating a diagnostic report based on the predicted response to the inhibitor of Mps1, optionally wherein the diagnostic report is provided to a medical professional) for providing guidance on selection of a cancer treatment to be administered.
  • the method further comprises administering to the subject the compound.
  • a method of treating a PBRM1-defective cancer in an individual in need thereof comprising administering an effective amount of a compound for inhibiting Mps1: wherein the individual has been stratified as having an increased likelihood of efficacy of treatment with the compound for inhibiting Mps1 by a method according to any one of claims 1 to 12.
  • the variant PBRM1 protein comprises or the PBRM1 gene comprises a nucleic acid sequence encoding a PBRM1 protein comprising one or more variants selected from: R710*; R1160*; R921*; G1324Afs*8; K485Sfs*14; I1170Sfs*23; Y387Lfs*5; X79_splice; Y963*; X216_splice; R710*; I279Yfs*4; N258Mfs*25; X989_splice; E707*; R1496Pfs*12; X272_splice; E1538*; X1016_splice; Y417Ifs*3; R710*; E1189R f s*6; E1538*; E846*; E457*; R1160*; S371*; Y697*; R1027*; L1457
  • the variant PBRM1 protein comprises an amino acid sequence comprising a sequence at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to any one of: SEQ ID NO: 1; and/or the variant PBRM1 gene comprises a nucleic acid sequence comprising a sequence at least 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to any one of: SEQ ID NO: 2.
  • a kit comprising a reagent for detecting deficient PBRM1 in a sample from a subject and a compound for inhibiting Mps1.
  • the deficient PBRM1 comprises a variant PBRM1 nucleic acid and the reagent comprises a nucleic acid that hybridizes to a target nucleic acid comprising the variant PBRM1 nucleic acid; optionally wherein the reagent is a PCR primer set for amplifying the variant PBRM1 nucleic acid; and further optionally wherein the variant PBRM1 nucleic acid is a variant PBRM1 gene.
  • the variant PBRM1 gene comprises a nucleic acid sequence encoding a variant PBRM1 protein comprising one or more mutations selected from: R710*; R1160*; R921*; G1324Afs*8; K485Sfs*14; I1170Sfs*23; Y387Lfs*5; X79_splice; Y963*; X216_splice; R710*; I279Yfs*4; N258Mfs*25; X989_splice; E707*; R1496Pfs*12; X272_splice; E1538*; X1016_splice; Y417Ifs*3; R710*; E1189R f s*6; E1538*; E846*; E457*; R1160*; S371*; Y697*; R1027*; L1457Wfs*32; E
  • the deficient PBRM1 comprises a variant PBRM1 protein and the reagent comprises an antibody that specifically binds to the variant PBRM1 protein; optionally wherein the variant PBRM1 protein comprises one or more mutations selected from: R710*; R1160*; R921*; G1324Afs*8; K485Sfs*14; I1170Sfs*23; Y387Lfs*5; X79_splice; Y963*; X216_splice; R710*; I279Yfs*4; N258Mfs*25; X989_splice; E707*; R1496Pfs*12; X272_splice; E1538*; X1016_splice; Y417Ifs*3; R710*; E1189R f s*6; E1538*; E846*; E457*; R1160*; S371*
  • ccRCC clear cell renal cell carcinoma
  • PBRM1 proficient cell lines (786- O, Caki-1, 769-P) and PBRM1-mutated cells (RCC-FG2, RCC-4, Caki-2) are shown as indicated;
  • D R e presentative images from one of the experiments is shown;
  • E R e presentative western blot showing depletion of CCNB1 following siRNA transfection. ⁇ -tubulin was used as loading control.
  • Figure 2 shows that PBRM1 deficient cells are sensitive to CDK1 inhibition, but not to an inhibitor of CDK5:
  • B R e presentative images of colonies treated at increasing doses of RO-3306;
  • C Clonogenic survival of RPE1 parental and PBRM1 KOs when treated with the CDK5/2 inhibitor Roscovitine;
  • D R e presentative images of colonies treated at increasing doses of Roscovitine.
  • Figure 3 shows that PBRM1 deficient cells show mitotic abnormalities following CDK1 inhibition:
  • A Schematic indicating the experimental plan. Lower panel: representative images of severe nuclear defects quantified in treated cells;
  • B Quantification of cells with mild or severe nuclear defects. Data shown are 24 hours after 3 ⁇ M RO3306 treatment of RPE1 parental or PBRM1 KOs (mean ⁇ SEM);
  • C R e presentative images of nuclear morphologies following 24 hours of treatment with 3 ⁇ M RO3306;
  • D Quantification of the number of 53BP1 nuclear bodies (NBs) per cell in untreated or at the indicated recovery times following RO3306 treatment.
  • ⁇ -tubulin was used as loading control;
  • C R e presentative images showing centromere staining in CEN-CO- FISH chromosomes in parental (Par) and KO#1 (B3) PBRM1 KO. White arrow indicates abnormal centromere where a recombination event has occurred;
  • D Distance between centre point of centromeres in ⁇ m in RPE1 parental, PBRM1 KOs, or parental cells treated with scramble (scr) or CENP-A siRNAs.
  • Figure 6 shows a schematic showing reported mutations in cancer databases. The mutations are found across the entirety of the PBRM1 gene. This schematic was generated in accordance with Cerami et al. Cancer Discov.2012 May;2(5):401-4 using an online portal for cancer mutation data, cbioportal.org.
  • Figure 7 shows exemplary mutations of PBRM1 including citations. This figure was generated in accordance with Cerami et al. Cancer Discov.2012 May;2(5):401-4 using an online portal for cancer mutation data, cbioportal.org. Additional mutations including structural variants may be generated using said reference and database.
  • Figure 8 shows the generation of isogenic PBRM1 knockout (KO) cell lines identifies downregulation of peri/centromere protein levels as a common feature.
  • KO isogenic PBRM1 knockout
  • A Parental cell lines and number of PBRM1 knockout (KO) clones generated in each line.
  • B-E Characterization of the cell line panel. R e presentative images of Western blots (B), growth curves (C), FACS profiles (D) and microscopy images (E).
  • F Waterfall plot of log2FC in protein levels determined by mass spectroscopy in the KO cells relative to the parental control (RPE1- hTERT shown here). PBRM1 and peri/centromere associated proteins are indicated.
  • G Schematic of centromere associated protein complexes.
  • H Bar chart of log2FC of indicated proteins in the PBRM1 KO cells relative to parental (RPE1-hTERT) of peri/centromere associated proteins.
  • Protein complexes as in (G) are indicated at the top of the graph.
  • (I) Transcript levels of peri/centromere associated proteins do not show significant down- regulation in the PBRM1 KO cells relative to the parental cells. Volcano plot of log2FC of peri/centromere associated transcripts measured by RNA-seq in the PBRM1 KO cells relative to parental (RPE1-hTERT). The significance (p adj) is plotted on the Y axis.
  • J Heat map of relative protein abundance of peri/centromere associated proteins in CCLE cell line whole proteome datasets ordered according to PBRM1 abundance, showing a correlation between PBRM1 protein levels and peri/centromere protein levels.
  • Figure 9 shows PBRM1 KO cells are sensitive to mitotic perturbation.
  • A,B PBRM1 KO cells show increased sensitivity to depletion of Cyclin B1 when compared with parental RPE1- hTERT.
  • A 20 Quantification and (B) representative images of clonogenic survival assays.
  • C PBRM1- deficient renal cancer cells display increased sensitivity to depletion of Cyclin B1 when compared with PBRM1-proficient renal cancer cell lines. Depletion of Cyclin B1 (CCNB1) was performed with two different siRNAs (si1 and si2) and survival was measured relative to cells treated with a non-targeting control (scr).
  • FIG. 1 Western blot analysis of PBRM1 from cell extracts 25 prepared from cell lines used in (C).
  • E R e presentative images of clonogenic survival assays as quantified in (C).
  • F PBRM1 KO cells show increased sensitivity to chronic CDK1 inhibitor (RO-3306) exposure when compared with parental RPE1-hTERT.
  • G R e presentative images of clonogenic survival assays as quantified in (F).
  • H-I PBRM1 KO cells show increased mitotic aberrations after acute exposure to CDK1 inhibitor (RO-3306) when compared with parental 30 RPE1-hTERT cells.
  • H Schematic of experimental design.
  • FIG. 1 Western blot analysis of two PBRM1 KO clones (B3 and B16) in the mouse B16 melanoma cell line.
  • E PBRM1 KO clones in mouse B16 display downregulation of peri/centromere associated proteins. Log2FC of protein levels in KO clones relative to the parental cells is 40 plotted. Associated complex of each protein is indicated at the top of the graph.
  • F-H PBRM1 KO clones in mouse B16 cells show increased sensitivity to Mps1 inhibitors. Clonogenic survival assays were performed in cells treated with AZ3146 (F) or BOS172722 (G) relative to cells treated with vehicle (DMSO) alone.
  • FIG. 1 R e presentative images of clonogenic survival assays is shown in (H).
  • FIG. 1 Schematic of experimental design.
  • F Survival curves show that PBRM1 KO tumours respond better to Mps1 inhibitor treatment.
  • Figure 11 shows loss of PBRM1 leads to centromere fragility.
  • A,B Centromeres in PBRM1 KO cells show altered centromere structure compared with parental cells. Fluorescence in situ 5 hybridization (FISH) was performed in parental RPE1 and PBRM1 KO cells using probes to alpha-satellite sequences from Chromosome 2 or 10. Quantification of FISH signals for chromosome 2 (A) and 10 (B) and representative images (C).
  • D Cen-CO-FISH methodology.
  • E-G PBRM1 KO cells show increased aberrant centromere signals compared with the parental cells. Percent of cells with abnormal mitotic centromere signals were quantified (E). CenpA 10 depletion was used as a positive control and compared with cells treated with a non-targeting siRNA (scr). R e presentative images of mitotic spreads are shown (F) and the highlighted boxes are shown at higher magnification (G) with aberrant signals indicated with an arrow.
  • Figure 12 shows PBRM1 directs PBAF to centromeres to regulate centromere associated 15 transcription.
  • A IGV screenshot of Cut&Run data from SMARCA4 (top two rows) and CenpB (bottom two rows) performed in parental or PBRM1 KO cells across a centromere HOR. Background reads from the negative control are layered onto the maps in light grey.
  • B IGV screenshot of Cut&Run data from SMARCA4 (top two rows) and CenpB (bottom two rows) performed in parental or PBRM1 KO cells across a centromere transition arm. Background reads from the negative control are layered onto the maps in light grey.
  • C Model of PBRM1 function at centromeres. See text for details. The patent, scientific and technical literature referred to herein establish knowledge that was available to those skilled in the art at the time of filing.
  • the methods may be methods of stratifying patients who suffer from cancer or are at risk of cancer. Stratifying patients based on whether the subject suffers from PBRM1-defective cancer as determined by the methods described herein may also allow for a clinician to determine a differential treatment plan. For example, help determine whether the subject should be administered a compound for inhibiting Msp1 or whether an alternative treatment should be administered. As such, also provided are methods of determining a treatment plan for a PBRM1-defective cancer.
  • the terms “response” or “responsiveness” refers to an anti-cancer response, e.g. in the sense of reduction of tumour size or inhibiting tumour growth.
  • the terms can also refer to an improved prognosis, for example, as reflected by an increased time to recurrence, which is the period to first recurrence censoring for second primary cancer as a first event or death without evidence of recurrence, or an increased overall survival, which is the period from treatment to death from any cause.
  • an improved prognosis for example, as reflected by an increased time to recurrence, which is the period to first recurrence censoring for second primary cancer as a first event or death without evidence of recurrence, or an increased overall survival, which is the period from treatment to death from any cause.
  • To respond or to have a response means there is a beneficial endpoint attained when exposed to a stimulus. Alternatively, a negative or detrimental symptom is minimized, mitigated or attenuated on exposure to a stimulus.
  • evaluating the likelihood that a tumour or subject will exhibit a favourable response is equivalent to evaluating the likelihood that the tumour or subject will not exhibit favourable response (i.e., will exhibit a lack of response or be non-responsive).
  • the use of the term response may be synonymous with efficacy of treatment.
  • a positive or favourable response may be used to refer to a high efficacy of treatment.
  • the treatment is effective in at least reducing the symptoms of the cancer, increasing overall survival, decreasing occurrence of death, improving prognosis, reducing tumour size, reducing tumour score or grade and/or decreasing time to remission. For example, reducing the size of a cancerous tumour.
  • non-response or unfavourable response may be used to refer to a lack of reduced efficacy of treatment.
  • the treatment has little to no effect on the cancer.
  • the methods of stratifying an individual described herein further comprise generating a diagnostic report based on the likelihood of efficacy of treatment with the compound for inhibiting Mps1.
  • the diagnostic report may be provided to a medical professional for providing guidance as to whether a subject would be or is likely to be responsive to treatment with a compound for inhibiting Mps1 as described herein.
  • the methods of stratifying described herein may also include administering a compound for inhibiting Mps1 as described herein to the subject.
  • the methods of stratifying described herein may include the steps of any of the methods of treatment as described herein.
  • the method may then include administering a compound for inhibiting Mps1 as described herein.
  • a report is generated and analyzed by a medical professional.
  • the methods may include determining the probability of a positive response to a compound for inhibiting Mps1 as described herein. For example, predicting whether a compound for inhibiting Mps1 as described herein will be effective in treating the cancer of the subject.
  • the method may include determining whether a subject has PBRM1-defetcive cancer by detecting the presence of defective PBRM1 in a sample obtained from the subject.
  • the presence of defective PBRM1 and thus detection of a PBRM1-defective cancer may indicate or predict that the subject will have a favorable or positive response to treatment with a compound for inhibiting Mps1 as described herein.
  • presence of a PBRM1-defective cancer may be used to evaluate a subject that may be selected for treatment with a MSP1 inhibiting compound as described herein, and/or evaluate a response to a treatment with a MSP1 inhibiting compound as described herein.
  • predictive includes the use of a PBRM1 nucleic acid and/or protein status, e.g., over- or under-activity and/or expression for determining the likelihood of response of a cancer to treatment with a MSP1 inhibiting compound as described herein.
