NZ749459A - TATĸ-CDKL5 FUSION PROTEINS, COMPOSITIONS, FORMULATIONS, AND USE THEREOF - Google Patents
TATĸ-CDKL5 FUSION PROTEINS, COMPOSITIONS, FORMULATIONS, AND USE THEREOFInfo
- Publication number
- NZ749459A NZ749459A NZ749459A NZ74945917A NZ749459A NZ 749459 A NZ749459 A NZ 749459A NZ 749459 A NZ749459 A NZ 749459A NZ 74945917 A NZ74945917 A NZ 74945917A NZ 749459 A NZ749459 A NZ 749459A
- Authority
- NZ
- New Zealand
- Prior art keywords
- cdkl5
- polypeptide
- fusion protein
- tatk
- seq
- Prior art date
Links
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Abstract
Disclosed herein are compositions and formulations containing a TATĸ-CDKL5 fusion protein. Also disclosed are methods of producing a TATĸ-CDKL5 fusion protein from vectors containing a TATĸ-CDKL5 cDNA and methods of transducing cells with the vectors containing a TATĸ-CDKL5 cDNA and the TATĸ-CDKL5 fusion protein. Also disclosed are uses of TATĸ-CDKL5 fusion proteins for treating CDKL5 deficiencies by systemic or intravenous administration of the fusion proteins. usion protein. Also disclosed are uses of TATĸ-CDKL5 fusion proteins for treating CDKL5 deficiencies by systemic or intravenous administration of the fusion proteins.
Description
TATK-CDKLS FUSION PROTEINS, COMPOSITIONS, ATIONS, AND USE
THEREOF
BACKGROUND
Cyclin-dependent kinase-like 5 (CDKL5) mutation/deficiency, also known as atypical
Rett syndrome, is a debilitating postnatal neurological disorder that occurs worldwide in 1 of
every 17,000 to 38,000 female . Males are also affected at a lower incidence. This
disorder is not limited to ethnic or racial origin. Symptoms of CDKL5 on/deficiency
range from mild to severe and present as early onset seizure, cognitive disability, hypotonia as
well as autonomic, sleep and gastrointestinal disturbances. ms of disease result from
the ency of a functional CDKL5 protein.
Mutations in the X-linked CDKL5 gene or deficiencies in the CDKL5 protein in
individuals are implicated in the development of atypical or congenital Rett syndrome. See
Bertani et a1., J. biol. Chem. 2006, 281:32048-320 56, Scala et a1., J. Med. Gen., 2005. 42:103-
107, and Kalscheuer et al., Am. J. Hum. Genet. 2003. 72:1401-1411. The CDKL5 gene is
located on the X-chromosome and encodes a protein that is essential for normal brain
development and function. CDKL5 protein is a multifunctional n that has multiple effects
in a neuronal cell. For e, CDKL5 can act as a kinase and phosphorylate MeCP2.
MeCP2 is the target of non-atypical Rett syndrome. Girls affected by the CDKL5 mutations or
deficiencies typically have a normal prenatal history; irritability and drowsiness in the perinatal
period; early-onset sy with onset before 5 months of age, Rett-like features, including
deceleration of head growth, stereotypies, poor to absent voluntary hand use, and sleep
disturbances, and severe mental retardation with poor eye contact and virtually no language.
See Bahi—Buisson and Bienvenu. 2012. Mol. Syndromol. 22137-152.
Current ents for CDKL5 mutations/deficiencies are primarily d on
ng symptoms. However, there are currently no treatments that improve the neurological
outcome of subjects with CDKL5 ons or deficiencies. As such, there exists a need for
development of therapies for treating the CDKL5 ons and deficiencies.
SUMMARY
Described herein are fusion proteins having a CDKL5 polypeptide sequence, wherein
the CDKL5 polypeptide sequence has about 50% to 100% sequence identity to SEQ ID NO: 2
or SEQ ID NO: 16, and a TATK polypeptide sequence, wherein the TATK polypeptide
sequence has about 90% to about 100% sequence identity to SEQ ID NO: 4, wherein the TATK
polypeptide is ively coupled to the CDKL5 polypeptide. In some aspects, the CDKL5
polypeptide sequence has at least 98%, at least 99% or at least 99.5% sequence identity to SEQ
ID NO: 2 or SEQ ID NO: 16. In some aspects, the fusion protein can contain an ng-chain
leader sequence polypeptide, wherein the ng-chain leader ce is operatively coupled to
the CDKL5 polypeptide. In further aspects, the fusion protein can contain a reporter protein
polypeptide, wherein the reporter protein polypeptide is operatively coupled to the CDKL5
polypeptide. In other aspects, the fusion n can contain a protein tag polypeptide, wherein
the protein tag polypeptide is operatively coupled to the CDKL5 polypeptide. In some aspects,
the fusion proteins can increase neurite growth, elongation, dendritic spine , branch
number, or branch y in a brain of a subject as ed to a control. In other s, the
fusion proteins can reduce al apoptosis in the brain of a subject as compared to a
control. In some aspects the fusion protein can have a polypeptide sequence according to SEQ
ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
Also provided herein are ceutical formulations containing a therapeutically
effective amount of a fusion protein having a CDKL5 ptide ce, wherein the
CDKL5 polypeptide sequence has about 50% to 100% sequence identity to SEQ ID N02 or
SEQ ID NO: 16, and a TATK polypeptide sequence, wherein the TATK polypeptide sequence
has about 90% to about 100% sequence identity to SEQ ID NO: 4, n the TATK
ptide is operatively coupled to the CDKL5 polypeptide and a pharmaceutically
acceptable carrier. In some aspects, the CDKL5 polypeptide sequence has at least 98%, at least
99% or at least 99.5% sequence identity to SEQ ID NO: 2 or SEQ ID NO: 16. In some aspects
the fusion protein contained in the pharmaceutical formulations can contain an ng—chain leader
sequence polypeptide, wherein the IgK—chain leader sequence is operatively coupled to the
CDKL5 polypeptide. In some aspects, the fusion protein contained in the pharmaceutical
formulations can contain a reporter protein polypeptide, wherein the reporter n
polypeptide is operatively coupled to the CDKL5 polypeptide. In further aspects, the fusion
protein contained in the pharmaceutical formulations can have a ptide sequence
according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14. In further
aspects, the therapeutically effective amount of the fusion protein can treat one or more
symptoms of a CDKL5 deficiency, Rett me, or Rett syndrome variant in a subject as
compared to a control. In additional aspects, the eutically effective amount of the fusion
protein can increase neurite growth, elongation, dendritic spine number, branch number, or
branch density in a brain of a subject as compared to a control. In other s, the
therapeutically effective amount of the fusion protein can reduce neuronal apoptosis in the
brain of a subject as ed to a control. In additional aspects, the therapeutically effective
amount of the fusion protein can improve motor function in a subject as compared to a control.
In some s, the therapeutically ive amount of the fusion protein can improve
cognitive function in a t as compared to a control. In additional aspects, the
therapeutically effective amount of the fusion protein can increase neural activity in the visual
cortex of a subject as compared to a control.
Provided herein are methods of administering to a subject in need thereof a
therapeutically effective amount of a pharmaceutical formulation ning an amount of a
fusion protein, where the fusion protein contains a CDKL5 polypeptide sequence, wherein the
CDKL5 polypeptide sequence has about 50% to 100% sequence identity to SEQ ID N02 or
SEQ ID NO: 16 and a TATK polypeptide sequence, wherein the TATK polypeptide sequence
has about 90% to about 100% sequence identity to SEQ ID NO: 4, wherein the TATK
polypeptide is operatively coupled to the CDKL5 polypeptide, and a pharmaceutically
acceptable carrier. In some aspects, the subject in need f has or is ted of having a
CDKL5 deficiency, Rett me, or a Rett syndrome variant. In some aspects, the CDKL5
polypeptide sequence has at least 98%, at least 99% or at least 99.5% sequence identity to SEQ
ID NO: 2 or SEQ ID NO: 16. In other aspects of the method of administering a therapeutically
effective amount of the pharmaceutical formulation, the therapeutically effective amount of the
fusion protein can treat one or more symptoms of a CDKL5 deficiency, Rett syndrome, or Rett
me variant in a subject as compared to a control.
Also provided herein are uses of fusion proteins for the treatment of a CDKL5
deficiency, Rett syndrome, or Rett me variant, by systemically administering the fusion
protein or a pharmaceutical ation comprising the fusion protein. In some aspects, the
fusion protein or ceutical formulation comprising the fusion protein is administered
intravenously.
Also provided herein are uses of fusion proteins for sing neural activity in the
visual cortex of a patient having a CDKL5 deficiency, Rett syndrome, or Rett syndrome
variant, by systemically administering the fusion protein or a pharmaceutical formulation
comprising the fusion protein. In some aspects, the fusion n or pharmaceutical
formulation comprising the fusion protein is administered intravenously.
Also provided herein are uses of fusion proteins for increasing neurite growth,
tion, tic spine number, branch number, or branch y in a brain of a patient
having a CDKL5 deficiency, Rett syndrome, or Rett syndrome variant, by systemically
administering the fusion n or a pharmaceutical ation comprising the fusion protein.
In some aspects, the fusion n or pharmaceutical formulation comprising the fusion
n is administered intravenously.
Also provided herein are uses of fusion proteins for reducing neuronal apoptosis in a
brain of a patient having a CDKL5 ency, Rett syndrome, or Rett me variant, by
systemically administering the fusion protein or a pharmaceutical formulation comprising the
fusion protein. In some aspects, the fusion protein or pharmaceutical formulation comprising
the fusion protein is administered intravenously.
Also provided herein are uses of fusion proteins for improving motor on of a
patient having a CDKL5 deficiency, Rett syndrome, or Rett syndrome variant, by systemically
administering the fusion protein or a pharmaceutical formulation comprising the fusion protein.
In some aspects, the fusion protein or ceutical formulation comprising the fusion
protein is administered intravenously.
BRIEF DESCRIPTION OF THE DRAWINGS
Fig. 1 shows one embodiment of a method to produce a CDKL5 fusion protein,
wherein the CDKL5 fusion protein is produced by the cultured cell and secreted into the
surrounding culture media.
Fig. 2 shows one embodiment of a method of producing a CDKL5 fusion protein
wherein the CDKL5 fusion protein is not secreted into the surrounding cell culture media.
Fig. 3 shows one embodiment of method of delivering a CDKL5 fusion protein to a
subject via a transduced or transfected (not specifically shown) autologous cell.
Figs. 4A and 4B demonstrate western blot analysis results from TATK—CDKL5115
protein expression in transfected HEK 293T cells. TATK-CDKL5115 fusion protein was tagged
with an eGFP protein to allow for western blot analysis using an anti-GFP antibody. Fig. 4A
demonstrates GFP-CDKL5115 fusion protein expression in cell t from transfected
HEK 293T cells. Fig. 4B demonstrates TATK—eGFP—CDKL5115 fusion protein purification
from 20X concentrated cell culture medium from TATK-eGFP-CDKL5115-transfected HEK
293T cells.
Figs. 5A and 5B demonstrate results from a kinase activity assay (Fig. 5A)
demonstrating that TAT-eGFP—CDKLSHS fusion protein retains CDKL5 autophosphorylation
activity. TATK-eGFP-CDKL5115 fusion protein was purified from culture medium on a Ni-
NTA resin.
Fig. 6 shows the effect of tion time on transduction efficiency of one
embodiment of a TATK—eGFP-CDKL5115 fusion protein in HEK 293T cells.
Fig. 7A and 7B shows localization of CDKL5 in GFP-CDKL5115 treated HEK
293T cells (Fig. 7B). Figs. 7A and 7B demonstrate the efficiency of transduction of HEK 293T
cells with a TATK—eGFP—CDKL5115 fusion protein as compared to the control (Fig. 7A) (panel
on the left). Immunodetection was conducted using an anti-GFP antibody and cells were
counterstained with DAPI. The White arrows indicate transduced HEK 293T cells.
Fig. 8 is an image demonstrating a serial of 12 images (1-12) from al microscopy
trating TATK-eGFP-CDKL5115 transduction into SH-SY5Y cells d with purified
TATK-eGFP-CDKL5115 protein for 30 minutes. Z stack size was 0.4 pm. Fig. 8 demonstrates
the efficiency of transduction of SH—SY5Y cells with a TATK-eGFP-CDKL5115 fusion protein.
Figs. 9A and 9B demonstrate the effect of transduced CDKL5 in neuroblastoma cells
(SH-SYSY) on cell proliferation. TATK—eGFP-CDKL5115 treated cells (Fig. 9B) were observed
to have sed proliferation as compared to TATK-eGFP (control) treated cells (Fig. 9A).
The white arrows indicate mitotic nuclei.
Fig. 10 shows a graph trating the mitotic index of SH-SY5Y cells treated with
GFP or TATK-eGFP-CDKL5115 fusion proteins. The y-aXis show mitotic cells/total
cells as expressed as % GFP. Data are shown as mean i S.E. *** P<0.001 (t-test).
Fig. 11A-11B are images demonstrating a representative phase contrast image of
TATK-eGFP treated ol) Y cells (Fig. 11A), and TATK-eGFP-CDKL5115 treated
SH-SY5Y cells (Fig. 11B). Neurite growth was observed to be greater in TATK-eGFP-
CDKL5115 d SH-SY5Y cells as compared to control cells.
Fig. 12 shows a graph demonstrating the quantification of neurite outgrowth of SH-
SY5Y cells treated with, TATK-eGFP fusion protein (control), or TATK-eGFP-CDKL5115.
Data is shown as mean i S.E. * P < 0.05 (t-test). The y-axis shows neuritic length/cell in
microns.
Figs. 13A-13B show images demonstrating the dendritic morphology and the number
of newborn ampal granule cells as shown by immunohistochemistry for doublecortin
(DCX) in 45-day-old male CDKL5 wild-type (+/Y) (Fig. 13A) and CDKL5 knockout (KO)
male mice (-/Y), which are hemizygous (Fig. 13B). Scale bar = 50 um. Abbreviations: GR,
granular layer; H, Hilus.
Figs. 14A-14B show double-fluorescence images of differentiated al precursor
cells (NPCs) demonstrating a ion in the generation and maturation of new neurons (red
cells) in neuronal cultures derived from old homozygous female CDKL5 knockout mice
(—/—) (Fig. 14B) as compared to female wild-type (+/+) (Fig. 14A) neuronal cultures. Cells with
a neuronal phenotype are immunopositive for B—tubulin 111 (red), and cells with an astrocytic
phenotype are immunopositive for GFAP (green). Cell nuclei were stained using Hoechst dye
(blue). Scale bar = 25 um.
Fig. 15A-15C shows representative images of neuronal sor cultures generated
from cells derived from 2-day-old homozygous CDKL5 knockout mice (-/-) (Figs. 15B and
15C), transduced with TATK—eGFP (Figure 15B) or GFP-CDKL5115 (Fig. 15C), as
well as neuronal precursor cultures from wild-type mice (+/+) (Fig. 15A). Scale bar = 20 um.
Fig. 16 shows a graph demonstrating quantification of neural maturation as measured
by the total neuritic length of differentiated neurons (neurons positive for beta-tubulin III) in
neuron sor cultures derived from n (2-day-old) wild-type female (+/+) and
homozygous CDKL5 KO (-/-) mice. Cultured and differentiated cells were treated with either
TATK-eGFP or TATK-eGFP-CDKL5115. Values ent mean 1 SE* *p<0.01 as compared to
wild-type condition; #p<0.01 as compared to untreated KO samples (Bonferroni test after
ANOVA).
Figs. 17A—17F show images demonstrating detection of CDKL5 in the brains
of mice (postnatal day 7) systemically treated (one single sub-cutaneous injection) with the
concentrated culture medium (vehicle) (Fig. 17A and 17D), TATK-eGFP (Fig. 17B and 17E),
and TATK-eGFP-CDKL5115 (Fig. 17C and 17F). Samples were collected 4 hours post
injection. Figs. 17D—17F rate magnifications of the dotted boxes in Fig. 17A—17C,
respectively. Localization of TATK-eGFP-CDKL5115 and TATK-eGFP in the brain was
evaluated by immunohistochemistry using an FP dy (red). Images were taken at
the level of the sensory—motor cortex. Scale bar = 60 um (lower magnification) and 20 um
(higher magnification).
Figs. 18A-18D show images of cerebellar sections demonstrating immunodetection of
TATK—eGFP-CDKL5115 in the brains of mice (postnatal day 7) systemically treated as in Figs.
l7A-17F with the culture medium (vehicle) (Fig. 18A and 18B) and TATK-eGFP-CDKL5115
(Fig. 18C and 18D). Samples were collected 4 hours post injection. Localization of TATK-
eGFP-CDKL5115 in the brain was evaluated by immunohistochemistry using an anti—GFP
antibody (Fig. 18A-18B). Slides were mounted with DAPI to stain cell nuclei (Fig. 18B—18C).
Abbreviations: EGL, external granular layer; IGL, internal granular layer; ML, molecular
layer; PL, Purkinje layer. Scale bar = 60 um.
Fig. 19 demonstrates the placement of the a for the intraventricular
administration of the TATK-eGFP-CDKL5115 fusion protein to mice.
Fig. 20 shows a cartoon depicting the implant and the fusion n injection le
for the study demonstrated in Figs. 21-34. The mice are 4-6 months old at the time of
implantation.
Figs. 21A-21C show images of hippocampal dentate gyrus ns immunostained for
DCX demonstrating reduced e length and number of newborn granule cells in CDKL5
knockout male mice (-/Y) as compared to male ype mice (+/Y) (Figs. 21B and 21A,
respectively). TATK-eGFP-CDKL5115 fusion protein administered intraventricularly on five
consecutive days was observed to increase e length and number of newborn granule cells
in male CDKL5 knockout mice (Fig. 21C) to levels similar to wild-type (Fig. 21A). Scale bar
= 70 um.
Figs. C illustrate magnifications of the images in Fig. 21 at the level of the
granule layer of the dentate gyrus. Scale bar = 25 um.
Figs. 23A-23C show examples of the reconstructed dendritic tree of newborn granule
cells of CDKL5 wild-type (WT) male mice (also referred to herein as CDKL5 +/Y or +/Y)
(Fig. 23A), CDKL5 ut (KO) male mice (also referred to herein as CDKL5 -/Y or -/Y)
(Fig. 23B), and CDKL5 KO male mice treated with a TATK-eGFP-CDKL5115 fusion protein
via intraventricular injections given once a day for 5 consecutive days (-/Y + TATK-eGFP-
CDKL5115) (Fig. 23C).
Figs. 24A-24B show graphs demonstrating quantification of the mean total dendritic
length (Fig. 24A), and mean number of tic segments (Fig. 24B) of newborn granule cells
(DCX-positive cells) of the dentate gyrus of CDKL5 WT male mice (+/Y), CDKL5 KO male
mice (—/Y), and CDKL5 KO male mice treated with GFP-CDKL5115 fusion protein via
intraventricular injections given once a day for 5 consecutive days (-/Y + TATK-eGFP-
CDKL5). Values represent mean i SE. ** p < 0.01; *** p < 0.001 as ed to +/Y; # p <
0.05 as compared to the —/Y samples (Bonferroni’s test after ANOVA).
Figs. 25A-25B show graphs demonstrating quantification of the mean length (Fig. 25A)
and mean number (Fig. 25B) of es of the different orders of newborn granule cells of the
e gyrus of CDKL5 wild-type male mice (+/Y), CDKL5 KO male mice (-/Y), and
CDKL5 KO male mice treated with TATK-eGFP—CDKL5115 fusion protein via intraventricular
ions given once a day for 5 consecutive days (-/Y + TATK-eGFP-CDKLS). Values
represent mean i SE. * p < 0.05; ** p < 0.01 as ed to +/Y; # p < 0.05 as compared to
the -/Y samples (Bonferroni’s test after ANOVA).
Fig. 26 shows a graph demonstrating quantification of apoptotic cells (caspase-3
positive cells) in CDKL5 ype male mice (+/Y), CDKL5 KO male mice (-/Y), and
CDKL5 KO male mice treated with TATK-eGFP-CDKLSUS fusion protein via intraventricular
injections given once a day for 5 consecutive days (-/Y + TATK-eGFP-CDKLS). Values
represent mean i SE. * P < 0.05 as compared to +/Y; # p < 0.05 as ed to the -/Y
samples (Bonferroni’s test after .
Figs. 27 shows a graph demonstrating quantification of the number of DCX positive
cells in the DG of CDKL5 wild-type male mice (+/Y), CDKL5 KO male mice (-/Y), and
CDKL5 KO male mice treated with TATK-eGFP-CDKL5115 fusion protein via intraventricular
injections given once a day for 5 consecutive days (-/Y + TATK-eGFP-CDKL5). Data are
expressed as number of cells/mm2 * p < 0.05 as compared to +/Y; # p < 0.05 as compared to
the -/Y samples (Bonferroni’s test after ANOVA).
Figs. 28A-28C show representative images demonstrating brain sections processed for
synaptophysin (SYN) immunofluorescence from the molecular layer of the dentate gryrus
(DG) from a CDKL5 wild-type male mouse (+/Y) (Fig. 28A), a CDKL5 KO male mouse (-/Y)
(Fig. 28B), and a CDKL5 KO male mouse treated with TATK-eGFP-CDKL5115 fusion protein
via intraventricular injections given once a day for 5 utive days (-/Y + TATK-eGFP-
CDKL5) (Fig. 28C). Scale bare = 80 um. Abbreviation: GR, granular layer; M01, molecular
layer.
Figs. 29A-29C show representative images demonstrating brain sections processed for
phospho—AKT (P—AKT) immunofluorescence from the molecular layer of the dentate gryrus
(DG) from a CDKL5 wild-type male mouse (+/Y) (Fig. 29A), a CDKL5 KO male mouse (-/Y)
2017/039692
(Fig. 29B), and a CDKL5 KO male mouse treated with TATK-eGFP-CDKL5115 fusion protein
via entricular injections given once a day for 5 consecutive days (-/Y + TATK—eGFP-
CDKL5) (Fig. 29C). Scale bare = 80 um. Abbreviation: GR, granular layer; Mol, molecular
layer.
Figs. 30A-30B show graphs demonstrating the fication of synaptophysin (SYN)
optical y in the molecular layer of the hippocampus (Fig. 30A) and layer 111 of the cortex
(Fig. 30B) in CDKL5 wild-type male mice (+/Y), CDKL5 KO male mice (-/Y), and CDKL5
KO male mice treated with TATK-eGFP-CDKL5115 fusion protein via intraventricular
injections given once a day for 5 consecutive days (-/Y + TAT-eGFP-CDKLS). Data are given
as fold difference vs. the corresponding zone of the molecular layer or cortex of wild-type
mice. Values represent mean i SD. >“*p < 0.01; ***p < 0.001 as compared to +/Y; # p < 0.05
as compared to the -/Y samples (Bonferroni’s test after .
Figs 3lA-31B show graphs demonstrating the quantification of the optical y of
Ser437 phosphorylated-AKT (PAKT) in the molecular layer of the hippocampus (Fig. 31A)
and layer V of the cortex (Fig. 31B) in CDKL5 wild-type male mice (+/Y), CDKL5 KO male
mice (-/Y), and CDKL5 KO male mice treated with TATK-eGFP—CDKL5115 fusion protein Via
entricular injections given once a day for 5 consecutive days (-/Y + TATK—eGFP-
CDKL5). Data are given as fold difference vs. the ponding zone of the molecular layer
or cortex of wild-type mice. Values represent mean 1- SD. **p < 0.01 as compared to +/Y; # p
< 0.01 as compared to the -/Y samples (Bonferroni’s test after ANOVA).
Fig. 32 shows a graph demonstrating tic mean total dendritic length of Golgi-
stained granule cells in CDKL5 wild-type male mice (+/Y) and CDKL5 KO male mice (—/Y)
treated with a e or TATK—eGFP-CDKL5115 via intraventricular injections given once a
day for 5 consecutive days. On the right scheme of a hippocampal slice showing the different
layers and the position of CA1 pyramidal cells and granule cells. The molecular layer (Mol) of
the dentate gyrus (DG) contains the granule cell dendrites. Values represent mean i SE. **p <
0.01 as compared to +/Y; # p < 0.05 as compared to the -/Y samples (Bonferroni’s test after
ANOVA).
Fig. 33 shows images of Golgi-stained dendritic branches of granule cells of CDKL5
wild-type male mice (+/Y) and CDKL5 KO male mice (-/Y) treated with vehicle or TATK-
eGFP-CDKL5115 Via intraventricular injections given once a day for 5 consecutive days.
Fig. 34 shows a graph demonstrating the fication of number of dendritic spines
of granule cells of CDKL5 wild—type male mice (+/Y) and CDKL5 KO male mice (-/Y) treated
with vehicle or TATK-eGFP-CDKL5115 via intraventricular injections given once a day for 5
consecutive days. Values represent mean i SE. ** p < 0.01 as compared to +/Y; # p < 0.05 as
compared to the —/Y samples (Bonferroni’s test after ANOVA).
Fig. 35 shows a n depicting the implant and the fusion protein injection schedule
for the behavioral study trated in Figs. 36—38. The mice are 4-6 months old at the time
of implantation.
Fig. 36 shows a graph demonstrating the quantification of the learning phase as
determined via the Morris Water Maze test in CDKL5 ype male mice (+/Y; n=8),
CDKL5 KO male mice (—/Y; n=8), and CDKL5 KO male mice treated with a TATK-eGFP-
CDKL5115 fusion protein (-/Y + TATK-eGFP-CDKLS; n=6). Values represent mean i SE. * P
< 0.05, ** P < 0.01 as ed to the untreated Wild-type condition and # P < 0.01 as
compared to the untreated CDKL5 knockout condition as tested with Fisher LSD after
ANOVA.
Figs. 37A-37B show graphs demonstrating memory ability as determined by a passive
avoidance test in CDKL5 wild—type male mice (+/Y; n=8), CDKL5 KO male mice (-/Y; n=8),
and CDKL5 KO male mice treated with a TATK-eGFP-CDKL5115 fusion protein (—/Y + TATK-
eGFP-CDKLS; n=6). Graphs show the latency time for entering the dark compartment on the
first day (Fig. 37A) and on the second day (Fig. 37B) of the behavioral procedure. Values
represent mean 1 SE. *** P < 0.001 as compared to the untreated wild-type condition and # P
< 0.01 as compared to the untreated CDKL5 knockout mice as tested with Fisher LSD after
ANOVA.
Figs. 38A-38B show a graph trating quantification of motor y as
determined by a clasping test in which total amount of time spent limb clasping during a 2
minute interval was measured in CDKL5 wild-type male mice (+/Y; n=8), CDKL5 KO male
mice (-/Y; n=8), and CDKL5 KO male mice treated with a TATK-eGFP-CDKL5115 fusion
protein (-/Y + TATK-CDKLS; n=8) according to the injection schedule in Fig. 35. Values
represent mean i SD. ***p < 0.001 as compared to +/Y; # p < 0.001 as compared to the -/Y
samples (Bonferroni’s test after .
Fig. 39 trates body weight (in grams) of CDKL5 wild-type male (+/Y) and
CDKL5 knockout male (-/Y) mice treated with a GFP-CDKL5115 fusion protein
according to the treatment schedule of Fig. 20 (+/Y; n=8) or Fig. 35 (-/Y; n=6). Mice were left
to recover for 7 days after cannula tation.
Figs. 40A-40F demonstrate a comparison of Allograft Inflammatory Factor 1 (AIF—l)
staining in untreated animals and d with TATK-eGFP-CDKL5115 for 5 days or 10 days by
intraventricular injection. Mice receiving injections were 4-6 months old.
Fig. 41 shows an image of a western blot demonstrating secretion (lanes 1-4) and
sion (lanes 5-8) of a TATK-eGFP—CDKL5115 or TATK-eGFP-CDKL5107 fusion protein
in HEK 293T cells cultured in DMEM and a comparison of the expression and secretion
n of TATK—eGFP-CDKL5115 and GFP-CDKL5107. Extracts were produced from
HEK 293T cells or medium from cultured HEK 293T cells that were transiently transfected.
About 15 ug total protein extracts for HEK 293T cells were loaded on the gel, 20 uL of a 40x
concentrated DMEM medium was loaded to show protein secretion. The arrows te the
respective CDKL5 fusion proteins.
Figs. 42A-42B show graphs demonstrating CDKL5 fusion protein stability in HEK
293T (Fig. 42A) and neuroblastoma cells (Fig. 42B). HEK 293T or neuroblastoma cells were
transfected with a plasmid containing polynucleotides encoding TATK-eGFP-CDKL5115 or
GFP-CDKL5107. -four hours later cells were incubated with cycloheximide
(Chx; 50 ug/ml) for the indicated times (3, 6 or 8 hours). cally expressed CDKL5 was
detected by CDKL5 immunoblotting.
Fig. 43 shows an image of a western blot demonstrating protein ity of TATK-
DKLSHS or TATK-eGFP-CDKL5107 in HEK 293T cells. HEK 293T cells were
transfected with TATK-eGFP-CDKL5115 or TATK-eGFP—CDKL5107. Twenty-four hours later
cells were incubated with cycloheximide (Chx; 50 ug/ml) for the indicated times (3 and 6
hours).
Fig. 44 shows a graph comparing the effect of TATK-eGFP-CDKL5115, TATK-
CDKL5115 and TATK-eGFP-CDKL5107 on neuroblastoma cell proliferation. SH—SY5Y cells
were treated with TATK-eGFP, TATK-eGFP-CDKL5115, TATK-CDKL5115 or TATK-eGFP-
CDKL5107. After 24 hours from transfection, the mitotic index was evaluated as number of
mitotic cells on total cell number as expressed as % TATK-eGFP. Note that the two CDKL5
isoforms show a similar activity of inhibition of SH—SYSY mitosis compared to TATK—eGFP
treated control cells. Values represent mean 1- SEM. ***
p < 0.001 as compared to TATK-
eGFP treated cells (t-test).
Figs. 45A-45D show localization of CDKL5 in TATK-eGFP-CDKL5107 d
hippocampal neuronal cultures. Figs. 45A and 45C demonstrate the efficiency of transduction
and the subcellular localization of a TATK-eGFP control protein. Figs. 45B and 45D
demonstrate the efficiency of transduction and the subcellular localization of a TATK-eGFP-
CDKL5107 protein. Immunodetection was conducted using an anti-GFP dy and cells
were counterstained with DAPI. Higher magnification shows an enlargement of a dendrite
segment.
Figs. 46A-46C show images by laser confocal microscopy of a dendrite t of a
hippocampal neuron treated with TATK—eGFP—CDKL5107. Images show co-localization of
TATK-eGFP-CDKL5107 protein with a postsynaptic protein (PSD-95). eGFP-CDKL5
immunodetection was conducted using an anti-GFP antibody (Fig. 45A).
Fig. 47 shows a graph demonstrating dendritic length of CDKL5 KO (-/Y)
hippocampal neurons after treatment with TATK—eGFP, TATK—eGFP-CDKL5115 or TATK-
eGFP-CDKL5107 fusion proteins. Values represent mean 1' SEM. *** p < 0.001 as compared to
CDKL5 wild-type (+/Y) neurons; # p < 0.05 as compared to the -;'Y neurons rroni’s test
after ANOVA).
Fig. 48 shows a graph demonstrating number of synaptophysin puncta in hippocampal
neurons of CDKL5 KO (-/Y) hippocampal neurons after treatment with TATK-eGFP, TATK-
eGFP-CDKL5115 or GFP-CDKL5107 fusion proteins. Values represent mean i SEM.
***
p < 0.001 as compared to CDKL5 wild-type (+/Y) neurons; # p < 0.05 as compared to the
-/Y neurons (Bonferroni’s test after ANOVA).
Figs. 49A-49B show ns depicting a treatment schedule and route of
administration of the CDKL5 fusion protein. Male CDKL5 wild-type (CDKL5 +/Y; +/Y)
mice received treatment with TATK-eGFP (n=6) while KO (CDKL5 —/Y; -/Y) mice were
treated with GFP (n=6) or TATK-eGFP-CDKL5107 (n=6) as indicated above.
ent period consisted of a single daily injection (10m injection, approximately 50
ng/injection) for 5 consecutive days, followed by a two day rest period and then 5 additional
days of a single ion. There was a total of 10 injections which were done in a 12 day
. Mice were 4-6 months old at the time of implantation. The treatment schedule, route of
administration, and age of mice used in Figs. 49A-49B apply to Figs. 51—59.
Fig. 50 shows a graph demonstrating results from Morris Water Maze g after
receiving the TATK-eGFP-CDKL5107 fusion protein as described in Figs. 49A-49B. Values
represent mean i SE. * p < 0.05, ** p < 0.01, as compared to the CDKL5 wild-type mice (+/Y)
treated with TATK-eGFP (+/Y + TATK—eGFP); # p < 0.01 as compared to CDKL5 KO mice (-
/Y) treated with TATK-eGFP (-/Y + TATK-eGFP) (Fisher LSD test after ANOVA).
Figs. 51A-51C show graphs demonstrating spatial memory from measuring (Fig. 51A)
latency to enter the former platform quadrant, Fig. 51B) ncy of entrances into the former
platform quadrant, (Fig. 51C) percentage of time spent in the former platform quadrant.
Performance in all ters was ly impaired in TATK-eGFP treated CDKL5 KO mice
(-/Y + TATK-eGFP). TATK-eGFP-CDKL5107 treated CDKL5 KO mice (-/Y + TATK-eGFP-
CDKL5107) showed statistically significant improvement in all parameters, Figs. 51A, 51B, and
51C. Values represent mean 1- SE. * p < 0.05, ** p < 0.01, *** p < 0.001 as compared to the
CDKL5 wild-type mice; # p < 0.01 as compared to the TATK-eGFP treated CDKL5 KO mice
(Fisher LSD test after ANOVA).
Figs. 52A-52B show graphs demonstrating the effect of treatment on learning and
memory using a passive avoidance (PA) test. After treatment period and a two day rest period,
mice received e avoidance (PA) testing. The experiment utilized a test cage with two
chambers (light and dark). On the first day, s were placed in the light chamber and
instinctively move into the dark chamber where they are ioned with a single adverse
event (foot-shock). Fig. 52A indicates that the latency time to enter the dark chamber was
similar for all groups. On the second day (testing period) animals are again placed in the light
chamber. Memory of the adverse event was measured by latency time to enter the dark
chamber and ented in Fig. 52B. GFP treated CDKL5 KO male mice (—/Y +
GFP) were ly impaired in this task, as shown by a reduced latency to enter the
dark compartment in comparison with CDKL5 wild-type male mice treated with TATK-eGFP
(+/Y + TATK-eGFP). TATK-eGFP-CDKL5107 treated CDKL5 KO male mice (—/Y + TATK-
eGFP-CDKL5107) showed similar latency time as compared to wild-type male mice (Fig. 52B).
These differences were statistically significant in comparison to TATK-eGFP treated CDKL5
KO male mice (-/Y + GFP). ** p < 0.01 as compared to the CDKL5 wild-type male
condition; # p < 0.01 as compared to the TATK-eGFP treated CDKL5 KO male condition
(Fisher LSD test after ANOVA).
Figs. 53A-53B show (Fig. 53A) a cartoon of a Y-maze used to evaluate the effect of
treatment on learning and memory and (Fig. 53B) a graph trating the results from the Y
maze test. CDKL5 KO mice treated with TATK-eGFP-CDKL5107 (-/Y + TATK-eGFP-
CDKL5107) showed performance similar to CDKL5 wild-type mice treated with TATK-eGFP
(+/Y + TATK—eGFP). * p < 0.05, ** p < 0.01 as ed to the wild—type condition; # p <
0.05 as compared to the TATK-eGFP treated CDKL5 KO ion (-/Y + TATK-eGFP)
(Fisher LSD test after ANOVA).
Figs. B show (Fig. 54A) a graph and (Fig. 54B) an image demonstrating
clasping (right mouse) vs. unclasping (left mouse) in a hind limb clasping test used to evaluate
the effect of treatment on motor function. Treatment of CDKL5 KO mice with TATK-eGFP-
CDKL5107 ( -/Y + TATK-eGFP-CDKL5107) led to a statistically significant ion in
clasping time as compared to TATK-eGFP treated CDKL5 KO (-/Y + TATK-eGFP) Values
represent mean i SE. *** p < 0.001 as compared to the wild-type condition (+/Y + TATK-
eGFP); ## p < 0.001 as compared to the GFP treated CDKL5 KO (Fisher LSD test
after .
Figs. 55A and 55B show graphs demonstrating breathing disturbances in treated TATK-
DKL5107) and untreated (+ TATK-eGFP) CDKL5 wild-type (+/Y) or CDKL5 KO (-/Y)
mice as measured by the number of apneas during non-rapid eye movement (NREM) (Fig.
55A) and rapid eye movement (REM) (Fig. 55B) sleep. Apneas were measured using whole
body plethysmography. * p < 0.01; ** p < 0.01 as compared to the wild—type condition; # p <
0.01 as compared to the CDKL5 KO -/Y condition (t-test).
Figs. 56A-56D show a graph (Fig. 56A) and (Figs. D) reconstructed dendritic
trees of newborn granule cells demonstrating the effect of treatment with TATK-eGFP-
CDKL5107 fusion protein (+ TATK-eGFP-CDKL5107) or TATK-eGFP (+TATK-eGFP) on
CDKL5 wild-type (+/Y) or CDKL5 KO (—/Y) mice. Values represent mean 1- SE. ** p < 0.01
as compared to the wild-type condition; # p < 0.01 as compared to the TATK-eGFP treated
CDKL5 KO condition (Bonferroni test after ANOVA).
Fig. 57 trates quantification of the number of DCX positive cells in the
hippocampus (dentate gyrus) of CDKL5 wild-type male mice (+x’Y) d with TATK-eGFP
(+/Y + TATK-eGFP), CDKL5 KO male mice (-/Y) (-/Y + TATK-eGFP), and CDKL5 KO male
mice treated with TATK-eGFP—CDKL5107 (-/Y + TATK-eGFP-CDKLSW). Treatment period
ted of once daily intraventricular injection for 5 days followed by a two day rest period
then an additional 5 injections. Animals were iced 10 days after the last injection. Data
are expressed as number of cells/mm p < 0.01 as compared to +/Y; ##p < 0.001 as
compared to the CDKL5 KO samples (Bonferroni’s test after ANOVA). Data suggest that the
WO 05617
positive impact of treatment with GFP-CDKLS on the number of DCX-positive cells is
retained 10 days after treatment completion.
Fig. 58 demonstrates quantification of the total number of cleaved Caspase 3 positive
cells in the hippocampus (dentate gyms) of CDKL5 ype male mice (+/Y) treated with
TATK-eGFP (+/Y + TATK-eGFP), CDKL5 KO male mice (-/Y) (-/Y + TATK-eGFP), and
CDKL5 KO male mice treated with TATK-eGFP-CDKL5107 (-/Y + TATK-eGFP-CDKL5107).
The treatment protocol was a once daily intraventricular injection given for 5 days followed by
a two day rest period then an additional 5 injections. Animals were sacrificed 10 days after the
last injection.
Fig. 59 shows a graph demonstrating body weight of CDKL5 KO (-/Y) and CDKL5
wild-type (+/Y) mice treated with GFP (+TATK—eGFP) or CDKL5 KO (-/Y) mice
treated with or TATK-eGFP-CDKL5107 (-/Y + TATK-eGFP-CDKL5107) via once daily
intraventricular injection. Mice were d to recover for 7 days after cannula tation
and sacrificed 10 days after the last injection.
Figs. C show images by laser confocal microscopy of a dendrite t of a
hippocampal neuron transduced with TATK-eGFP-CDKL5107. Images show co-localization of
TATK—eGFP-CDKL5107 protein with a presynaptic protein (synaptophysin; SYN). eGFP-
CDKL5 immunodetection was conducted using an anti-GFP dy (Fig. 64A). Figs. 60A-
60C were produced using the protocol as described in relation to Fig. 45.
Fig. 61 shows a graph demonstrating dendritic spine number of CDKL5 wild—type
(+/Y) or CDKL5 KO (-/Y) hippocampal neurons in Golgi-stained sections after treatment with
TATK-eGFP (+ TATK-eGFP), TATK-eGFP-CDKL5115 (+TATK—eGFP-CDKL5115) or TATK-
eGFP-CDKL5107 (+ TATK-eGFP-CDKL5107) fusion proteins. Values represent mean '1’ SEM.
** p < 0.01 as compared to wild—type (+/Y) neurons; # p < 0.05 as compared to the CDKL5 (-
/Y) neurons (Bonferroni’s test after ANOVA).
Fig. 62 shows a treatment schedule for systemic administration of the CDKL5 fusion
ns. To mimic a daily human dose administration we used an infusion method which is
based on a programmable pump implanted under the skin with a refillable reservoir. CDKL5 -
/Y mice were treated with GFP or TATK-eGFP-CDKL5107. n is injected through
a cannula directly into the internal carotid artery. This system allowed us to apply a twice a day
infusion protocol (morning and evening; 20111 injection, approximately 50ng/injection) for the
duration of 10 days. Mice were 4-6 months of age at the time of implantation. The treatment
schedule and age of mice described with respect to Fig. 62 apply to Figs. 63A-72.
Figs. 63A-63B show images of ampal dentate gyrus sections stained for
DCX. TATK-eGFP-CDKL5107 fusion protein administered systemically on ten consecutive
days to mice that were 4—6 months old was observed to increase neurite length and number of
newborn granule cells in CDKL5 KO male mice (Fig. 63B).
Fig. 64 shows a graph demonstrating the effect of systemic treatment of 4—6 month old
mice with a GFP-CDKL51O7 fusion protein on breathing bances as measured by
the number of apneas during NREM sleep.
Fig. 65 is graph showing mean total tic length of newborn (doublecortin-positive)
granule cells of untreated CDKL5 +/Y and CDKL5 -/Y mice, and CDKL5 -/Y mice treated
with TATK-eGFP or TATK-eGFP-CDKL5107. Values represented as means i SE. ** p < 0.01;
p < 0.001 as compared to the untreated CDKL5 +/Y condition; # p < 0.05 as compared to
the untreated CDKL5 -/Y samples (Fisher LSD test after ANOVA).
Fig. 66 is a graph showing mean total dendritic length of Golgi-stained granule cells of
untreated CDKL5 +/Y and CDKL5 -/Y mice, and CDKL5 -/Y mice treated with TATK-eGFP
** ***
or GFP—CDKL5107. Values represented as means i SE. p < 0.01; p < 0.001 as
compared to the untreated CDKL5 +/Y condition; # p < 0.05 as compared to the untreated
CDKL5 -/Y samples (Fisher LSD test after ANOVA).
Fig. 67 is a graph showing the number of g bouts of untreated CDKL5 +/ and
CDKL5 -/Y mice, and CDKL5 —;’Y mice treated with TATK-eGFP or TATK-eGFP-CDKL51O7.
Values represented as means i SE. ** p < 0.01; as compared to the ted CDKL5 +/Y
condition; # p < 0.05 as compared to the untreated CDKL5 -/Y samples (Fisher LSD test after
ANOVA).
Fig. 68 is a graph showing the nest quality of untreated CDKL5 +/ and CDKL5 -/Y
mice, and CDKL5 -/Y mice treated with TATK-eGFP or TATK-eGFP—CDKL5107. Values
represented as means i SE. ** p < 0.01; as compared to the untreated CDKL5 +/Y condition; #
p < 0.05 as compared to the untreated CDKL5 -/Y samples (Fisher LSD test after .
Fig. 69 are a series of representative images of neural activity in the visual cortex
collected at different time points in one CDKL5 -/Y mouse treated with either GFP or
TATK-eGFP-CDKL5107.
Fig. 70 is a graph showing the mean amplitude of visually evoked responses measured
before and after 6 and 10 days of treatment in CDKL5 -/Y mice d with either TATK-
eGFP or TATK-eGFP-CDKL5107. The persistence of the effect was ted with an
additional measurement 6-10 days after treatment ion (washout). As a reference, the 95%
confidence interval of untreated wild-type response amplitude over time is shown in the
ned area. Error bars represent standard error of the mean. Two-way ANOVA (repeated
measures for the factor time) revealed a time X treatment interaction p<0.05; post-hoc Holm-
Sidak's multiple comparisons test: * p<0.05, **p<0.01.
Fig. 71 is a graph showing the dendritic spine density of the primary visual cortex (V1)
pyramidal neurons (layer 2/3) from untreated CDKL5 +/Y and CDKL5 -/Y mice, and CDKL5
—/Y mice treated with TATK-eGFP or TATK-eGFP—CDKL5107 (n = 5) and sacrificed at the end
of treatment (short term) or with TATK-eGFP or TATK-eGFP—CDKL5107 and sacrificed 10
days after treatment cessation (long term). Values are represented as means i SE. * p< 0.05; **
p < 0.01; p < 0.001 as compared to the untreated CDKL5 +/Y ion; # p < 0.05 as
compared to the untreated CDKL5 -/Y samples (Fisher LSD test after ANOVA).
Fig. 72 is a graph showing the number of fluorescent puncta per um2 exhibiting PSD-95
immunoreactivity in the primary visual cortex (V1) of untreated CDKL5 +/Y (n = 3) and
CDKL5 -/Y (n = 3) mice, and CDKL5 —/Y mice treated with TATK-eGFP (n = 4) or TATK-
DKL5107 (n = 6) and sacrificed at the end of treatment (short term), or with TATK-
eGFP (n = 4) or GFP—CDKL5107 (n = 4) and sacrificed 10 days after treatment
cessation (long term). Values are represented as means i SE. ** p < 0.01 as compared to the
untreated CDKL5 +/Y condition; # p < 0.05 as ed to the untreated CDKL5 -/Y samples
(Fisher LSD test after ANOVA).
DETAILED PTION
Provided herein are TATK-CDKLS fusion protein compositions and formulations and
methods for their use in the treatment of CDKL5—mediated disease and disorders, particularly
disorders and diseases due to CDKL5 mutations and/or deficiencies. Also provided herein are
methods for ing TATK-CDKLS fusion protein compositions and formulations. These
methods provide for ed experimental tools for the research of CDKL5-mediated
neurological disorders as well as improved treatment options for ts suffering disorders
related to CDKL5 dysfunction. Also provided herein are methods of using such TATK-CDKLS
fusion protein compositions and formulations for treating CDKL5—mediated diseases and
disorders. Also provided herein are methods of increasing neural ty in the visual cortex
in a patient having a mediated disease or disorder. Also provided herein are methods
of increasing neurite growth, elongation, dendritic spine , branch number, or branch
density in a brain of a patient having a CDKL5-mediated e or disorder. Also provided
herein are methods of reducing neuronal apoptosis in the brain of a patient having a CDKL5-
mediated disease or disorder. Also provided herein are methods of improving motor function
of a patient having a CDKL5-mediated disease or disorder.
Definitions
As used herein, "about, H Happroximately," and the like, when used in connection with a
numerical variable, generally refers to the value of the variable and to all values of the variable
that are within the experimental error (e.g., within the 95% confidence al for the mean) or
Within +;’- 10% of the indicated value, whichever is greater.
As used herein, “active agent” or “active ingredient” refers to a substance, compound,
or molecule, which is biologically active or otherwise, s a ical or physiological
effect on a subject to which it is stered to. In other words, “active agent” or “active
ingredient” refers to a component or components of a composition to which the whole or part
of the effect of the composition is attributed.
As used herein, “additive ” refers to an effect arising between two or more
les, compounds, substances, factors, or compositions that is equal to or the same as the
sum of their individual effects.
The term “amphiphilic,” as used herein, refers to a molecule combining hydrophilic and
lipophilic (hydrophobic) properties.
As used herein, “antibody” refers to a glycoprotein comprising at least two heavy (H)
chains and two light (L) chains inter-connected by disulfide bonds, or an antigen binding
portion thereof. Each heavy chain is comprised of a heavy chain variable region (abbreviated
herein as VH) and a heavy chain constant region. Each light chain is sed of a light
chain le region and a light chain nt region. The VH and VL regions retain the
binding specificity to the antigen and can be further subdivided into regions of
hypervariability, termed complementarity ining regions (CDR). The CDRs are
interspersed with regions that are more ved, termed framework regions (FR). Each VH
and VL is composed of three CDRs and four framework regions, arranged from amino-
terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3,
and FR4. The variable regions of the heavy and light chains contain a binding domain that
interacts with an antigen.
As used herein, “anti-infective” refers to compounds or molecules that can either kill an
infectious agent or inhibit it from spreading. nfectives include, but are not limited to,
antibiotics, cterials, antifungals, rals, and antiprotozoans.
As used herein, “aptamer” refers to single-stranded DNA or RNA molecules that can
bind to pre-selected targets including proteins with high affinity and specificity. Their
specificity and teristics are not directly determined by their primary sequence, but
d by their tertiary structure.
The term “biocompatible”, as used herein, refers to a material that along with any
metabolites or degradation products thereof that are generally non-toxic to the recipient and do
not cause any significant adverse effects to the recipient. lly speaking, biocompatible
materials are materials which do not elicit a significant atory or immune response
when administered to a patient.
As used herein “biodegradable” generally refers to a material that will e or erode
under physiologic conditions to smaller units or chemical species that are capable of being
metabolized, ated, or excreted by the subject. The degradation time is a function of
composition and morphology. Degradation times can be from hours to weeks.
The term “hydrophilic”, as used herein, refers to nces that have strongly polar groups
that readily interact with water.
As used herein, “cDNA” refers to a DNA sequence that is complementary to a RNA
transcript in a cell. It is a man-made molecule. Typically, cDNA is made in vitro by an
enzyme called reverse-transcriptase using RNA transcripts as templates.
As used herein, “CDKLS deficiency” refers to any deficiency in the biological function
of the protein. The deficiency can result from any DNA on in the DNA coding for the
protein or a DNA related regulatory region or any change in the function of the protein due to
any changes in epigenetic DNA modification, including but not limited to DNA methylation or
histone cation, any change in the secondary, tertiary, or quaternary structure of the
CDKL5 protein, or any change in the ability of the CDKL5 protein to carry out its ical
on as compared to a wild—type or normal subject.
As used herein, “CDKL5 mutation” refers to any change in the nucleotide sequence of
the coding region of the CDKL5 protein.
As used , “cell,” ”cell line,” and ”cell culture" include progeny. It is also
understood that all progeny may not be precisely identical in DNA content, due to deliberate or
inadvertent mutations. Variant progeny that have the same function or biological ty, as
ed for in the originally transformed cell, are included.
As used herein, "composition” refers to a combination of active agent and at least one
other compound or molecule, inert (for example, a detectable agent or label) or active, such as
an adjuvant.
As used herein, “concentrated” refers to a molecule, including but not limited to a
polynucleotide, peptide, polypeptide, protein, antibody, or nts thereof, that is
distinguishable from its naturally ing counterpart in that the concentration or number of
molecules per volume is greater than that of its naturally occurring counterpart.
As used herein, “control” is an alternative subject or sample used in an experiment for
comparison purpose and included to minimize or distinguish the effect of les other than
an independent variable.
As used herein, “chemotherapeutic agent” or “chemotherapeutic” refer to a therapeutic
agent utilized to prevent or treat cancer.
As used herein, “culturing” refers to maintaining cells under ions in which they
can erate and avoid senescence as a group of cells. “Culturing” can also include
conditions in which the cells also or alternatively differentiate.
As used herein, “deoxyribonucleic acid (DNA)” and ucleic acid (RNA)”
generally refer to any polyribonucleotide or polydeoxribonucleotide, which may be unmodified
RNA or DNA or modified RNA or DNA. RNA may be in the form of a tRNA (transfer RNA),
snRNA (small nuclear RNA), rRNA (ribosomal RNA), mRNA (messenger RNA), anti-sense
RNA, RNAi (RNA interference construct), siRNA (short interfering RNA), or ribozymes.
As used herein, “DNA molecule” includes nucleic acids/polynucleotides that are made
of DNA.
As used herein, “derivative” refers to any compound having the same or a r core
structure to the compound but having at least one structural ence, including substituting,
2017/039692
deleting, and/or adding one or more atoms or functional groups. The term “derivative” does not
mean that the derivative is synthesized from the parent compound either as a starting material
or intermediate, gh this may be the case. The term “derivative” can include prodrugs, or
metabolites of the parent compound. Derivatives include compounds in which free amino
groups in the parent compound have been derivatized to form amine hydrochlorides, ene
sulfoamides, benzoxycarboamides, t-butyloxycarboamides, thiourethane-type derivatives,
roacetylamides, chloroacetylamides, or ides. Derivatives include nds in
which carboxyl groups in the parent compound have been derivatized to form methyl and ethyl
esters, or other types of esters or ides. Derivatives include compounds in which
hydroxyl groups in the parent nd have been derivatized to form O-acyl or O—alkyl
derivatives. Derivatives include compounds in which a hydrogen bond donating group in the
parent nd is replaced with another hydrogen bond donating group such as OH, NH, or
SH. Derivatives include replacing a hydrogen bond or group in the parent compound
with another hydrogen bond acceptor group such as esters, ethers, ketones, carbonates, ry
amines, imine, thiones, sulfones, tertiary amides, and sulfides. “Derivatives” also includes
extensions of the replacement of the cyclopentane ring with saturated or unsaturated
cyclohexane or other more complex, e.g., nitrogen-containing rings, and extensions of these
rings with side s groups.
As used herein, “differentiate” or “differentiation,” refers to the process by which
sor or progenitor cells (e. g., neuronal progenitor cells) differentiate into specific cell
types (e. g., neurons).
As used herein, “differentially expressed,” refers to the differential tion of RNA,
including but not limited to mRNA, tRNA, miRNA, siRNA, snRNA, and piRNA transcribed
from a gene or regulatory region of a genome or the protein product encoded by a gene as
compared to the level of production of RNA by the same gene or regulator region in a normal
or a control cell. In another context, “differentially expressed,” also refers to nucleotide
sequences or proteins in a cell or tissue which have different temporal and/or spatial expression
profiles as compared to a normal or control cell.
As used herein, “diluted” refers to a molecule, including but not limited to a
polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, that is
distinguishable from its naturally occurring counterpart in that the concentration or number of
molecules per volume is less than that of its lly occurring counterpart.
As used herein, “dose,7: 66 unit dose,’ a or e” refers to physically discrete units
suitable for use in a subject, each unit containing a predetermined ty of the CDKL5
fusion protein, a composition containing the CDKL5 fusion n, and/or a pharmaceutical
formulation thereof calculated to produce the d response or ses in association with
its administration.
As used herein, “effective amount” is an amount sufficient to effect beneficial or
desired biological, emotional, medical, or clinical response of a cell, , system, animal, or
human. An effective amount can be administered in one or more administrations, applications,
or dosages. The term also includes within its scope s effective to enhance normal
logical function.
As used herein, “expansion” or “expanded” in the context of cell refers to an increase in
the number of a teristic cell type, or cell types, from an initial population of cells, which
may or may not be identical. The initial cells used for expansion need not be the same as the
cells generated from expansion. For instance, the expanded cells may be produced by ex vivo
or in vitro growth and differentiation of the initial population of cells.
As used herein, “expression” refers to the process by which polynucleotides are
transcribed into RNA ripts. In the context of mRNA and other translated RNA species,
“expression” also refers to the process or ses by which the transcribed RNA is
subsequently translated into peptides, polypeptides, or proteins.
As used herein, “fusion protein” refers to a protein formed from the combination of at
least two different proteins or protein fragments. A fusion protein is encoded by a recombinant
DNA molecule. As such, a “CDKL5 fusion protein” refers to a recombinant protein having a
human CDKL5 polypeptide or variant thereof operatively linked to other polypeptide
sequences.
As used herein, “gene” refers to a hereditary unit corresponding to a sequence of DNA
that occupies a specific location on a chromosome and that contains the genetic instruction for
a characteristic(s) or trait(s) in an organism.
As used herein, “green cent n,79 44yellow fluorescent protein,” 44red
fluorescent n” and the like and their abbreviations include, without limitation, all forms
of such proteins as they are routinely modified, derivitized, and generally known to those of
ordinary skill in the art. For example “green fluorescent protein” includes, without limitation,
enhanced green fluorescent protein (eGFP), redox sensitive GFP (roGFP), and all color
mutants.
As used herein, “HEK 293T” and is a term of art to refer to human embryonic kidney
(HEK) 293 cells that express large T antigen and are generally known in the art and
commercially available h vendors such as American Tissue Type Culture tion.
The term phobic”, as used herein, refers to substances that lack an affinity for
water; tending to repel and not absorb water as well as not dissolve in or mix with water.
As used herein, “identity,” is a relationship between two or more polypeptide sequences, as
determined by comparing the sequences. In the art, “identity” also refers to the degree of
sequence relatedness n polypeptide as determined by the match between s of such
sequences. “Identity” can be readily calculated by known methods, including, but not limited
to, those described in (Computational Molecular Biology, Lesk, A. M., Ed., Oxford University
Press, New York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., Ed.,
Academic Press, New York, 1993; Computer Analysis of Sequence Data, Part I, Griflin, A. M.,
and Grzfiin, H. G., Eds, Humana Press, New Jersey, 1994; ce Analysis in Molecular
Biology, von Heinje, G., Academic Press, 1987; and Sequence Analysis , ov, M.
and Devereux, 1., Eds., M Stockton Press, New York, 1991; and Carillo, H., and , D.,
SIAM J. Applied Math. 1988, 48: 1073. Preferred methods to determine ty are designed
to give the largest match between the sequences tested. Methods to determine identity are
codified in publicly available computer programs. The t identity between two sequences
can be determined by using analysis software (e.g., Sequence Analysis Software Package of
the Genetics Computer Group, Madison Wis.) that incorporates the Needelman and Wunsch,
(J. Mol. Biol, 1970, 48: 443-453,) thm (e.g., NBLAST, and XBLAST). The default
parameters are used to determine the identity for the polypeptides of the present disclosure.
As used herein, “immunomodulator,” refers to an agent, such as a therapeutic agent,
which is capable of modulating or regulating one or more immune on or response.