  • Such predictive use of the PBRM1 may be confirmed by, e.g., (1) increased or decreased copy number (e.g., by FISH, FISH plus SKY, single-molecule sequencing, e.g., as described in the art at least at J.
  • PBRM1 nucleic acid e.g., by ISH, Northern Blot, or qPCR
  • PBRM1 protein e.g., by IHC
  • activity e.g., in more than about 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, or more of assayed human cancers types or cancer samples; (2) its absolute or relatively modulated presence or absence in a biological sample, e.g., a sample containing tissue, whole blood, serum, plasma, buccal scrape, saliva, cerebrospinal fluid, urine, stool, or bone marrow, from a subject, e.g.
  • PBRM1 refers to protein Polybromo-1, which is a subunit of ATP-dependent chromatin-remodeling complexes. PBRM1 functions in the regulation of gene expression as a constituent of the evolutionary-conserved SWI/SNF chromatin remodeling complexes (Eus Wegn et al. (2012) J. Biol. Chem.287:30897-30905).
  • PBRM1 is one of the unique components of the SWI/SNF-B complex, also known as polybromo/BRG1-associated factors (or PBAF), absent in the SWI/SNF-A (BAF) complex (Xue et al. (2000) Proc Natl Acad Sci USA.97:13015-13020; Brownlee et al. (2012) Biochem Soc Trans.40:364-369).
  • PBAF polybromo/BRG1-associated factors
  • PBRM1 mutations are most predominant in renal cell carcinomas (RCCs) and have been detected in over 40% of cases, placing PBRM1 second (after VHL) on the list of most frequently mutated genes in this cancer (Varela et al. (2011) Nature 469:539-542; Hakimi et al. (2013) Eur Urol.63:848-854; Pena-Llopis et al. (2012) Nat Genet.44:751-759; Pawlowski et al. (2013) Int J Cancer.132:E11-E17).
  • PBRM1 mutations have also been found in a smaller group of breast and pancreatic cancers (Xia et al. (2008) Cancer Res.68:1667-1674; Shain et al.
  • PBRM1 mutations are more common in patients with advanced disease stage (Hakimi et al. (2013), supra), and loss of PBRM1 protein expression has been associated with advanced tumour stage, low differentiation grade and worse patient outcome (Pawlowski et al. (2013), supra). In another study, no correlation between PBRM1 status and tumour grade was found (Pena-Llopis et al. (2012), supra).
  • PBRM1-mutant tumours are associated with better prognosis than BAP1-mutant tumours, tumours mutated for both PBRM1 and BAP1 exhibit the greatest aggressiveness (Kapur et al. (2013) Lancet Oncol.14:159-167).
  • PBRM1 is ubiquitously expressed during mouse embryonic development (Wang et al. (2004), supra) and has been detected in various human tissues including pancreas, kidney, skeletal muscle, liver, lung, placenta, brain, heart, intestine, ovaries, testis, prostate, thymus and spleen (Xue et al. (2000), supra; Horikawa and Barrett (2002) DNA Seq.13:211-215).
  • PBRM1 protein localises to the nucleus of cells (Nicolas and Goodwin (1996) Gene 175:233- 240). As a component of the PBAF chromatin-remodelling complex, it associates with chromatin (Thompson (2009) Biochimie.91:309-319), and has been reported to confer the localisation of PBAF complex to the kinetochores of mitotic chromosomes (Xue et al. (2000), supra). Human PBRM1 gene encodes a 1582 amino acid protein, also referred to as BAF180. Six bromodomains (BD1-6), known to recognize acetylated lysine residues and frequently found in chromatin-associated proteins, constitute the N-terminal half of PBRM1.
  • PBRM1 The C- terminal half of PBRM1 contains two bromo-adjacent homology (BAH) domains (BAH1 and BAH2, present in some proteins involved in transcription regulation.
  • BAH bromo-adjacent homology
  • BAH2 high mobility group
  • HMG domain is located close to the C-terminus of PBRM1. HMG domains are found in a number of factors regulating DNA-dependent processes where HMG domains often mediate interactions with DNA.
  • PBRM1 is intended to include fragments, variants (e.g., allelic variants), and derivatives thereof of a PBRM1 encoding nucleic acid or protein.
  • a PBRM1 nucleic acid may be a PBRM1 gene, such as the human gene or an RNA, such as an mRNA transcript produced from transcription of a PBRM1 encoding gene.
  • R e presentative human PBRM1 cDNA and human PBRM1 protein sequences are well-known in the art and are publicly available from the National Center for Biotechnology Information (NCBI).
  • NCBI National Center for Biotechnology Information
  • a PBRM1 gene may have a sequence as set forth in the NCBI Gene ID: 55193.
  • a PBRM1 protein may comprise an amino acid sequence as set forth in UniProt ID: Q86U86 or any of the isoforms described therein.
  • PBRM1 The nucleic acid and amino acid sequences of wildtype PBRM1 are known in the art and readily available on public databases, such as the National Center for Biotechnology Information (NCBI).
  • NCBI National Center for Biotechnology Information
  • the PBRM1 gene is a human PBRM1 gene, also known as protein polybromo- 1, polybromo- ID, BRG1 -associated factor 180 (BAF180) or PB1.
  • An exemplary PBRM1 gene is represented by NCBI Gene ID No. 55193.
  • Exemplary nucleic acid sequences of human PBRM1 include, for example, human PBRM1 transcript variant 1 cDNA sequence (NCBI R e ference sequence: NM_018313.4), human PBRM1 transcript variant 2 cDNA sequence (NCBI R e ference sequence: NM 181042.4), and mouse PBRM1 cDNA sequence (NCBI R e ference sequence: NM 001081251.1).
  • RNA nucleic acid sequences corresponding to the PBRM1 cDNA sequences described herein nucleic acid molecules encoding orthologues of the encoded proteins, as well as DNA or RNA nucleic acid sequences comprising a nucleic acid sequence having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or more identity across their full length with the nucleic acid sequences described herein, or a portion thereof.
  • Exemplary amino acid sequences of PBRM1 protein include, for example, human PBRM1 variant 1 amino acid sequence (NCBI Reference sequence: NP_ 060783.3), human PBRM1 variant 2 amino acid sequence (NCBI R e ference sequence: NP 851385.1), and mouse PBRM1 protein sequence (NP 001074720.1).
  • orthologues of the proteins as well as polypeptide molecules comprising an amino acid sequence having at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or more identity across their full length with an amino acid sequence of any PBRM1 proteins, or a portion thereof.
  • PBRM1 defective PBRM1
  • PBRM1- defective refers to a nucleic acid or protein that encodes a PBRM1 gene, gene product or protein that has a reduced activity in comparison to a control or reference PBRM1 nucleic acid or protein.
  • a control or reference nucleic acid may be a PBRM1 gene according to SEQ ID NO: 2.
  • a control or reference protein may be a PBRM1 protein according to SEQ ID NO: 1.
  • references to “deficiency” or “deficient” PBRM1 includes any means by which the function of the gene product is lost within cells.
  • a PBRM1 protein comprises a sequence according to SEQ ID NO: 1.
  • a PBRM1 gene comprises a sequence according to SEQ ID NO: 2.
  • this may be selected from the group consisting of: a loss of copy numbers of the PBRM1 gene; a mutation or modification reducing transcription or translation of the PBRM1 gene; and a mutation reducing function of the PBRM1 gene product (i.e. a PBRM1 mRNA or protein).
  • a deficiency assessed with respect to a reduction in transcription or translation of gene of interest may cause a reduction of the relevant parameter by at least 5%, by at least 10%, by at least 20%, or by at least 30%.
  • a deficiency may cause a reduction of the relevant parameter by at least 40%, at least 50%, at least 60%, at least 70% or more.
  • a deficiency may be a total loss (100% reduction) as compared to a suitable comparator.
  • Activity of a particular gene may be characterized by a measure of gene transcript (e.g. mRNA), by a measure of the quantity of translated protein, or by a measure of gene product activity.
  • PBRM1 expression can be monitored in a variety of ways, including by detecting mRNA levels, protein levels, or protein activity, any of which can be measured using standard techniques. Detection can involve quantification of the level of gene expression (e.g., genomic DNA, cDNA, mRNA, protein, or enzyme activity), or, alternatively, can be a qualitative assessment of the level of gene expression, in particular in comparison with a control level. Many techniques are known in the art for determining absolute and relative levels of gene expression, commonly used techniques suitable for use include Northern analysis, RNase protection assays (RPA), microarrays and PCR-based techniques, such as quantitative PCR and differential display PCR.
  • RPA RNase protection assays
  • PCR-based techniques such as quantitative PCR and differential display PCR.
  • control may be a level of expression of PBRM1 and “defective PBRM1” refers to a reduced level of expression in comparison to the control (e.g. expression of PBRM1 in a control sample).
  • control comprises an activity of a reference PBRM1 gene and “defective PBRM1” refers to a reduced activity of a PBRM1 gene in comparison to the control (e.g. a reference PBRM1 gene in a control sample).
  • the control comprises an activity of a reference PBRM1 protein and defective PBRM1 comprises a reduced activity of a PBRM1 protein in comparison to the control (e.g. a reference PBRM1 protein).
  • defective PBRM1 refers to a variant PBRM1 protein.
  • the variant PBRM1 protein may comprise one or more deleterious mutations in comparison to SEQ ID NO: 1.
  • defective PBRM1 refers to a variant PBRM1 gene.
  • the variant PBRM1 may comprise one or more deleterious mutations in comparison to SEQ ID NO: 2.
  • Exemplary deleterious mutations include, but are not limited to, nucleic acid mutations including single-base substitutions, multi-base substitutions, insertion mutations, deletion mutations, frameshift mutations, missense mutations, nonsense mutations, splice-site mutations, epigenetic modifications (e.g., methylation, phosphorylation, acetylation, ubiquitylation, sumoylation, histone acetylation, histone deacetylation, and the like), and combinations thereof.
  • the mutation is a "nonsynonymous mutation," meaning that the mutation alters the amino acid sequence of PBRM1.
  • Such mutations reduce or eliminate PBRM1 protein amounts and/or function by eliminating proper coding sequences required for proper PBRM1 protein translation and/or coding for PBRM1 proteins that are non-functional or have reduced function (e.g., deletion of enzymatic and/or structural domains, reduction in protein stability, alteration of sub-cellular localization, and the like).
  • Mutations contemplated herein include germline mutations and somatic mutations. Both biallelic and monoallelic mutations are contemplated herein.
  • the deleterious mutation of PBRM1 is a loss-of-function mutation in the PBRM1 gene.
  • the deleterious mutation of PBRM1 is a nonsense, frameshift, or splice-site mutation.
  • the deleterious mutation of PBRM1 is loss of a PBRM1 allele.
  • the deleterious mutation of PBRM1 is biallelic loss of PBRML
  • the deleterious mutation of PBRM1 is monoallelic loss of PBRML.
  • the deleterious mutation of PBRM1 is a mutation that results in truncation of the PBRM1 protein.
  • the a variant gene may encode a protein including or the variant protein may include any one or more mutations selected from: R710*; R1160*; R921*; G1324Afs*8; K485Sfs*14; I1170Sfs*23; Y387Lfs*5; X79_splice; Y963*; X216_splice; R710*; I279Yfs*4; N258Mfs*25; X989_splice; E707*; R1496Pfs*12; X272_splice; E1538*; X1016_splice; Y417Ifs*3; R710*; E1189R f s*6; E1538*; E846*; E457*; R1160*; S371*; Y697*; R1027*; L1457Wfs*32; E368*; R58*; Q779
  • PBRM1 human PBRM1 as identified by UniProt ID NO: Q86U86.
  • Other deleterious mutations of PBRM1 may also be applicable, for example, see the inactivating mutations of PBRM1 described in WO2018/132287, which is incorporated herein by reference in its entirety.
  • other mutations may be found in publicly available cancer databases such as at the cBioPortal for Cancer Genomics (Cerami, Ethan, et al. "The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.” Cancer discovery 2.5 (2012): 401-404. which is incorporated herein by reference in its entirety).
  • defective PBRM1 may include a variant PBRM1 protein comprising at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or more sequence identity to the amino acid according to SEQ ID NO: 1.
  • defective PBRM1 may include a variant PBRM1 gene comprising at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or more sequence identity to the nucleic acid according to SEQ ID NO: 2.
  • defective PBRM1 reduced the expression level of PBRM1 protein by any one of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • the defective PBRM1 results in no expression of PBRM1 protein.
  • Expression level of PBRM1 gene products can be determined using known methods in the art, for example, by quantitative polymerase chain reaction (qPCR) or RNA sequencing for measuring RNA levels, or by western blot for measuring protein levels.
  • defective PBRM1 reduces activity of a PBRM1 protein by any one of at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, or more.
  • the activity of PBRM1 protein can be measured using activity assays known in the art, for example, by assessing binding to acetylated Lys-14 of histone H3 (H3K14ac).
  • the methods described herein may further comprises detecting one or more epigenetic modifications to PBRM1 gene of the individual.
  • the individual has one or more epigenetic modifications to PBRM1 gene.
  • the one or more epigenetic modifications comprise methylations, such as methylations to the promoter, enhancer, and/or coding regions of the PBRM1 gene.
  • the one or more epigenetic modifications comprise histone modification.
  • the one or more epigenetic modifications to PBRM1 gene may contribute to altered (e.g., lower) expression and/or activity level of PBRM1 gene products.
  • a biological sample is tested for the presence of copy number changes in genomic loci containing the genomic marker.
  • Methods of evaluating the copy number of a gene locus include, but are not limited to, hybridization-based assays.
  • Hybridization-based assays include, but are not limited to, traditional “direct probe” methods, such as Southern blots, in situ hybridization (e.g., FISH and FISH plus SKY) methods, and “comparative probe” methods, such as comparative genomic hybridization (CGH), e.g., cDNA-based or oligonucleotide-based CGH.
  • CGH comparative genomic hybridization
  • the methods can be used in a wide variety of formats including, but not limited to, substrate (e.g.