As used herein “induces,” “inducing,” or “induced” refers to activating or stimulating a
process or pathway within a cell, such as endocytosis, secretion, and exocytosis.
As used herein, “isolated” means separated from constituents, cellular and otherwise, in
which the polynucleotide, peptide, polypeptide, protein, antibody, or fragments thereof, are
normally associated with in . A non-naturally occurring polynucleotide, peptide,
polypeptide, protein, antibody, or fragments thereof, do not require “isolation” to distinguish it
from its naturally occurring counterpart.
The term “lipophilic,” as used herein, refers to compounds having an affinity for lipids.
As used , “mammal,” for the purposes of ents, refers to any animal
classified as a mammal, including human, domestic and farm animals, nonhuman primates, and
zoo, sports, or pet animals, such as, but not limited to, dogs, horses, cats, and cows.
As used herein, “matrix” refers to a material, in which one or more specialized
structures, molecules, or compositions, are ed.
The term “molecular weight”, as used herein, generally refers to the mass or average
mass of a material. If a polymer or oligomer, the lar weight can refer to the relative
average chain length or relative chain mass of the bulk r. In practice, the molecular
weight of polymers and oligomers can be estimated or characterized in various ways including
gel permeation chromatography (GPC) or capillary viscometry. GPC molecular weights are
reported as the weight-average molecular weight (MW) as d to the number-average
molecular weight (Mn). ary viscometry provides estimates of lar weight as the
inherent viscosity determined from a dilute polymer solution using a particular set of
tration, temperature, and solvent conditions.
As used , “negative control” refers to a “control” that is designed to e no
effect or result, provided that all reagents are oning properly and that the experiment is
ly conducted. Other terms that are interchangeable with “negative control” include
“sham,93 44placebo,” and “mock.”
As used herein, “nucleic acid” and “polynucleotide” generally refer to a string of at
least two ugar-phosphate combinations and refers to, among others, single-and double-
stranded DNA, DNA that is a e of single-and double-stranded regions, single— and
double-stranded RNA, and RNA that is mixture of single- and double-stranded regions, hybrid
molecules comprising DNA and RNA that may be single—stranded or, more typically, double-
stranded or a mixture of single- and double-stranded regions. Also, polynucleotide, as used
herein, refers to triple-stranded regions comprising RNA or DNA or both RNA and DNA. The
strands in such regions may be from the same molecule or different les. The regions
may include all of one or more of the molecules, but more typically involve only a region of
some of the molecules. One of the molecules of a triple-helical region often is an
oligonucleotide. “Polynucleotide” and “nucleic acids” also encompasses such chemically,
tically or metabolically ed forms of polynucleotides, as well as the chemical
forms of DNA and RNA characteristic of viruses and cells, including simple and complex
cells, among other . For instance, the term polynucleotide includes DNAs or RNAs as
described above that contain one or more modified bases. Thus, DNAs or RNAs comprising
unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two
es, are polynucleotides as the term is used herein. “Polynucleotide” and “nucleic acids”
also includes PNAs (peptide nucleic acids), phosphorothioates, and other variants of the
phosphate ne of native nucleic acids. Natural nucleic acids have a phosphate backbone,
artificial nucleic acids may contain other types of backbones, but contain the same bases.
Thus, DNAs or RNAs with backbones modified for stability or other reasons are “nucleic
acids” or ”polynucleotide” as that term is intended herein.
As used herein, “nucleic acid sequence” and nucleotide” also encompasses a
nucleic acid and polynucleotide as defined above. As used herein, "organism," ”host," and
"subject" refers to any living entity comprised of at least one cell. A living organism can be as
simple as, for example, a single isolated eukaryotic cell or cultured cell or cell line, or as
complex as a mammal, including a human being, and animals (e.g., vertebrates, amphibians,
fish, mammals, e.g., cats, dogs, horses, pigs, cows, sheep, rodents, s, squirrels, bears,
primates (e.g., chimpanzees, gorillas, and humans). ”Subject" may also be a cell, a population
of cells, a tissue, an organ, or an organism, preferably to human and tuents f. As
used herein, “overexpressed” or “overexpression” refers to an increased expression level of an
RNA or n product encoded by a gene as compared to the level of expression of the RNA
or protein product in a normal or control cell.
As used herein, "operatively linked” can indicate that the tory sequences useful
for expression of the coding sequences of a nucleic acid are placed in the nucleic acid molecule
in the appropriate positions relative to the coding sequence so as to effect expression of the
coding sequence. This same definition is sometimes applied to the arrangement of coding
sequences and/or transcription control elements (e. g. promoters, enhancers, and termination
elements), and/or selectable markers in an expression vector.
As used herein, nt” refers to an organism, host, or subject in need of treatment.
As used herein “peptide” refers to chains of at least 2 amino acids that are short,
relative to a protein or polypeptide.
As used herein, “pharmaceutical formulation” refers to the combination of an active
agent, compound, or ingredient with a pharmaceutically acceptable carrier or excipient, making
the composition suitable for diagnostic, therapeutic, or preventive use in vitro, in vivo, or ex
vivo.
As used herein, “pharmaceutically able carrier or excipient” refers to a carrier or
excipient that is useful in preparing a pharmaceutical formulation that is generally safe, non-
toxic, and is neither biologically or otherwise undesirable, and includes a carrier or excipient
that is acceptable for veterinary use as well as human pharmaceutical use. A “pharmaceutically
acceptable carrier or ent” as used in the specification and claims includes both one and
more than one such carrier or ent.
As used herein, “pharmaceutically able salt” refers to any acid or base addition
salt whose counter-ions are non-toxic to the subject to which they are administered in
pharmaceutical doses of the salts.
As used herein, “plasmid” as used herein refers to a non-chromosomal double-stranded
DNA sequence including an intact “replicon” such that the d is replicated in a host cell.
As used herein, ive control” refers to a “control” that is designed to produce the
desired result, provided that all reagents are functioning properly and that the experiment is
properly ted.
As used herein, “preventative” and “prevent” refers to hindering or stopping a disease
or ion before it occurs, even if undiagnosed, or while the disease or condition is still in
the inical phase.
As used herein, “protein” as used herein refers to a large molecule composed of one or
more chains of amino acids in a specific order. The term protein is used interchangeable with
“polypeptide.” The order is determined by the base sequence of nucleotides in the gene coding
for the n. Proteins are required for the structure, function, and regulation of the body’s
cells, tissues, and organs. Each protein has a unique function.
As used herein, “purified” or “purify” is used in reference to a nucleic acid sequence,
peptide, or polypeptide that has increased purity relative to the natural nment.
As used herein, the term “recombinant” generally refers to a non-naturally occurring
nucleic acid, c acid construct, or polypeptide. Such non-naturally ing nucleic
acids may include natural nucleic acids that have been modified, for example that have
deletions, substitutions, inversions, insertions, eta, and/or combinations of nucleic acid
ces of different origin that are joined using molecular biology technologies (e.g., a
nucleic acid sequences encoding a fusion protein (e. g., a protein or polypeptide formed from
the combination of two different proteins or protein fragments), the combination of a nucleic
acid encoding a polypeptide to a promoter sequence, where the coding sequence and promoter
sequence are from different sources or otherwise do not typically occur together naturally (e.g.,
a c acid and a constitutive promoter), etc.). Recombinant also refers to the polypeptide
encoded by the recombinant nucleic acid. Non-naturally occurring nucleic acids or
ptides include c acids and polypeptides ed by man.
As used herein, “Rett syndrome variant,a: 4‘variant of Rett syndrome,” and the like
refers to an atypical form of Rett syndrome with similar clinical signs to Rett syndrome but an
n gy.
As used herein, “separated” refers to the state of being physically divided from the
original source or population such that the separated compound, agent, particle, or molecule
can no longer be considered part of the original source or population.
As used , “specifically binds” or “specific g” refers to binding that occurs between
such paired species such as enzyme/substrate, receptor/agonist or antagonist, antibody/antigen,
lectin/carbohydrate, oligo DNA primers/DNA, enzyme or proteinfDNA, and/or RNA molecule
to other nucleic acid (DNA or RNA) or amino acid, which may be mediated by covalent or
non-covalent interactions or a combination of nt and valent interactions. When
the interaction of the two s produces a non-covalently bound complex, the binding that
occurs is typically electrostatic, hydrogen-bonding, or the result of lipophilic interactions.
ingly, ”specific binding" occurs between a paired species where there is interaction
n the two which produces a bound complex having the characteristics of an
antibody/antigen, enzyme/substrate, DNA/DNA, DNA/RNA, DNA/protein, RNA/protein,
RNA/amino acid, receptor/substrate interaction. In particular, the specific binding is
characterized by the binding of one member of a pair to a particular species and to no other
species within the family of compounds to which the corresponding member of the binding
member belongs. Thus, for example, an antibody preferably binds to a single epitope and no
other epitope within the family of proteins.
As used herein, “specific g partner” or “binding partner” is a compound or
molecule to which a second compound or molecule binds with a higher affinity than all other
molecules or compounds.
As used interchangeably herein, “subject, 73 4"individual,”
or “patient” refers to a
vertebrate organism.
As used herein, "substantially pure” means an object species is the predominant species
present (i.e., on a molar basis it is more abundant than any other individual species in the
composition), and preferably a substantially ed fraction is a ition wherein the
object species comprises about 50 percent of all species present. Generally, a substantially
pure composition will comprise more than about 80 percent of all s present in the
ition, more preferably more than about 85%, 90%, 95%, and 99%. Most preferably,
the object species is purified to essential homogeneity (contaminant species cannot be detected
in the composition by conventional detection methods) n the composition consists
essentially of a single species.
As used , “substantially pure cell tion” refers to a population of cells
having a specified cell marker characteristic and differentiation potential that is about 50%,
preferably about 75-80%, more preferably about 85-90%, and most preferably about 95% of
the cells making up the total cell population. Thus, a "substantially pure cell population" refers
to a population of cells that contain fewer than about 50%, preferably fewer than about 20-
%, more preferably fewer than about 10-15%, and most preferably fewer than about 5% of
cells that do not display a specified marker characteristic and entiation potential under
designated assay conditions.
The terms “sufficient” and “effective,” as used interchangeably herein, refer to an
amount (e.g. mass, volume, dosage, concentration, and/or time period) needed to achieve one
or more desired result(s). For example, a therapeutically effective amount refers to an amount
needed to achieve one or more therapeutic effects.
As used herein, “synergistic effect,73 c;synergism,”
or “synergy” refers to an effect
arising between two or more molecules, compounds, substances, s, or compositions that
is greater than or ent from the sum of their individual effects.
As used herein, “therapeutic” refers to treating, healing, and/or ameliorating a e,
er, condition, or side effect, or to decreasing in the rate of advancement of a disease,
disorder, condition, or side effect. The term also includes within its scope enhancing normal
physiological function, palliative treatment, and partial remediation of a e, disorder,
condition, side effect, or symptom thereof. The e or disorder can be a CDKL5 deficiency
and/or Rett Syndrome.
2017/039692
As used herein, “therapeutically effective amount” refers to the amount of a CDKL5-
fusion protein, a composition containing a CDKL5 fusion protein, a pharmaceutical
formulation thereof, auxiliary agent, or secondary agent bed herein that will elicit the
biological or medical response of a , system, animal, or human that is being sought by the
researcher, veterinarian, medical doctor or other ian. “Therapeutically effective amount”
includes that amount of a CDKL5-fusion protein, a composition containing a CDKL5 fusion
protein, a pharmaceutical formulation f that, when administered alone or co—administered
with a secondary agent, is sufficient to prevent development of, reduce or alleviate to some
extent, one or more of the symptoms of CDKL5 deficiency and/or Rett syndrome.
peutically effect amount” includes that amount of CDKL5—fusion protein, a composition
containing a CDKL5 fusion protein, a pharmaceutical formulation thereof that, when
administered alone or co—administered with a secondary agent, is sufficient to increase neuron
survival, neuron number, e growth, elongation, dendritic spine number, and/or branch
density in a region of the brain of a subject as compared to a control. “Therapeutically effect
amount” includes that amount of CDKL5-fusion protein, a composition containing a CDKL5
fusion protein, a pharmaceutical formulation thereof that, when administered alone or co-
administered with a secondary agent, is sufficient to increase ng ability in a subject as
compared to a control. “’Iherapeutically effect amount” includes that amount of CDKL5-fusion
protein, a composition containing a CDKL5 fusion protein, a pharmaceutical formulation
thereof that, when administered alone or co-administered with a secondary agent, is sufficient
to increase memory ability in a subject as compared to a control. peutically effect
amount” includes that amount of CDKL5-fusion protein, a composition containing a CDKL5
fusion protein, a pharmaceutical formulation thereof that, when administered alone or co-
administered with a secondary agent, is sufficient to e motor function in a subject as
compared to a control. “Therapeutically effect amount” includes that amount of CDKL5-fusion
protein, a composition containing a CDKL5 fusion protein, a pharmaceutical formulation
thereof that, when administered alone or co-administered with a secondary agent, is ient
to restore learning ability, memory ability, and/or motor function to levels that are substantially
similar to wild-type or normal levels. “Therapeutically effect amount” includes that amount of
CDKL5-fusion n, a composition containing a CDKL5 fusion protein, a pharmaceutical
ation f that, when administered alone or co-administered with a secondary agent,
is sufficient to e neuron number, neuron survival, e growth, neurite elongation,
dendritic spine number, neurite branch number, and/or neurite branch density in a region of the
brain to levels that are substantially similar to ype or normal levels. The therapeutically
effective amount will vary depending on the exact chemical structure of the fusion
protein, a composition containing a CDKL5 fusion protein, a pharmaceutical formulation
thereof, the CDKL5 deficiency, Rett syndrome or symptom thereof being treated, the route of
administration, the time of administration, the rate of excretion, the drug combination, the
judgment of the treating physician, the dosage form, and the age, weight, general health, sex
and/or diet of the subject to be treated.
The terms ”treating” and ”treatment” as used herein refer generally to obtaining a
desired pharmacological and/or logical effect. The effect may be prophylactic in terms
of preventing or partially ting a disease, symptom or condition f, such as disease
or ers resulting from CDKL5 mutations and/or deficiencies, the CDKL5 variant of Rett
syndrome, or other CDKL5-mediated neurological disorder, and/or may be therapeutic in
terms of a partial or complete cure of a disease, condition, symptom or adverse effect attributed
to the e, er, or condition. The term "treatment" as used herein covers any treatment
of CDKL5-mediated neurological disorder in a mammal, particularly a human, and includes:
(a) preventing the e from ing in a subject which may be predisposed to the disease
but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its
development; or (c) relieving the disease, i.e., mitigating or ameliorating the disease and/or its
symptoms or conditions. The term ”treatment" as used herein refers to both therapeutic
treatment and prophylactic or preventative measures. Those in need of treatment include those
already with the disorder as well as those in which the disorder is to be prevented.
As used herein, “tangible medium of expression” refers to a medium that is physically
tangible and is not a mere abstract thought or an unrecorded spoken word. Tangible medium of
expression includes, but is not limited to, words on a cellulosic or plastic material or data
stored on a suitable device such as a flash memory or CD—ROM.
As used herein, “transduced” refers to the direct introduction of a protein into a cell.
As used herein, the term “transfection” refers to the introduction of an ous
and/or recombinant nucleic acid sequence into the interior of a ne enclosed space of a
living cell, including uction of the nucleic acid ce into the l of a cell as well
as the interior space of a mitochondria, nucleus, or chloroplast. The nucleic acid may be in the
form of naked DNA or RNA, it may be associated with various proteins or regulatory elements
2017/039692
(e.g., a promoter and/or signal element), or the nucleic acid may be incorporated into a vector
or a chromosome. It may be incorporated into a viral particle.
As used herein, formation” or “transformed” refers to the introduction of a
nucleic acid (e. g., DNA or RNA) into cells in such a way as to allow expression of the coding
portions of the introduced nucleic acid.
As used herein, “underexpressed” or “underexpression” refers to decreased expression
level of an RNA or protein product encoded by a gene as compared to the level of expression
of the RNA or protein product in a normal or control cell.
As used herein, “variant” refers to a ptide that differs from a reference
polypeptide, but retains essential properties. A typical t of a polypeptide differs in amino
acid sequence from r, reference ptide. Generally, differences are d so that
the sequences of the reference polypeptide and the variant are closely similar overall and, in
many regions, identical. A variant and reference polypeptide may differ in amino acid
sequence by one or more modifications (e. g., substitutions, additions, and/or deletions). A
substituted or inserted amino acid residue may or may not be one encoded by the genetic code.
A variant of a polypeptide may be naturally occurring such as an allelic variant, or it may be a
variant that is not known to occur naturally. “Variant” includes functional and structural
variants.
As used herein, the term “vector” or is used in reference to a vehicle used to introduce
an exogenous nucleic acid sequence into a cell. A vector may include a DNA molecule, linear
or circular (e. g. plasmids), which includes a segment ng a polypeptide of interest
operatively linked to additional segments that e for its transcription and translation upon
introduction into a host cell or host cell organelles. Such additional segments may include
promoter and terminator sequences, and may also include one or more origins of replication,
one or more selectable markers, an enhancer, a polyadenylation signal, etc. Expression vectors
are generally derived from yeast or bacterial genomic or plasmid DNA, or viral DNA, or may
contain elements of both.
As used herein, “wild-type” is the typical form of an sm, variety, , gene,
protein, or characteristic as it occurs in nature, as guished from mutant forms that may
result from selective breedng or transformation with a transgene.
Unless ise defined herein, all technical and ific terms used herein have the
same meaning as commonly understood by one of ordinary skill in the art.
Discussion
TATIc-CDKLS Fusion Genes and Proteins
In human CDKL5 the first two ed splice variants differ in the 5’UTRs and
produce the same 115 kDa protein. They are referred to as isoform I, containing exon 1, which
is transcribed in a wide range of tissues, and isoform II, including exon 1a and 1b, which is
limited to testis and fetal brain (Kalscher et al. 2003. Am J Hum Genet, 72: 1401-11 and
Williamson et al. 2012. Hum Genet, 131: 187-200).The resulting CDKL5 transcript generates a
protein of 1030 amino acids with lar weight of 115 kDa (CDKL5115) and is mainly
expressed in the testis. More recently ative splicing events have been identified, leading
to at least three distinct human protein ms. One of these ms is, characterized by an
altered C-terminal region and is refered to as CDKL5107. u et al. 2011. J. Hum Genet,
56:52-57, Williamson et al. 2012, Hector et. al. 2016. PLoS One. 11(6): e0157758). CDKL5107
is the predominant isoform in human and mouse brains. In all human tissues CDKL5107 is the
most abundant transcript, with tissues expressing 10- to 100-fold or more 07 than
. In particular, in the whole brain, there is 37-fold more of CDKL51O7 than
CDKL5115. Testis is the exception, with only 25-fold more CDKL5107 than 15
reflecting the relative abundance of CDKL5115 in this tissue. The inus of CDKL5, which
is different in the two isoforms, is important in modulating its subcellular zation, and the
accumulation of truncated protein in the nucleus. (Bertani et al. 2006. J Biol Chem, 281:32048-
56 and Rusconi et al. 2008. J Biol Chem, 283:30101-11).
The cellular distribution of the CDKL5107 isoform has been examined, ing
subcellular localization and catalytic activity that overlap greatly, but not completely, with that
of the previously studied human CDKL5115 protein. In vitro data indicate that proteasomal
degradation of the CDKL5115 isoform is mediated by a signal between amino acids 904 and
1030, exclusively present in this isoform, whereas CDKL5107 is more stable and less prone to
ation through the proteasome pathway.
Fusion Genes and Proteins
Disclosed herein are recombinant cDNA sequences, which code for various CDKL5
fusion proteins containing a modified TAT (TATK) sequence. The CDKL5 included in the
fusion protein can be the CDKL5115 isoform. The CDKL5 included in the fusion protein can be
the CDKL51O7 isoform. SEQ ID NO: 2 corresponds to the CDKL5115 isoform polypeptide and
SEQ ID NO: 16 corresponds to the CDKL51O7 isoform polypeptide. In one embodiment the
fusion protein contains a human CDKL5 polypeptide operatively coupled to a TATK
polypeptide. The cDNA sequence, which codes for the CDKL5 fusion protein, can have a
sequence according to any one of SEQ ID NOs: 1, 7, 9, 11, 13, or a variant thereof described
herein. The CDKL5 fusion protein can have a polypeptide sequence according to any one of
SEQ ID NOs: 8, 10, 12, 14, or a t thereof describe herein.
In some embodiments, the human CDKL5 cDNA sequence can be according to SEQ
ID NOs: 1 or 15. In further embodiments, the human CDKL5 cDNA can be about 90% to
about 100%, 80% to about 90%, or about 50% to about 80%, identical to SEQ ID NOs: 1 or
15. In some embodiments, the human CDKL5 cDNA sequence can code for an amino acid
sequence according to SEQ ID NO: 2 or 16. In further embodiments, the human CDKL5
cDNA sequence can code for an amino acid ce that is about 90% to about 100%, 80% to
about 90%, or about 50% to about 80% identical to SEQ ID NO: 2 or 16.
In some embodiments, the human CDKL5 cDNA sequence can be a fragment of at
least 12 consecutive nucleotides that are about 90% to 100% identical to 12 consecutive
nucleotides in SEQ ID NO: 1. In some embodiments, the human CDKL5 cDNA sequence can
be a fragment of at least 12 consecutive tides that are about 80% to 90% identical to 12
consecutive nucleotides in SEQ ID NO: 1. In some embodiments, the cDNA sequence can be a
fragment of at least 12 consecutive nucleotides that are about 50% to 80% identical to 12
consecutive nucleotides in SEQ ID NO: 1.
In some ments, the human CDKL5 cDNA sequence can be a fragment of at
least 12 consecutive tides that are about 90% to 100% identical to 12 consecutive
nucleotides in SEQ ID NO: 15. In some embodiments, the human CDKL5 cDNA ce can
be a fragment of at least 12 consecutive nucleotides that are about 80% to 90% identical to 12
consecutive tides in SEQ ID NO: 15. In some embodiments, the cDNA sequence can be
a fragment of at least 12 consecutive nucleotides that are about 50% to 80% identical to 12
consecutive nucleotides in SEQ ID NO: 15.
The CDKL5 fusion protein contains a modified trans-acting tion of transcription
(TAT) protein transduction domain (PTD) (TATK) operatively coupled to the human CDKL5
polypeptide. The TATK can have a cDNA sequence according to SEQ ID NO: 3 and an amino
acid sequence according to SEQ ID NO: 4. TATK is a modified TAT-PTD. fied TAT-
PTD mediates the transductions of peptides and proteins into cells. r, unmodified
TAT-PTD does not allow TAT-PTD fusion proteins to be secreted by the cell. Unmodified
D is cleaved from the fusion protein by furin endoprotease at furin recognition
sequences located within unmodified TAT-PTD. In contrast, TATK is ed such that it
does not contain the furin recognition sequences. As such, the CDKL5 fusion ns
described herein containing TATK can be secreted in its full form by eukaryotic cells.
In some ments, the TATK cDNA sequence can be about 90% to 100% or about
80% to about 90% cal to SEQ ID NO: 3. In some embodiments, the TATK cDNA can
code for a ptide sequence that is about 90% to 100% or about 80% to about 90%
identical to SEQ ID NO: 4. The TATK cDNA can be operatively coupled to a cDNA that
encodes a CDKL5 fusion protein.
The CDKL5 fusion n can optionally contain an IgK-chain leader sequence to
direct the polypeptide down the secretory pathway during production by a cell. In some
embodiments, the IgK-chain leader sequence can be operatively coupled at the N—terminus of
the human CDKL5 polypeptide. The IgK-chain leader sequence can have a cDNA sequence
according to SEQ ID NO: 5 or a variant thereof described herein and can have an amino acid
sequence according to SEQ ID NO: 6 or variant thereof described herein. The IgK-chain leader
sequence cDNA can be operatively coupled to a cDNA that encodes a CDKL5 fusion protein.
In other embodiments, the IgK-chain leader sequence cDNA can be about 90% to
100%, about 80% to about 90%, or about 80% to 90% cal to SEQ ID NO: 5. In some
embodiments, the IgK-chain leader sequence can have an amino acid sequence that is about
90% to about 100%, about 80% to about 90%, or about 50% to about 80% identical to SEQ ID
NO: 6.
The CDKL5 fusion protein can optionally n one or more protein tags operatively
coupled to the CDKL5 fusion protein. These types of tags are amino acid sequences that allow
for affinity purification, solubilization, chromatographical separation, and/or immunodetection
of the fusion protein. Suitable protein tags include, but are not limited to, chitin binding n
(CBP), maltose binding protein (MBP), glutathione-S-transferase (GST), poly(His),
thioredoxin (TRX), poly(NANP), FLAG—tag (including any FLAG—tag variant, 6. g. 3x FLAG),
V5-tag, Myc-tag, HA-tag, S-tag, SBP—Tag, Sftag l, Softag 3, Tc tag, Xpress tag, Strep-tag,
Isopeptag, Spy Tag, Ty tag, Biotin Carboxyl Carrier Protein , and Nus tag. A CDKL5
fusion protein cDNA according SEQ ID NO: 7, 9, or 11 having an amino acid sequence
according to SEQ ID NO: 8, 10, or 12, respectively, demonstrate miting embodiments of
a CDKL5 fusion protein ning a TATK, and Myc-tag and a poly(HIS) tag. A CDKL5
fusion protein cDNA according SEQ ID NO: 13, having an amino acid sequence according to
SEQ ID NO: 14 demonstrate a non-limiting embodiment of a CDKL5 fusion protein having a
FLAG—tag.
The CDKL5 fusion protein can optionally contain one or more er proteins
operatively coupled to the CDKL5 polypeptide. Suitable reporter genes include, but are not
limited to, fluorescent proteins (6. g. green fluorescent protein (GFP), red fluorescent protein
(RFP), yellow fluorescent protein (YFP), blue fluorescent n (BFP), and cyan fluorescent
protein (CFP)), beta-galactosidase, luciferase (bacterial, , and renilla luciferase),
otic-resistance genes (e. g. chloramphenicol acetyltransferase, neomycin
otransferase, and NPT-II), p-glucuronidase, and alkaline phosphatase. Inclusion of a
reporter protein allows, among other things, for direct and/or indirect characterization of the
fusion protein and function of the fusion protein, as well as affinity purification of the protein.
The reporter protein can be operatively linked to the N-terminus and/or the C-terminus of the
human CDKL5 polypeptide. In other embodiments, the reporter protein can be operatively
linked to N-terminus and/or the C-terminus of the CDKL5 fusion protein. A CDKL5 fusion
protein cDNA according SEQ ID NO: 9 or 11 and having an amino acid sequence according to
SEQ ID NO: 10 or 12 respectively, demonstrate non-limiting embodiments of a CDKL5 fusion
protein containing a fluorescent reporter protein.
Recombinant Vectors
The CDKL5 fusion cDNA ce can be incorporated into a suitable expression
vector. The expression vector can contain one or more tory sequences or one or more
other sequences used to tate the expression of the CDKL5 fusion cDNA. The expression
vector can contain one or more regulatory ces or one or more other sequences used to
facilitate the replication of the CDKL5 fusion expression vector. The expression vector can be
le for expressing the CDKL5 fusion protein in a bacterial cell. In other embodiments, the
expression vector can be suitable for expressing the CDKL5 fusion protein in a yeast cell. In
further embodiments, the expression vector can be suitable for expressing the CDKL5 fusion
protein in a plant cell. In other embodiments, the sion vector can be suitable for
expressing the CDKL5 fusion n in a mammalian cell. In another embodiment, the vector
can be suitable for expressing the CDKL5 fusion protein in a fungal cell. In further
embodiments, the vector can be suitable for sing the CDKL5 fusion n in an insect
cell. Suitable expression s are generally known to those of ordinary skill in the art.
TATIC-CDKLS Protein Production
In some ments, the CDKL5 fusion n is produced in vitro in a cell culture
system. The cell culture system can contain one or more bacterial, yeast, insect, fungal, plant,
or mammalian cells. In some embodiments, the CDKL5 fusion protein is ed by the
cultured cell(s) into the cell culture media. In other embodiments, the CDKL5 fusion protein is
contained within the cytoplasm or a membrane of the cultured cell(s).
With that said, ion is directed to Fig. l, which shows one embodiment of a
method to produce a CDKL5 fusion protein, wherein the CDKL5 fusion protein is produced by
the cultured cell and secreted into the surrounding culture medium. The method begins by
transfecting or otherwise delivering a suitable vector containing a CDKL5 fusion protein
cDNA sequence to a cell or cells in culture (6000). The cells are then cultured (6010) using
generally known methods to allow the transfected cells to produce the CDKL5 fusion protein
from the vector and e the CDKL5 fusion protein into the surrounding cell culture
medium. In other embodiments, stably—transfected cell lines expressing one or more of the
vectors containing a CDKL5 fusion protein cDNA can be ted using techniques generally
known by those of ordinary skill in the art. These cells can be cultured (6010) using generally
know methods to allow the cells to produce the CDKL5 fusion protein.
After a suitable amount of time, the e medium that contains the secreted CDKL5
fusion protein is collected (6020). In some embodiments the cells are cultured from about 12 h
to about 96 h. At this point, it is determined whether or not the CDKL5 fusion protein needs to
be further purified from the culture medium (6030). In some embodiments, the medium
containing the CDKL5 fusion n is not further purified and is used directly to transduce
one or more cells (6050). In other embodiments, the CDKL5 fusion protein is further purified
from and/or concentrated in the culture media. In some embodiments, the CDKL5 fusion
protein is purified and/or concentrated using a suitable method. Suitable methods include, but
are not limited to solvent partitioning salting in or g out, affinity-based methods, and
chromatographic separation methods such as hydrophobic interaction, ion exchange, mixed
mode, dye g, and size exclusion, as ified in Kameshita et al. (Biochemical and
Biophysical Research Communications 377, 1162-1167 (2008)), Sekiguchi er al. (Archives of
mistry and Biophysics 535, 257-267 (2013)), and Katayama et a]. (Biochemistry, 54,
2975-2987 ), which are incorporated by nce.
With an tanding of a secretory method of production in mind, attention is
directed to Fig. 2, which shows one embodiment of a method of producing a CDKL5 fusion
protein wherein the CDKL5 fusion protein is not secreted into the nding cell culture
media. The method begins by transfecting or otherwise delivering a suitable vector containing
a CDKL5 fusion protein cDNA sequence to a cell or cells in culture (6000). The cells are then
cultured (6010) using generally known methods to allow the transfected cells to produce the
CDKL5 fusion protein from the vector. After a suitable amount of time, the cells are lysed
using rd methods (7000). In some ments, the cells are cultured from 12 h to 96 h
before being lysed.
Next, it is determined if the CDKL5 fusion protein is integrated within the cell
membrane or the asm (7010). If the CDKL5 fusion protein is in the membrane fraction,
then the membrane fraction is collected (7020). After the membrane fraction is collected
(7020), the CDKL5 fusion protein is separated from the membrane fraction using suitable
method (6040) for purifying and/or concentrating the CDKL5 fusion protein.
In embodiments where the CDKL5 fusion protein is present in the cytoplasm, the
supernatant containing the CDKL5 fusion protein is collected (7030). After the supernatant is
collected (7030), it is determined if the CDKL5 fusion protein should be further purified and/or
trated. If it is determined that that the CDKL5 fusion protein should be further purified
and/or concentrated, then the CDKL5 fusion protein is purified and/or concentrated using a
le method (6040). Suitable methods e, but are not limited to, affinity purification,
size exclusion separation, and chromatographical separation methods. In other embodiments
where it is determined that the CDKL5 should not be further purified and/or concentrated from
the supernatant, the supernatant containing the CDKL5 fusion protein is used directly to
transduce cells (6050).
Compositions and Formulations containing TATk-CDKL5 Fusion Protein
Also within the scope of this disclosure are compositions and formulations ning a
CDKL5 fusion protein as described herein. The composition can be the media or atant
containing the CDKL5 fusion protein that can be produced according to a method described
herein.
The CDKL5 fusion proteins described herein can be provided to a subject in need
thereof alone or as such as an active ingredient, in a pharmaceutical formulation. As such, also
described herein are pharmaceutical formulations containing an amount of a CDKL5 fusion
protein. In some embodiments, the pharmaceutical formulations contain a therapeutically
effective amount of a CDKL5 fusion n. The ceutical formulations described
herein can be administered to a subject in need thereof. The subject in need thereof can have a
CDKL5 deficiency, Rett syndrome, and/or a symptom thereof. In other ments, the
CDKL5 fusion protein can be used in the manufacture of a medicament for the treatment or
tion of a CDKL5 deficiency, Rett syndrome, and/or a symptom thereof.
Pharmaceutically Acceptable Carriers and Auxiliary Ingredients and Agents
The pharmaceutical formulations containing a therapeutically effective amount of a
CDKL5 fusion protein described herein can further include a pharmaceutically acceptable
carrier. le pharmaceutically acceptable carriers include, but are not limited to, water, salt
solutions, ls, gum arabic, vegetable oils, benzyl alcohols, polyethylene glycols, gelatin,
ydrates such as lactose, amylose or starch, magnesium stearate, talc, silicic acid, viscous
paraffin, perfume oil, fatty acid esters, hydroxy methylcellulose, and polyvinyl pyrrolidone,
which do not deleteriously react with the active composition.
The pharmaceutical formulations can be sterilized, and if desired, mixed with auxiliary
agents, such as lubricants, preservatives, stabilizers, wetting , emulsifiers, salts for
influencing osmotic pressure, buffers, coloring, flavoring and/or aromatic substances, and the
like which do not deleteriously react with the active composition.
In addition to the therapeutically effective amount of a of a CDKL5 fusion protein
described herein, the pharmaceutical formulation can also include an effective amount of an
auxiliary active agent, including but not limited to, DNA, RNA, amino acids, peptides,
polypeptides, antibodies, aptamers, ribozymes, guide sequences for ribozymes that inhibit
translation or transcription of essential tumor proteins and genes, hormones,
immunomodulators, antipyretics, anxiolytics, ychotics, analgesics, antispasmodics, anti-
inflammatories, anti-histamines, anti-infectives, and chemotherapeutics.
Suitable es include, but are not limited to, acid d hormones (e. g.
melatonin and thyroxine), small e hormones and protein es (e. g. ropin-
releasing hormone, Vasopressin, insulin, growth hormone, luteinizing hormone, le-
stimulating hormone, and thyroid-stimulating hormone), eiconsanoids (e. g. arachidonic acid,
lipoxins, and prostaglandins), and steroid hormones (e.g. estradiol, testosterone, tetrahydro
testosteron cortisol).
Suitable immunomodulators include, but are not limited to, sone, azathioprine, 6-
MP, cyclosporine, tacrolimus, methotrexate, interleukins (e. g. IL—2, IL-7, and IL—12), cytokines
(e. g. erons (e. g. IFN—(x, IFN-B, IFN-a, IFN-K, IFN—@, and IFN-y), granulocyte colony-
stimulating , and mod), chemokines (e. g. CCL3, CCL26 and CXCL7), cytosine
ate-guanosine, oligodeoxynucleotides, s, antibodies, and aptamers).
Suitable antipyretics include, but are not limited to, non-steroidal anti-inflammants (e. g.
fen, naproxen, ketoprofen, and nimesulide), aspirin and related salicylates (e. g. choline
salicylate, magnesium salicylae, and sodium salicaylate), paracetamol/acetaminophen,
metamizole, nabumetone, phenazone, and quinine.
Suitable ytics include, but are not limited to, benzodiazepines (e. g. alprazolam,
bromazepam, chlordiazepoxide, epam, clorazepate, diazepam, flurazepam, lorazepam,
oxazepam, temazepam, triazolam, and tofisopam), serotenergic antidepressants (e. g. selective
serotonin reuptake inhibitors, tricyclic antidepresents, and monoamine oxidase inhibitors),
mebicar, afobazole, selank, bromantane, emoxypine, azapirones, barbiturates, hydroxyzine,
pregabalin, validol, and beta blockers.
Suitable ychotics include, but are not limited to, benperidol, bromoperidol,
droperidol, haloperidol, moperone, pipaperone, timiperone, fluspirilene, penfluridol, pimozide,
acepromazine, romazine, cyamemazine, dizyrazine, fluphenazine, levomepromazine,
mesoridazine, perazine, azine, perphenazine, pipotiazine, prochlorperazine, promazine,
promethazine, pendyl, thioproperazine, thioridazine, trifluoperazine, triflupromazine,
chlorprothixene, clopenthixol, flupentixol, tiotixene, zuclopenthixol, clotiapine, loxapine,
prothipendyl, carpipramine, clocapramine, one, mosapramine, sulpiride, veralipride,
amisulpride, amoxapine, aripiprazole, asenapine, clozapine, blonanserin, iloperidone,
lurasidone, one, nemonapride, olanzaprine, paliperidone, perospirone, quetiapine,
remoxipride, risperidone, sertindole, trimipramine, ziprasidone, ne, alstonie, befeprunox,
bitopertin, brexpiprazole, cannabidiol, cariprazine, pimavanserin, pomaglumetad methionil,
vabicaserin, xanomeline, and zicronapine.
Suitable analgesics e, but are not d to, paracetamoliacetaminophen, non-
steroidal anti-inflammants (e. g. ibuprofen, en, ketoprofen, and nimesulide), COX-2
inhibitors (e.g. rofecoxib, celecoxib, and etoricoxib), opioids (e.g. morphine, codeine,
oxycodone, hydrocodone, dihydromorphine, pethidine, orphine), tramadol,
norepinephrine, flupiretine, nefopam, adrine, pregabalin, gabapentin, cyclobenzaprine,
scopolamine, methadone, ketobemidone, piritramide, and aspirin and related salicylates (e. g.
choline salicylate, magnesium salicylate, and sodium salicylate).
Suitable antispasmodics include, but are not limited to, rine, papverine,
cyclobenzaprine, carisoprodol, orphenadrine, tizanidine, metaxalone, methodcarbamol,
chlorzoxazone, baclofen, dantrolene, baclofen, tizanidine, and lene.
Suitable anti-inflammatories include, but are not limited to, prednisone, non-steroidal
nflammants (e. g. ibuprofen, naproxen, ketoprofen, and nimesulide), COX—2 inhibitors
(e. g. rofecoxib, celecoxib, and etoricoxib), and immune selective anti-inflammatory derivatives
(6. g. submandibular gland e—T and its derivatives).
Suitable istamines include, but are not limited to, Hl-receptor antagonists (e. g.
acrivastine, azelastine, bilastine, brompheniramine, buclizine, bromodiphenhydramine,
carbinoxamine, zine, chlorpromazine, cyclizine, chlorpheniramine, clemastine,
eptadine, desloratadine, dexbromapheniramine, dexchlorpheniramine, dimenhydrinate,
dimetindene, diphenhydramine, doxylamine, ebasine, embramine, fexofenadine, hydroxyzine,
levocetirzine, loratadine, meclozine, mirtazapine, adine, adrine, phenindamine,
pheniramine, phenyltoloxamine, promethazine, pyrilamine, quetiapine, rupatadine,
tripelennamine, and triprolidine), Hz—receptor antagonists (e. g. cimetidine, famotidine,
lafutidine, nizatidine, rafitidine, and roxatidine), tritoqualine, in, cromoglicate,
nedocromil, and B2-adrenergic agonists.
Suitable anti-infectives include, but are not limited to, amebicides (e. g. nitazoxanide,
paromomycin, metronidazole, tinidazole, chloroquine, miltefosine, amphotericin b, and
iodoquinol), aminoglycosides (e. g. paromomycin, tobramycin, icin, in,
cin, and neomycin), anthelmintics (e. g. pyrantel, mebendazole, ctin,
praziquantel, abendazole, thiabendazole, oxamniquine), antifungals (e.g. azole antifungals (e. g.
itraconazole, fluconazole, posaconazole, ketoconazole, clotrimazole, miconazole, and
voriconazole), echinocandins (e.g. caspofungin, anidulafungin, and micafungin), griseofulvin,
terbinafine, flucytosine, and polyenes (e. g. nystatin, and amphotericin b), antimalarial agents
((3. g. pyrimethamine/sulfadoxine, anemether/lumefantrine, atovaquone/proquanil, quinine,
hydroxychloroquine, mefloquine, chloroquine, doxycycline, pyrimethamine, and halofantrine),
antituberculosis agents (e.g. aminosalicylates (e.g. aminosalicylic acid), isoniazid/rifampin,
2017/039692
isoniazid/pyrazinamide/rifampin, bedaquiline, isoniazid, ethambutol, in, rifabutin,
rifapentine, mycin, and cycloserine), antivirals (e.g. amantadine, rimantadine,
abacavir/lamivudine, emtricitabine/tenofovir, cobicistat/elvitegravir/emtricitabine/tenofovir,
efavirenz/emtricitabine/tenofovir, avacavir/lamivudine/zidovudine, lamivudine/zidovudine,
emtricitabine/tenofovir, emtricitabine/opinavir/ritonavir/tenofovir, interferon v/ribavirin,
peginterferon alfa-2b, maraviroc, raltegravir, dolutegravir, enfuvirtide, foscarnet, rsen,
mivir, zanamivir, nevirapine, efavirenz, etravirine, rilpivirine, delaviridine, pine,
entecavir, lamivudine, adefovir, sofosbuvir, didanosine, vir, avacivr, zidovudine,
stavudine, emtricitabine, xalcitabine, telbivudine, simeprevir, boceprevir, telaprevir,
lopinavir/ritonavir, fosamprenvir, dranuavir, ritonavir, tipranavir, atazanavir, nelfinavir,
amprenavir, indinavir, sawuinavir, rin, valcyclovir, acyclovir, famciclovir, ganciclovir,
and valganciclovir), carbapenems (e. g. doripenem, meropenem, ertapenem, and
cilastatin/imipenem), cephalosporins (e.g. cefadroxil, cephradine, lin, cephalexin,
cefepime, ceflaroline, loracarbef, cefotetan, cefuroxime, cefprozil, loracarbef, cefoxitin,
cefaclor, ceftibuten, ceftriaxone, cefotaxime, cefpodoxime, cefdinir, cefixime, cefditoren,
cefizoxime, and ceftazidime), glycopeptide antibiotics (e. g. vancomycin, ancin,
oritavancin, and telvancin), glycylcyclines (e. g. cline), leprostatics (e, g. clofazimine and
thalidomide), lincomycin and derivatives f (e.g. clindamycin and lincomycin ),
macrolides and derivatives thereof (6. g. telithromycin, fidaxomicin, mycin, azithromycin,
clarithromycin, dirithromycin, and ndomycin), linezolid, sulfamethoxazole/trimethoprim,
rifaximin, chloramphenicol, fosfomycin, metronidazole, aztreonam, acin, penicillins
(amoxicillin, ampicillin, bacampicillin, carbenicillin, piperacillin, ticarcillin,
amoxicillin/clavulanate, ampicillin/sulbactam, piperacillin/tazobactam, clavulanate/ticarcillin,
penicillin, procaine penicillin, oxaxillin, dicloxacillin, and nafcillin), quinolones (e. g.
lomefloxacin, norfloxacin, ofloxacin, qatifloxacin, moxifloxacin, ciprofloxacin, levofloxacin,
gemifloxacin, moxifloxacin, cinoxacin, nalidixic acid, enoxacin, grepafloxacin, gatifloxacin,
trovafloxacin, and sparfloxacin), sulfonamides (e. g. sulfamethoxazole/trimethoprim,
sulfasalazine, and sulfasoxazole), tetracyclines (e.g. doxycycline, ocycline,
minocycline, doxycycline/salicyclic acid, doxycycline/omega-3 polyunsaturated fatty acids,
and tetracycline), and urinary anti-infectives (e.g. nitrofurantoin, methenamine, fosfomycin,
cinoxacin, nalidixic acid, trimethoprim, and methylene blue).
Suitable chemotherapeutics include, but are not limited to, paclitaxel, brentuximab
vedotin, doxorubicin, 5—FU uracil), everolimus, pemetrexed, melphalan, pamidronate,
anastrozole, exemestane, bine, ofatumumab, bevacizumab, belinostat, tositumomab,
carmustine, cin, bosutinib, busulfan, zumab, irinotecan, vandetanib,
bicalutamide, lomustine, daunorubicin, clofarabine, cabozantinib, dactinomycin, ramucirumab,
cytarabine, n, cyclophosphamide, decitabine, dexamethasone, docetaxel, yurea,
decarbazine, leuprolide, icin, oxaliplatin, asparaginase, estramustine, cetuximab,
vismodegib, asparginase Erwinia chrysanthemi, amifostine, etoposide, flutamide, toremifene,
fulvestrant, letrozole, degarelix, pralatrexate, methotrexate, floxuridine, obinutuzumab,
gemcitabine, ib, imatinib mesylatem, carmustine, eribulin, trastuzumab, altretamine,
topotecan, ponatinib, idarubicin, ifosfamide, ibrutinib, axitinib, interferon alfa-2a, gefitinib,
romidepsin, ixabepilone, ruxolitinib, cabazitaxel, ado-trastuzumab emtansine, carfilzomib,
chlorambucil, mostim, cladribine, mitotane, vincristine, procarbazine, megestrol,
inib, mesna, strontium-89 de, mechlorethamine, mitomycin, busulfan,
gemtuzumab ozogamicin, Vinorelbine, stim, pegfilgrastim, sorafenib, nilutamide,
tatin, tamoxifen, mitoxantrone, pegaspargase, denileukin diftitox, alitretinoin,
carboplatin, pertuzumab, cisplatin, pomalidomide, prednisone, aldesleukin, mercaptopurine,
zoledronic acid, lenalidomide, rituximab, octretide, dasatinib, regorafenib, histrelin, sunitinib,
imab, omacetaxine, thioguanine (tioguanine), dabrafenib, erlotinib, bexarotene,
temozolomide, thiotepa, omide, BCG, temsirolimus, bendamustine hloride,
triptorelin, aresnic trioxide, lapatinib, valrubicin, panitumumab, Vinblastine, bortezomib,
tretinoin, azacitidine, pazopanib, teniposide, orin, crizotinib, capecitabine, enzalutamide,
ipilimumab, lin, vorinostat, idelalisib, ceritinib, abiraterone, epothilone, tafluposide,
azathioprine, doxifluridine, vindesine, and all-trans retinoic acid
Efiective Amounts of the CDKL5 Fusion n and Auxiliary Agents
The pharmaceutical formulations can contain a therapeutically effective amount of a
CDKL5 fusion n, and optionally, a therapeutically effective amount of an auxiliary agent.
The precise dosage will vary with the age, size, sex and condition of the subject, the nature and
severity of the disorder to be treated, and the like; thus, a precise effective amount cannot be
specified in advance and will be determined by the caregiver. However, the therapeutically
effective amount of the CDKL5 fusion protein can generally range from about 1 ug/kg to about
mg/kg. In further embodiments, the therapeutically effective amount of the CDKL5 fusion
2017/039692
n can range from 1 ng/g bodyweight to about 0.1 mg/g bodyweight. The therapeutically
effective amount of the CDKL5 fusion protein can range from about 1 pg to about 10 g. In
some embodiments, the eutically effective amount of the CDKL5 fusion protein or
ceutical composition containing the CDKL5 fusion protein can range from about 10 nL
to about 10 mL. In other embodiments the therapeutically effective amount of the CDKL5
fusion protein or pharmaceutical composition from about 10 nL to about 1 uL.
In some embodiments, the therapeutically effective amount can also range from about
to about 50 ng per injection, such as for an intraventricular injection. In other embodiments,
the therapeutically effective amount can be about 10 microliters per injection, such as for
intraventricular injection. In further embodiments, the therapeutically effective amount can be
about 5ng/uL, such as for intraventricular injection. In yet further embodiments, the
therapeutically ive amount can be about 1.9 ug/kg of bodyweight for intraventricular
injection. In other embodiments, the therapeutically effective amount can be from about 1 to 3
ug/kg of bodyweight for intraventricular injection.
In other embodiments, the therapeutically effective amount can be from about 1 to
about 2 micrograms per ion, such as for a systemically stered injection. In some
embodiments, the therapeutically effective amount can be about 5 ng/uL, such as for systemic
injections. For some embodiments, the therapeutically effective amount can be about 1 to
about 1.5 pg per 5 g of ight.
In one or more ments, the systemic administration is intravenous administration.
The intravenous ation can be administered by direct intravenous injection (i.V. bolus) or
can be administered by infusion by addition to an appropriate infusion solution such as 0.9%
sodium chloride injection or other compatible infusion solution. The most commonly used IV
infusion system consists of a bag filled with IV fluids, a drip chamber, roller clamp (variable
resistance controller) for control of the flow and tubing connected to an IV catheter. The
elevated IV bag in this system serves as a pressure source, the roller clamp as a user-controlled
resistor, and the IV catheter as a fixed resistor.
Most commonly, the rate of IV fluids flow is determined by the rate at which drops of
liquid are observed falling through a drip chamber. y infusion of the parenteral solution
is accomplished by suspending the solution container several feet above the patient and
connecting the solution container to the venopuncture site via a disposable enous
administration set which includes a drip chamber and flexible delivery tube.
In ments where there is an auxiliary active agent contained in the
pharmaceutical formulation in addition to the CDKLS fusion n, the eutically
effective amount of the auxiliary active agent will vary depending on the auxiliary active
agent. In some embodiments, the effective amount of the auxiliary active agent ranges from
0.001 micrograms to about 1 milligram. In other embodiments, the effective amount of the
auxiliary active agent ranges from about 0.01 IU to about 1000 IU. In further embodiments, the
effective amount of the auxiliary active agent ranges from 0.001 mL to about lmL. In yet other
embodiments, the effective amount of the auxiliary active agent ranges from about 1% w/w to
about 50% w/w of the total pharmaceutical formulation. In additional embodiments, the
effective amount of the auxiliary active agent ranges from about 1% v/v to about 50% v/v of
the total pharmaceutical formulation. In still other embodiments, the effective amount of the
auxiliary active agent ranges from about 1% w/v to about 50% w/v of the total pharmaceutical
formulation.
Dosage Farms
In some ments, the pharmaceutical formulations described herein may be in a
dosage form. The dosage forms can be adapted for stration by any appropriate route.
Appropriate routes include, but are not limited to, oral (including buccal or sublingual), rectal,
epidural, intracranial, intraocular, inhaled, intranasal, topical (including buccal, sublingual, or
transdermal), vaginal, intraurethral, parenteral, intracranial, aneous, intramuscular,
intravenous, intraperitoneal, intradermal, intraosseous, intracardiac, intraarticular,
intracavemous, intrathecal, intravireal, intracerebral, and intracerebroventricular and
intradermal. Such formulations may be prepared by any method known in the art.
Dosage forms adapted for oral administration can be discrete dosage units such as
capsules, pellets or tablets, powders or granules, solutions, or suspensions in aqueous or non-
aqueous s; edible foams or whips, or in oil-in-water liquid emulsions or water-in-oil
liquid emulsions. In some embodiments, the ceutical formulations adapted for oral
stration also include one or more agents which flavor, preserve, color, or help disperse
the pharmaceutical formulation. Dosage forms prepared for oral administration can also be in
the form of a liquid solution that can be delivered as foam, spray, or liquid solution. In some
ments, the oral dosage form can n about 1 mg to 1000 g of a pharmaceutical
formulation containing a therapeutically effective amount or an appropriate fraction thereof of
the CDKL5 fusion protein or composition containing the CDKL5 fusion protein The oral
dosage form can be administered to a subject in need thereof.
Where appropriate, the dosage forms bed herein can be microencapsulated. The
dosage form can also be prepared to prolong or sustain the release of any ingredient. In some
ments, the CDKL5 fusion protein is the ingredient whose e is d. In other
embodiments, the release of an optionally included auxiliary ingredient is delayed. Suitable
methods for delaying the release of an ingredient include, but are not limited to, coating or
embedding the ingredients in material in polymers, wax, gels, and the like. Delayed release
dosage formulations can be prepared as described in standard references such as
“Pharmaceutical dosage form tablets,” eds. Liberman et. al. (New York, Marcel Dekker, Inc.,
1989), “Remington — The science and practice of pharmacy”, 20th ed., Lippincott Williams &
Wilkins, Baltimore, MD, 2000, and “Pharmaceutical dosage forms and drug delivery systems”,
6th Edition, Ansel et al., (Media, PA: Williams and Wilkins, 1995). These references provide
information on excipients, materials, equipment, and processes for preparing s and
capsules and delayed release dosage forms of tablets and pellets, capsules, and granules. The
delayed release can be anywhere from about an hour to about 3 months or more.
Examples of suitable coating materials e, but are not limited to, cellulose
polymers such as cellulose acetate phthalate, hydroxypropyl cellulose, ypropyl
methylcellulose, hydroxypropyl methylcellulose phthalate, and hydroxypropyl methylcellulose
acetate succinate; polyvinyl acetate phthalate, c acid polymers and copolymers, and
methacrylic resins that are commercially available under the trade name EUDRAGIT® (Roth
Pharma, stadt, Germany), zein, c, and polysaccharides.
Coatings may be formed with a different ratio of water e polymer, water
ble polymers, andlor pH dependent polymers, with or without water insoluble/water
soluble non polymeric excipient, to produce the desired release profile. The coating is either
performed on the dosage form x or simple) which includes, but is not limited to, s
(compressed with or without coated beads), capsules (with or without coated beads), beads,
le compositions, “ingredient as is” formulated as, but not limited to, suspension form or
as a sprinkle dosage form.
Dosage forms adapted for topical stration can be formulated as ointments,
creams, suspensions, lotions, s, solutions, pastes, gels, sprays, aerosols, or oils. In some
embodiments for treatments of the eye or other external tissues, for example the mouth or the
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skin, the pharmaceutical formulations are applied as a topical ointment or cream. When
formulated in an ointment, the CDKL5 fusion protein, auxiliary active ingredient, and/or
pharmaceutically acceptable salt thereof can be formulated with a paraffinic or water-miscible
ointment base. In other embodiments, the active ingredient can be formulated in a cream with
an oil-in-water cream base or a water-in-oil base. Dosage forms d for topical
administration in the mouth include es, les, and mouth washes.
Dosage forms adapted for nasal or inhalation administration include aerosols, solutions,
suspension drops, gels, or dry powders. In some ments, the CDKL5 fusion protein, the
composition containing a CDKL5 fusion n, auxiliary active ingredient, and/or
pharmaceutically acceptable salt thereof in a dosage form adapted for inhalation is in a
particle-size-reduced form that is obtained or obtainable by micronization. In some
ments, the particle size of the size reduced (e.g. micronized) compound or salt or
solvate thereof, is defined by a D50 value of about 0.5 to about 10 s as measured by an
appropriate method known in the art. Dosage forms adapted for administration by inhalation
also include particle dusts or mists. Suitable dosage forms n the r or excipient is a
liquid for administration as a nasal spray or drops include aqueous or oil solutions/suspensions
of an active ingredient, which may be generated by various types of metered dose pressurized
aerosols, nebulizers, or insufflators.
In some embodiments, the dosage forms are aerosol formulations suitable for
administration by inhalation. In some of these ments, the aerosol formulation contains a
solution or fine sion of the CDKL5 fusion protein, the composition containing a CDKL5
fusion protein, and/or pharmaceutically acceptable salt thereof, and a pharmaceutically
acceptable aqueous or non-aqueous solvent. Aerosol formulations can be presented in single or
multi-dose quantities in sterile form in a sealed container. For some of these embodiments, the
sealed container is a single dose or multi-dose nasal or an aerosol dispenser fitted with a
metering valve (e.g. metered dose inhaler), which is intended for al once the contents of
the container have been exhausted.
Where the aerosol dosage form is contained in an aerosol dispenser, the dispenser
contains a suitable propellant under pressure, such as compressed air, carbon dioxide, or an
organic propellant, including but not limited to a hydrofluorocarbon. The l formulation
dosage forms in other embodiments are contained in a pump-atomizer. The pressurized aerosol
formulation can also contain a solution or a suspension of a CDKL5 fusion protein,
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composition containing a CDKL5 fusion protein, or a pharmaceutical formulation thereof. In
further embodiments, the aerosol formulation also contains co-solvents andlor modifiers
incorporated to improve, for example, the stability and/or taste and/or fine le mass
characteristics (amount and/or profile) of the formulation. stration of the aerosol
formulation can be once daily or l times daily, for example 2, 3, 4, or 8 times daily, in
which 1, 2, or 3 doses are delivered each time.
For some dosage forms suitable and/or d for inhaled administration, the
pharmaceutical ation is a dry powder inhalable formulation. In addition to the CDKL5
fusion protein, the composition containing a CDKL5 fusion protein, an auxiliary active
ingredient, and/or pharmaceutically acceptable salt thereof, such a dosage form can contain a
powder base such as lactose, glucose, trehalose, manitol, and/or . In some of these
embodiments, the CDKL5 fusion protein, the composition containing a CDKL5 fusion protein,
auxiliary active ingredient, and/or pharmaceutically acceptable salt thereof is in a particle—size
reduced form. In further embodiments, a performance modifier, such as L-leucine or another
amino acid, cellobiose octaacetate, and/or metals salts of c acid, such as magnesium or
calcium stearate.
In some embodiments, the aerosol formulations are arranged so that each metered dose
of aerosol contains a predetermined amount of an active ingredient, such as the one or more of
the CDKL5 fusion proteins or compositions ning the CDKL5 fusion n described
herein.
Dosage forms d for vaginal administration can be presented as pessaries,
tampons, creams, gels, pastes, foams, or spray formulations. Dosage forms adapted for rectal
administration include suppositories or enemas.