  • the invention makes use of the analysis of a PBRM1 gene and the products there of. These include analysis for a deficiency (such as loss of gene copy number), analysis for the presence of mutations (either generally or specifically) within genes of interest, analysis for activity of a gene or gene product and analysis for elevated expression of the gene. Analysis will be performed in respect of a suitable sample from a patient. Such a sample may, for example, be a cell of the cancer of interest. R e sults obtained by the chosen method of analysis may be compared with suitable reference values, to identify any gene-associated changes that are present.
  • PBRM1 gene copy number in a sample involves a Southern Blot.
  • genomic DNA typically fragmented and separated on an electrophoretic gel
  • probe specific for the target region is hybridized to a probe specific for the target region.
  • control probe signal from analysis of normal genomic DNA e.g., a non-amplified portion of the same or related cell, tissue, organ, etc.
  • a Northern blot may be utilized for evaluating the copy number of encoding nucleic acid in a sample.
  • mRNA is hybridized to a probe specific for the target region. Comparison of the intensity of the hybridization signal from the probe for the target region with control probe signal from analysis of normal RNA (e.g., a non-amplified portion of the same or related cell, tissue, organ, etc.) provides an estimate of the relative copy number of the target nucleic acid.
  • RNA can be used, such that higher or lower expression relative to an appropriate control (e.g., a non-amplified portion of the same or related cell tissue, organ, etc.) provides an estimate of the relative copy number of the target nucleic acid.
  • An alternative means for determining genomic copy number is in situ hybridization (e.g., Angerer (1987) Meth. Enzymol 152: 649).
  • the probes are typically labeled, e.g., with radioisotopes or fluorescent reporters.
  • probes are sufficiently long so as to specifically hybridize with the target nucleic acid(s) under stringent conditions. Probes generally range in length from about 200 bases to about 1000 bases.
  • tRNA, human genomic DNA, or Cot-I DNA is used to block non-specific hybridization.
  • Analysis for mutations of genes of interest Analysis for mutations of a selected gene, or to identify the presence of one or more specific mutations of interest as described herein, may be performed by any suitable means known to the skilled person. Examples of such mutations that may be investigated in connection with the various aspects or embodiments of the invention, are set out in elsewhere in the present specification. The following illustrative methods can be used to identify the presence of a structural alteration in a PBRM1 nucleic acid and/or PBRM1 protein molecule in order to, for example, identify defective PBRM1 genes or proteins as described herein.
  • detection of the alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Pat. Nos.4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci.
  • PCR polymerase chain reaction
  • LCR ligation chain reaction
  • This method can include the steps of collecting a sample of cells from a subject, isolating nucleic acid (e.g., genomic, mRNA or both) from the cells of the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a PBRM1 gene under conditions such that hybridization and amplification of the PBRM1 gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample.
  • nucleic acid e.g., genomic, mRNA or both
  • Alternative amplification methods include: self-sustained sequence replication (Guatelli, J. C. et al. (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh, D. Y. et al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta R e plicase (Lizardi, P. M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art.
  • Mutations in a PBRM1 nucleic acid from a sample can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA.
  • genetic mutations in a PBRM1 nucleic acid can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotide probes (Cronin, M. T. et al. (1996) Hum. Mutat.7:244-255; Kozal, M. J. et al. (1996) Nat. Med.2:753-759).
  • PBRM1 genetic mutations can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin et al. (1996) supra.
  • Such PBRM1 genetic mutations can be identified in a variety of contexts, including, for example, germline and somatic mutations.
  • any variety of sequencing reactions known in the art can be used to directly sequence a PBRM1 gene and detect mutations by comparing the sequence of the sample PBRM1 with the corresponding wild-type (control) sequence (e.g. SEQ ID NO:2).
  • Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert (1977) Proc. Natl. Acad. Sci. USA 74:560 or Sanger (1977) Proc. Natl. Acad Sci. USA 74:5463.
  • any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays (Naeve (1995) Biotechniques 19:448-53), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr.36:127- 162; and Griffin et al. (1993) Appl. Biochem. Biotechnol.38:147-159).
  • Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension.
  • oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163; Saiki et al. (1989) Proc. Natl. Acad. Sci. USA 86:6230).
  • Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
  • Analysis for elevated expression of genes of interest Analysis for elevated expression of a gene of interest may be performed by any suitable means known to the skilled person.
  • genes that may be analysed with reference to their elevated expression are set out in elsewhere in the present specification. Analysis may be limited to only transcripts of the gene of interest, or the entire transcriptome may be analysed, and results compared in respect of the gene of interest. Merely by way of example, suitable analysis may be performed using any of the following techniques: RNA sequencing, for example by next generation sequencing analysis; quantitative RT-PCR; and immunolabelling (carried out in respect of the relevant gene products).
  • PBRM1 expression may be assessed by any of a wide variety of well-known methods for detecting expression of a transcribed molecule or protein.
  • Non-limiting examples of such methods include immunological methods for detection of secreted, cell-surface, cytoplasmic, or nuclear proteins, protein purification methods, protein function or activity assays, nucleic acid hybridization methods, nucleic acid reverse transcription methods, and nucleic acid amplification methods.
  • detecting or determining expression levels of PBRM1, including a fragment or genetic alteration thereof (e.g., in regulatory or promoter regions thereof) comprises detecting or determining RNA levels for PBRM1.
  • one or more cells from the subject to be tested are obtained and RNA is isolated from the cells.
  • Northern analysis involves running a preparation of RNA on a denaturing agarose gel, and transferring it to a suitable support, such as activated cellulose, nitrocellulose or glass or nylon membranes. Radiolabeled cDNA or RNA is then hybridized to the preparation, washed and analyzed by autoradiography.
  • In situ hybridization visualization may also be employed, wherein a radioactively labeled antisense RNA probe is hybridized with a thin section of a biopsy sample, washed, cleaved with RNase and exposed to a sensitive emulsion for autoradiography.
  • the samples may be stained with hematoxylin to demonstrate the histological composition of the sample, and dark field imaging with a suitable light filter shows the developed emulsion.
  • Non-radioactive labels such as digoxigenin may also be used.
  • mRNA expression can be detected on a DNA array, chip or a microarray. Labeled nucleic acids of a test sample obtained from a subject may be hybridized to a solid surface comprising PBRM1 DNA.
  • Types of probes that can be used in the methods described herein include cDNA, riboprobes, synthetic oligonucleotides and genomic probes.
  • the type of probe used will generally be dictated by the particular situation, such as riboprobes for in situ hybridization, and cDNA for Northern blotting, for example.
  • the probe is directed to nucleotide regions unique to the RNA.
  • the probes may be as short as is required to differentially recognize PBRM1 mRNA transcripts, and may be as short as, for example, 15 bases; however, probes of at least 17, 18, 19 or 20 or more bases can be used.
  • the primers and probes hybridize specifically under stringent conditions to a DNA fragment having the nucleotide sequence corresponding to the PBRM1.
  • stringent conditions means hybridization will occur only if there is at least 95% identity in nucleotide sequences. In another example, hybridization under “stringent conditions” occurs when there is at least 97% identity between the sequences. Analysis for a deficiency in respect of a gene of interest The skilled person will be aware of many suitable techniques by which a deficiency in respect of a gene of interest may be identified. The skilled person may make use of any such suitable technique in order to practice the invention.
  • a deficiency in a gene of interest may arise for one or more reasons, including loss of copy numbers of the gene; a mutation or modification reducing transcription or translation of the gene; or a mutation reducing function of the gene product.
  • Suitable techniques may be selected with reference to the nature of the deficiency.
  • suitable analysis may be performed using any of the following techniques: RNA sequencing (as considered above), quantitative RT-PCR; immunolabelling.
  • Analysis for a deficiency in respect of a gene product e.g. PBRM1 protein
  • the activity or level of a PBRM1 protein can be detected and/or quantified by detecting or quantifying the expressed protein.
  • the protein can be detected and quantified by any of a number of means well known to those of skill in the art. Any method known in the art for detecting polypeptides can be used. Such methods include, but are not limited to, immunodiffusion, immunoelectrophoresis, radioimmunoassay (MA), enzyme-linked immunosorbent assays (ELISAs), immunofluorescent assays, Western blotting, binder-ligand assays, immunohistochemical techniques, agglutination, complement assays, high performance liquid chromatography (HPLC), thin layer chromatography (TLC), hyperdiffusion chromatography, and the like (e.g., Basic and Clinical Immunology, Sites and Terr, eds., Appleton and Lange, Norwalk, Conn.
  • MA radioimmunoassay
  • ELISAs enzyme-linked immunosorbent assays
  • immunofluorescent assays Western blotting, binder-ligand assays, immunohistochemical techniques, agg
  • binder-ligand immunoassay methods including reacting antibodies with an epitope or epitopes and competitively displacing a labeled polypeptide or derivative thereof.
  • ELISA and MA procedures may be conducted such that a desired PBRM1 protein standard is labeled (with a radioisotope such as 125 I or 35 S, or an assayable enzyme, such as horseradish peroxidase or alkaline phosphatase), and, together with the unlabelled sample, brought into contact with the corresponding antibody, whereon a second antibody is used to bind the first, and radioactivity or the immobilized enzyme assayed (competitive assay).
  • a radioisotope such as 125 I or 35 S
  • an assayable enzyme such as horseradish peroxidase or alkaline phosphatase
  • a method for measuring PBRM1 protein levels comprises the steps of: contacting a biological specimen with an antibody or variant (e.g., fragment) thereof which selectively binds the PBRM1 protein (for example specifically binds to a PBRM1 variant as described herein), and detecting whether said antibody or variant thereof is bound to said sample and thereby measuring the levels of the PBRM1 protein.
  • control refers to any reference standard suitable to provide a comparison to a PBRM1 gene or gene product (e.g. a PBRM1 mRNA or protein) in a test sample.
  • a control sample may comprise any suitable sample, including but not limited to a sample from a control cancer patient (can be stored sample or previous sample measurement) with a known outcome; normal tissue or cells isolated from a subject, such as a normal patient or the cancer patient, cultured primary cells/tissues isolated from a subject such as a normal subject or the cancer patient, adjacent normal cells/tissues obtained from the same organ or body location of the cancer patient, a tissue or cell sample isolated from a normal subject, or a primary cells/tissues obtained from a depository.
  • control comprises obtaining a “control sample” from which expression product levels are detected and compared to the expression product levels from the test sample (i.e. sample obtained from the patient).
  • a control sample may comprise any suitable sample, including but not limited to a sample from a control cancer patient (can be stored sample or previous sample measurement) with a known outcome; normal tissue or cells isolated from a subject, such as a normal patient or the cancer patient, cultured primary cells/tissues isolated from a subject such as a normal subject or the cancer patient, adjacent normal cells/tissues obtained from the same organ or body location of the cancer patient, a tissue or cell sample isolated from a normal subject, or a primary cells/tissues obtained from a depository.
  • the control may comprise a reference standard expression product level from any suitable source, including but not limited to housekeeping genes, an expression product level range from normal tissue (or other previously analyzed control sample), a previously determined expression product level range within a test sample from a group of patients, or a set of patients with a certain outcome (for example, survival for one, two, three, four years, etc.) or receiving a certain treatment (for example, standard of care cancer therapy).
  • a certain outcome for example, survival for one, two, three, four years, etc.
  • a certain treatment for example, standard of care cancer therapy.
  • the control may comprise normal or non-cancerous cell/tissue sample.
  • control may comprise an expression level for a set of patients, such as a set of cancer patients, or for a set of cancer patients receiving a certain treatment, or for a set of patients with one outcome versus another outcome.
  • the specific expression product level of each patient can be assigned to a percentile level of expression, or expressed as either higher or lower than the mean or average of the reference standard expression level.
  • control may comprise normal cells, cells from patients treated with combination chemotherapy, and cells from patients having benign cancer.
  • control may also comprise a measured value for example, average level of expression of the PBRM1 gene in a population compared to the level of expression of a housekeeping gene in the same population.
  • control comprises a control sample which is of the same lineage and/or type as the test sample.
  • control may comprise expression product levels grouped as percentiles within or based on a set of patient samples, such as all patients with cancer.
  • a control expression product level is established wherein higher or lower levels of expression product relative to, for instance, a particular percentile, are used as the basis for predicting responsiveness to treatment with an Mps1 inhibiting compound as described herein.
  • a control expression product level is established using expression product levels from cancer control patients with a known outcome, and the expression product levels from the test sample are compared to the control expression product level as the basis for predicting responsiveness to treatment with an Mps1 inhibiting compound as described herein.
  • the activity and/or amount of a PBRM1 gene, protein, gene product may be compared to a pre-determined amount and/or activity measurement(s) (i.e. a reference amount and/or activity).
  • the pre-determined amount and/or activity may be determined in populations of patients with or without cancer.
  • the pre- determined amount and/or activity measurement(s) can be a single number, equally applicable to every patient, or the pre-determined amount and/or activity measurement(s) can vary according to specific subpopulations of patients. Age, weight, height, and other factors of a subject may affect the pre-determined amount and/or activity measurement(s) of the individual. Furthermore, the pre-determined amount and/or activity can be determined for each subject individually. In one example, the amounts determined and/or compared in a method described herein are based on absolute measurements. In another example, the amounts determined and/or compared in a method described herein are based on relative measurements, such as ratios (e.g., serum PBRM1 normalized to the expression of a housekeeping or otherwise generally constant biomarker).
  • ratios e.g., serum PBRM1 normalized to the expression of a housekeeping or otherwise generally constant biomarker.
  • the pre-determined amount and/or activity measurement(s) can be any suitable standard.
  • the pre-determined amount and/or activity measurement(s) can be obtained from the same or a different human from whom a sample is being assessed.
  • the pre-determined biomarker amount and/or activity measurement(s) can be obtained from a previous assessment of the same subject.
  • the control can be obtained from an assessment of another subject or multiple subject, e.g., selected groups of humans, if the subject is a human.
  • PBRM1-defective cancer refers to any cancer wherein the subject has been determined to have defective PBRM1 as described herein.
  • the PBRM1-defective may be selected from but not limited to the group consisting of: pancreatic ductal adenocarcinoma; pancreatic cancer; breast cancer; melanoma; non-small cell lung cancer; small cell lung cancer; nasopharyngeal cancer; hepatocellular cancer; colorectal cancer; oesophageal cancer; gastric cancer; anal cancer; small intestine cancer; mesothelioma; kidney cancer; renal cell carcinoma; bladder cancer; prostate cancer; ovarian cancer; vulval cancer; cervical cancer; penile cancer; uveal melanoma; retinoblastoma; sarcoma; osteosarcoma; glioblastoma; adrenocortical carcinoma; neuroblastoma; Wilms tumour; endometrial cancer; and thyroid cancer.
  • the PBRM1-defective cancer is selected from the group consisting of: clear cell renal cell carcinoma, chordoma, cholangiocarcinoma, mesothelioma, endometrial carcinoma, non–small cell lung cancer and skin cutaneous melanoma.
  • the PBRM1-defective cancer is clear cell renal cell carcinoma.
  • the term “renal cell carcinoma” generally refers to a type of kidney cancer that starts in the lining of the proximal convoluted tubule, a part of the very small tubes in the kidney that transport waste molecules from the blood to the urine. RCC is the most common type of kidney cancer in adults, responsible for approximately 90-95% of cases.
  • R e nal cell carcinoma is the most common type of kidney cancer in adults. It occurs most often in men 50 to 70 years old.
  • the different types of RCC are generally distinguished by the way that cancer cells appear when viewed under a microscope, such as clear cell RCC (ccRCC), papillary RCC, chromophobe RCC, oncocytoma RCC, collecting duct RCC, and other unclassified RCC.
  • clear cell RCC or conventional RCC the cells have a clear or pale appearance.
  • CCRCC classically has apical nuclei, i.e. the nucleus is adjacent to the luminal aspect (Bing and Tomaszewski (2011) Case Rep Transplant.2011:387645).
  • mRCC Metastatic renal cell carcinoma
  • mRCC has a poor prognosis compared to other cancers, though average survival times have increased in the last few years due to treatment advances. Average survival time in 2008 for the metastatic form of the disease was under a year and by 2013 this improved to an average of 22 months. Despite this improvement, the 5-year survival rate for mRCC remains under 10%. About 20-25% of suffers remain unresponsive to all treatments and in these cases, the disease has a rapid progression.
  • the known risk factors of kidney cancer include, e.g., smoking, obesity, dialysis treatment, family history of the disease, high blood pressure, horseshoe kidney, long-term use of certain medicines, such as pain pills or water pills (diuretics), polycystic kidney disease, von Hippel-Lindau disease (a hereditary disease that affects blood vessels in the brain, eyes, and other body parts), etc.
  • Symptoms of RCC may include any of the following: abdominal pain and swelling, back pain, blood in the urine, swelling of the veins around a testicle (varicocele), flank pain, weight loss, excessive hair growth in females, pale skin, vision problems, etc.
  • RCC paraneoplastic syndromes
  • PNSs seen in people with RCC are: high blood calcium levels, polycythaemia (the opposite of anaemia, due to an overproduction of erythropoietin), thrombocytosis (too many platelets in the blood, leading to an increased tendency for blood clotting and bleeds) and secondary amyloidosis.
  • a physical exam may reveal mass or swelling of the abdomen and/or a varicocele in the male scrotum. Diagnostic tests include, e.g., abdominal CT scan, blood chemistry, complete blood count (CBC), intravenous pyelogram (IVP), liver function tests, renal arteriography, ultrasound of the abdomen and kidney, and urine tests.
  • CBC complete blood count
  • IVP intravenous pyelogram
  • Tests for detecting spread RCC may include abdominal CT scan, adominal MM, bone scan, chest x-ray or CT scan, and PET scan.
  • Availabe treatment for RCC may include surgery to remove of all or part of the kidney (nephrectomy). This may include removing the bladder, surrounding tissues, or lymph nodes.
  • Chemotherapy or radiation therapy is generally not effective for treating kidney cancer.
  • Current immunotherapies include the immune system medicines interleukin-2 (IL-2) and nivolumab, developed after observing that in some cases there was spontaneous regression (Davar et al. (2013) “Immunotherapy for R e nal Cell Carcinoma”. Renal Cell Carcinoma Clinical Management. Humana. pp. 279- 302).
  • tyrosine kinase inhibitors e.g., cabozantinib (CabometyxTM), pazopanib (Votrient®), sorafenib (Nexavar), axitinib (INLYTA®) and sunitinib (Sutent®)
  • mTOR inhibitors e.g., Everolimus (Afinitor®) and temsirolimus)
  • sample in vitro methods that are performed using a sample that has already been obtained from the subject (i.e. the sample is provided for the method, and the steps taken to obtain the sample from the subject are not included as part of the method).
  • the methods may therefore include the step of providing a sample from a subject.
  • “provide”, “obtain” or “obtaining” can be any means whereby one comes into possession of the sample by "direct” or "indirect” means.
  • Directly obtaining a sample means performing a process (e.g., performing a physical method such as extraction) to obtain the sample.
  • Indirectly obtaining a sample refers to receiving the sample from another party or source (e.g., a third party laboratory that directly acquired the sample).
  • DNA may be extracted from a sample from the subject to be utilized directly for identification of the individual's genetic variations.
  • nucleic acid analysis methods are: direct sequencing or pyrosequencing, massively parallel sequencing, high-throughput sequencing (next generation sequencing), high performance liquid chromatography (HPLC) fragment analysis, capillarity electrophoresis and quantitative PCR (as, for example, detection by Taqman® probe, ScorpionsTM ARMS Primer or SYBR Green).
  • the DNA may be amplified by PCR prior to incubation with the probe and the amplified primer extension products can be detected using procedure and equipment for detection of the label.
  • biological sample refers to a sample obtained or derived from a subject.
  • the sample is, or comprises, a biological fluid (also referred to herein as a bodily fluid) sample.
  • biological fluid sample encompasses a blood sample.
  • a blood sample may be a whole blood sample, or a processed blood sample e.g. buffy coat. Methods for obtaining biological fluid samples (e.g. whole blood,) from a subject are well known in the art.
  • methods for obtaining blood samples from a subject are well known and include established techniques used in phlebotomy.
  • the obtained blood samples may be further processed using standard techniques.
  • methods for obtaining biological fluid samples from a subject are typically low-invasive or non-invasive.
  • a whole blood sample is defined as a blood sample drawn from the human body and from which (substantially) no constituents (such as platelets or plasma) have been removed.
  • the relative ratio of constituents in a whole blood sample is substantially the same as a blood in the body.
  • substantially the same allows for a very small change in the relative ratio of the constituents of whole blood e.g.
  • Whole blood contains both the cell and fluid portions of blood.
  • a whole blood sample may therefore also be defined as a blood sample with (substantially) all of its cellular components in plasma, wherein the cellular components (i.e. at least comprising the requisite white blood cells, red blood cells, platelets of blood) are intact.
  • Subject As used herein the, “individual”, “individual in need thereof” “subject(s)” and/or “patient(s)”, suitably refer to mammals (e.g. humans and non-human mammals such as livestock (cows, sheep, goats) or companion animals (cats, dogs, horses, rabbits).
  • the subject(s) and/or patient(s) are human(s).
  • the subject may be referred to herein as a patient.
  • the terms “subject”, “individual”, and “patient” are used herein interchangeably.
  • the subject can be symptomatic (e.g., the subject presents symptoms associated with cancer), or the subject can be asymptomatic (e.g., the subject does not present symptoms associated with cancer).
  • the subject may be diagnosed with, or present with symptoms of cancer.
  • the subject may have, or be suspected of having (e.g. present with symptoms or a history indicative or suggestive of), cancer. Accordingly, in some examples, the subject has cancer. In some examples, the subject has early stage cancer.
  • MPS1 inhibitor refers to a chemical or biological agent capable of inhibiting MPS1 (monopolar spindle) kinase.
  • MPS1 inhibitors are selective for MPS1 over other kinases.
  • the MPS1 inhibitors herein have nanomolar IC50s at MPS1.
  • the MPS1 inhibitors are chemical compounds, e.g. a drug or a drug-like molecule.
  • BAY 1161909 refers to the following compound: .
  • the term “BAY 1217389” refers to the following compound: .
  • NMS-P715 refers to the following compound: .
  • AZ3146 refers to the following compound: .
  • MPS1-IN-3 refers to the following compound: .
  • MPS1-IN-2 refers to the following compound: .
  • CFI-402257 refers to the following compound: .
  • CCT289346 refers to N2-(2-ethoxy-4-(4-methyl-4H-1,2,4-triazol-3- yl)phenyl)-6-methyl-N8-neopentylpyrido[3,4-d]pyrimidine-2,8-diamine.
  • the compounds and intermediates described herein may be named according to either the IUPAC (International Union for Pure and Applied Chemistry) or CAS (Chemical Abstracts Service) nomenclature systems. It should be understood that unless expressly stated to the contrary, the terms “compounds of Formula I” and the more general term “compounds” refer to and include any and all compounds described by and/or with reference to Formula I.
  • hydrocarbon-containing moieties may be described using a prefix designating the minimum and maximum number of carbon atoms in the moiety, e.g. “(Ca-b)” or “Ca-Cb” or “(a-b)C”.
  • (Ca-b)alkyl indicates an alkyl moiety having the integer “a” to the integer “b” number of carbon atoms, inclusive.
  • Certain moieties may also be described according to the minimum and maximum number of members with or without specific reference to a particular atom or overall structure.
  • a to b membered ring or “having between a to b members” refer to a moiety having the integer “a” to the integer “b” number of atoms, inclusive.
  • alkyl and “alkyl group” refer to a branched or unbranched saturated hydrocarbon chain.
  • alkyl groups typically contain 1-10 carbon atoms, such as 1-6 carbon atoms or 1-4 carbon atoms or 1-3 carbon atoms, and can be substituted or unsubstituted.
  • Representative examples include, but are not limited to, methyl, ethyl, n-propyl, i-propyl, n-butyl, i-butyl, s- butyl, t-butyl, n-pentyl, n-hexyl, n-heptyl, n-octyl, n-nonyl, n-decyl, isopropyl, tert-butyl, isobutyl, etc.
  • alkylene and alkylene group refer to a branched or unbranched saturated hydrocarbon chain. Unless specified otherwise, alkylene groups typically contain 1-10 carbon atoms, such as 1-6 carbon atoms or 1-3 carbon atoms, and can be substituted or unsubstituted.
  • R e presentative examples include, but are not limited to, methylene (–CH 2 –), the ethylene isomers (–CH(CH 3 )– and – CH 2 CH 2 –), the propylene isomers (–CH(CH 3 )CH 2 –, –CH(CH 2 CH 3 )–, –C(CH 3 )3–, and – CH 2 CH 2 CH 2 –), etc.
  • alkenyl and “alkenyl group” refer to a branched or unbranched hydrocarbon chain containing at least one double bond.
  • alkenyl groups typically contain 2-10 carbon atoms, such as 2-6 carbon atoms or 2-4 carbon atoms, and can be substituted or unsubstituted.
  • R e presentative examples include, but are not limited to, ethenyl, 3-buten-1-yl, 2-ethenylbutyl, and 3-hexen-1-yl.
  • alkynyl and alkynyl group refer to a branched or unbranched hydrocarbon chain containing at least one triple bond.
  • alkynyl groups typically contain 2-10 carbon atoms, such as 2-6 carbon atoms or 2-4 carbon atoms, and can be substituted or unsubstituted.
  • R e presentative examples include, but are not limited to, ethynyl, 3-butyn-1-yl, propynyl, 2- butyn-1-yl, and 3-pentyn-1-yl.
  • aromatic refers to monocyclic and polycyclic ring systems containing 4n+2 pi electrons, where n is an integer. Aromatic should be understood as referring to and including ring systems that contain only carbon atoms (i.e.
  • aryl as well as ring systems that contain at least one heteroatom selected from N, O or S (i.e. “heteroaromatic” or “heteroaryl”).
  • An aromatic ring system can be substituted or unsubstituted.
  • non-aromatic refers to a monocyclic or polycyclic ring system having at least one double bond that is not part of an extended conjugated pi system.
  • non-aromatic refers to and includes ring systems that contain only carbon atoms as well as ring systems that contain at least one heteroatom selected from N, O or S.
  • a non-aromatic ring system can be substituted or unsubstituted.
  • aryl and aryl group refer to phenyl and 7-15 membered bicyclic or tricyclic hydrocarbon ring systems, including bridged, spiro, and/or fused ring systems, in which at least one of the rings is aromatic.
  • Aryl groups can be substituted or unsubstituted. Unless specified otherwise, an aryl group may contain 6 ring atoms (i.e., phenyl) or a ring system containing 9 to 15 atoms, such as 9 to 11 ring atoms, or 9 or 10 ring atoms.
  • R e presentative examples include, but are not limited to, naphthyl, indanyl, 1,2,3,4-tetrahydronaphthalenyl, 6,7,8,9-tetrahydro-5H- benzocycloheptenyl, and 6,7,8,9-tetrahydro-5H-benzocycloheptenyl.
  • an aryl group is phenyl and naphthyl, suitably phenyl.
  • arylene and arylene group refer to a phenylene (–C6H4–) or to 7 to 15 membered bicyclic or tricyclic hydrocarbon ring systems, including bridged, spiro, and/or fused ring systems, in which at least one of the rings is aromatic.
  • Arylene groups can be substituted or unsubstituted.
  • an arylene group may contain 6 (i.e., phenylene) ring atoms or be a ring system containing 9 to 15 atoms; such as 9 to 11 ring atoms; or 9 or 10 ring atoms.
  • Arylene groups can be substituted or unsubstituted.
  • alkylaryl and alkylaryl group refer to an alkyl group in which a hydrogen atom is replaced by an aryl group, wherein alkyl group and aryl group are as previously defined, such as, for example, benzyl (C6H5CH 2 –). Alkylaryl groups can be substituted or unsubstituted.
  • carbbocyclic group and “carbocycle” refer to monocyclic and polycyclic ring systems that contain only carbon atoms in the ring(s), i.e., hydrocarbon ring systems, without regard or reference to aromaticity or degree of unsaturation.