Dosage forms adapted for parenteral administration and/or adapted for any type of
injection (e. g. intravenous, intraperitoneal, aneous, intramuscular, intradermal,
intraosseous, epidural, intracardiac, intraarticular, intracavernous, intrathecal, intravireal,
intracerebral, and intracerebroventricular) can include aqueous and/or non-aqueous sterile
injection solutions, which can contain anti—oxidants, buffers, bacteriostats, solutes that render
the composition isotonic with the blood of the t, and aqueous and non-aqueous sterile
suspensions, which can include suspending agents and thickening agents. The dosage forms
adapted for parenteral administration can be presented in a single-unit dose or multi-unit dose
ners, including but not limited to sealed ampoules or vials. The doses can be 1yophilized
and resuspended in a sterile carrier to reconstitute the dose prior to administration.
Extemporaneous injection solutions and suspensions can be prepared in some embodiments,
from sterile powders, es, and tablets.
Dosage forms adapted for ocular administration can include aqueous and/or non-
aqueous sterile solutions that can optionally be adapted for ion, and which can optionally
contain anti-oxidants, buffers, bacteriostats, solutes that render the composition isotonic with
the eye or fluid contained n or around the eye of the subject, and aqueous and non-
aqueous sterile sions, which can include suspending agents and thickening .
For some embodiments, the dosage form contains a predetermined amount of the
CDKL5 fusion protein or composition containing a CDKL5 fusion protein per unit dose. In an
embodiment, the predetermined amount of the CDKL5 fusion protein or composition
ning a CDKL5 fusion protein is a eutically ive amount of the CDKL5 fusion
protein or composition containing a CDKL5 fusion protein to treat or prevent a CDKL5
deficiency, Rett me, and/or a symptom thereof. In other embodiments, the
predetermined amount of the CDKL5 fusion protein or composition containing a CDKL5
fusion protein can be an appropriate fraction of the eutically effective amount of the
active ingredient. Such unit doses may, therefore, be administered once or more than once a
day. Such pharmaceutical formulations may be ed by any of the methods well known in
the art.
Treatment of Neurological Disorders with TATIc-CDKLS Compositions and
Formulations
The CDKL5 fusion protein and pharmaceutical formulations thereof described herein
can be used for the treatment and/or tion of a disease, er, syndrome, or a symptom
thereof in a subject. In some embodiments, the CDKL5 fusion protein and pharmaceutical
formulations thereof can be used to treat and/or prevent a CDKL5 deficiency, Rett syndrome,
variants of Rett syndrome, and/or a symptom thereof. In some embodiments, the subject has a
CDKL5 deficiency, Rett syndrome, variants of Rett syndrome, and/or a m thereof. In
some embodiments, the CDKL5 fusion protein and pharmaceutical formulations thereof can be
used to increase neural activity in the visual cortex in a patient having a CDKL5 deficiency,
Rett syndrome, variants of Rett syndrome, and/or a symptom thereof. In some embodiments,
the CDKL5 fusion protein and pharmaceutical formulations thereof can be used to increase
neurite growth, tion, dendritic spine number, branch number, or branch density in a
brain of a patient having a CDKL5 deficiency, Rett syndrome, variants of Rett syndrome,
and/or a symptom thereof. In some embodiments, the CDKL5 fusion protein and
pharmaceutical formulations thereof can be used to reduce neuronal apoptosis in the brain of a
patient having a CDKL5 ency, Rett syndrome, variants of Rett syndrome, and/or a
symptom thereof. In some embodiments, the CDKL5 fusion protein and pharmaceutical
formulations thereof can be used to improve motor function of a patient having a CDKL5
deficiency, Rett syndrome, variants of Rett syndrome, and/or a symptom thereof.
An amount of the CDKL5 fusion protein, itions, and pharmaceutical
formulations f described herein can be administered to a subject in need thereof one or
more times per day, week, month, or year. In some ments, the amount stered can
be the therapeutically effective amount of the CDKL5 fusion protein, compositions, and
pharmaceutical formulations thereof. For example, the CDKL5 fusion n, compositions,
and pharmaceutical formulations thereof can be administered in a daily dose. This amount may
be given in a single dose per day. In other embodiments, the daily dose may be stered
over multiple doses per day, in which each containing a fraction of the total daily dose to be
administered (sub-doses). In some embodiments, the amount of doses delivered per day is 2, 3,
4, 5, or 6. In further embodiments, the compounds, formulations, or salts thereof are
administered one or more times per week, such as l, 2, 3, 4, 5, or 6 times per week. In other
embodiments, the CDKL5 fusion protein, itions, and pharmaceutical formulations
thereof can be administered one or more times per month, such as l to 5 times per month. In
still further embodiments, the CDKL5 fusion protein, compositions, and pharmaceutical
formulations thereof can be administered one or more times per year, such as l to 11 times per
year.
The CDKL5 fusion proteins, compositions, and pharmaceutical formulations f
can be co—administered with a secondary agent by any convenient route. The secondary agent
is a separate compound and/or formulation from the CDKL5 fusion ns, compositions,
and pharmaceutical formulations thereof. The secondary agent can be administered
simultaneously with the CDKL5 fusion proteins, compositions, and pharmaceutical
formulations thereof. The secondary agent can be administered tially with the CDKL5
fusion proteins, compositions, and pharmaceutical formulations thereof. The secondary agent
can have an additive or synergistic effect to the CDKL5 fusion proteins, compositions, and
pharmaceutical formulations thereof. Suitable secondary agents include, but are not limited to,
DNA, RNA, amino acids, peptides, polypeptides, antibodies, aptamers, ribozymes, guide
sequences for ribozymes that t translation or ription of ial tumor proteins and
genes, es, immunomodulators, antipyretics, anxiolytics, antipsychotics, analgesics,
antispasmodics, anti-inflammatories, anti-histamines, nfectives, and chemotherapeutics.
In some embodiments the secondary agent is DCA.
Suitable hormones include, but are not d to, amino—acid derived hormones (e. g.
melatonin and thyroxine), small peptide hormones and protein hormones (e. g. thyrotropin-
releasing hormone, vasopressin, n, growth hormone, luteinizing hormone, follicle-
stimulating hormone, and thyroid-stimulating hormone), eiconsanoids (e. g. arachidonic acid,
lipoxins, and prostaglandins), and steroid hormones (e.g. estradiol, testosterone, tetrahydro
testosteron cortisol).
Suitable immunomodulators include, but are not limited to, prednisone, azathioprine, 6-
MP, cyclosporine, tacrolimus, methotrexate, interleukins (e. g. IL—2, IL-7, and IL-12), cytokines
(e. g. interferons (e. g. IFN-(x, IFN-B, IFN-s, IFN-K, IFN-(o, and IFN—y), granulocyte colony-
ating factor, and imiquimod), chemokines (e. g. CCL3, CCL26 and , cytosine
phosphate-guanosine, oligodeoxynucleotides, glucans, antibodies, and aptamers).
Suitable antipyretics include, but are not limited to, non-steroidal anti-inflammants (e. g.
ibuprofen, naproxen, ketoprofen, and nimesulide), n and related salicylates (e. g. choline
salicylate, magnesium salicylae, and sodium ylate), paracetamol/acetaminophen,
metamizole, nabumetone, one, and quinine.
Suitable anxiolytics include, but are not limited to, benzodiazepines (e. g. alprazolam,
bromazepam, chlordiazepoxide, clonazepam, clorazepate, diazepam, flurazepam, lorazepam,
oxazepam, temazepam, lam, and tofisopam), serotenergic antidepressants (e. g. selective
nin reuptake inhibitors, tricyclic antidepresents, and ine oxidase inhibitors),
r, afobazole, selank, bromantane, emoxypine, azapirones, urates, hydroxyzine,
pregabalin, l, and beta blockers.
Suitable antipsychotics include, but are not limited to, benperidol, bromoperidol,
droperidol, haloperidol, moperone, pipaperone, timiperone, fluspirilene, penfluridol, pimozide,
acepromazine, chlorpromazine, cyamemazine, dizyrazine, fluphenazine, levomepromazine,
mesoridazine, ne, pericyazine, perphenazine, pipotiazine, prochlorperazine, promazine,
promethazine, prothipendyl, thioproperazine, thioridazine, trifluoperazine, triflupromazine,
chlorprothixene, clopenthixol, flupentixol, tiotixene, zuclopenthixol, clotiapine, loxapine,
pendyl, carpipramine, clocapramine, one, amine, sulpiride, veralipride,
amisulpride, ine, aripiprazole, ine, clozapine, blonanserin, iloperidone,
lurasidone, melperone, nemonapride, olanzaprine, ridone, perospirone, quetiapine,
remoxipride, risperidone, sertindole, trimipramine, ziprasidone, zotepine, alstonie, befeprunox,
bitopertin, brexpiprazole, cannabidiol, cariprazine, pimavanserin, pomaglumetad methionil,
vabicaserin, xanomeline, and zicronapine.
Suitable analgesics include, but are not limited to, paracetamol/acetaminophen, non-
steroidal anti-inflammants (e. g. ibuprofen, naproxen, ketoprofen, and nimesulide), COX-2
inhibitors (e.g. rofecoxib, celecoxib, and etoricoxib), opioids (e.g. morphine, codeine,
oxycodone, hydrocodone, dihydromorphine, pethidine, buprenorphine), tramadol,
norepinephrine, flupiretine, nefopam, orphenadrine, pregabalin, gabapentin, cyclobenzaprine,
scopolamine, methadone, ketobemidone, piritramide, and aspirin and d salicylates (e. g.
choline salicylate, magnesium salicylate, and sodium salicylate).
Suitable antispasmodics include, but are not limited to, mebeverine, papverine,
cyclobenzaprine, carisoprodol, orphenadrine, tizanidine, metaxalone, methodcarbamol,
oxazone, baclofen, dantrolene, baclofen, tizanidine, and dantrolene.
Suitable nflammatories e, but are not limited to, prednisone, non-steroidal
anti-inflammants (e. g. ibuprofen, naproxen, ketoprofen, and nimesulide), COX-2 inhibitors
(e. g. rofecoxib, celecoxib, and etoricoxib), and immune selective anti-inflammatory derivatives
(e. g. submandibular gland peptide-T and its tives).
Suitable anti-histamines include, but are not limited to, Hl-receptor antagonists (e. g.
acrivastine, azelastine, bilastine, brompheniramine, buclizine, bromodiphenhydramine,
carbinoxamine, cetirizine, chlorpromazine, cyclizine, chlorpheniramine, clemastine,
cyproheptadine, desloratadine, dexbromapheniramine, dexchlorpheniramine, dimenhydrinate,
dimetindene, diphenhydramine, doxylamine, ebasine, ine, fexofenadine, hydroxyzine,
levocetirzine, dine, meclozine, mirtazapine, olopatadine, orphenadrine, phenindamine,
pheniramine, phenyltoloxamine, promethazine, pyrilamine, quetiapine, rupatadine,
ennamine, and triprolidine), Hz-receptor antagonists (e. g. cimetidine, famotidine,
lafutidine, nizatidine, dine, and dine), tn'toqualine, catechin, licate,
nedocromil, and B2-adrenergic agonists.
Suitable anti-infectives include, but are not limited to, amebicides (e. g. nitazoxanide,
paromomycin, metronidazole, tinidazole, chloroquine, osine, amphotericin b, and
iodoquinol), lycosides (e. g. paromomycin, tobramycin, gentamicin, amikacin,
kanamycin, and neomycin), anthelmintics (e. g. pyrantel, mebendazole, ivermectin,
praziquantel, abendazole, thiabendazole, oxamniquine), antifungals (e.g. azole antifungals (e. g.
itraconazole, fluconazole, posaconazole, nazole, clotrimazole, miconazole, and
voriconazole), echinocandins (e. g. caspofungin, anidulafungin, and micafungin), griseofulvin,
terbinafine, flucytosine, and polyenes (e. g. nystatin, and amphotericin b), antimalarial agents
(6. g. pyrimethamine/sulfadoxine, artemether/lumefantrine, atovaquone/proquanil, quinine,
hydroxychloroquine, mefloquine, chloroquine, doxycycline, pyrimetharnine, and halofantrine),
antituberculosis agents (e.g. aminosalicylates (e.g. aminosalicylic acid), isoniazid/rifampin,
isoniazid/pyrazinamide/rifampin, bedaquiline, isoniazid, ethambutol, rifampin, rifabutin,
rifapentine, capreomycin, and cycloserine), antivirals (e.g. amantadine, rimantadine,
abacavir/lamivudine, emtricitabine/tenofovir, cobicistat/elvitegravir/emtricitabine/tenofovir,
efavirenz/emtricitabine/tenofovir, avacavir/lamivudine/Zidovudine, lamivudine/zidovudine,
emtricitabine/tenofovir, emtricitabine/opinavir/ritonavir/tenofovir, interferon alfa-2v/ribavirin,
peginterferon alfa-2b, maraviroc, raltegravir, dolutegravir, enfuvirtide, net, fomivirsen,
oseltamivir, zanamivir, nevirapine, efavirenz, rine, rilpivirine, delaviridine, nevirapine,
entecavir, lamivudine, adefovir, sofosbuvir, didanosine, tenofovir, avacivr, zidovudine,
stavudine, itabine, xalcitabine, telbivudine, simeprevir, boceprevir, telaprevir,
lopinavir/ritonavir, fosamprenvir, dranuavir, vir, tipranavir, atazanavir, nelfinavir,
amprenavir, indinavir, sawuinavir, ribavirin, valcyclovir, acyclovir, famciclovir, ganciclovir,
and valganciclovir), carbapenems (e. g. doripenem, meropenem, nem, and
cilastatin/imipenem), cephalosporins (e. g. cefadroxil, cephradine, lin, cephalexin,
cefepime, ceflaroline, loracarbef, cefotetan, xime, cefprozil, loracarbef, cefoxitin,
cefaclor, uten, axone, cefotaxime, cefpodoxime, ir, cefixime, cefditoren,
cefizoxime, and ceftazidime), glycopeptide antibiotics (e. g. vancomycin, ancin,
oritavancin, and telvancin), glycylcyclines (e.g. tigecycline), leprostatics (e.g. clofazimine and
thalidomide), lincomycin and derivatives thereof (e.g. clindamycin and lincomycin ),
ides and derivatives thereof (6. g. telithromycin, fidaxomicin, erthromycin, azithromycin,
clarithromycin, dirithromycin, and troleandomycin), linezolid, sulfamethoxazole/trimethoprim,
min, chloramphenicol, fosfomycin, metronidazole, aztreonam, bacitracin, penicillins
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(amoxicillin, ampicillin, icillin, carbenicillin, piperacillin, ticarcillin,
illin/clavulanate, ampicillin/sulbactam, piperacillin/tazobactam, clavulanate/ticarcillin,
penicillin, procaine penicillin, oxaxillin, acillin, and nafcillin), quinolones (e. g.
lomefloxacin, norfloxacin, ofloxacin, qatifloxacin, moxifloxacin, ciprofloxacin, levofloxacin,
gemifloxacin, moxifloxacin, cinoxacin, xic acid, in, grepafloxacin, gatifloxacin,
trovafloxacin, and sparfloxacin), sulfonamides (e.g. sulfamethoxazole/trimethoprim,
sulfasalazine, and sulfasoxazole), tetracyclines (e.g. cline, demeclocycline,
minocycline, doxycycline/salicyclic acid, doxycycline/omega-3 polyunsaturated fatty acids,
and tetracycline), and urinary anti-infectives (e.g. nitrofurantoin, amine, fosfomycin,
cinoxacin, nalidixic acid, trimethoprim, and methylene blue).
Suitable chemotherapeutics include, but are not limited to, paclitaxel, brentuximab
vedotin, doxorubicin, 5—FU (fluorouracil), everolimus, pemetrexed, melphalan, pamidronate,
anastrozole, exemestane, nelarabine, ofatumumab, bevacizumab, belinostat, tositumomab,
carmustine, bleomycin, bosutinib, busulfan, alemtuzumab, irinotecan, vandetanib,
bicalutamide, lomustine, daunorubicin, clofarabine, cabozantinib, dactinomycin, rumab,
cytarabine, cytoxan, cyclophosphamide, bine, dexamethasone, docetaxel, hydroxyurea,
decarbazine, leuprolide, icin, oxaliplatin, asparaginase, estramustine, cetuximab,
Vismodegib, asparginase a chrysanthemi, amifostine, etoposide, flutamide, toremifene,
fulvestrant, letrozole, degarelix, pralatrexate, methotrexate, floxuridine, obinutuzumab,
gemcitabine, afatinib, imatinib mesylatem, carmustine, eribulin, trastuzumab, altretamine,
can, ponatinib, idarubicin, ifosfamide, nib, axitinib, interferon alfa—2a, gefitinib,
romidepsin, ixabepilone, tinib, cabazitaxel, ado-trastuzumab emtansine, carfilzomib,
chlorambucil, sargramostim, cladribine, ne, Vincristine, procarbazine, megestrol,
trametinib, mesna, strontium—89 chloride, mechlorethamine, mitomycin, busulfan,
gemtuzumab ozogamicin, Vinorelbine, filgrastim, pegfilgrastim, sorafenib, nilutamide,
pentostatin, tamoxifen, mitoxantrone, pegaspargase, denileukin diftitox, alitretinoin,
carboplatin, pertuzumab, cisplatin, pomalidomide, prednisone, aldesleukin, mercaptopurine,
zoledronic acid, lenalidomide, rituximab, octretide, dasatinib, regorafenib, histrelin, sunitinib,
siltuximab, omacetaxine, thioguanine (tioguanine), dabrafenib, nib, bexarotene,
temozolomide, thiotepa, thalidomide, BCG, temsirolimus, bendamustine hydrochloride,
triptorelin, aresnic trioxide, nib, valrubicin, panitumumab, Vinblastine, bortezomib,
tretinoin, azacitidine, pazopanib, teniposide, leucovorin, crizotinib, tabine, enzalutamide,
ipilimumab, goserelin, vorinostat, idelalisib, ceritinib, abiraterone, epothilone, tafluposide,
azathioprine, doxifluridine, vindesine, and all-trans retinoic acid.
In embodiments where the CDKL5 fusion proteins, itions, and pharmaceutical
ations thereof are simultaneously co-administered with a secondary agent, the CDKL5
fusion proteins, compositions, and pharmaceutical formulations thereof can be administered to
the subject at substantially the same time as the secondary agent. As used in this context
“substantially the same time” refers to administration of the CDKL5 fusion proteins,
compositions, and pharmaceutical formulations thereof and a secondary agent where the period
of time between administration of the CDKL5 fusion protein, composition, or ceutical
formulation thereof and the secondary agent is between 0 and 10 minutes.
In embodiments where the CDKL5 fusion protein, composition, or pharmaceutical
formulations thereof is tially co—administered with a ary agent, the CDKL5
fusion protein, composition, or ceutical formulations thereof can be administered first,
and followed by administration of the ary agent after a period of time. In other
embodiments where the CDKL5 fusion protein, composition, or pharmaceutical formulations
thereof is sequentially co-administered with a secondary agent, the secondary agent can be
administered first, and followed by administration of the CDKL5 fusion protein, composition,
or pharmaceutical formulations thereof after a period of time. In any embodiment, the period of
time between stration of the CDKL5 fusion protein, composition, or pharmaceutical
formulations f and the secondary agent can range from 10 minutes to about 96 hours. In
some embodiments, the period of time can be about 10 minutes, about 30 minutes, about 1
hour, about 2 hours, about 4 hours, about 6 hours, about 8 hours, about 10 hours, or about 12
hours. The sequential administration can be repeated as necessary over the course of the period
of treatment.
The amount of the CDKL5 fusion proteins, compositions, pharmaceutical formulations
thereof that can be stered are bed elsewhere herein. The amount of the secondary
agent will vary depending on the secondary agent. The amount of the secondary agent can be a
therapeutically effective amount. In some embodiments, the effective amount of the secondary
agent ranges from 0.001 micrograms to about 1 milligram. In other embodiments, the amount
of the secondary agent ranges from about 0.01 IU to about 1000 IU. In r embodiments,
the amount of the secondary agent ranges from 0.001 mL to about 1mL. In yet other
ments, the amount of the secondary agent ranges from about 1% w/w to about 50%
w/w of the total pharmaceutical formulation. In additional embodiments, the amount of the
ary agent ranges from about 1% v/v to about 50% v/v of the total pharmaceutical
formulation. In still other embodiments, the amount of the secondary agent ranges from about
1% w/v to about 50% w/v of the total ary agent composition or pharmaceutical
formulation.
In some embodiments, the composition or formulation containing the CDKL5 fusion
protein is administered to a patient via and injection. Suitable methods of injection e,
but are not limited to, intravenous, intraperitoneal, subcutaneous, intramuscular, intradermal,
intraosseous, epidural, intracardiac, intraarticular, intracavernous, intrathecal, ireal,
intracerebral, and intracerebroventricular injection Other suitable methods of administration of
the composition or formulation containing the CDKL5 fusion protein include, but are not
d to, topical, transdermal, nasal, or oral delivery. In some ments, the dosage of the
CDKL5 fusion protein ranges from about 0.01 ug/g ight to about 10 mg/g bodyweight.
In other embodiments, the CDKL5 fusion n can be delivered to a patient in need
of treatment Via cell therapy. With this in mind, attention is directed to Fig. 3, which shows
one embodiment of method of delivering a CDKL5 fusion protein via an autologous cell. The
method begins by culturing cells in vitro (8000). Preferably, the cells are autologous cells. In
one embodiment, the autologous cells are neurons or neuronal precursor cells, such as neural
stem cells. In some embodiments, the autologous cells are neurons that are derived from
induced pluripotent stem cells. In other embodiments, the autologous cells are neurons that are
derived from umbilical cord blood stem cells.
Next, the cultured cells are transduced With a purified CDKL5 fusion protein (8010).
In other embodiments, the cultured cells are transduced by exposing the culture cells to media
containing a CDKL5 fusion protein as previously described. In further embodiments, the
ed cells are transfected with a suitable vector containing a CDKL5 fusion protein cDNA.
The cells are then cultured for a suitable amount of time to allow for expression of the CDKL5
fusion protein . In some embodiments, the cells are cultured for about 6 h to about 96 h.
After the cells are cultured, one or more transduced cells are administered to a patient.
In one ment, transduced gous s are delivered to the brain using
surgical techniques. In some embodiments, one or more transduced cells are administered to a
patient via injection. In some embodiments, one or more transduced cells are included in a
formulation. In one embodiment, the formulation containing one or more transduced cells also
WO 05617
includes a pharmaceutically acceptable r and/or an active agent. In some embodiments
the formulation containing the one or more transduced cells is administered to a patient via
injection or using a surgical technique.
Kits containing the CDKL5 Fusion Protein and Formulations f
The CDKL5 fusion protein, compositions containing the CDKL5 fusion protein, and
pharmaceutical formulations thereof described herein can be presented as a ation kit.
As used herein, the terms “combination kit” or “kit of parts” refers to the CDKL5 fusion
protein, compositions containing the CDKL5 fusion protein, and pharmaceutical formulations
f described herein and additional components that are used to package, sell, market,
deliver, and/or administer the combination of elements or a single element, such as the active
ient, contained therein. Such additional components include but are not limited to,
packaging, syringes, blister packages, bottles, and the like. When one or more of the
components (e.g. active agents) contained in the kit are administered simultaneously, the
combination kit can contain the active agents in a single pharmaceutical ation (e.g. a
tablet) or in separate pharmaceutical formulations.
The combination kit can contain each agent, compound, pharmaceutical formulation or
component thereof, in separate compositions or pharmaceutical formulations. The separate
compositions or pharmaceutical formulations can be ned in a single package or in
separate packages within the kit. Also provided in some embodiments, are buffers, diluents,
lization reagents, cell culture media and other reagents. These additional ents can
be contained in a single package or in separate packages Within the kit.
In some ments, the combination kit also includes instructions printed on or
otherwise ned in a tangible medium of expression. The instructions can provide
information regarding the content of the CDKL5 fusion protein, itions containing the
CDKL5 fusion n, and pharmaceutical formulations f and/or other auxiliary and/or
secondary agent contained therein, safety information regarding the content of the CDKL5
fusion protein, compositions containing the CDKL5 fusion protein, and pharmaceutical
formulations thereof and/or other auxiliary and/or secondary agent contained therein,
information regarding the dosages, indications for use, andfor recommended treatment
regimen(s) for the CDKL5 fusion protein, compositions containing the CDKL5 fusion protein,
and ceutical formulations thereof andi’or other auxiliary and/or secondary agent
contained therein. In some ments, the instructions can e directions for
administering the CDKLS fusion protein, compositions containing the CDKLS fusion n,
and pharmaceutical formulations thereof and/or other auxiliary and/or secondary agent to a
t having a CDKLS deficiency, Rett syndrome, and/or a symptom thereof.
Without further elaboration, it is believed that one skilled in the art can, based on the
description herein, utilize the present disclosure to its fullest . It is emphasized that the
embodiments of the present disclosure, particularly any “preferred” embodiments, are merely
possible examples of the implementations, merely set forth for a clear understanding of the
principles of the disclosure. Many variations and modifications may be made to the disclosed
embodiment(s) of the sure without departing substantially from the spirit and principles
of the disclosure. All such modifications and ions are within the scope of this disclosure.
All publications and patents cited in this specification are herein orated by
reference as if each individual ation or patent were specifically and individually
indicated to be incorporated by reference and are incorporated herein by reference to disclose
and describe the methods and/or materials in connection with which the publications are cited.
The citation of any publication is for its disclosure prior to the filing date and should not be
construed as an admission that the present disclosure is not entitled to antedate such
publication by virtue of prior disclosure. r, the dates of publication provided could be
different from the actual publication dates that may need to be independently confirmed.
As will be apparent to those of skill in the art upon g this disclosure, each of the
individual embodiments described and illustrated herein has discrete ents and features
which may be readily separated from or combined with the features of any of the other several
embodiments without departing from the scope or spirit of the present disclosure. Any recited
method can be carried out in the order of events recited or in any other order that is logically
possible.
Embodiments of the present disclosure will employ, unless otherwise indicated,
techniques of molecular biology, microbiology, nanotechnology, organic chemistry,
biochemistry, botany and the like, which are within the skill of the art. Such techniques are
ned fully in the literature.
EXAMPLES
The following examples are put forth so as to provide those of ry skill in the art
with a complete disclosure and description of how to perform the methods and use the
compositions and compounds disclosed and claimed . The specific examples below are
to be construed as merely illustrative, and not limitative of the remainder of the disclosure in
any way whatsoever. Efforts have been made to ensure accuracy with respect to numbers (e. g.
amounts, temperature, etc), but some errors and deviations should be ted for. Unless
indicated otherwise, parts are parts by , temperature is in 0C, and pressure is at or near
atmospheric. Standard temperature and pressure are defined as 20°C and 1 atmosphere.
Example 1: Production andpurification ofthe TATIc-CDKLS115 and DKLS107 fusion
proteins.
To produce a deliverable TAT-CDKL5 fusion protein a synthetic TATK-PTD in which
mutation of the furin recognition sequences in the TAT domain allows secretion of
recombinant proteins was used. The secreted protein was ed to be successfully taken up
by the target cells. TATK-CDKL5115 or DKL5107 fusion gene containing a human
CDKL5115 or CDKL5107was cloned into the expression plasmid pSecTag2 (Life Technologies).
This plasmid is designed to allow expression of genes in mammalian hosts and high expression
levels of target proteins. Proteins expressed from pSecTag2 are fused at the N—terminus to the
murine IgK chain leader ce for protein secretion in culture medium. The TATK-CDKLS
fusion proteins were tagged with an eGFP protein to allow for western blot analysis using an
FP antibody. To facilitate protein purification, the TATK-CDKLS fusion proteins were
configured to include a myc-tag, 6xHis tag, and/or a FLAG tag at the C-terminal region of the
TATK-eGFP-CDKL5115 or TATK-eGFP—CDKL5107 gene. HEK 293T cells were transfected
with the TATK-eGFP-CDKL5115 or TATK-eGFP—CDKL5107 expression plasmid using rd
plasmid delivery methods. After transfection cells were left to grow in serum-free medium
(High glucose Dulbecco's Modified Eagle Medium). After 48 hours medium was collected,
diafiltered and concentrated with Amicon ultra centrifugal filters (50kDa cut-off). This method
allows buffer exchange and enrichment of the secreted n.
Figs. 4A and 4B demonstrate western blot is results from TATK-eGFP-
CDKL5115 protein expression in transfected HEK 293T cells. Fig. 4A demonstrates TATK-
eGFP—CDKL5115 fusion n sion in cell homogenates from transfected HEK
lls. Fig. 4B demonstrates TATK-eGFP—CDKL5115 fusion protein accumulation in
concentrated (20X) cell culture medium from transfected HEK 293T cells. Although not
shown in Figs. 4A-4B similar results were obtained with the TATK-eGFP-CDKL5107 fusion
protein.
Example 2: Validation of TATIc-CDKL5115 kinase activity.
In order to purify the TATK-eGFP-CDKL5115 protein, a myc-tag and a 6xHis tag were
added at the C—terminal region of the TATK-eGFP-CDKL5115 gene. TATK-eGFP-CDKL5115
fusion n was purified from culture medium on a Ni-NTA resin. It has been shown that
the CDKL5 kinase has a high osphorylation activity. As shown in Figs. 5A and 5B,
which shows the results from an in vitro kinase activity assay, purified TATK-eGFP—CDKL5115
protein preserves its autophosphorylation ty. This trates that the purified fusion
protein retains its kinase activity.