  • carbocyclic group should be understood as referring to and including ring systems that are fully saturated (such as, for example, a cyclohexyl group), ring systems that are aromatic (such as, for example, a phenyl group), as well as ring systems having fully saturated, aromatic and/or unsaturated portions (such as, for example, cyclohexenyl, 2,3-dihydro-indenyl, and 1,2,3,4-tetrahydro-naphthalenyl).
  • the terms carbocyclic and carbocycle further include bridged, fused, and spirocyclic ring systems.
  • cycloalkyl and cycloalkyl group refer to a non-aromatic carbocyclic ring system, that may be monocyclic, bicyclic, or tricyclic, saturated or unsaturated, and may be bridged, spiro, and/or fused.
  • a cycloalkyl group may be substituted or unsubstituted.
  • a cycloalkyl group typically contains from 3 to 12 ring atoms. In some instances a cycloalkyl group may contain 4 to 10 ring atoms (e.g., 4 ring atoms, 5 ring atoms, 6 ring atoms, 7 ring atoms, etc.).
  • R e presentative examples include, but are not limited to, cyclopropyl, cyclopropenyl, cyclobutyl, cyclobutenyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, norbornyl, norbornenyl, bicyclo[2.2.1]hexane, bicyclo[2.2.1]heptane, bicyclo[2.2.1]heptene, bicyclo[3.1.1]heptane, bicyclo[3.2.1]octane, bicyclo[2.2.2]octane, bicyclo[3.2.2]nonane, bicyclo[3.3.1]nonane, and bicyclo[3.3.2]decane.
  • cycloalkyl groups are selected from cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl groups.
  • alkylcycloalkyl and alkylcycloalkyl group refer to an alkyl group in which a hydrogen atom is replaced by a cycloalkyl group, wherein alkyl group and cycloalkyl group are as previously defined, such as, for example, cyclohexylmethyl (C6H11CH 2 –).
  • Alkylcycloalkyl groups can be substituted or unsubstituted.
  • haloalkyl and haloalkyl group refer to alkyl groups in which one or more hydrogen atoms are replaced by halogen atoms.
  • Haloalkyl includes both saturated alkyl groups as well as unsaturated alkenyl and alkynyl groups.
  • Haloalkyl groups can be substituted or unsubstituted.
  • a haloalkyl group is selected from CHF 2 and CF 3 , suitably CF 3 .
  • haloalkoxy and haloalkoxy group refer to alkoxy groups (i.e. O-alkyl groups) in which one or more hydrogen atoms are replaced by halogen atoms.
  • Haloalkoxy includes both saturated alkoxy groups as well as unsaturated alkenyl and alkynyl groups.
  • Haloalkoxy groups can be substituted or unsubstituted.
  • a haloalkyoxy group is selected from –OCHF 2 and –OCF 3 , suitably –OCF 3 .
  • halo and “halogen” include fluorine, chlorine, bromine and iodine atoms and substituents.
  • heteroaryl and heteroaryl group refer to (a) 5 and 6 membered monocyclic aromatic rings, which contain, in addition to carbon atom(s), at least one heteroatom, such as nitrogen, oxygen or sulfur, and (b) 7 to15 membered bicyclic and tricyclic rings, which contain, in addition to carbon atom(s), at least one heteroatom, such as nitrogen, oxygen or sulfur, and in which at least one of the rings is aromatic.
  • a heteroaryl group can contain two or more heteroatoms, which may be the same or different.
  • Heteroaryl groups can be substituted or unsubstituted, and may be bridged, spiro, and/or fused.
  • a heteroaryl group may contain 5, 6, or 8 to 15 ring atoms.
  • a heteroaryl group may contain 5 to 10 ring atoms, such as 5, 6, 9, or 10 ring atoms.
  • R e presentative examples include, but are not limited to, 2,3-dihydrobenzofuranyl, 1,2-dihydroquinolinyl, 3,4-dihydroisoquinolinyl, 1,2,3,4- tetrahydroisoquinolinyl, 1,2,3,4-tetrahydroquinolinyl, benzoxazinyl, benzthiazinyl, chromanyl, furanyl, 2-furanyl, 3-furanyl, imidazolyl, isoxazolyl, isothiazolyl, oxadiazolyl, oxazolyl, pyridinyl, 2-, 3-, or 4-pyridinyl, pyrimidinyl, 2-, 4-, or 5-pyrimidinyl, pyrazolyl, pyrrolyl, 2- or 3-pyrrolyl, pyrazinyl, pyridazinyl, 3- or 4-pyridazinyl, 2-pyrazinyl, thi
  • a heteroaryl is a 5- or 6-membered heteroaryl ring comprising one, two or three heteroatoms selected from N, O or S.
  • alkylheteroaryl and alkylheteroaryl group refer to an alkyl group in which a hydrogen atom is replaced by a heteroaryl group, wherein alkyl group and heteroaryl group are as previously defined. Alkylheteroaryl groups can be substituted or unsubstituted. Where carbon numbers are provided, e.g. (Cn-m)alkylheteroaryl, the range refers to the whole group.
  • the consitutent alkyl group has 1-6 carbons, suitable 1-3 carbons.
  • heterocyclic group and heterocycle refer to monocyclic and polycyclic ring systems that contain carbon atoms and at least one heteroatom selected from nitrogen, oxygen, sulfur or phosphorus in the ring(s), without regard or reference to aromaticity or degree of unsaturation.
  • heterocyclic group should be understood as referring to and including ring systems that are fully saturated (such as, for example, a piperidinyl group), ring systems that are aromatic (such as, for example, a pyrindinyl group), as well as ring systems having fully saturated, aromatic and/or unsaturated portions (such as, for example, 1,2,3,6-tetrahydropyridinyl and 6,8- dihydro-5H-[1,2,4]triazolo[4,3-a]pyrizinyl).
  • the terms heterocyclic and heterocycle further include bridged, fused, and spirocyclic ring systems.
  • heterocycloalkyl and “heterocycloalkyl group” refer to 3 to 15 membered monocyclic, bicyclic, and tricyclic non- aromatic ring systems, which contain, in addition to carbon atom(s), at least one heteroatom, such as nitrogen, oxygen, sulfur or phosphorus. Heterocycloalkyl groups may be fully saturated or contain unsaturated portions and may be bridged, spiro, and/or fused ring systems. In some instances a heterocycloalkyl group may contain at least two or heteroatoms, which may be the same or different. Heterocycloalkyl groups can be substituted or unsubstituted.
  • a heterocycloalkyl group may contain from 3 to 10 ring atoms or from 3 to 7 ring atoms or from 5 to 7 ring atoms, such as 5 ring atoms, 6 ring atoms, or 7 ring atoms.
  • R e presentative examples include, but are not limited to, tetrahydrofuranyl, pyrrolidinyl, pyrrolinyl, imidazolidinyl, imidazolinyl, pyrazolidinyl, pyrazolinyl, piperidyl, piperazinyl, indolinyl, isoindolinyl, morpholinyl, thiomorpholinyl, homomorpholinyl, homopiperidyl, homopiperazinyl, thiomorpholinyl-5-oxide, thiomorpholinyl-S,S-dioxide, pyrrolidinyl, tetrahydropyranyl, piperidinyl, tetrahydrothienyl, homopiperidinyl, homothiomorpholinyl-S,S-dioxide, oxazolidinonyl, dihydropyrazolyl, dihydropyrrolyl, dihydropyrazinyl, dihydr
  • a heterocyclylalkyl group as defined herein is a monocyclic, bicyclic or spiro heterocyclyl group comprising one, two or three heteroatoms selected from N, O or S.
  • heterocycloalkylene and “heterocycloalkylene group” refer to 3 to15 membered monocyclic, bicyclic, or tricyclic non-aromatic ring systems, which contain, in addition to carbon atom(s), at least one heteroatom, such as nitrogen, oxygen, sulfur or phosphorus.
  • Heterocycloalkylene groups may be fully saturated or contain unsaturated portions and may be bridged, spiro, and/or fused.
  • Heterocycloalkylene groups can be substituted or unsubstituted.
  • a heterocycloalkylene group may contain from 3 to 10 ring atoms; such as from 3 to 7 ring atoms.
  • a heterocycloalkylene group may contain from 5 to 7 ring atoms, such as 5 ring atoms, 6 ring atoms, or 7 ring atoms.
  • alkylheterocycloalkyl and “alkylheterocycloalkyl group” refer to an alkyl group in which a hydrogen atom is replaced by a heterocycloalkyl group, wherein alkyl group and heterocycloalkyl group are as previously defined, such as, for example, pyrrolidinylmethyl (C4H8NCH 2 –).
  • Alkylheteroycloalkyl groups can be substituted or unsubstituted. Where carbon numbers are provided, e.g. (Cn-m)alkylheterocycloalkyl, the range refers to the whole group.
  • the consitutent alkyl group has 1-6 carbons, suitable 1-3 carbons.
  • stable and “chemically stable” refer to a compound that is sufficiently robust to be isolated from a reaction mixture with a useful degree of purity. The present application is directed solely to the preparation of stable compounds.
  • substituents include members which, owing to valency requirements, chemical stability, or other reasons, cannot be used to substitute a particular group, the list is intended to be read in context to include those members of the list that are suitable for substituting the particular group. For example, when considering the degree of optional substitution of a particular moiety, it should be understood that the number of substituents does not exceed the valency appropriate for that moiety.
  • R 1 is a methyl group (-CH 3 ), it can be optionally substituted by 1 to 3 R 5 .
  • substituted indicates that a hydrogen atom on a molecule has been replaced with a different atom or group of atoms and the atom or group of atoms replacing the hydrogen atom is a “substituent.” It should be understood that the terms “substituent”, “substituents”, “moiety”, “moieties”, “group”, or “groups” refer to substituent(s).
  • the MPS1 inhibitor is a compound capable of inhibiting MPS1 kinase.
  • the compound has an IC50 at MPS1 kinase of 100nM or less.
  • the compound has an IC50 at MPS1 kinase of 75nM or less.
  • the compound has an IC50 at MPS1 kinase of 50nM or less.
  • the compound has an IC50 at MPS1 kinase of 25nM or less.
  • the compound has an IC50 at MPS1 kinase of 10nM or less.
  • the compound has an IC50 at MPS1 kinase of 8nM or less.
  • the compound has an IC50 at MPS1 kinase of 5nM or less.
  • the compound has an IC50 at MPS1 kinase of 3nM or less.
  • the IC50 at MPS1 kinase may be determined by any suitable method.
  • the IC50 may be determined by in vitro enzyme inhibition assay comprising full length MPS1, a suitable fluorophore, test compound and an assay buffer.
  • IC50s are determined by testing the compounds at a range of concentrations.
  • the fluorophore can be a fluorescent labelled peptide, for example, H236, which has the sequence: 5FAM-DHTGFLTEYVATR-CONH 2 .
  • the enzyme inhibition assay is carried out at room temperature (21°C ⁇ 3°C) for about one hour.
  • the enzyme inhibition assay (total volume 10 ⁇ l) was carried out in black 384- well low volume plates containing full length MPS1 (12.5nM or 3nM), fluorescent labelled peptide [known as H236, which has the sequence: 5FAM-DHTGFLTEYVATR-CONH 2 ] (5 ⁇ M), ATP(10 ⁇ M), either DMSO (1% v/v) or the test compound (in the range 0.25nM-100 ⁇ M in 1% DMSO) and assay buffer (50mM HEPES (pH 7.0), 0.02% NaN3, 0.01% BSA, 0.1mM Orthovandate, 10 ⁇ M MgCl2, 1 ⁇ M DTT, Roche protease inhibitor).
  • H236 fluorescent labelled peptide
  • ATP 10 ⁇ M
  • DMSO 1% v/v
  • test compound in the range 0.25nM-100 ⁇ M in 1% DMSO
  • assay buffer 50mM HEPES (pH 7.0), 0.02% NaN3, 0.01%
  • the reaction was carried out for 60min at room temperature and stopped by the addition of buffer (10 ⁇ l) containing 20mM EDTA, 0.05% (v/v) Brij-35, in 0.1M HEPES-buffered saline (Free acid, Sigma, UK).
  • the plate was read on a Caliper EZ reader II (Caliper Life Sciences).
  • the reader provides a Software package (‘R e viewer’) which converts the peak heights into % conversion by measuring both product and substrate peak and also allows selection of control well which represent 0% and 100% inhibition, respectively.
  • the % inhibition of the compounds is calculated relative to the means of selected control wells.
  • IC50s are determined by testing the compounds at a range of concentrations from 0.25 nM -100 ⁇ M.
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, S 81694 (NMS-P153), AZ3146, BAY 1217389, BAY 1161909, MPS1-IN-3, MPS1-IN-2, CFI- 402257, CCT289346, a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or a pharmaceutically acceptable salt or solvate thereof; wherein formula I is: I wherein: W is N or C-R 3 ; X is CH or N; Z is N or C-H; R 1 is selected from chloro, (1-6C)alkyl, (1-8C)hetero
  • X is CH or N; Y is N or C-H; R 2 is selected from (1-6C)alkyl, (1-8C)heteroalkyl, aryl, aryl(1-2C)alkyl, a 5 or 6 membered heteroaryl, a 5 or 6 membered heteroaryl(1-2C)alkyl, a 3 to 6 membered heterocyclyl, a 3 to 6 membered heterocyclyl(1-2C)alkyl, (3-8C)cycloalkyl, (3-8C)cycloalkyl(1-2C)alkyl, NR 11 R 12 , OR 13 , C(O)R 13 , C(O)OR 13 , OC(O)R 13 , N(R14)OR 13 , N(R14)C(O)OR 13 , C(O)N(R14)R 13 , N(R14)C(O)R 13 , S(O)xR 13 (where x is 0, 1 or 2), SO 2 N(
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, S 81694 (NMS-P153), AZ3146, BAY 1217389, BAY 1161909, MPS1-IN-3, MPS1-IN-2 and CFI- 402257. In some examples, the MPS1 inhibitor is selected from the group consisting of NMS-P715, BAY 1217389 and BAY 1161909.
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, S 81694 (NMS-P153), AZ3146, BAY 1217389, BAY 1161909, CFI-402257, CCT289346, a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or a pharmaceutically acceptable salt or solvate thereof.
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, AZ3146, BAY 1217389, BAY 1161909, CFI-402257, CCT289346, a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or a pharmaceutically acceptable salt or solvate thereof.
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, BAY 1217389, BAY 1161909, CCT289346, a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or pharmaceutically acceptable salts or solvates thereof.
  • the MPS1 inhibitor is not selected from the group consisting of a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or pharmaceutically acceptable salts or solvates thereof.
  • the MPS1 inhibitor is selected from the group consisting of a compound of formula I, a compound of formula II, a compound of formula III and a compound of formula IV, or pharmaceutically acceptable salts or solvates thereof.
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, BAY 1217389, BAY 1161909 and CCT289346.
  • the MPS1 inhibitor is selected from the group consisting of a compound of formula I or a compound of formula II, or pharmaceutically acceptable salts or solvates thereof.
  • the MPS1 inhibitor is selected from a compound of formula V: wherein R a is hydrogen; R b is C 1-6 alkyl, optionally substituted with halogen; or R a and R b together with the nitrogen to which they are attached from a 4 to 10 membered heterocyclic ring optionally substituted by one or more groups selected from hydrogen, C 1-6 alkyl, O-C 1-6 alkyl, CN, C 1-6 haloalkyl and O-C 1-6 haloalkyl; R c is C 1-3 alkyl; and Ar 1 is a 5- or 6-membered heteroaryl ring optionally substituted with one or more substituents independently selected from C 1-6 alkyl, O-C 1-6 alkyl, CN, C 1-6 haloalkyl and O-C 1-6 haloal
  • R b is C 1-6 alkyl, suitably C 5 and C 6 alkyl.
  • R a and R b together with the nitrogen to which they are attached form an azetidinyl group which may optionally be substituted with one or more groups selected from C 1-6 alkyl, O-C 1-6 alkyl, CN, C 1-6 haloalkyl and O-C 1-6 haloalkyl, or linked through a spiro carbon atom to a further 4-, 5- or 6-membered carbocyclic or heterocyclic ring to form a spiro bicyclic ring system, which may optionally be substituted with one or more groups selected from hydrogen, C 1-6 alkyl, O-C 1-6 alkyl, CN, C 1-6 haloalkyl and O-C 1-6 haloalkyl.
  • R c is selected from methyl and ethyl, suitably ethyl.
  • Ar 1 is a 5-membered heteraryl group, suitably 1,2,4-triazole, optionally substituted with one or more substituents independently selected from C 1-6 alkyl, O- C 1-6 alkyl, CN, C 1-6 haloalkyl and O-C 1-6 haloalkyl.
  • Ar 1 is a 1,2,4-triazole, substituted with one or more C1-3 alkyl substituents, suitably methyl.
  • the MPS1 inhibitor is selected from NMS-P715, BAY 1217389, BAY 1161909 and a compound of formula V, or pharmaceutically acceptable salts thereof.
  • the MPS1 inhibitor is selected from NMS-P715, BAY 1217389, BAY 1161909 and 5-(furan-2-yl)-N-(4-methoxyphenyl)isoquinolin-3-amine; N-(4-methoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine; N-(2-methoxy-4-((1-methylpiperidin-4-yl)oxy)phenyl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin- 3-amine; N-(2,4-dimethoxyphenyl)-5-(1-methyl-1H-pyrazol-4-yl)isoquinolin-3-amine; 3-chloro-N,N-dimethyl-4
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715 and N-cyclopropyl-4-(6-(2,3-difluoro-4-methoxyphenoxy)-8-((3,3,3- trifluoropropyl)amino)imidazo[1,2-b]pyridazin-3-yl)-2-methylbenzamide; (R)-2-(4-fluorophenyl)-N-(4-(2-((2-methoxy-4-(methylsulfonyl)phenyl)amino)- [1,2,4]triazolo[1,5-a]pyridin-6-yl)phenyl)propanamide; N2-(4-(4,5-dimethyl-4H-1,2,4-triazol-3-yl)-2-ethoxyphenyl)-6-methyl-N8-neopentylpyrido[3,4- d]pyrimidine-2,8-diamine; (S)-N8-(
  • the MPS1 inhibitor is selected from the group consisting of NMS-P715, BAY 1217389, BAY 1161909 and N2-(2-ethoxy-4-(4-methyl-4H-1,2,4-triazol-3-yl)phenyl)-6- methyl-N8-neopentylpyrido[3,4-d]pyrimidine-2,8-diamine, or pharmaceutically acceptable salts thereof.
  • the MPS1 inhibitor is selected from the group consisting of: N-cyclopropyl-4-(6-(2,3-difluoro-4-methoxyphenoxy)-8-((3,3,3- trifluoropropyl)amino)imidazo[1,2-b]pyridazin-3-yl)-2-methylbenzamide; (R)-2-(4-fluorophenyl)-N-(4-(2-((2-methoxy-4-(methylsulfonyl)phenyl)amino)- [1,2,4]triazolo[1,5-a]pyridin-6-yl)phenyl)propanamide; N2-(4-(4,5-dimethyl-4H-1,2,4-triazol-3-yl)-2-ethoxyphenyl)-6-methyl-N8-neopentylpyrido[3,4- d]pyrimidine-2,8-diamine; (S)-N8-(3,3-dimethyl
  • the MPS1 inhibitor is selected from the group consisting of: N-cyclopropyl-4-(6-(2,3-difluoro-4-methoxyphenoxy)-8-((3,3,3- trifluoropropyl)amino)imidazo[1,2-b]pyridazin-3-yl)-2-methylbenzamide; and (R)-2-(4-fluorophenyl)-N-(4-(2-((2-methoxy-4-(methylsulfonyl)phenyl)amino)- [1,2,4]triazolo[1,5-a]pyridin-6-yl)phenyl)propanamide; or a pharmaceutically acceptable salt or solvate thereof.
  • the MPS1 inhibitor is selected from the group consisting of : N2-(4-(4,5-dimethyl-4H-1,2,4-triazol-3-yl)-2-ethoxyphenyl)-6-methyl-N8-neopentylpyrido[3,4- d]pyrimidine-2,8-diamine; (S)-N8-(3,3-dimethylbutan-2-yl)-N2-(2-ethoxy-4-(4-methyl-4H-1,2,4-triazol-3-yl)phenyl)-6- methylpyrido[3,4-d]pyrimidine-2,8-diamine; 8-(3,3-dimethylazetidin-1-yl)-N-(2-ethoxy-4-(4-methyl-4H-1,2,4-triazol-3-yl)phenyl)-6- methylpyrido[3,4-d]pyrimidin-2-amine; N-(2-ethoxy-4-(4-methyl-4-methyl-4
  • Biomarker Panel Also provided herein is a signature biomarker panel that may be used for determining a subject’s response or the likelihood of a positive response to treatment with a Msp1 inhibiting compound as described herein .
  • the panel may be characteristic of the probability of a subject’s positive or favorable response to treatment with a compound for inhibiting Mps1 as described herein.
  • the biomarker panel may be capable of detecting or configured to detect reduced expression of PBRM1 in a subject in comparison to a control.
  • the panel may be capable of detecting or configured to detect a reduced activity of a PBRM1 protein in comparison to a control.
  • the panel may be capable of detecting or configured to detect one or more variant PBRM1 proteins.
  • the panel may be capable of detecting or configured to detect one or more variant PBRM1 genes.
  • the variant protein or gene may be any of the variants described herein.
  • the level of expression and/or activity may be compared to a control as described herein. For example, in comparison to an expression level of PBRM1 in a healthy individual.
  • a reference PBRM1 protein for example a wild type protein.
  • a PBRM1 protein comprising an amino acid sequence according to SEQ ID NO: 1.
  • the panel may detect a variant PBRM1 gene or protein in a subject by comparison to wild-type or reference sequence.
  • the variant PBRM1 gene may include one or more mutations as described herein in comparison to a PBRM1 gene comprising an nucleic acid sequence according to SEQ ID NO: 2.
  • the variant PBRM1 protein may include one or more mutations as described herein in comparison to a PBRM1 protein comprising an amino acid sequence according to SEQ ID NO: 1.
  • the signature biomarker panel may include all or a fragment of one or more of variant PBMR1 genes as described herein.
  • the polynucleotides can be attached to a substrate, such as a glass slide or microarray chip.
  • detection of at least one variant PBMR1 gene may be by detecting hybridization (or a lack thereof) of at least a fragment of a subject’s genetic material corresponding to the gene encoding PBRM1.
  • the panel detects defective PBRM1 as described herein and provides an indication (for example to a medical practitioner) whether the treatment with a compound for inhibiting Mps1 as described herein may be effective in treating the individual.
  • a biomarker panel may detect defective PBRM1 using any suitable strategy, such as any strategy described herein for detecting defective PBRM1.
  • kits Also provided herein is a kit of parts including a reagent for detecting deficient PBRM1 in a sample from a subject.
  • reagents include reagents such as probes or antibodies that are capable of selectively binding to a PBRM1 nucleic acid or protein or variant thereof, such as a defective PBRM1 nucleic acid or protein as described herein.
  • the kit may a further include a compound for inhibiting Mps1 as described herein.
  • the kit may also further include instructions for how to use the kit.
  • the deficient PBRM1 comprises a variant PBRM1 nucleic acid and the reagent comprises a nucleic acid that hybridizes to a target nucleic acid comprising the variant PBRM1 nucleic acid.
  • the reagent may be a PCR primer set for amplifying the variant PBRM1 nucleic acid.
  • the target nucleic acid comprises a fragment of a variant PBRM1 gene as described herein.
  • the target nucleic acid may include at least the part of the gene wherein a mutation or modification occurs and the reagent comprises a nucleic acid probe that is capable of hybridising to the mutant nucleic acid sequence. For example, under stringent conditions, thus indicating the presence of the variant in the sample.
  • the deficient PBRM1 includes a variant PBRM1 protein and the reagent comprises an antibody that specifically binds to the variant PBRM1 protein.
  • the variant PBRM1 protein comprises one or more variants described herein.
  • the reagent may be a fragment of an antibody capable of binding to at least a portion of a variant PBRM1 protein.
  • capable of binding to a mutated sequence thus indicating the presence of a defective PBRM1 protein.
  • the kit may include a biomarker panel as described herein.
  • the method of treatment may comprise administering an effective amount of a compound for inhibiting MPS1, wherein the individual has been stratified as having an increased likelihood of efficacy of treatment with the compound for inhibiting MPS1 by any method of stratification as disclosed herein.
  • the compounds for inhibiting MPS1 described herein may be for use treating a PBRM-1 defective cancer in an individual in need thereof. Therefore, the compounds for inhibiting MPS1 described herein may be for use in methods of treating a PBRM1-defective cancer in an individual in need thereof, the method comprising administering an effective amount of the compound to the individual.
  • R e ference to a method of treatment may mean a treatment of the human and animal body by therapy.
  • a method of treatment may cover a compound e.g., MPS1 inhibitor, for use in a method of treatment as disclosed herein, vice versa.
  • a method of treatment may also contemplate an MPS1 inhibitor for use in a method of treatment.
  • the present invention may also cover an MPS1 inhibitor for use in a method of treating a PBRM-1 defective cancer in an individual in need thereof, wherein the method of treatment may comprise administering an effective amount of a compound for inhibiting MPS1 and the individual has been stratified as having an increased likelihood of efficacy of treatment with the compound for inhibiting MPS1 by any method of stratification as disclosed herein.
  • reference to a method of treatment may also cover the use of a substance e.g., MPS1 inhibitor, in the preparation of a medicament for the treatment of PBRM1-defective cancer, vice versa.
  • the present invention may also contemplate the use of an MPS1 inhibitor in the preparation of a medicament for the treatment of PBRM1-defective cancer in an individual in need thereof, wherein the method of treatment may comprise administering an effective amount of a compound for inhibiting MPS1 and the individual has been stratified as having an increased likelihood of efficacy of treatment with the compound for inhibiting MPS1 by any method of stratification as disclosed herein.
  • treating may refer to medical actions and results and includes prophylactic, ameliorative, palliative, and curative actions and results.
  • the terms “treating”, “treated”, and “treatment” refer to curative actions and results as well as actions and results that diminish or reduce the severity of a particular condition, characteristic, symptom, disorder, or disease described herein.
  • treatment can include diminishment of several symptoms of a condition or disorder or complete eradication of said condition or disorder.
  • prophylactic as used herein is not absolute but rather refers to actions and results where the administration of a compound or composition diminishes the likelihood or seriousness of a condition, symptom, or disease state, and/or delays the onset of a condition, symptom, or disease state for a period of time.
  • Treating/treatment As used herein, the terms “treat”, “treating” and “treatment” are taken to include an intervention performed with the intention of preventing the development or altering the pathology of a condition, disorder or symptom (i.e. in this case PBRM1-defective cancer).
  • treatment refers to both therapeutic treatment and prophylactic or preventative measures, wherein the object is to prevent or slow down (lessen) the targeted condition, disorder or symptom.
  • Treatment therefore encompasses a reduction, slowing or inhibition of the symptoms of a cancer as disclosed herein, e.g., a PBRM1-defective cancer, for example of at least 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90% or 100% when compared to the symptoms before treatment.
  • appropriate treatment may include surgery and/or therapy.
  • Effective amount An effective amount of the agents (i.e.
  • MPS1 inhibitors of the methods herein is an amount sufficient to treat or prevent cancer referred to herein, slow disease progression and/or reduce the symptoms associated with the condition, e.g., PBRM1-defective cancer.
  • therapeutic refers to an amount a compound, composition or medicament that (a) inhibits or causes an improvement in a particular disease, condition or disorder (e.g., PBRM1-defective cancer); (b) attenuates, ameliorates or eliminates one or more symptoms of a particular disease, condition or disorder (e.g., PBRM1-defective cancer); (c) or delays the onset of one or more symptoms of a particular disease, condition or disorder described herein (e.g., PBRM1-defective cancer).
  • a therapeutically effective amount can be determined experimentally in a laboratory or clinical setting, or a therapeutically effective amount may be the amount required by the guidelines of the United States Food and Drug Administration (FDA) or equivalent foreign regulatory body, for the particular disease and subject being treated. It should be appreciated that determination of proper dosage forms, dosage amounts, and routes of administration is within the level of ordinary skill in the pharmaceutical and medical arts.