Example 3: Internalization of TATK-CDKL5115 by HEK 293T cells.
To evaluate the efficiency of the transduction of the TATK-eGFP-CDKL5115 fusion
protein HEK 293T cells were ted with the ed/concentrated fusion protein. Briefly,
the TATK-eGFP—CDKL5115 fusion protein was produced and purified as described in Example
1. HEK 293T cells were incubated in concentrated medium containing the fusion protein. After
different incubation times cells were lysed and total protein extracts were separated by SDS-
PAGE and transferred to a nitrocellulose membrane for blotting for TATK-eGFP-
CDKL5115 protein fication. As shown in Fig. 6, TATK-eGFP-CDKL5115 is internalized
by cells after only about 30 minutes of incubation. Other cultures were treated in parallel and
were fixed and immunostained with an anti-GFP specific antibody to visualize the transduced
TATK-eGFP-CDKL5115 protein. As demonstrated in Figs. 7A-7B, TATK-eGFP-CDKL5115
protein was efficiently translocated into the cells. The internalization in target cells was
confirmed by al copy (Fig. 8). SH-SY5Y neuroblastoma cells were incubated in
concentrated media containing the fusion n for 30 minutes. Fig. 8 shows an image of a
series of confocal images (1-12) of TATK-eGFP-CDKL5115 transduced SH-SY5Y cells,
demonstrating that TATK-eGFP—CDKL5115 protein is internalized by target cells and localized
both in the nucleus and cytoplasm of SH-SY5Y cells (Fig. 8).
Example 4: TATIc-CDKLS115 induces differentiation and inhibits proliferation of the
SHSY5Y neuroblastoma cell line
In spite of the clear importance of CDKL5 for the central nervous system, the
biological functions of this kinase remain largely n. The CDKL5 n can affect
both eration and differentiation of neural cells (See e.g. Valli et al., 2012. Biochim
s Acta. 1819:1173-1185, and Rizzi et al., 2011. Brain Res. 1415:23-33). lastoma
cells share several features with normal neurons and thus are considered a good in vitro model
to study the biochemical and functional properties of neuronal cells, particularly when they are
induced to entiate upon treatment with agents such as retinoic acid (RA) (See e. g., Singh,
2007 Brain Res. 1154 p 8-21; Melino, 1997 J. Neurooncol. 31 pp 65-83). For these reasons,
neurobastoma cells were employed to study the CDKL5 function in Vitro.
SH-SY5Y cells were treated with purified TATK-eGFP-CDKLS similar to the treatment
as described in Example 3. Here, SH—SY5Y cells were incubated with the trated media
containing the purified TATK-eGFP-CDKLSHS protein for about 24 hours. Cell proliferation
was evaluated as mitotic index (the ratio between the number of cells in a population
undergoing mitosis to the total number of cells) using Hoecsht nuclear staining. Differentiation
was ted by examining neurite growth, which is a sign of neuronal differentiation. For
analysis of neurite growth, cells were grown for an additional 1-2 days in the presence or
absence of the pro-differentiation agent, RA. Neurite outgrowth was measured using an image
analysis system.
Induction of CDKL5 expression (by TATK-eGFP-CDKL5115 protein) caused a strong
inhibition of cell proliferation (e. g., Figs. 9A-9B, and 10) with no increase in apoptotic cell
death (data not shown) ed to controls. Further, as shown in Figs. llA—llB and 12,
TATK-eGFP-CDKL5115 promotes neuroblastoma cell differentiation as indicated by neurite
outgrowth in SH-SY5Y cells. These s demonstrate that TATK-eGFP-CDKL5115 is
onal in an in Vitro neuronal model.
Example 5: Characterization ofthe CDKL5-K0 mouse model
A CDKL5 knockout mouse model has been recently created by the EMBL in
Monterotondo, Italy, by the group led by Dr. Cornelius Gross (Amendola, 2014 PLoS One.
9(5):e9l6l3). To establish the effect of CDKL5-loss of function on dendritic development of
newborn neurons, the dendritic morphology of newborn hippocampal granule cells derived
from the CDKL5 KO mouse was ed. Dendritic morphology of newborn neurons was
analyzed with immunohistochemistry for doublecortin (DCX), taking advantage of the
expression of this protein in the cytoplasm of immature neurons during the period of e
elongation. As shown in Figs. 13A—13B, DCX-positive cells of CDKL5 KO mice (-/Y)
ted a dendritic tree with a highly immature pattern (Fig. 13B) compared to the CDKL5
wild-type (+/Y) counterparts (Fig. 13A). A highly immature pattern can be evidenced by little
branching and elongation. Absence of CDKL5 resulted in a decrease in the number of DCX-
positive cells (Fig. 13B) due to an increase in apoptotic cell death (data not shown) that was
observed to affect postmitotic immature granule neurons (DCX—positive cells) , 2014
iol Dis. 70 p53—68). These data suggests that CDKL5 plays a fundamental role on
postnatal neurogenesis, by affecting neural precursor survival and maturation of newborn
neurons. Cultures of neuronal precursor cells (NPCs) from the subventricular zone (SVZ) of
CDKL5 knockout mice were observed to exhibit the same defects observed in vivo in
llar granule cell precursors. Namely, in cultures of neuronal precursor cells derived from
female wild-type mice (+/+) there were more s (B-tubulin III positive cells, red cells)
than in cultures of neuronal sor cells derived from homozygous CDKL5 KO female
mice (—/—) (Figs. 14A and 14B). This suggests that the loss of CDKL5 decreases the survival of
post-mitotic neurons. Assessment of neurite wth in B-tubulin 111 positive cells
demonstrated that neurons generated from Cdk15 knockout NPCs were less differentiated
compared to female wild-type (+/+) neurons (Figs. 14A and 14B). These results suggest that
post-mitotic NPCs from CDKL5 ut mice have an intrinsic , not only in cell
survival, but also in neuronal tion.
e 6: TATE-CDKL5115 protein restores neurite development of neuronal cell
precursors derivedfrom a CDKL5 K0 mouse.
Neuronal precursor cells cultures from the female homozygous CDKL5 KO (-/-) mouse
and wild-type (+/+) mouse were treated with TATK-eGFP—CDKL5115 or TATK-eGFP.
Neuronal maturation was evaluated by measuring the total neuritic length of differentiated
neurons (positive for B-tubulin III). Evaluation of neurite length was performed by using the
image is system Image Pro Plus (Media Cybernetics, Silver Spring, MD 20910, USA).
The average neurite length per cell was calculated by dividing the total neurite length by the
number of cells counted in the areas. As shown in Figs. C and 16, absence of CDKL5
causes a reduction in the maturation of new neurons and treatment with TATK-eGFP-
CDKL5115 restores neurite pment. For Figs. lSA-l6, cells were isolated from the
subventricular zone (SVZ) of newborn (2-day-old) mice. For differentiation is,
neurospheres obtained after three passages in vitro were dissociated and plated on cover slips
coated with 15 ug/ml poly-l-ornithine ) at a density 20’000 cells/well. Cells were grown
for 2 days and then transferred to a differentiating medium (EGF and FGF free plus 1% foetal
bovine serum) from day 3 for 7 days. TATK-CDKL5115 fusion protein was administered daily
at a final 10x concentration after buffer exchange with DMEM-Fl2, avoiding complete change
of culture medium. Every 3 days, half of the medium was replenished with fresh differentiating
medium.
Example 7: Delivery of TATk-CDKL5115 into the mouse brain.
Seven-day old mouse pups were subcutaneously injected with a single dose of culture
medium of HEK 293T cells ected with TATK-eGFP-CDKL5115, GFP or medium
from untransfected cells (vehicle) (single dose corresponded to about 200 pl of 200x
concentrated medium; which contained about 1-1.5 ug of the fusion protein). Culture medium
was collected after 48 hours from transfection and was diafiltered and concentrated with
Amicon ultra centrifugal filters (50kDa cut-off). Mice were sacrificed 4 hours post-
administration of the treatment. Brains were stored in the fixative for 24 hours, cut along the
e and kept in 20% e in phosphate buffer for an additional 24 hours. heres
were frozen and stored at -80°C. The right hemisphere was cut with a freezing ome in
-um-thick coronal sections. histochemistry was carried out on free-floating sections.
Localization of TATK—eGFP-CDKL5115 and TATK-eGFP in the brain was evaluated by
immunohistochemistry using an anti-GFP antibody and a TSA amplification kit. Images were
taken at the level of the sensory-motor cortex and the llum. Cells were counterstained
using 4',6~diamidinw2~pheriylindole (DAPI). Representative images demonstrating presence
of the TATK-eGFP-CDKL5115 n in the sensory-motor cortex and cerebellum of mice are
shown in Figs. l7A-17F and Figs. 18A—18D, respectively. Given that the TATK-eGFP-
CDKL5115 protein was subcutaneously administered, these data demonstrates that the TATK-
eGFP-CDKL5115 protein is effectively transported across the blood brain barrier and enters into
brain cells.
Example 8: Effect of CDKLS115 Fusion Protein in vivo on Neuronal Maturation,
Survival and tivity
Adult mice (4-6 months of age) were intraventricularly injected (Fig. 19) for 5
consecutive days (see 6.g. Fig. 20 for mental schedule) with TATK-eGFP—CDKL5115 or
TATK-eGFP. , mice were anesthetized with ketamine (100—125 mg/kg) and xylazine
(IO—12.5 mg/kg). Cannulas (0.31-mm er, Brain Infusion Kit 111; Alzet Cupertino, CA)
were stereotaxically implanted into the lateral ventricles (A/P —0.4-mm caudal, M/L 1.0 mm,
D/V —2.0 mm; Fig. 19). Seven days after implantation mice were infused for 5 consecutive
days with 10 u] (about 50 ng) of TATK—eGFP-CDKL5115 or TATK-eGFP in PBS by using a
Hamilton syringe connected to a motorized jector (at a rate of 0.5 ul/min). Four hours
after the last injection animals were sacrificed, and the dendritic morphology of newborn
ampal granule cells was analyzed with immunohistochemistry for DCX. Figs. 21A-21C
and 22A-22C demonstrate that DCX positive neurons of male CDKL5 KO mice had shorter
ses than those of their wild-type rparts (Figs 21A-21B and 22A-22B). TATK-
DKL5115 fusion protein administered intraventricularly on five consecutive days was
observed to increase neurite length and branch number in CDKL5 knockout male mice (Fig.
22C) to levels similar to wild-type (Fig. 22A). Figs. 23A—23B show examples of the
reconstructed dendritic tree of newborn granule cells of wild-type (+/Y) (Fig. 23A), CDKL5
knockout male mice (-/Y) (Fig. 23B), and CDKL5 knockout male mice treated with a TATK-
eGFP-CDKL5 115 fusion protein.
Quantification of the tic size of DCX positive cells demonstrate that CDKL5 KO
male mice (-/Y) mice had a shorter tic length (Fig. 24A) and a reduced number of
segments (Fig. 24B) than wild-type male mice (Figs 24A and 24B). In TATK-eGFP-CDKL5115
treated CDKL5 knockout male mice mice there was an increase in both parameters that
became even larger in comparison with wild-type male mice (Figs. 24A-24B). The effects of
GFP-CDKL5115 treatment on details of the dendritic architecture were examined by
evaluating each dendritic order separately. A striking feature of CDKL5 KO mice was the
absence of branches of higher order (Figs. 25A-25B; red arrows). While wild-type male mice
had up to 10 orders of branches, CDKL5 knockout male mice lacked branches of orders 8-10
(Fig. 25A, arrows). In addition, CDKL5 knockout male mice showed a reduced branch length
of orders 5-8 (Fig. 25A) and a reduced number of branches of orders 6-8 (Fig. 25B). Taken
together, these data indicate that in CDKL5 KO male mice the dendritic tree of the newborn
granule cells is hypotrophic and that this defect is due to a reduction in the number and length
of branches of ediate order and a lack of branches of higher order. All these defects were
observed to be completely rescued by TATK-eGFP-CDKL5115 ent (Figs. 25A to 25B).
In order to evaluate the effect of TATK-eGFP—CDKL5115 treatment on apoptotic cell
death, we counted the number of apoptotic cells expressing cleaved caspase-3 in the
hippocampal dentate gyrus (Fig. 26). Quantification of cleaved caspase-3 cells shows that
TATK-eGFP-CDKL5115 treatment completely normalized apoptotic cell death in CDKL5
ut amle mice (-/Y) (Fig. 26). It was ed that CDKL5 knockout male mice had
fewer post-mitotic s (DCX—positive cells) than wild-type male mice in the hippocampal
dentate gyrus (Fig. 27). TATK-eGFP-CDKLS115—treated CDKL5 knockout mice underwent an
increase in the number of post-mitotic neurons that became similar to those of wild-type male
mice (Fig. 27). This indicates that the increased death of post-mitotic immature granule cells
that characterizes CDKL5 knockout mice is rescued by TATK—eGFP-CDKL5115 treatment.
Taken together, these data demonstrate that treatment with TATK-eGFP-CDKL5115 in CDKL5
ut mice sed neurite length and survival of n cells in the ampus
ting that injected TATK-CDKLS diffused from the lateral ventricle to the hippocampus
and restored maturation and survival of post-mitotic granule cells.
Without being bound by any one theory, a ion in connectivity may be the
counterpart of the dendritic hypotrophy that characterizes the newborn granule cells of CDKL5
KO mice. Synaptophysin (SYN; also known as p38) is a synaptic vesicle glycoprotein that is a
specific marker of presynaptic terminals. Here, it was observed in CDKL5 knockout male mice
that the optical density of SYN was icantly lower than in wild-type male mice in the
molecular layer of the hippocampus (Figs. 28 and 30A), suggesting that CDKL5 KO male
mice had fewer synaptic contacts in the dentate gyrus. Figs. 28A-28C show representative
images trating brain sections processed for synaptophysin (SYN) immunofluorescence
from the molecular layer (MOI) of the dentate gryrus (DG) from a wild-type male mouse (+/Y)
(Fig. 28A), a CDKL5 knockout male mouse (-/Y) (Fig. 28B), and a CDKL5 knockout male
mouse treated with TATK—eGFP—CDKL5115 fusion protein via intraventricular injections given
once a day for 5 consecutive days (-/Y + TATK-eGFP-CDKLS) (Fig. 28C). One out of six 30-
um-thick coronal sections from the DG of animals were processed for immunohistochemistry.
Immunohistochemistry was carried out on free—floating sections for the frozen brains. For
Synaptophysin immunohistochemistry, sections were incubated for 48 hours at 4°C with
mouse monoclonal anti—SYN (SY38) antibody (1:1000, MAB 5258, Millipore Bioscience
Research Reagents) and for 2 hours with a Cy3 conjugated anti—mouse IgG secondary antibody
(1:200; Jackson Immunoresearch). ity of immunoreactivity (IR) was determined by
optical ometry of immunohistochemically d sections. Fluorescence images were
captured using a Nikon Eclipse E600 microscope equipped with a Nikon Digital Camera
DXM1200 (ATI system). Densitometric analysis in the molecular layer and cortex was carried
out using Nis-Elements Software 3.21.03 (Nikon). For each image, the intensity threshold was
estimated by ing the distribution of pixel intensities in the image areas that did not
contain IR. This value was then subtracted to calculate IR of each sampled area. Values are
given as a percentage of the optical density of control CDKL5 ype male mice (mean +
rd error).
Dendritic arborization is significantly reduced in cortical pyramidal neurons of CDKL5
KO mice compared to their wild—type counterparts (Amendola, 2014 PLoS One. 9(5):e91613).
A similar lower level of SYN immunoreactivity in the layer III of the neocortex was observed
(Fig. 30B). In CDKL5 KO male mice treated with TATK-CGFP-CDKL5115 these defects were
fully rescued (Fig. 28 and Figs. 30A and 30B), suggesting that the positive impact of treatment
with TATK-eGFP-CDKL5115 on dendritic structure was paralleled by restoration of the input to
neurons.
Example 9: Effect of TATk-CDKL5115 Fusion Protein in vivo 0n P-AKT
AKT is a central signaling kinase associated with multiple cellular pathways.
Phosphorylated AKT (P—AKT) is significantly reduced in CDKL5 knockout animals, CDKL5
ency and Rett syndrome. Figs. 29A-29C show representative images demonstrating brain
sections processed for P—AKT immunofluorescence from the molecular layer (Mol) of the
dentate gryrus (DG) from a ype male mouse (+/Y) (Fig. 29A), a CDKL5 ut male
mouse (—/Y) (Fig. 29B), and a CDKL5 knockout male mouse treated with TATK-eGFP-
CDKL5115 fusion protein via intraventricular injections given once a day for 5 consecutive
days (-i’Y + TATK-eGFP—CDKLS) (Fig. 29C). For phospho-AKT immunohistochemistry,
ns were incubated for 24 hours at 40C with mouse monoclonal hospho-AKT-
Ser473 antibody 0, Cell Signaling Technology) and for 2 hours with a Cy3 conjugated
anti-mouse IgG secondary antibody (1:200; Jackson Immunoresearch). Intensity of
immunoreactivity (IR) was determined by l densitometry of immunohistochemically
d sections. scence images were captured using a Nikon Eclipse E600 cope
equipped with a Nikon Digital Camera DXM1200 (ATI system).
In CDKL5 knockout male mice (-/Y) the optical y of P-AKT in the molecular
layer of the DG (Fig. 31A) and in the layer V of the cortex (Fig. 31B) was observed to be
significantly lower than in +/Y mice. In CDKL5 knockout male mice (-/Y) intraventricular
injected with TATK-eGFP-CDKL5115 for five consecutive days these defects were fully
rescued (Figs. 31A and 31B), demonstrating that treatment with GFP-CDKL5115 in
CDKL5 knockout mice restores AKT activity.
Example 10: Effect of TATk—CDKLSI15 Fusion Protein in vivo on tic architecture of
mature neurons.
The effects of treatment on the dendritic architecture of mature neurons were analyzed.
To this end Golgi—stained granule neurons located in the middle portion of the granule cell
layer were ed. While CDKL5 KO male mice show a r length of dendritic
branches compared to wild-type male mice, these defects were completely rescued by
treatment with TATK-eGFP-CDKL5115 (Fig. 32). In both treated (—/Y) and (+/Y) mice total
dendritic length became even larger in ison with ted (+/Y) mice. These results
show that the impaired tic ecture of mature granule neurons observed in CDKL5
KO male mice was restored by treatment with TATK-eGFP-CDKL5115 protein.
In Golgi-stained sections, spines of granule cells were counted and spine density was
measured on dendritic segments in the inner and outer half of the molecular layer. Untreated
CDKL5 KO adult male mice showed a lower spine density compared to wild-type mice, while
treatment with TATK-eGFP-CDKL5115 protein fully restored density, erasing the difference
between knockout and wild-type conditions. Representative images are shown in Fig. 33 and
the relative quantification can be observed in the histogram on the right Fig. 34.
Taken together, these data demonstrate that treatment with TATK-eGFP—CDKL5115
completely recovers connectivity in CDKL5 KO male mice, by restoring synaptophysin
expression and by correcting dendritic spine number and maturation.
Example 11: Effect of TATK-CDKL5115 Fusion Protein on Learning and Memory Ability.
Male CDKL5 knockout mice exhibit learning and memory deficits as compared to
wild-type mice (see e. g. Figs. 36, and 37A-37B).
To examine memory and learning ability, CDKL5 knockout male mice were
administered daily intraventricular injections of a TATK—eGFP-CDKL5115 fusion protein for 10
days (see e. g. Fig. 35 for mental schedule). After a two day rest period at the conclusion
of 10 days of injections, mice in all groups ed the Morris Water Maze (MWM) testing
(Fig. 36). MWM measures the ability to find and recall the on of a hidden platform
submerged in water. Mice were trained in the MWM task to locate a hidden escape platform in
a circular pool. The apparatus ted of a large circular water tank (1.00 m diameter, 50 cm
height) with a transparent round escape platform (10 cm2). The pool was Virtually divided into
four equal quadrants identified as northeast, est, southeast, and southwest. The tank was
filled with tap water at a temperature of 22°C up to 0.5 cm above the top of the platform and
the water was made opaque with milk. The platform was placed in the tank in a fixed position
(in the middle of the north-west quadrant). The pool was placed in a large room with a number
of intra- (squares, triangles, circles and stars) and extra-maze Visual cues. After training, each
mouse was tested for two sessions of 4 trials each per day, for 5 consecutive days with an inter-
session interval of 40 minutes (acquisition phase). A Video camera was placed above the center
of the pool and connected to a Videotracking system ision 3.1; Noldus Information
Technology B.V., Wageningen, Netherlands). Mice were released facing the wall of the pool
from one of the following starting points: North, East, South, or West and allowed to search for
up to 60 seconds for the platform. If a mouse did not find the platform, it was gently guided to
it and allowed to remain there for 15 seconds. The latency to find the hidden platform was used
as a measure of ng. All experimental sessions were carried out between 9:00 am. and
3:00 pm.
The s of this test are demonstrated in Fig. 36. Fig. 36 shows a graph
demonstrating the quantification of the learning phase as determined Via the Morris Water
Maze test in wild-type male mice (+/Y), CDKL5 KO male mice (-/Y), and CDKL5 KO male
mice treated with a TATK—eGFP—CDKL5115 fusion protein (-/Y + TATK-eGFP-CDKLS). Wild-
type mice learned to find the platform by the second day, but no significant learning was
detected in CDKL5 KO mice. CDKL5 KO male mice treated with a TATK-eGFP—CDKL5115
fusion protein began to r learning y at day 4 with continued ement at day 5.
Memory and learning ability as further ed in response to TATK-eGFP-
CDKL5115 fusion protein treatment using a passive avoidance test. After 10 consecutive days
of treatment and a two day rest period, mice of the various groups received passive avoidance
testing (Fig. 37). The experiment utilized a test cage with two chambers (light and dark). On
day one (conditioning period), animals are placed in the light chamber and instinctively move
into the dark chamber where they are conditioned with a single adverse event (foot shock). For
the passive avoidance test we used a tilting—floor box (47x18x26 cm) divided into two
compartments by a sliding door and a control unit incorporating a shocker (Ugo Basile, Italy).
This classic instrument for Pavlovian conditioning exploits the tendency in mice to escape
from an illuminated area into a dark one (step-through method). On the first day mice were
individually placed into the illuminated compartment. After a 60 second habituation period, the
connecting door between the rs opened. In general, mice step quickly through the gate
and enter the dark compartment e mice prefer to be in the dark. Upon ng the dark
compartment, mice received a brief foot shock (0.7 mA for 3 seconds) and were removed from
the chamber after 15 seconds of latency. If the mouse ed in the light compartment for
the duration of the trial (358 s), the door closed and the mouse was removed from the light
compartment. The chambers were cleaned with 70% ethanol between testing of individual
mice. After a 24 hour retention period, mice were placed back into the light compartment and
the time it took them to er the dark compartment (latency) was measured up to 358
seconds.
Figs. B demonstrate the results from the passive nce test. Fig. 37A
tes that the latency time to enter the dark chamber was similar for all groups. On day two
(testing ) (Fig. 37B) animals were again placed in the light chamber. Memory of the
adverse event was measured by latency time to enter the dark chamber. CDKL5 knockout male
mice (-/Y) were severely ed at performing this task, as demonstrated by a reduced
latency to enter the dark compartment in comparison with GDKLS male wild-type mice (+/Y).
TATK-eGFP-CDKL5115 treated CDKL5 knockout male mice showed a similar latency time as
ed to wild-type mice.
In sum, the data demonstrate that TATK—eGFP—CDKL5115 can increase and restore
learning and memory y in CDKL5 knockout male mice to levels similar to that observed
in their untreated wild-type counterparts.
e 12: Effect of TATk-CDKL5115 Fusion Protein on Motor Function.
CDKL5 knockout male mice exhibited prolonged limb ng when suspended (see
e.g. Figs. 38A-38B).
To examine the effect of TATK—eGFP—CDKL5115 fusion protein on motor function,
mice were administered daily intraventricular injections of TATK-eGFP-CDKL5115 for 10
consecutive days (Fig. 38). 10 days ing the completion of the dosing protocol, s
were suspended in the air by the tail (Fig. 38A and Fig. 38B). All animals were suspended for
about 2 minutes and total time of limb clasping was measured. Results from this experiment
are demonstrated in Figs. 38A-38B.
Figs. 38A-38B show a graph demonstrating quantification of motor ability as
determined by a clasping test in which total amount of time spent limb clasping during a 2
minute al was measured in wild-type male mice (+/Y), CDKL5 knockout male mice (-
fY), and CDKL5 KO male mice d with a TATK-eGFP-CDKL5115 fusion protein (—/Y +
TATK-eGFP-CDKLS) according to the injection schedule in Fig. 35. In sum, the data
demonstrate that treatment with TATK-eGFP-CDKLSlls improved motor function in CDKL5
KO male mice.
Body weight of wild-type (+/Y) and CDKL5 KO (-/Y) male mice injected for 5 (+/Y)
or 10 (-/Y) days with TATK-eGFP-CDKL5115 protein was measured and results are
trated in Fig. 39. No significant changes in body weight during the injection period
were observed, suggesting that there were no side effects caused by TATK-eGFP-CDKL5115
protein administration.
Comparison of Allograft Inflammatory Factor 1 (AIF-l) ng in ted animals
and treated with TATK-eGFP-CDKL5115 for 5 days or 10 days by intraventricular injection is
shown in Figs. 40A-40F. Data show that treatment does not provoke microglial activation,
ting the absence of inflammatory response to the prolonged TATK-eGFP-CDKL5115
treatment.
Example 13: Comparison of expression and activity between TA Tic-CDKL5 isoforms.
Alternative splice isoforms for the CDKL5 gene have been described (Kilstrup-Nielsen,
2012). The original CDKL5 transcript generates a n of 1030 amino acids (CDKL5115;
115 kDa). While CDKL5115 was the first characterized CDKL5 isoform, a recently identified
107 kDa isoform has been demonstrated to contain an d C—terminal region and is thought
to be involved with brain function (CDKL51O7) (Williamson et al., 2012). As described above,
the CDKL5 fusion protein can be formed using any suitable isoform (e.g. a variant as
described ere herein). For this Example, the CDKL5 fusion protein was formed by
operatively liking the CDKL5115 isoform (SEQ ID NO: 2) or the CDKL5107 isoform (SEQ ID
NO: 16) to TATK using similar methods described elsewhere herein.
To compare the levels of production and activity of the two CDKL5 isoforms (115 and
107), TATK-eGFP-CDKL5115 or TATK-eGFP-CDKL5107 was transiently or stably expressed in
HEK 293T cells. It was observed that the recovery of GFP-CDKL5107 fusion protein
from culture medium was higher than that of TATK-eGFP—CDKL5115 (Fig. 41).
It was observed that the two CDKL5 isoforms have similar intracellular stability. Figs.
42A-42B show graphs demonstrating intracellular stability of expressed TATK-eGFP-
CDKL5115 or TATK-eGFP-CDKL5107 fusion proteins in HEK 293T cells (Fig. 42A) and
SKNBE cells (Fig. 42B). HEK 293T and SKNBE cells were transfected with GFP-
CDKL5115 or TATK-eGFP-CDKL5107. Twenty-four hours later cells were incubated with
cycloheximide (Chx; 50 ug/ml) for the indicated times (3, 6 or 8 hours). Ectopically expressed
CDKL5 was detected by CDKL5 immunoblotting.
antly, at a functional level, we found that the two isoforms have a comparable
physiological activity. The in vitro activity of TATK-eGFP-CDKL5115 was tested in el to
a DKL5115 and TATK—eGFP-CDKL5115. SH—SY5Y cells were treated with purified
TATK-CDKLSHS or TATK-eGFP-CDKL5115 and TATK—eGFP (as a control) the day after
seeding. In particular, cells were incubated with the concentrated media containing the
concentrated/purified protein for about 24 hours. Cell proliferation was evaluated as a mitotic
index (the ratio n the number of cells in a population undergoing s to the total
number of cells) using Hoechst nuclear staining. As shown in Fig. 52, we demonstrated that
both CDKL5 isoforms have the same effect on SH-SY5Y lastoma cells in terms of
inhibition of proliferation. We tested the in vitro activity of TATK—eGFP-CDKL5115 in parallel
to a TATK-CDKL5115 protein without eGFP. As shown in Fig. 52, we demonstrated that both
the proteins have the same effect on SH-SYSY neuroblastoma cells in terms of tion of
proliferation, ting that the eGFP-tag does not alter CDKL5 activity.
e 14: TATIc-CDKLS protein has the same subcellular zationas the native
CDKL5 and restores neurite development of hippocampal neurons derived from a CDKL5
K0 mouse.
It has been shown that in hippocampal neurons CDKL5 has mainly a cytoplasmic
localization with an enrichment at the postsynaptic compartment. We found that in these
neurons internalized TATK-eGFP-CDKL5107 localizes mainly in the cytoplasm and, in
particular, at the dendritic level it specifically localizes to the dendritic spine (Figs. 45A-45D).