  • a therapeutic agent or other treatment When a therapeutic agent or other treatment is administered, it is administered in an amount and/or for a duration that is effective to treat the cancer disclosed herein.
  • An effective amount is a dosage of the therapeutic agent sufficient to provide a medically desirable result.
  • the effective amount will vary with the particular condition being treated, the age and physical condition of the subject being treated, the severity of the condition, the duration of the treatment, the nature of the concurrent therapy (if any), the specific route of administration and the like factors within the knowledge and expertise of the health care practitioner. For example, an effective amount can depend upon the degree to which a subject has abnormal levels of certain analytes that are indicative of cancer. It should be understood that the therapeutic agents described herein are used to treat and/or prevent cancer e.g., PBRM1-defective cancer.
  • a “pharmaceutical product” refers to a product comprising a pharmaceutical.
  • examples of a pharmaceutical product include a medical device, a pharmaceutical composition and a kit comprising one or more medical device and/or pharmaceutical composition.
  • the pharmaceutical product is a pharmaceutical composition.
  • the MPS1 inhibitors may be administered/for administration to the subject by any convenient route of administration. Routes of administration include, but are not limited to, oral (e.g., by ingestion); buccal; sublingual; transdermal (including, e.g., by a patch, plaster, etc.); transmucosal (including, e.g., by a patch, plaster, etc.); intranasal (e.g., by nasal spray); ocular (e.g., by eye drops); pulmonary (e.g., by inhalation or insufflation therapy using, e.g., via an aerosol, e.g., through the mouth or nose); rectal (e.g., by suppository or enema); vaginal (e.g., by pessary); parenteral, for example, by injection, including subcutaneous, intradermal, intramuscular, intravenous, intra-art
  • the route of administration is selected from oral and parenteral injection.
  • the treatments described herein can be administered to the subject by any conventional route, including injection or by gradual infusion over time.
  • the administration may, for example, be by infusion or by intramuscular, intravascular, intracavity, intracerebral, intralesional, rectal, subcutaneous, intradermal, epidural, intrathecal, percutaneous administration.
  • the medications may also be given in e.g. tablet form or in solution. Several appropriate medications and means for administration of the same are well known for treatment of cancer.
  • the therapeutic agents (i.e. MPS1 inhibitors) for use in the methods herein may be in a form suitable for administration to a subject.
  • lozenges for oral use tablets, lozenges, hard or soft capsules, aqueous or oily suspensions, emulsions, dispersible powders or granules, syrups or elixirs; for topical use creams, ointments, gels, or aqueous or oily solutions or suspensions); for administration by inhalation a finely divided powder or a liquid aerosol; for administration by insufflation a finely divided powder); or for parenteral administration a sterile aqueous or oily solution for intravenous, subcutaneous, intramuscular, intraperitoneal or intramuscular dosing; or as a suppository for rectal dosing.
  • compositions intended for oral use may contain, for example, one or more colouring, sweetening, flavouring and/or preservative agents.
  • An effective amount of the agents (i.e. MPS1 inhibitors) of the methods herein is an amount sufficient to treat or prevent said cancer referred to herein, slow disease progression and/or reduce the symptoms associated with the condition, e.g., PBRM1-defective cancer.
  • the amount of active ingredient that is combined with one or more excipients to produce a single dosage form will necessarily vary depending upon the individual treated and the particular route of administration.
  • a formulation intended for oral administration to humans will generally contain, for example, from 0.5 mg to 0.5 g of active agent (more suitably from 0.5 to 100 mg, for example from 1 to 30 mg) compounded with an appropriate and convenient amount of excipients which may vary from about 5 to about 98 percent by weight of the total composition.
  • active agent more suitably from 0.5 to 100 mg, for example from 1 to 30 mg
  • excipients which may vary from about 5 to about 98 percent by weight of the total composition.
  • the size of the dose for therapeutic or prophylactic purposes of an agent will naturally vary according to the nature and severity of the conditions, the age and sex of the animal or patient and the route of administration, according to well-known principles of medicine. It is to be noted that dosages and dosing regimens may vary with the type and severity of the condition to be alleviated, and may include the administration of single or multiple doses, i.e.
  • Example 1 materials and methods Cell culture All cell lines were purchased from ATCC, CLS, or ECACC. Cells were cultured in the indicated medium (Table 1) in a humidified incubator with 5% CO2. All cell lines were regularly tested for mycoplasma contamination. CRISPR/Cas9 targeting of cells for gene knockout
  • the CRISPR-Cas9 plasmid pSpCas9(BB)-2A-GFP (PX458) was a gift from Professor Feng Zhang (Addgene plasmid #48138).
  • sgRNA sequences targeting PBRM1 were designed using the Benchling CRISPR sgRNA designing tool (https://www.benchling.com/crispr/) and purchased from Sigma.
  • the sgRNAs were cloned into the Cas9-sgRNA expressing plasmid pSpCas9(BB)-2A-GFP (PX458) according to Ran et al., 2013 (Ran et al. 2013). Cells were seeded in 10 cm dish to reach 70% confluence at the time of transfection. For each 10 cm dish, 10 ⁇ g of plasmid with specific sgRNA cloned was transfected into the cells with 20 ⁇ l of Lipofectamine 3000 reagent (Invitrogen) and 20 ⁇ l of P3000 reagent (Invitrogen) according to the manufacturer’s protocol.
  • siRNA transfection Single CCNB1 and scramble (control) siRNAs were purchased from Dharmacon, Horizon Discovery.
  • CENPA siRNAs were purchased as a pool of 4 individual siRNAs from Dharmacon, and a corresponding non-targeting siRNA pool was used as control.
  • Cells were transfected with the indicated siRNA(s) at a final concentration of 50nM using Lipofectamine RNAiMAX transfection reagent (Invitrogen) according to the manufacturer’s protocol.
  • Clonogenic survival assay Cells were trypsinised, counted, and diluted to a single cell suspension at the appropriate cell concentration (300-1,500 cells/dish, depending on cell line), and cells were seeded to 6cm2 dishes. Colonies were allowed to grow for 10-14 days, depending on the cell line, and were then stained with methylene blue (1% methylene blue (Sigma), 70% methanol) for 1 hour at room temperature. Colony number was counted using a Stuart Digital Colony Counter. All conditions were seeded in technical triplicates.
  • clonogenic survival assays following siRNA transfection, cells were transfected with the indicated siRNA for 48 hours before trypsinisation, dilution, and seeding to 6 cm2 dishes. For clonogenic survival assays in the presence of a drug, the compound was added at the indicated concentration 24 hours after seeding.
  • Protein samples were prepared for Western blot analysis by mixing with NuPAGETM LDS sample buffer (Life Technology) and 1.25% ⁇ -Mercaptoethanol (Sigma) and were denatured at 95 °C for 5 minutes prior to electrophoresis on either NovexTM 4% to 20% Tris-Glycine gel (Thermo Fisher Scientific) or 8% Tris-Glycine gel with Precision Plus Protein Standards (Bio- Rad). R e solved proteins were transferred onto 0.45 ⁇ m nitrocellulose membrane (GE Healthcare) followed by Western blot analysis with the indicated antibodies (Table 2).
  • Drug treatments Compounds for inhibition of CDK1 (RO-3306, Merck), pan-CDK (roscovitine, BioVision), or Mps1 (reversine, Merck; AZ3146, Stratech; and BOS172722, MedChemExpress) were dissolved in the appropriate volume of DMSO to a stock solution of 5-20mM, depending on the compound. The corresponding volume of DMSO alone was used as control in experiments.
  • Immunofluorescence imaging Cells were seeded on 18 mm x 18 mm coverslips 24 hours before addition of drug. Coverslips were fixed in 100% ice-cold methanol for at least 1 hour at -20 °C.
  • 53BP1 nuclear bodies were quantified using Fiji and were classed as 53BP1 foci with a Prominence > 135.
  • CEN-CO-FISH assay CEN-CO-FISH was performed as described in (Giunta and Funabiki 2017; Giunta 2018). Briefly, cells were incubated overnight with 3:1 BrdU:BrdC. Colcemid was then added for 4 hours to accumulate mitotic cells. Following trypsinisation, cells were incubated in hypotonic KCl solution, fixed in 3:1 methanol:acetic acid, and dropped from a height onto humid Superfrost Plus slides (ThermoFisher Scientific).
  • RNAse A (Roche), UV treated with 365nm UV light for 30 minutes (Analytik Jena), and Exonuclease III (New England Biolabs) digested.
  • FW single-stranded forward
  • RV reverse
  • Slides were mounted using ProLong Gold antifade mounting medium and cured overnight protected from light. Cells were imaged as described above. Statistical analyses Statistical details of experiments are included in the Figure legends; 2-way ANOVA or t-test was used as appropriate.
  • Cyclin B1 (CCNB1) was identified in a screen for genes that are synthetic lethal with PBRM1 (Hopkins, DNA R e pair).
  • PBRM1 Hopkins, DNA R e pair.
  • ccRCC clear cell renal cell carcinoma
  • Example 3 Mitotic abnormalities are elevated in PBRM1 deficient cells following CDK1 inhibition Because Cyclin B1-CDK1 functions to regulate mitotic progression, the ability of PBRM1 deficient cells to progress through mitosis following CDK1 inhibition as interrogated. To do this, parental and PBRM1 knockout cells were treated for 24h with the RO-3306 CDK1 inhibitor. Nuclear morphology as then monitored as a readout of successful mitotic progression at time points following inhibitor removal ( Figure 3A). Morphological defects were categorised as mild (2 or fewer micronuclei per cell) or severe (multiple micronuclei or the presence of multinucleated, binuclear, polylobular, or catastrophically micronucleated cells; Figure 3A).
  • pericentromeric heterochromatin was disrupted when the catalytic subunit of PBAF was deleted in murine fibroblasts (Bourgo et al. 2009). Defects in centromere chromatin can impair kinetochore assembly, leading to problems with microtubule attachments. Therefore, one potential explanation for the sensitivity of PBRM1 deficient cells to Cyclin B1-CDK1 activity is that aberrant centromere structure in the absence of PBRM1 leads to increased reliance on the spindle assembly checkpoint, which relies on Cyclin B1-CDK1 activity, in order to allow more time to assemble appropriate attachments.
  • R e versine is an Mps1 inhibitor that has been used extensively in the literature to override the SAC (Santaguida et al.2010). It was determined that PBRM1 knockout cells survived less well than the parental cells when treated with R e versine (Figure 5A). While Reversine has activity against Mps1, it also shows activity against other kinases (Hiruma et al.2016). Therefore tested two additional inhibitors with better specificity towards Mps1 were tested; AZ3146 and BOS172722 (Anderhub et al. 2019). Again, the PBRM1 deficient cells showed increased sensitivity to these inhibitors when compared with the isogenic parental control cell line (Figure 5B, C).
  • PBRM1 deficient cells were more dependent on the activity of the SAC than PBRM1 proficient cells.
  • Example 6 - Discussion the inventors have shown that PBRM1 loss results in synthetic lethality with Cyclin B1, which together with CDK1, forms a kinase that is central to mitotic progression in eukaryotic cells. Sensitivity of PBRM1 deficient cells to CDK1 inhibition was also seen. Moreover, the PBRM1 deficient cells showed increased mitotic aberrations following CDK1 inhibitor treatment when compared with the parental cells. It was further determined that PBRM1 is important for protecting the integrity of centromeric DNA by showing increased recombination events at centromeres when PBRM1 is absent.
  • PBRM1 deficient cells are dependent on the SAC because of compromised centromere structure, and as described above, there is evidence that the PBRM1-containing PBAF remodelling complex acts at centromeres.
  • One possibility as to how PBAF remodelling contributes to the establishment or maintenance of centromeric chromatin is that PBAF is required for the transcription of genes involved in the establishment of centromere structure, such as CENP-A.
  • PBAF could act on chromatin at centromeres to promote transcription of centromere repeats, which are required for establishing centromere structure and kinetochore attachments. There is evidence to support both models, which are not mutually exclusive.
  • PBRM1 deficient cancers are predicted to respond to MPS1 inhibitors. Loss of function PBRM1 mutations are found in approximately 40% of ccRCC (Harrod et al.2020).
  • immune checkpoint inhibitor (ICI) therapy is used to treat these patients.
  • ICI immune checkpoint inhibitor
  • anti-mitotic drug treatment can lead to immunogenic cell death (Serrano-Del Valle et al.2021), which could enhance ICI response.
  • Potent and selective MPS1 inhibitors have been developed and brought into clinical trials (Faisal et al.2017; Serrano-Del Valle et al. 2021).
  • PBRM1 directs PBAF to centromeres to constrain transcription and protect genome integrity
  • Example 7 – R e sults To identify core functions of PBRM1, the inventors generated a panel of 17 cell lines with CRISPR-Cas9 engineered loss of function mutations in PBRM1 across five different cell line backgrounds, which included both cancer-derived and immortalized non-cancerous parental cell lines ( Figure 8A and (8)). The growth rate, cell cycle profile, and morphology changes in the KO cells were analyzed relative to the parental lines ( Figure 8B-E).
  • the inventors interrogated the proteomic datasets for peri/centromere-associated proteins, including CenpA interacting proteins, the constitutive centromere-associated network (CCAN) complex, the outer kinetochore, the chromosomal passenger complex (CPC), pericentromeric heterochromatin proteins, and other annotated centromere associated proteins (Figure 8G). Strikingly, it was found that proteins belonging to all of these categories were modestly but consistently downregulated in all cell line backgrounds except for the 786- O renal cancer line ( Figure 8F, H). In contrast, transcription levels of these genes were not consistently downregulated in the PBRM1 knockout cells, indicating that the misregulation of protein levels was not being driven by misregulation of gene expression (Figure 8I).
  • centromere fragility an assay in which centromeres were labelled in a strand specific manner to identify sister chromatid exchanges and other centromere specific rearrangements (termed Cen-CO-FISH (11) was used; Figure 11D).
  • CenpA was depleted, which protects centromere integrity (11).