Confocal es show GFP-CDKLS co-localization with presynaptic
(synaptophysin; SYN Figs. 60A-6OC) and postsynaptic (PSD—95; Figs. 46A—46D). This
indicates that the exogenous protein localizes at the same subcellular sites of the native
CDKL5.
To establish whether TATK-eGFP-CDKL5107 retains CDKL5 physiological activity,
hippocampal neuronal cultures from CDKL5 knockout male mice (-/Y) were grown in the
presence of TATK-eGFP-CDKL5107 (added to the culture medium) for 8 days. In these neurons
an absence of CDKL5 causes a reduction in neuronal maturation, as shown by reduced
dendritic length (Fig. 47), number of synaptic connections (Fig. 48) and spine density (Fig.
61). Treatment with GFP-CDKLS restores e pment (Figs. 47—48 and 61),
ting that the fusion protein has ed the physiological activity of CDKL5.
Example 15: Effect of TATk-CDKL5107 Fusion Protein on Behavior.
Figs. 49A—49B show cartoons depicting a treatment schedule and route of
administration of the CDKL5 fusion protein for behavioral testing. Male CDKL5 ype
mice (+lY) received treatment with TATK-eGFP (n=6) while CDKL5 KO male mice (-/Y)
were treated with TATK-eGFP (n=6) or TATK-eGFP-CDKL5107 (n=6) as ted above.
Treatment period consisted of a single daily injection (10 pl ion, approximately
50ng/injection) for 5 consecutive days, followed by a two day rest period and then 5 additional
days of a single injection. There was a total of 10 injections which were done in a 12 day
period.
Fig. 50 shows a graph demonstrating results from Morris Water Maze testing after
receiving the TATK-eGFP-CDKL5107 fusion protein as described in Figs. 49A-49B. After the
treatment period and a two day rest period, mice received Morris Water Maze (MWM) testing.
This test measures the ability to find and recall the position of a hidden platform ged in
water. Mice were tested for their ability to learn for 5 days (learning phase) and were
subjected to the probe test on day 6 (Page 4). TATK-eGFP d wild-type (+/Y) male mice
learned to find the platform by the third day, but no significant learning was detected in
CDKL5 KO male mice d with TATK-eGFP, indicative of a learning deficit. TATK-eGFP-
CDKL5107 d CDKL5 KO male mice began to recover learning ability on day 3 and
reached performance similar to WT at days 4 and 5. Values represent mean 1- SE. * p < 0.05,
p < 0.01 as compared to the wild-type condition; # p < 0.01 as compared to the TATK—eGFP
treated CDKL5 KO (-/Y) condition (Fisher LSD test after ANOVA).
Figs. 51A-51C show graphs demonstrating spatial memory from measuring (Fig. 51A)
latency to enter the former platform quadrant, (Fig. 51B) ncy of entrances into the
former platform nt, (Fig. 51C) percentage of time spent in the former platform quadrant.
Performance in all parameters was ly impaired in GFP treated CDKL5 KO male
mice. TATK-eGFP-CDKL5107 treated CDKL5 KO male mice showed statistically icant
improvement in all parameters, Figures A, B and C. Values ent mean 1- SE. * p < 0.05,
** ***
p < 0.01, p < 0.001 as compared to the ype condition; # p < 0.01 as ed to
the TATK-eGFP treated Cdk15 KO -/Y condition (Fisher LSD test after ANOVA).
Figs. 52A-52B show graphs demonstrating the effect of treatment on learning and
memory using a passive avoidance (PA) test. After treatment period and a two day rest period,
mice received passive avoidance (PA) testing. The experiment utilized a test cage with two
chambers (light and dark). On the first day, animals are placed in the light chamber and
instinctively move into the dark chamber where they are conditioned with a single adverse
event (foot-shock). Fig. 52A indicates that the latency time to enter the dark chamber was
similar for all groups. On the second day (testing period) animals are again placed in the light
r. Memory of the adverse event was measured by latency time to enter the dark
chamber and represented in Fig. 52B. TATK-eGFP treated CDKL5 KO male (-/Y) mice were
severely impaired in this task, as shown by a reduced latency to enter the dark compartment in
comparison with wild-type male (+/Y) mice. TATK—eGFP—CDKL5107 treated CDKL5 KO male
mice showed similar latency time as compared to wild-type mice (Fig. 52B). These
differences were statistically significant in ison to TATK-eGFP treated CDKL5 KO
male mice. ** p < 0.01 as compared to the wild-type male condition; # p < 0.01 as compared to
the TATK-eGFP d CDKL5 KO -/Y condition (Fisher LSD test after ANOVA).
Figs. 53A-42B show (Fig. 53A) a cartoon of a Y-maze used to evaluate the effect of
treatment on learning and memory and (Fig. 53B) a graph demonstrating the results from the Y
maze test. After the ent period and a two day rest period, mice received Y maze testing.
Y Maze Spontaneous Alternation was used for measuring the willingness of mice to explore
new environments and represents hippocampus—dependent spatial reference memory. Each
mouse was placed at the distal part of one arm facing the center of the maze. Each of the three
arms was 34 cm X 5 cm x 10 cm height, angled 1200 from the others and made of grey opaque
plastic. After introduction into the maze, the animal is allowed to freely explore the three arms
for 8 minutes. Over the course of the multiple arm entries, the subject should show a tendency
to enter a less recently visited arm. Arm s were defined by the presence of all four—paws
in an arm. The percentage of spontaneous alternations is d as: (total altemations/total
arm entries-2) X 100. One alternation is defined as consecutive entries in three different arms.
TATK-eGFP treated CDKL5 KO male (—/Y) mice were impaired in this task, as shown by a
reduced tage of spontaneous ations in comparison with TATK-eGFP treated wild-
type male (+/Y) mice. CDKL5 KO male mice treated with TATK-eGFP—CDKL51O7 showed
performance similar to WT treated with TATK-eGFP. * p < 0.05, ** p < 0.01 as compared to
the wild-type male condition; # p < 0.05 as compared to the GFP treated CDKL5 KO
male ion (Fisher LSD test after ANOVA).
Figs. 54A-54B show (Fig. 54A) a graph and (Fig. 54B) an image demonstrating
clasping (right mouse) vs. unclasping (left mouse) in a hind limb clasping test used to evaluate
the effect of treatment on motor function. After the treatment period, animals were suspended
in air by the tail. All animals were suspended for 2 minutes and total time of hind—limb
clasping was measured. The figure above reports time of hind-limb clasping as a percentage of
the total time suspended. Treatment with TATK-eGFP-CDKL5107 led to a statistically
significant reduction in clasping time as compared to TATK-eGFP treated CDKL5 KO male (-
fY) mice. Values ent mean 1- SE. *** p < 0.001 as compared to the wild-type condition;
## p < 0.001 as ed to the TATK-eGFP treated CDKL5 KO male condition r LSD
test after ANOVA).
Figs. 55A and 55B show graphs demonstrating breathing disturbances in CDKL5 KO (-
fY) male mice as ed by the number of apneas during non-REM (NREM) (Fig. 55A) and
REM (Fig. 55B) sleep. Treatment with TATK-eGFP-CDKL5107 led to a drastic reduction in the
number of apneas during non-REM (NREM) (Fig. 55A) and REM (Fig. 55B) sleep in CDKL5
KO male mice.
Body weight of male wild-type (+/Y) and CDKL5 KO mice injected for 10 (-/Y) days
with TATK-eGFP-CDKL5107 protein was measured and results are demonstrated in Fig. 59. No
significant changes in body weight during the injection period were observed, suggesting that
there were no side effects caused by TATK-eGFP—CDKLS protein administration.
e 16: Long lasting effect of TATE-CDKL5107 in vivo treatment on neuronal
maturation and survival.
A protein ement therapy needs to be continued during the whole life span of the
patient. With the idea of possibly reducing the frequency of injections in view of a future
treatment protocol in humans, we evaluated the persistence of positive s after treatment
cessation.
Figs 56A-56D show a graph (Fig. 56A) and (Figs. 56B—56D) reconstructed dendritic
trees of newborn granule cells demonstrating the effect of treatment with TATK-eGFP-
CDK5107 fusion protein. Twelve days after the completion of the treatment period, granule cell
dendritic logy was analyzed with immunohistochemistry for DCX, a protein t in
the cytoplasm during the period of neurite elongation (from one to four weeks after neuron
birth). Figure A represents mean total dendritic length of male wild-type (+/Y) (WT) and male
CDKL5 KO (-/Y) mice treated with TATK-eGFP and male CDKL5 KO (-/Y) mice treated with
TATK—eGFP-CDKL5107. Figures 56B, 56C and 56D show examples of the reconstructed
dendritic tree of newborn e cells of male wild-type (+/Y) mice treated with GFP,
male CDKL5 KO (-/Y) mice treated with TATK-eGFP and male CDKL5 KO (-/Y) mice
treated with TATK-eGFP—CDKL5107 respectively. Data te treatment with TATK-eGFP-
CDKL5107 leads to a morphological change that is durable for at least 12 days from time when
dosing was discontinued. Values represent mean 1- SE. ** p < 0.01 as compared to the wild-
type condition; # p < 0.01 as compared to the TATK-eGFP treated (-/Y) ion (Bonferroni
test after .
Fig. 57 demonstrates quantification of the number of DCX positive cells in the
hippocampus (dentate gyrus) of wild-type (WT) male mice (+/Y), CDKL5 KO male mice (-
/Y), and CDKL5 KO male mice treated with TATK-eGFP-CDKL5107. The treatment period
consisted of once daily intraventricular ion for 5 days followed by two a day rest period
then an additional once daily injection for 5 days. Animals were sacrificed 10 days after the
last injection. Data **
are sed as number of cells/um p < 0.01 as compared to the
number of cells/um in the +/Y + TATK-eGFP samples; ##p < 0.001 as compared to the number
of cells/um in the -/Y + GFP s (Bonferroni’s test after ANOVA). Data suggest
that the positive impact of treatment with GFP-CDKLS on the number of DCX-
positive cells is retained 10 days after treatment completion.
Fig. 58 demonstrates quantification of the total number of cleaved Caspase 3 positive
cells in the hippocampus (dentate gyrus) of wild-type (WT) male mice (+/Y), CDKL5 KO
male mice (-/Y), and CDKL5 KO male mice treated with TATK-eGFP-CDKL5107. The
treatment period consisted of a once daily intraventricular injection for 5 days followed by two
a day rest period then an additional once daily injection for 5 days. Animals were sacrificed 10
days after the last injection.
Example 17: Efi‘ect of systemically administered CDKLS107 protein on
al development and behavior.
Fig. 62 shows a treatment schedule for systemic administration of the CDKL5 fusion
ns. To mimic a daily human dose administration we used an innovative infusion method
which is based on a programmable pump implanted under the skin with a able reservoir.
The pump was connected to a cannula implanted in the carotid artery. This system allowed us
to apply a twice a day infusion protocol (morning and evening) for the duration of 10 days.
Male CDKL5 KO (-/Y) mice were infused twice a day with TATK-eGFP (20 1.11 + 20 1.11) or
TATK-eGFP-CDKL5107 (20 Ml + 20 111) for the duration of 10 days. The two periods of
infusion were 9—10 am. and 9-10 pm. This treatment schedule was used to generate the data
shown in Figs. 63A-72. In Figs. 65-68 and 70-72, values are represented as means i SE. * p <
0.05; ** p < 0.01; *** p < 0.001 as compared to the untreated CDKL5 +/Y condition; # p <
0.05 as compared to the untreated CDKL5 -/Y samples (Fisher LSD test after ANOVA).
As shown in Figs. 17A—17F, the CDKL5 fusion n 115 isoform can cross the
blood-brain barrier when administered systemically. Figs. 63A-63B demonstrate the effect of
systemic treatment with the TATK—eGFP—CDKL5107 on newborn granule cell maturation. One
hour after the last injection animals were sacrificed, and the dendritic morphology of newborn
hippocampal granule cells was analyzed with immunohistochemistry for DCX. Figs. 63A-63B
demonstrate that DCX positive neurons of treated male CDKL5 knockout mice had longer
processes than those of untreated male CDKL5 KO mice. Fig. 64 shows that apneas during
sleep are cally reduced in the mice treated with TATK-eGFP-CDKL5107, indicating a
ve effect of the treatment.
Fig. 65 shows the total dendritic length of newborn ecortin-positive) granule cells
of untreated CDKL +/Y (n = 5) and CDKL5 —/Y (n = 5) mice, and CDKL5 -/Y mice treated
with TATK-eGFP (n = 6) or TATK-eGFP-CDKL5107 (n = 6). Fig. 66 shows the total dendritic
length of Golgi—stained granule cells of untreated CDKL5 +/Y (n = 5) and CDKL5 -/Y (n = 5)
mice, and CDKL5 -/Y mice treated with TATK-eGFP (n = 4) or TATK-eGFP-CDKL5107 (n =
). As can be seen from Figs. 65 and 66, systemic administration of the CDKL5 fusion protein
significantly increased dendritic length compared to the untreated CDKL5 +/Y mice.
Fig. 67 shows the number of digging bouts of untreated CDKL5 +/Y (n = 24) and
CDKL5 —/Y (n = 11) mice, and CDKL5 —/Y mice treated with TATK-eGFP (n = 6) or TATK-
eGFP-CDKL5107 (n = 5). As can be seen from Fig. 67, systemic administration of the CDKL5
fusion protein significantly increased the number of digging bouts compared to the untreated
CDKL5 +/Y mice.
Fig. 68 shows the nest quality of untreated CDKL5 +/Y (n = 6) and CDKL5 -/Y (n =
) mice, and CDKL5 -/Y mice treated with TATK-eGFP (n = 6) or TATK-eGFP-CDKL5107 (n
= 5). As can be seen from Fig. 68, systemic administration of the CDKL5 fusion protein
significantly increased the nest quality compared to the untreated CDKL5 +/Y mice.
Fig. 69 shows representative images of neural activity in the visual cortex ted at
different time points in one CDKL5 -/Y mouse treated with either TATK-eGFP or TATK-
eGFP-CDKL5107. In Fig. 69, a darker image shows a higher level of neural activity and a
lighter image shows a lower level of neural activity. As can be seen from Fig. 69, the mouse
treated with TATK-eGFP had very little neural ty in the visual cortex, whereas the mouse
treated with TATK-eGFP—CDKL5107 regained visual activity hout the 10-day treatment
period and retained visual activity during the t period.
Fig. 70 shows the mean ude of visually evoked responses ed before and
after 6 and 10 days of treatment in CDKL5 -/Y mice treated with TATK-eGFP or TATK-eGFP-
CDKL5107. The persistence of the effect was ted with an additional measurement 6—10
days after treatment cessation (washout). As a reference, the 95% confidence interval of
untreated wild-type se amplitude over time is shown in the ned area. Error bars
represent standard error of the mean. y ANOVA (repeated measures for the factor
time) revealed a time X treatment interaction p<0.05; post-hoc Holm-Sidak‘s multiple
comparisons test: * p<0.05, **p<0.01. As can be seen from Fig. 70, systemic administration of
the CDKL5 fusion protein for 6 and 10 days significantly decreased the mean amplitude of
visually evoked ses compared to the CDKL5 +/Y mice treated with TATK-eGFP. This
trend continued even after the cessation of treatment.
Fig. 71 shows the dendritic spine density of the primary visual cortex (V1) pyramidal
neurons (layer 2/3) from untreated CDKL5 +/Y (n = 5) and CDKL5 —/Y (n = 5) mice and
CDKL5 -/Y mice treated with TATK-eGFP (n = 4) or TATK-eGFP-CDKL5107 (n = 5) and
sacrificed at the end of treatment (short term), or with TATK-eGFP (n = 3) or TATK-eGFP-
CDKL5107 (n = 3) and iced 10 days after treatment cessation (long term). As can be seen
from Fig. 71, systemic administration of the CDKL5 fusion n significantly increased the
dendritic spine density compared to the untreated CDKL5 +/Y mice. This trend continued even
after the cessation of ent.
Fig. 72 shows the number of fluorescent puncta per um2 exhibiting PSD—95
immunoreactivity in the y visual cortex (V1) of untreated CDKL5 +/Y (n = 3) and
CDKL5 —/Y (n = 3) mice, and CDKL5 —/Y mice treated with TATK-eGFP (n = 4) or TATK-
eGFP-CDKL5107 (n = 6) and sacrificed at the end of treatment (short term), or with TATK-
eGFP (n = 4) or TATK-eGFP-CDKLSW (n = 4) and sacrificed 10 days after treatment
cessation (long term). As can be seen from Fig. 72, systemic administration of the CDKL5
fusion protein significantly increased the number of PSD-95 fluorescent puncta per um2
ed to the untreated CDKL5 +/Y mice. This trend continued even after the cessation of
treatment.
These data support the systemic (e.g., intravenous) administration of CDKL5 fusion
proteins for the treatment of CDKL5 deficiencies, increasing te length, increasing neural
activity in the visual cortex, and improving behavior.
SEQUENCEIJSHNG
SEQ ID NO: 1 CDKLS 115 m cDNA (lacking the ATG start codon for the initiator
methionine)
aagattcctaacattggtaa vgtgaLgaaLaaatLLgagaLccttggggttg:aggtgaagga
gcctatggagttgtacttaaatgcagacacaaggaaacaca:gaaattgtggcgatcaagaaa
ttcaaggacagtgaagaaaatgaagaagtcaaagaaacgac:ttacgagagc:taaaatgctt
cggactctcaagcaggaaaacattgtggag :tgaaggaagcatttcg:cggaggggaaagttg
tacttggtgtttgagtatgttgaaaaaaatatgctcgaat :gctggaagaaa :gccaaatgga
gttccacc:gagaaagtaaaaagctacatc :atcagctaatcaaggc:attcactggtgccat
aagaatgatattgtccatcgagatataaaaccagaaaatc:Cttaatcagccacaatgatgtc
ctgtgtgactttggttttgctcg:aatctgtcagaaggcaa :aatgctaattacaca
gagtacgttgccaccagatggtatcggtccccagaactcttacttggcgctccctatggaaag
tccgtggacatnggvcgnggchgvat VCLtggggagcttagcga :ggacagcc vattL
cctggagaaagtgaaattgaccaactttttactattcagaaggtgctaggaccacttccatct
gagcagatgaagCLLvtCLacagLaaVCC vcgcthcatgggctccgg :ttccagc vngaaC
catcctcagtccttggaaagaagataccttggaattttgaatagtgttctacttgacctaatg
aagaatt:actgaag:tggacccagc:gacagatacttgacagaacag v9 VLLgaa vcaCCC:
acatttcaaacccagagacttctggatcgttctccttcaaggtcagcaaaaagaaaaccttac
cavgvggaaagcagcacaLLgchaa vagaaaccaagccggcaaaag vac ego tC:
caccacagatctaacagcaaggacatccagaacctgagtgtaggcctgccccgggctgacgaa
gng VCCCLgccaa:gaaagc:tcctaaatggaaaccttgctggagc wag VCL wag eccac v9
aaaacctaccaagcaagcagccagcctgggtctaccagcaaagatctcaccaacaac
aacataccacacc vcttagcccaaaagaagccaagtcaaaaacagagLt vga vttvaaLavL
gacccaaagccttcagaaggcccagggacaaagtacctcaagtcaaacagcagatctcagcag
aaccgccactcat:catggaaagctC:Caaagcaaagctgggacactgcagcccaatgaaaag
cagagtcggcatagctatattgacacaattccccagtcctc:aggagtccctcctacaggacc
aaggccaaaagccatggggcactgagegac vccaagtctgtgagcaacctttc:gaagccagg
gcccaaattgcggagcccagtaccagtagg :acttcccatc:agctgcttagacttgaattct
agcccaacccccaccagacacagtgacacgagaac:ttgctcagccc:tctggaaga
aataaccgaaatgagggaacgctggactcacgtcgaaccacaaccagacattCtaagacgatg
gaggaattgaagctgccggagcacatggacagtagccattcccattcactgtctgcacctcac
gaaLcttLLLottangacnggcLacaccagcccottttcttcccagcaacg:cctcatagg
cattctatgtatgtgacccgtgacaaagtgagagCcaagggcttggatggaagcttgagcata
gggcaagggatggcagctagagccaacagcctgcaactcttgtcaccccagcctggagaacag
ctccctcoagaga:gactgtggcaagatcttcggtcaaagagacctcoagagaaggcacctC:
catacacgccagaagtctgagggtggagtgtatcatgacccacactctgatgatggc
acagcccccaaagaaaatagacacctatacaatgatcctgtgccaaggagagttggtagctt:
tacagagtgccatctccacgtccagacaattctttccatgaaaataatgtgtcaactagagtt
tcvectcLaccaLcagagagcagttctggaaccaaccactcaaaaagacaaccagcattcga:
ccatggaaaagtcctgaaaatattagtcattcagagcaactcaaggaaaaagagaagcaagga
agchaaegaaaaagaaaaagaagaaatthaaacagtacccaattccgacagCCC:
gatcttctgacgttgcagaaatccavtcatectgcvagcactccaagcagcagaccaaaggag
tggcgccccgagaagatctcagatC:gcagacccaaagccagccattaaaatcactgcgcaag
ttgttacatctctcttcggcctcaaatcacccggc:tcctcagatccccgcveccagccctta
acagctcaacaaaccaaaaattcot:ctcagaaattcggattcaccccctgagccaggcctct
ggcgggagcagcaacatccggcaggaacccgcaccgaagggcaggccagCCC:Ccagctgcca
gacggtggatgtgatggcagaagacagagacaccaeectggaccccaagatagacgcttcatg
ttaaggacgacagaacaacaaggagaatacLectgcvgtggegacccaaagaagcctcacact
ccgtgcgtcccaaaccgagcccttcatcgtccaatctccag:cctgctccctatccagtactc
caggtccgaggcacttccatgtgcccgacaC:ccaggtccgaggcactgatgctttcagctgc
ccaacccagcaatccgggttctctttcttcgtgagacacgttatgagggaagccctgattcac
agggcccaggtaaaccaagctgcgctcctgacataccatgagaatgcggcactgacgggcaag
SEQ ID NO: 2 CDKL5 isoform 115 polypeptide (lacking the initiator methionine)
KIPNIGNVMNKFEILGVVGEGAYGVVAKCRHKElHELVALKKEKDSEENEEVKEILLREAKMJ
RT.KQEN"V?UK?AFRRRGKLYLVF7YVFKVWLELLWFMPNGVPPEKVKSY"YQU'KA"HWCiJ.
RD"KPEN.LISHNJVLKLCJFGFARNLSEGWNANYTEYVATRWYRSPEJLLGAPYGK
SVDMWSVGCTHGFWSDGQPTFPGFS?TDQLTTTQKVWGPLPSTQMKWTYSNPRFHGLRF?AVW
HPQSLERRYLGIJWSVLLJ.MKNL.KlDPAJRYLTEQCLN{PTFQTQRLLDRSPSRSAKRKPY
HVESSTLSNRNQAGKSTAAQSHHRSNSKDIQNLSVGAPRADEGLPANESFLNGNJAGASASPJ
HTKTYQASSQ?GSTSKDLTWNVIP .WSPKfiAKSKifiFDFW"JPKPSEGPGTKYLKSWSQSQQ
NRflSFMESSQSKAGTLQPNEKQSR.SYIDT:PQSSRSPSYRTKAKSflGALSDSKSVSNLSEAR
AQIAEPSTSRYFPSSCLDLWS?TS?T?TRHSDTRTWTSPSGRWNRNEGTLDSRRTTTQHSKTW
E?.K.PE WDSSHSHSLSAPHESFSYGLGYTSPFSSQQRPiRiSMYVTRDKVRAKGnJGSLS:
GQGMAARANSLQLLSPQPGEQAPPEMTVARSSVKETSREGTSSFHTRQKSEGGVYHDPHSDDG
TAPKjNRJ. PQRVGSFYRVPSPRPDNSFHENNVSTRVSSLPSESSSGTNHSKRQPAFJ
PWKSPENISHSEQLKjKEKQGEFRSMKKKKKKSQTVFNSDSPDLL-LQKSLHSASLPSSRPKE
WRPEKIS,LQTQSQPTKSLRKHLHLSSASNHPASSDPRFQPLTAQQTKNSFSEIR:H?LSQAS
RQEPAPKGRPALQLPDGGCDGRRQRHHSGPQDRRFM.RTTTQQGEYFCCGDPKKPHT
PCVPNRALHRPISSPAPYPVLQVRGiSMCPiLQVRGiDAhSCPiQQSGbSbeRHVMREALIH
RAQVNQAA ..TYH?NAALTGK
SEQ ID NO: 3 TATK polynucleotide sequence
tanccagaaaggCcgccaggcaggccagggca
SEQ ID NO: 4 TATK polypeptide sequence
YARKAARQARA
SEQ ID NO: 5 IgK-chain leader polynucleotide sequence
atggagacagacacactcctgctatgggtactgctgctctgggttccaggttccactggt
SEQ ID NO: 6 Ichhain leader polypeptide
METDTLLLWVLLLWVPGSTG
SEQ ID NO: 7 CDKL5 115 m fusion protein (IgK—TATK-CDKL5(115)—MYC—HIS)
polynucleotide
atggagacagacacactcc:gctatgggtactgctgctctgggttccaggttccactggtgac
gcggcccagccggCcaggcgcgcgcgccgtacgaagcttgcggcctacgccagaaaggcchC
aggcaggCcagggcaccggtgaagat:CctaacattggtaaCgtgaCgaaLaaatttgagatC
cttggggttgtaggtgaaggagcctatggagttgtacttaaatgcagacacaaggaaacacat
gaaattgtggcgatcaagaaattcaaggacagtgaagaaaa:gaagaagtcaaagaaacgact
ttacgagagcttaaaatgc chgaC:thaagcaggaaaacattgnganggaaggaagca
tttcgtcggaggggaaagttgtacttggtgtttgagtatgttgaaaaaaatatgctcgaattg
gaaatgccaaatggagttccaCC:gagaaagtaaaaagctacatcCaLcagC CaatC
aaggctaL CgccaCaagaaCgavaCtgLccatcgagatataaaaccagaaaatctC
ttaatcagccacaatgatgtcctaaaactgtgtgactttggttttgctcgtaatctgtcagaa
ggcaataa:gctaaCCacacagagtacgttgccaccagatggtatcggtccccagaac:Ctta
cttggchiccctatggaaagtccgtggacaCgtggchgnggctgtattcttggggagct
agcgatggacagcctttatttcctggagaaagtgaaattgaccaactttttactattcagaag
gCgCCaggaccaCCCccaLCLgagcagatgaagcttttctacagtaatcctcgcttccatggg
ctccggtt:CcagC:gttaaccatcctcagtccttggaaagaagataccttggaattC Cgaa
agtgttctacttgac
CCaaCgaagaatt:actgaagttggacccagctgacagatacttgacagaacagtgLC Cgaa
caccctacatttcaaacccagagacCtctggatcgttctccttcaaggtcagcaaaaagaaaa
cctvacca Cgtggaaagcagcacat:gtctaatagaaaccaagccggcaaaagtactgctttg
cag:Ctcaccacagatctaacagcaaggacatccagaacctgagtgtaggcctgccccgggc
gacgaagg:ctccctgccaatgaaagcttcctaaatggaaaccttgctggagctagtcttagt
40 ccactgcacaccaaaaCCtaccaagcaagcagccagcctgggtctaccagcaaagatctcaCC
aacaacaacataccacaccv Lct vagcccaaaagaagccaag:Caaaaacagagtttgatttt
aatattgacccaaagccttcagaaggcccagggacaaagtacctcaagtcaaacagcagatct
cagcagaaccgccactcat:Catggaaagctctcaaagcaaagctgggacactgcagcccaat
gaaaagcagagtcggcatagcta:attgacacaat:CcccagvchCvaggagtccctcctac
aaggccaaaagccatggggcactgagtgactccaagtctgtgagcaacctttctgaa
gccagggcccaaa:tgcggagcccagtaccagtaggtacttcccatC vagcvgcttagacttg
aa:tctcocaccagcccaacccccaccagacacag:gacacgagaac:ttgctcagcccttct
ggaagaaataaccgaaatgagggaacgctggactcacgtcgaaccacaaccagacattctaag
gaggaat:gaagc:gccggagcacatggacagtagccattcccat:Cactgtctgca
CC:Cacgaatctt:t
tcttatggactgggctacaccagccccttttcttcccagcaacgtcctcataggcattctatg
ta:gtgacccgtgacaaag:gagagccaagggcttggatggaagcttgagcatagggcaaggg
atggcagc:agagccaacagcctgcaactct:gtcaccccagcctggagaacagctccctcca
gagatgactgtggcaagatcttcggtcaaagagacctccagagaaggcacctcttccttccat
acacgccagaagtc:gagggtggagtgta: catgacccacactctgatgatggcacagccccc
aaagaaaa:agacacctatacaatgatccvgvgccaaggagagttggvagCLLvtacagagtg
ccatctccacgtccagacaattctttccatgaaaataatgtgtcaactagagtttcttctcta
cca:Cagagagcag:tctggaaccaaccactcaaaaagacaaccagcaLtcga vccavggaaa
agtcctgaaaatat:agtca:tcagagcaactcaaggaaaaagagaagcaaggattt:tcagg
tcaatgaaaaagaaaaagaagaaatctcaaacagtacccaattccgacagccctgatcttctg
acgttgcagaaa:Ccattca VLCLgC vagcaetccaagcagcagaccaaaggagtggcgcccC
gagaagatctcagaZctgcagacccaaagccagccattaaaatcactgcgcaagttg:tacat
ctc:cttcggcctcaaatcacccggcttcctcagatCCccgcttccagcccttaacagctcaa
caaaccaaaaatCccttctcagaaaL vcggaL vcaCCCCC:gagccaggcctctggcgggagc
agcaacatccggcaggaacccgcaccgaagggcaggccagccctccagctgccagacggtgga
ggcagaaga
cagagacaccattctggaccccaaga:agacgcttcatgttaaggacgacagaacaacaagga
gaatacttctgctgtggtgacccaaagaagcctcacactccgtgcgtcccaaaccgagccctt
ca:Cgtccaatctccagtcc:gctcc cta: ccagtactccaggtccgaggcacttccatgtgc
ccgacacCocaggtccgaggcacha vgcv LLcagcLgcccaacccagcaatccgggvvctCL
ttcttcgtgagacacgttatgagggaagccctgattcacagggcccaggtaaaccaagctgcg
CLCCVgaca vaccaLgagaa:gcggcactgacgggcaagtccgctcgaggagggcccgaacaa
avc vcagaagagga:ctgaa:agcgccgtcgaccatcatcatcatcatcattga
SEQ ID NO: 8 CDKL5 115 isoform fusion protein (IgK—TATK-CDKL5(115)-MYC—HIS)
[xflypepfide
METDTLLLWVLLLWVPGSTGJAAQPARRARRTKLAAYARKAARQARAPVKIPNIGNVMWKFE_:
40 GAYGVVLKCQHKETHEIVAIKKFKDSTENEEVKETTTREWKMT.RTTKQENTVEVKEA
FRRRGKLY_JVFEYVZ ESE *MPWGVPPEKVKSYTYQ.”KAIiWCHKND"VHRD_KPENL
ANDVLK EEGAPYGKSVJMWSVGCIEGEL
LRFPAVNHPQSLERRYWGILN
RSAKRKPYHVESSTLSNRWQAG
45 KSTALQSHARSNSKJIQNLSVGLPRA
SKDTTNNNT?HL.S?KEAKSKTEFDFVIDPKPSEG?GTKY.JKSNSRSQQNRHSFMESSQSKAG
TLQPNEKQSRflSY:JTIPQSSRSPSYRTKAKSHGA. HPSTSRYFPS
SCLDLNSPTSPTPTRHSDTRTLLSPSGRNNRNEGTA
HSLSAPHES?SYGLGYTSPFSSQQQP{RHSWYVTRDKVRAKGTDGSTSTGQGWAARA
SPQPGEQHPPEMTVARSSVK4TSR4GiSSbiiRQKS.LGGVYHDPHSDJGTAPK'iNRi
PRRVGSFYRVPSPRPDNSFHENNVSTRVSSAPSESSSGTNHSKRQPAFDPWKSPE ISHSEQL
KEKEKQGTFQSMKKKKKKSQTVPWSDSPDL .T.QKSTHSAST?SSRPK?WRP4KTSD
PLKSLRKHL NHPASSDPRFQPLTAQQTKNSFSEIa: {PLSQASGGSSWIRQEPAPKG
RPAAQLPDGGCDGRRQRHHSGPQDRRFMLRTTEQQGEYFCCGJPKKPHTPCVPNRAA
PAPYPVLQVRGTS WCPTLQVRGTDAFSCPTQQSGFSFFVRiVWREAL:HRAQVWQAA
HTGKSARGGP.EQKLIS4 4DLNSAVDHHHHHH
SEQ ID NO: 9 CDKLS 115 isoform fusion protein TK-eGFP-CDKL5(115)-MYC-
HIS) polynucleotide. Underline indicates codon for the initiator methionine.