  • PBRM1 KO clones showed significantly elevated levels of aberrant centromere signals when compared with the parental RPE1-hTERT cells, similar to levels in the CenpA- depleted cells (Figure 11E-G). These data indicated that loss of PBRM1 led to substantially increased genome instability at centromeres, even in the absence of any perturbations. As described above, there was no evidence to show that the lower levels of centromere associated proteins are a consequence of gene expression misregulation when PBRM1 is deficient. Rather, the data are consistent with a model in which PBRM1 promotes centromere organization and, in its absence, peri/centromere-associated proteins fail to assemble efficiently and are destabilized.
  • the inventors set out to determine whether PBAF associates with centromeric or pericentromeric chromatin and gain a comprehensive view of PBAF localization patterns.
  • Cut and Run was performed using both low and high salt conditions to ensure capture of heterochromatic regions such as the centromere (16).
  • SMARCA4 (BRG1) the catalytic subunit of PBAF, was mapped using both IgG and a SMARCA4 KO cell line as negative controls, and CenpB was mapped as a positive control.
  • SMARCA4 and CenpB in the PBRM1 KO cells was additionally mapped to interrogate changes to binding patterns when PBRM1 is absent.
  • centromere-associated reads can be mapped to multiple locations, making enrichment and peak calling challenging.
  • CenpB was analyzed relative to the IgG control as a positive control. When this was done, a total of 2200 k-mers associated with SMARCA4 and 971,000 k-mers associated with CenpB was found. As expected, the CenpB-associated k-mers mapped primarily to the active higher order repeats (HORs) where CenpB is known to bind, and motif analysis of the CenpB associated k-mers identified the CenpB box, providing support for the utility of this approach.
  • HORs active higher order repeats
  • PBRM1 is required to direct SMARCA4 to specific peri/centromere locations. Specifically, PBRM1-dependent SMARCA4 enriched k-mers are predominantly found in transition arms, and a modest but significant association with HORs was found. Interestingly, an impact on CenpB enriched k-mers when PBRM1 is absent was found suggesting that SMARCA4-dependent remodelling facilitates normal CenpB binding patterns. CenpB is important for creating DNA loops that are important for centromere compaction and clustering (2), and this defect could therefore be responsible for the change in centromere chromatin structure observed using alpha-satellite FISH probes in the PBRM1 KO cells ( Figure 11).
  • PBRM1 loss was identified as a genetic determinant for a chromosome instability signature that is associated with whole arm or whole chromosome changes (18). This is consistent with the role the inventors identify here in preventing centromere fragility, and suggests that this general feature of PBRM1 loss is a critical activity that contributes to tumorigenesis and cancer progression.
  • Example 9 Methods Cell culture All cell lines were obtained from ATCC unless otherwise specified.
  • hTERT-RPE1 cells were cultured in Dulbecco Modified Minimal Essential Medium (DMEM)/F-12 (Sigma) supplemented with 10% FBS (Gibco), 200 ⁇ M glutamax (Gibco), 0.26% sodium bicarbonate (Gibco), and 1% penicillin/streptomycin (P/S)(Sigma).
  • DMEM Dulbecco Modified Minimal Essential Medium
  • FBS FBS
  • Gibco 200 ⁇ M glutamax
  • 0.26% sodium bicarbonate Gibco
  • P/S penicillin/streptomycin
  • 1BR3-hTERT, Hek293TN, U2OS, A375, RCC4-VO, and B16-F10 cells were cultured in DMEM supplemented with 10% FBS and 1% P/S.
  • MOC-2 cells were cultured in DMEM supplemented with 5% FBS, 100 ⁇ M glutamax, and 1% P/S.786-O, 769-P, A704, and RCC-FG2 (Cell Lines Service, CLS GmbH) cells were cultured in RPMI 1640 medium (Sigma) supplemented with 10% FBS and 1% P/S.
  • Caki-1 and Caki-2 cells were cultured in McCoy’s 5A modified medium supplemented with 10% FBS and 1% P/S. All cells were maintained at 37oC in a humified incubator with 5% CO2 and were regularly tested for mycoplasma contamination.
  • PBRM1 re-expression plasmid PBRM1-TRIPZ-neo was a gift from Professor William Kaelin (Addgene plasmid #107406).
  • the lentiviral packaging and envelope plasmids psPAX2 and pMD2.G were gifts from Professor Didier Trono (Addgene plasmid #12259 & #12260).
  • CRISPR/Cas9-mediated gene knockout Single guide RNAs (sgRNAs) to target PBRM1 for knockout were designed using the Benchling CRISPR design tool (https://www.benchling.com/crispr).
  • sgRNAs (Sigma) were then cloned into the px458 construct and transfected into cells using Lipofectamine 3000 (Invitrogen), according to the manufacturer’s instructions. 48 hours after transfection, GFP- positive cells were single cell sorted into 96-well plates using a BD FACSAriaTM III sorter (BD). R e sulting clones were screened for loss of PBRM1 using western blotting. Validation of PBRM1 deletion was done by Sanger sequencing (Eurofins) of the targeted genomic region, as well by immunofluorescence microscopy and proteomic profiling. RPE1 SMARCA4 KO cells were generated and characterised as described previously (PMID: 35365638).
  • PBRM1- TRIPz-neo plasmid To exogenously express PBRM1 in cells, cells were transduced with the PBRM1- TRIPz-neo plasmid. To generate lentiviral particles expressing this construct, Hek293TN cells were cultured to 90% confluence, followed by co-transfection of PBRM1-TRIPz-neo, pMD2.G, and psPAX2 plasmids at equimolar amounts using Lipofectamine 3000, according to the manufacturer’s instructions. The resulting virus-containing medium was collected at 24 and 48 hours after transfection, centrifuged to remove cells and debris, passed through a 0.45 ⁇ m filter, aliquoted, and stored at -80oC.
  • Viral titer was estimated using Lenti-X GoStix Plus (Takara). Cells to be infected were cultured to 70% confluence and viral medium was added to cells at a range of concentrations with 6 ⁇ g/mL polybrene (Sigma). After 24 hours, fresh medium containing G418 (Sigma) at the appropriate concentration was added to cells to select for infected cells. R e sulting cells were screened for PBRM1 expression by inducing expression for 48 hours with 1 ⁇ g/mL doxycycline hyclate (Sigma), followed by screening and characterisation by western blotting, immunofluorescence microscopy, and proteomic profiling.
  • siRNA mediated gene depletion/RNA interference 100 ⁇ M of the specified siRNA (Dharmacon) were reverse transfected into cells using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer’s instructions. Single siRNAs or siRNA pools were used as indicated in figure legends. Multiple single siRNAs or an siRNA pool was used, as indicated. Corresponding single or pooled non-targeted siRNAs (Dharmacon) were used as control. Cells were assayed 24-72 hours after transfection. Clonogenic survival assay Cells in culture were diluted to the appropriate density (300-1,000 cells per dish, depending on the cell line) and seeded onto 6cm dishes in triplicate. For survival after drug treatments, drugs were added 24 hours after seeding.
  • RNAi For clonogenic survival after RNAi, cells were reverse transfected as described with the appropriate siRNA 24 hours before seeding in dishes for clonogenic survival assays. Cells were incubated in culture for 10-21 days (depending on the cell line), after which media was aspirated and colonies were fixed and stained with 1% methylene blue in 70% methanol for 1 hour at room temperature with gentle rocking. Dishes were washed extensively with water and allowed to dry overnight. Colony number was counted using a Digital Colony Counter (Stuart), and survival was defined as the % of colonies in treated conditions versus control conditions (vehicle only or control siRNA for drug treatments and RNAi respectively).
  • SRB Sulforhodamine B
  • Proliferation assays For cell growth assays, 1x10 5 cells were seeded to 6 well plates in triplicate. Every 24 hours, wells were trypsinised and counted, up to a total of 96 hours, to quantify the speed of proliferation. For RPE1 cells, the rate of proliferation was quantified using the Incucyte SX5 (Sartorius) using phase contrast images of cells taken every 4 hours.
  • Flow cytometry For flow cytometric analysis of cell cycle distribution, growth medium was collected, and cells were trypsinised and combined with cells suspended in growth medium. Cells were isolated by centrifugation and washed once with PBS. Cells were gently resuspended in remaining PBS and fixed by addition of 70% ethanol dropwise with gentle vortexing. Cells were fixed by incubating in ethanol at -20 o C overnight. Cell suspensions were centrifuged for 5 minutes at 300 x g and the ethanol removed. Pellets were washed twice in cold PBS and then resuspended in the appropriate volume of PBS containing 5 ⁇ g/mL propidium iodide (Sigma) and 0.1mg/mL RNase A.
  • Cells were either fixed with 100% ice-cold methanol for 15 minutes at -20oC, followed by rehydration with four 5-minute washes in PBS or by adding 4% paraformaldehyde (PFA) for 10 minutes at room temperature, followed by permeabilization with 0.2% TritonX-100 for 10 minutes at room temperature. Samples were blocked with 1% BSA in PBS for 1 hour at room temperature and incubated overnight at 4oC in primary antibody diluted in blocking solution. Following washes in PBS, cells were incubated with the appropriate secondary antibody and DNA stain Hoechst 33342 (Sigma) for 2 hours at room temperature.
  • PFA paraformaldehyde
  • Cells were then washed in PBS, mounted onto frosted glass microscope slides with ProLong Gold (Thermo Fisher Scientific), and cured overnight. Cells were imaged with an Advanced Spinning Disc Confocal microscope with SlideBook imaging software (3i). 1.02 ⁇ m Z-stacks were imaged using a 40x or 63x oil objective and exported for analysis as maximum intensity projections. Images were analysed using ImageJ or CellProfiler software. Metaphase spreads Cells in culture were treated with 0.1 ⁇ g/mL colcemid for 4-5 hours to accumulate cells in mitosis.
  • CEN-CO-FISH Centromeric chromosome orientation fluorescent in situ hybridisation
  • Cells were lysed on ice for 45 minutes followed by centrifugation at maximum speed for 15 minutes at 4oC. The resulting supernatant containing whole cell protein extracts was collected.
  • DTT 1,4-dithiothreitol
  • NP-40 1x cOmpleteTM EDTA-free protease inhibitor cocktail
  • PhosSTOPTM phosphatase inhibitor cocktail 1x PhosSTOPTM
  • Membranes were washed with Ponceau S to confirm transfer and total protein concentration and were blocked in 5% milk in TBS buffer containing 0.1% Tween-20 for 1 hour with gentle rocking. Successful protein transfer was confirmed by incubating membranes in Ponceau S solution (Sigma) for 5 minutes with rocking. Membranes were incubated in the appropriate antibody diluted in blocking buffer at 4o C overnight, washed 3 times with TBS buffer containing 0.1% Tween-20, and incubated in the appropriate horseradish peroxidase (HRP)-conjugated secondary antibody diluted in blocking buffer for 1 hour at room temperature. Proteins were visualised on an iBright CL750 imager (Thermo Fisher Scientific) using Immobilon Forte HRP substrate for chemiluminescence.
  • HRP horseradish peroxidase
  • RT-qPCR RNA was extracted from cells using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.0.5 ⁇ g of RNA was then reverse transcribed to cDNA with the High- Capacity cDNA R e verse Transcription kit (Applied Biosystems) according to the manufacturer’s protocol. 4ng of cDNA was used for each qPCR reaction, along with the forward and reverse primers (at 200nM concentration, and Power SYBR green PCR master mix (Applied Biosystems). Samples were run in triplicate in PLATES on a StepOne Plus R e al- Time PCR system (Applied Biosystems), according to the manufacturer’s protocol.
  • CUT&RUN sequencing CUT&RUN (Cleavage Under Targets & R e lease Using Nuclease) was performed according to the CUT&RUN Assay Kit protocol (Cell Signaling Technology) with the following modifications. Cells were detached with Accutase (Sigma). 2 ⁇ 10 5 cells were collected per experiment and pelleted by centrifugation for 5 minutes at 600 x g. Beads were incubated in the indicated primary antibody (Supplementary Table S2) on a nutator overnight at 4°C.
  • MNase digestion was carried out at 0°C in an ice water bath for 30 minutes. Salt fractionation and DNA purification were carried out according to the CUT&RUN.salt protocol (PMID: 29386331). After STOP buffer addition, samples were incubated at 4°C for 1 hour to release low-salt fragments. Beads were resuspended in low salt buffer (175mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20 ⁇ g/mL glycogen). High salt buffer (825mM NaCl, 10mM EDTA, 2mM EGTA, 0.1% TritonX-100, 20 ⁇ g/mL glycogen) was added dropwise with gently vortexing.
  • RNAse A (Thermo Fisher Scientific) was added to all samples and incubated at 37°C for 20 minutes. 3 ⁇ L 10% SDS and 2.5 ⁇ L 20mg/mL Proteinase K (Cell Signaling Technology #10012) were added and samples were incubated at 50°C for 1 hour. DNA was extracted using phenol/chloroform and precipitated in 100% ethanol.
  • SWI/SNF deficiency results in aberrant chromatin organization, mitotic failure, and diminished proliferative capacity.
  • Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint.
  • J Cell Biol 219. Lara-Gonzalez P, Pines J, Desai A.2021. Spindle assembly checkpoint activation and silencing at kinetochores. Semin Cell Dev Biol 117: 86-98. 17. Lukas C, Savic V, Bekker-Jensen S, Doil C, Neumann B, Pedersen RS, Grofte M, Chan KL, Hickson ID, Bartek J et al.2011.53BP1 nuclear bodies form around DNA lesions generated by mitotic transmission of chromosomes under replication stress. Nat Cell Biol 13: 243-253. 18.

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Abstract

La présente invention concerne une méthode de stratification d'un sujet souffrant d'un cancer pour un traitement avec un composé pour inhiber le fuseau monopolaire 1 (Mps1) et un composé pour inhiber Mps1 destiné à être utilisé dans une méthode de traitement d'un cancer déficient en PBRM1 chez un individu en ayant besoin. Un kit comprenant un réactif pour détecter un PBRM1 déficient dans un échantillon provenant d'un sujet et un composé pour inhiber Mps1 et un panel de biomarqueurs de signature caractéristique de la réponse au traitement d'un cancer avec un composé pour inhiber Mps1 sont également fournis.
PCT/GB2023/051429 2022-06-01 2023-05-31 Cancérothérapie WO2023233148A1 (fr)

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