gotagccaccatggagacagacacactcc:gctatgggtac:gctgctctgggttccaggttc
cactggtgaCgcggcccagccggccaggcgcgcgcgccgtacgaagcttgcggcctacgccag
aaaggccgccaggcaggccagggcaccgg:Cgccaccatgg:gagcaagggcgaggagctgtt
caccgggg:ggtgcccatcctggtcgagctggacggcgacg:aaacggccacaagttcagcgt
gtccggcgagggcgagggcgatgccacctacggcaagctgaccctgaagttca:Ctgcaccac
cggcaagc:gcccgtgccc:ggcccaccctcgtgaccaccc:gacctacggcg:gcagtgctt
cagccgctaccccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggcta
ggagcgcaccatcv vctLcaaggacgacggcaactacaagacccgcgccgaggtgaa
gttcgagggcgacaccctggtgaaccgcatcgagctgaagggcatcgacttcaaggaggacgg
caacatcctggggcacaagc:ggagtacaactacaacagccacaacg:Ctatatcatggccga
caagcagaagaacggcatcaaggtgaacttcaagatccgccacaaca:Cgaggacggcagcg
gcagctcgccgaccactaccagcagaacacccccatcggcgacggccccgtgctgctgcccga
caaccactacctgagcacccagtccgccc:gagcaaagaccccaacgagaagcgcgatcaca
ggtcctgctggagttcgtgaccgccgccgggatcactctcggcatggacgagctgtacaagtc
cggactcagatctcgagcgaagat:Cctaacattgg:aatgtgatgaataaatttgagatcc
tggggttg:aggtgaaggagccta eggagLLgtaCL vaaaLgcagacacaaggaaacacatga
aattgtggcgatcaagaaattcaaggacagtgaagaaaatgaagaagtcaaagaaacgacttt
gc:taaaatgcttcggactctcaagcaggaaaacattgtggagttgaaggaagcatt
tcgtcggaggggaaagttgtacttggtgtttgagtatgttgaaaaaaatatgctcgaattgct
ggaagaaa:gccaaatggagttccacctgagaaagtaaaaagctacatctatcagctaatcaa
ggc:attcactgg:gccataagaatgatattgtccatcgaga:ataaaaccagaaaatctct
aatcagccacaatgatgtcctaaaactgtgtgactttggttttgctcgtaatctgtcagaagg
LgCLaaL vacacagagtacgttgccaccagangLa ngg eccccagaactcttac
tggcgctccctatggaaagtccgtggacatgtggtcggtgggctgtattcttggggagcttag
40 cgatggacagcct vLatt ecctggagaaagtgaaa:tgaccaactt thaCLa agg
gctaggaccacttccatc:gagcagatgaagcttttotacagtaatcctchL eccanggC
ccggtttccagctgttaaccatcctcagtccttggaaagaagataccttggaattttgaatag
tgttctacttgacctaatgaagaatttactgaagttggacccagctgacagatacttgacaga
acagtgtttgaatcaccctacatttcaaacccagagacttctggatcgttctccttcaaggtc
agcaaaaagaaaaccttaccatgtggaaagcagcacattgtctaatagaaaccaagccggcaa
aagtacth:ttgcagtctcaccacagatctaacagcaaggacatccagaacctgagtgtagg
cctgccccgggctgacgaaggtctccctgccaatgaaagcttcctaaatggaaaccttgctgg
agcvagLCLvachcaCLgcacaccaaaacc:accaagcaagcagccagcctgggtC:accag
caaagatctcaccaacaacaacataccacaccttcttagcccaaaagaagccaagtcaaaaac
agagtttga:tttaatattgacccaaagcct:cagaaggcccagggacaaagtacctcaagtC
aaacagcagatctcagcagaaccgccactcattcatggaaagctctcaaagcaaagC:gggaC
gcccaatgaaaagcagagtcggcatagctatattgacacaattccccagtcctctag
gagtccctcctacaggaccaaggccaaaagccatggggcactgagtgactccaagtC:gtgag
caacctttctgaagccagggcccaaattgcggagcccagtaccagtaggtacttcccatctag
ctgcttagacttgaattctcccaccagcccaaccCccaccagacacagtgacacgagaacttt
gctcagCCC:tctggaagaaataaccgaaatgagggaacgctggactcacgtcgaaccacaac
cagacattctaagacgatggaggaattgaagctgccggagcacatggacagtagccattccca
ttcactgtC:gcacctcacgaatctttttCttatggactgggctacaccagcccctVLactLC
ccagcaacgtcctcataggcattctatgtatgtgacccgtgacaaagtgagagccaagggctt
ggatggaagcttgagcatagggcaagggatggcagc:agagccaacagcctgcaacWCvtgtc
accocagcc:ggagaacagctccctCcagagatgaC:gtggcaagatcttcggtcaaagagac
ctccagagaaggcacctcttccttccatacacgccagaagtctgagggtggagtgtatcatga
cocacacvcvgavgangcacagcccccaaagaaaatagacacctatacaatgatcctgtgcc
aaggagagttggtagcttttacagagtgccatctccacgtccagacaattctttccatgaaaa
taaLgtgvcaacvagagtvacttCLCLaccaLcagagagcagttctggaaccaaccactcaaa
aagacaaccagcattcga:ccatggaaaagtcctgaaaatattagtcattcagagcaactcaa
ggaaaaagagaagcaaggatttttcaggtcaatgaaaaagaaaaagaagaaatctcaaacagt
acccaattccgacagcccagaLCVLCLgacgvtgcagaaaaccatvcaLtCLgctagcactCC
aagcagcagaccaaaggagtggcgccccgagaagatctcagatctgcagacccaaagccagcc
attaaaa:cactgcgcaagttgttacatctthttcggccacaaavcacccggcttcctcaga
tccccgcv-Ccageccttaacagc:caacaaaccaaaaat:ccttctcagaaattcggattca
3O ccccctgagccaggcctctggcgggagcagcaacatccggcaggaacccgcaccgaagggcag
gccagccc:Ccagctgccagacggtggatgtgatggcagaagacagagacaccattctggacc
ccaagatagacgcttcatgttaaggacgacagaacaacaaggagaatacttctgctgtggtga
cccaaagaagcctcacactccgtgcgtcccaaaccgagcccttcatcgtccaatctccagtcc
tgc-CCCLaLccag-actccaggtccgaggcacttccatgtgcccgacactccaggtccgagg
cac:gatgctttcagctgcccaacccagcaatccgggttctctttcttcgtgagacacgttat
gagggaagccctgattcacagggcccaggtaaaccaagctgcgctcctgacataccatgagaa
actgacgggcaagtccgctcgaggagggcccgaacaaaaactcatctcagaagagga
tctgaatagcgccg:cgaccatcatcatcatcatcattga
SEQ ID NO: 10 CDKLS 115 isoform fusion protein ATK-eGFP-CDKL5(115)-MYC-
40 HIS) polypeptide. Translated from nucleotide 11 ator methionine) of SEQ ID NO: 9.
METJTLLLWVLLLWVPGSTGJAAQPARRARRTKLAAYARKAARQARAPVATMVSKG1%.ETGVJ.
VPLLVELDGDVNGHK1'SVSGLGEGDATYGKLTLKFICTTGKLPVPWPiLV-iL_YGVQCFSRY
PDHMKQHDFFKSAMTTGYVQTTTTFFKDDGWYKTRAFVKFFGDTT.VNT’ELKG'DFKTDGNTL
G {K.TYNYNSANVYLWADKQKNG"KVWFK‘RiNITJGSVQLAJHYQQWTPLGDGPV..PJNHY
LSTQSALSKDPNEKRDHMVLLLFVLAAG__LGMDLLYKSGLRSRAKIPNIGNVMNKFEILGVV
GEGAYGVVLKCRHKETHEIVAIKKFKDSFTWTTVKTTTLRT.KMLRT.KQFWVTLKTATRR?
GKLYIVEfiYViKNW.fiLLfifiMPNGVPPEKVKSYIYQ.IKA’{WCHKNJLVHRJLKPEWLLIS{
LFPGESTTJQLFTTQKV.GPLPSTQWKLTYSVPRF{GLRFPAVNHPQSLFRRYLGT.NSVL.
DLMKNLLKL,PADRYLTEQCLNHPTFQTQRLLJRSPSRSAKRKPYHVTSST.SNRNQAGKSTA
LQSHHRSWSKDIQVLSVGLPRADHGLPANHSFLNGNLAGASISPTHTKTYQASSQPGSTSKDL
TWNWTPH..S?KFAKSKTT 3T T PGTKYLKSNSRSQQNRiSFM_ESSQSKAGTLQP
NEKQSRHSYI3TIPQSSRSPSYRTKAKSHGALSDSKSVSNLSEARAQLAEPSTSRYFPSSCLJ
LWSPTSPTPTRHS3TRTLLSPSGRVWRNEGTLDSRRTTTRHSKTMEELKLPEHWDSSHSHS_LS
ATHESFSYGLGYTSPFSSQQR?HR{SWYVTRDKVRAKGLDGS_LSIGQGWAARAWSLQ..SPQP
GEQLPPEMTVARSSVKELSTAGlsSi{TRQKSEGGVYHDPASJDGTAPKENR{LYNDPVPRRV
GSFYRVPSPTPDNSFHEWWVSTRVS LPSESSSGTN{SKRQPAFDPWKSPEWISHSEQLKEKE
KQGFFRSMKKKKKKSQTVPWSDSP3..TLQKSIHSASTPSSRPKEWRPTK SD.QTQSQPLKS
LRKLLHLSSASNHPASSDPREQPLiAQQiKNS:'SLIRiHPLSQASGGSSNLRQLPAPKGRPAL
QLP3GGCDGTRQRHHSGPQDTTFMLTTTFQQGTYFCCGDPKKPHTPCVTNRALHTPISSTAPY
PVLQVRGTSWCPTLQVRGTDATSCPTQQSGFSTFVRiVMREALIHRAQVNQAA.LTYHTWAAL
TGKSARGGPLQKLISEEDLNSAVDH_{HHHH
SEQ ID NO: 11 CDKL5 107 isoform fusion protein ATK—eGFP—CDKLSG07)-MYC-
HIS) polynucleotide
acagacacactcctgctatgggtactgctgctctgggttccaggttccactggtgac
gcggcccagccggccaggcgcgcgcgccgtacgaagcttgcggcctacgccagaaaggccgcc
aggcaggccagggcaccgg:cgccaccatggtgagcaagggcgaggagctgLLcaccggggtg
gtgcccatcctggtcgagctggacggcgacgtaaacggccacaagttcagcgtgtccggcgag
ggcgagggcgatgccacctacggcaagctgaccctgaagttcatctgcaccaccggcaagctg
cccgthCC:ggcccaccC:cgtgaccaCCC:gacctacggcgtgcagLgcLLcagccgctac
cccgaccacatgaagcagcacgacttcttcaagtccgccatgcccgaaggctacgtccaggag
cgcaccaLCLtCLLcaaggacgacggcaactacaagacccgcgccgaggtgaagttcgagggc
gacaCCCZggtgaaccgca:cgagC:gaagggcatcgacttcaaggaggacggcaaca:cctg
gggcacaagctggagtacaactacaacagccacaacgtctatatcatggccgacaagcagaag
aacggcatcaagngaacLLcaaga:ccgccacaacatcgaggacggcagcgtgcagc:cgcc
gaccactaccagcagaacaccccca:cggcgacggcCccgtgctgctgcccgacaaccactaC
ctgagcacccagtCcgccctgagcaaagaccccaacgagaagcgcgatcacatggtcctgctg
gagttcgtgaccgccgccgggatcactctcggcatggacgagctgtacaag:ccggac:caga
tctcgagcgaagat:cctaacattggtaatgtgatgaataaatttgagatCCCtggggttgta
ggagcctangagLtgtacttaaatgcagacacaaggaaacacatgaaattgtggcg
atcaagaaattcaaggacagtgaagaaaatgaagaag:CaaagaaacgaCLL Lacgagagctt
aaaatgcttcggactctcaagcaggaaaacattgtggagttgaaggaagcat:tcgtcggagg
ttgtacttggtgtLtgagLatgttgaaaaaaatatgctcgaattgc:ggaagaaatg
ccaaatggagttcoacctgagaaagtaaaaagctacaLctaLcagCLaatcaaggctattcaC
tggtgccataagaatgatattgtccatcgagatataaaaccagaaaatctcttaatcagccac
aatgatgtcctaaaactngLgacLLtggLLLtgcchtaatctgtcagaaggcaataatgct
2017/039692
aavvacacagagtacgttgccaccagatggLavcggvccccagaactcttaC:tggch:CCC
tatggaaagtccgtggacatgtgg:cggtgggctg:attcttggggagcttagcgatggacag
CCVvtattvCctggagaaagtgaaa:tgaccaactvvttacvattcagaaggtgctaggacca
cttccatC:gagcagatgaagctLvvctacagvaavcctchLLccanggcvccgngvcca
gctgttaaccatcctcagtccttggaaagaagataccttggaattttgaatagtgttctactt
gacctaatgaagaavttaCLgaagvvggacccagc:gacagatacttgacagaacagtgtttg
aatcacccvacaLvvcaaacccagagacthvggavcgttctccttcaaggtcagcaaaaaga
aaaccttaccatgtggaaagcagcacattgtctaatagaaaccaagccggcaaaagtactgct
ttgcagtC:caccacagatctaacagcaaggacatccagaacctgag:gtaggcctgccccgg
gotgacgaaggtC:ccctgccaatgaaagct:cctaaatggaaaccvvgctggagctagtct:
agtccactgcacaccaaaacctaccaagcaagcagccagcctgggtctaccagcaaagatctc
aacaacataccacacctVCLvagcccaaaagaagccaag:caaaaacagagtttga:
tt:aatattgacccaaagcc:tcagaaggcccagggacaaagtaCC:caagtcaaacagcaga
tctcagcagaaccgccactcattcatggaaagctctcaaagcaaagctgggacactgcagccc
aatgaaaagcagagtcggcavagCLavatLgacacaattccccag:cctctaggagtccctcc
tacaggaccaaggccaaaagccatggggcactgagtgactccaagtctgtgagcaacctttC:
gaagccagggcccaaattgcggagcccagtaccagtaggtacttcccatctagctgcttagac
ttgaattctCccaccagcccaacccccaccagacacagtgacacgagaacVngctcagCCC:
tCtggaagaaataaccgaaatgagggaacgctggactcacg:cgaaccacaaccagacattc:
aagacgatggaggaattgaagctgccggagcacatggacag:agccattcccattcactgtct
gcacctcacgaaLCthtLCvLangachggctacaccagccchVLLCVVcccagcaacg:
cc:cataggcattC:atgtatgtgacccgtgacaaagtgagagccaagggcttggatggaagc
ttgagcatagggcaagggatggcagctagagccaacagcctgcaac:cttgtcaccccagcct
ggagaacagctccc:ccagagatgactgtggcaaga:cttcggtcaaagagacctccagagaa
ggcacctcttccttccatacacgccagaagtctgagggtggagtgtatcatgacccacactct
gatgatggcacagcccccaaagaaaatagacacctavacaavgatCC:gtgccaaggagagtt
ggvagctLvvacagagtgccatctccacg:ccagacaattcvVtccavgaaaataatgtgtca
gtttcttctctaccatcagagagcagttctggaaccaaccactcaaaaagacaacca
gcattcga:Ccatggaaaagtcctgaaaa:attagtcattcagagcaactcaaggaaaaagag
aagcaaggavttLvcaggLcaatgaaaaagaaaaagaagaaa:ctcaaacagtacccaattcc
gacagccctgatcttctgacgttgcagaaatccattcattctgctagcactccaagcagcaga
ccaaaggag:ggcgccccgagaaga:ctcagatctgcagacccaaagccagccattaaaatca
ctgcgcaagvtgtvacatctctcttcggcctcaaatcacccggcttcctcagatccccgcttc
ttaacagctcaacaaaccaaaaattccttctcagaaattcggattcaccccctgagc
caggcctctggcgggagcagcaaca:ccggcaggaacccgcaccgaagggcaggccagccctC
cagctgccaggtcagatggatcctggttggcatgtgtcctctgtgaccaggagtgccacagag
ggcccttcctactctgaacagctgggtgccaaaagtgggccaaatgggcacccctataacaga
acaaatcgctcacgaatgccaaatC:gaatgatttaaaagagacagccttgtccgctcgagga
gggcccgaacaaaaactcatctcagaagaggatctgaatagcgccgtcgaccatcatcatcat
catcattga
SEQ ID NO: 12 CDKLS 107 isoform fusion n (IgK-TATK-eGFP—CDKL5(107)-MYC-
HIS) polypeptide
METJTLLLWVLLLWVPGSTGDAAQPARRARRTKLAAYARKAARQARAPVATMVSKGEELTTGV
VP".VELDGDVNGHKFSVSG_EGEGDATYGK.TLKFCTTGKLPVPWPTLVTTJTYGVQCFSRY
PDHMKQHDFFKSAMPEGYVQERT_FFKDDGNYK'_RALVKthGDi’LVNRiELKGiDtKhDGNLL
GHKJEYNYNSHNVY_MADKQKNG'KVNFK RHN'FDGSVQLADHYQQNTP:GDGPVL_4P3NHY
LSTQSALSKDPNEKRDHMVLLEFVTAAG"TLGMD3.YKSGLRSRAKIPNIGNVMNKFH"1GVV*J
GEGAYGVVLKCRHKEiHEiVAiKKEKJSEENEjVKEi_LRELKMLR_LKQENIVELKEAERRR
GKT.YT.VFFYV3KNWL3LT.F3MPNGVPREKVKSYTYQL3KAT{WCHKNDTVHRDTKPFNLLISH
NJVLKLCDFGFARNLSEGNNANYi_LYVA'- 3.LLGAPYGKSVJMWSVGCILG3.SDGQ
PLFPGESEIDQLFTIQKVLGPLPSEQMKLFYSNPRF.iGLRFPAVNHPQSLERRYLGILNSVLL
DLMKNLLKLDRADRY.TFQC.NHPTFQTQRLJDRSPSRSAKRKPYHVESSTLSNRNQAGKSTA
LQSiHRSNSKJIQN.SVG.PRADEGLPANESELNGN.AGAS.SPLiTKTYQASSQPGSTSKD_4
TNNN_PHLLSPKEAKSKiEbDbNiDPKPSEGPGlKYLKSNSRSQQNRHSFMESSQSKAGTLQP
NEKQSRHSYI3TIPQSSRSPSYRTKAKSHGALSDSKSVSN.S3ARAQAEPSTSRYFPSSCLD
LNSPTSPTPTRHSDTRTLJSPSGRNNRNEGT_JJSRRTTTR SKi'ME3TKLP3 WJSSiSHSLS
APHESFSYGLGYTSPFSSQQRPHRHSWYVTRDKVRAKGLDGSLSIGQGMAARANSLQLLSPQP
G3 VARSSVKETSREGTSSFHTRQKSE.GGVYHDP PKENR LYNDPVPRRV
GSFYRVPSPRPDNSFHENNVSTRVSSLPSESSSGTN{SKRQPA3DPWKSPENISdSEQLKEKE
KQGFFRSMKKKKKKSQTVPNSDSPDLLTLQKSIHSASTPSSRPKFWRPPK SDLQTQSQPLKS
.SSASNHPASSDPRFQPLTAQQTKNS3S33RTHP.SQASGGSSN'RQ3RAPKGRPAL
QLPGQMDPGW.{VSSVTRSATEGPSYSEQLGAKSGPNGHPYNRTNRSRMPNLNDLKETALSARG
GPEQKLISEEDLNSAVDHHHHHH
SEQ ID NO: 13 CDKL5 107 isoform fusion protein (ng-TATK-CDKL5(107)-3XFLAG
polynucleotide. Underline indicates codon for the initiator nine.
go:agccaccggggagacagacacactcctgctatgggtac:gctgc:ctgggttccaggttC
caC:ggtgacgcggcocagccggccaggcgcgcgcgccgtacgaagC:tgcggcctacgccag
aaaggccgccaggcaggccagggcaccggtgaagattcctaacattggtaatgtgatgaataa
ateegagaLCcttggggttgtaggtgaaggagcctatggag:tgtaCttaaatgcagacacaa
ggaaacacatgaaattgtggcgatcaagaaa:tCaaggacag:gaagaaaatgaagaagtcaa
agaaacgactttacgagagcttaaaatgcttcggactctcaagcaggaaaacattgtggagtt
gaaggaagcatttcgtcggaggggaaagtvgvactngthVegagvatgtvgaaaaaaatat
aLvgctggaagaaatgccaaatggagttCcaCctgagaaagtaaaaagctacatcta
tcagctaatcaaggctattcactggtgccataagaatgatattgtccatcgagatataaaacc
agaaaatc:cttaatcagccacaaegatgvcctaaaactgvgvgacevtggVVLtgcvcgtaa
totgtcagaaggcaataatgctaavvacacagagtacgttgccaccagatggtatcggtcccc
agaactcttacttggcgctccctatggaaagtccgtggacatgtggtcggtgggctgtattct
tggggagcvvagcgatggacagccvvLateecctggagaaagegaaangaccaacLvthaC
tavvcagaaggtgc:aggaccact:ccatC:gagcagatgaagcttVectacagtaa:cctcg
cttccatgggctccggtttccagctgttaaccatcctcagtccttggaaagaagataccttgg
aavthgaavangvectacvtgaccvaavgaagaathachaagveggacccagC:gacag
atacttgacagaacagtgtLegaavcacccvacatv-Caaacccagagacttctgga:cgttc
tCcttcaaggtcagcaaaaagaaaacCttaccatgtggaaagcagcacattgtctaatagaaa
ccaagccggcaaaagvacngLtLgcagLCvcaCcacagatctaacagcaaggacatccagaa
cctgagtgtaggcctgccccgggCZgacgaaggtthcctgccaatgaaagCCtcctaaatgg
aaaccttgctggagctagtcttag:Ccactgcacaccaaaacctaccaagcaagcagccagcc
tgggtctaccagcaaaga:ctcaccaacaacaacataccacacctLCvvagcccaaaagaagc
caagtcaaaaacagagtttgattttaatattgacccaaagccttcagaaggcccagggacaaa
gtacctcaagtcaaacagcagatC:cagcagaaccgccactcattcatggaaagctC:caaag
caaagctgggacactgcagcccaatgaaaagcagagtcggcaLagCLavaLegacacaattcc
ccagtcctctaggagtccctcctacaggaccaaggccaaaagccatggggcactgagtgactc
caagtctgtgagcaacctttctgaagccagggcccaaattgcggagcccagtaccag:aggta
WO 05617
CLLcccaLCLagCLgcttagacttgaattctcccaccagcccaacccocaccagacacagtga
cacgagaactttgctcagcccttctggaagaaataaccgaaatgagggaacgctggactcacg
tcgaaccacaaccagacat:ctaagacgatggaggaattgaagctgccggagcacatggacag
tagccatecccaLLcactgtctgcacctcacgaaLCLLtLLCLLangaCvgggctacaccag
ccccttttcttcccagcaacgtcctcataggcattctatgtatgtgacccgtgacaaagtgag
agccaagggcttggatggaagcttgagcatagggcaagggatggcagctagagccaacagcct
gcaactcvLgtcacoccagcctggagaacagctcCC:ccagagatgactgtggcaaga:cttC
ggtcaaagagacctccagagaaggcacctcttccttccatacacgccagaagtctgagggtgg
agtgtatcatgacccacactctga:gatggcacagcccccaaagaaaatagacacctatacaa
tgatcctgtgccaaggagathggLagctLLLacagagtgccatC:ccacgtccagacaattc
tgaaaataatgtgtcaactagagtttcttctctaccatcagagagcagttctggaac
caaccactcaaaaagacaaccagcaLchaeccangaaaagtCC:gaaaa:attagtcattc
agagcaac:caaggaaaaagagaagcaaggaLttvLcaggLcaatgaaaaagaaaaagaagaa
atctcaaacagtacccaattccgacagccctgatcttctgacgttgcagaaatccattcattc
tgc:agcac:ccaagcagcagaccaaaggagtggcgccccgagaaga:ctcagatctgcagac
ccaaagccagccattaaaatcactgcgcaagLtgtvacatctctcttcggcctcaaatcaccc
ggcttcctcagatccccgcttccagcccttaacagctcaacaaaccaaaaattccttctcaga
aaLLoggaLLcaccccctgagccaggcctctggcgggagcagcaaca:ccggcaggaacccgc
gggcaggccagccctccagctgccaggtcagatggatcctggttggcatgtgtcctC
tgtgaccaggagtgccacagagggccCttcctactctgaacagctgggtgccaaaagtgggcc
aaatgggcacccctataacagaacaaatcgctcacgaatgccaaatCtgaatgatttaaaaga
gacagccttgtctagaggatcccgggctgactacaaagaccatgacggtgattataaagatca
tgacatcgaCtacaaggatgacgatgacaagtag
SEQ ID NO: 14 CDKL5 107 isoform fusion protein (IgK-TATK-CDKLS(107)-3XFLAG
polynucleotide
MFTJTLLLWVLLLWVPGSTG 3AAQPA?RARRTKLAAYARKAARQARAPVKIPNIGNVMWKFE_:
LGVVGEGAYGVVLKCRHKji{LIVA_KKbKJSLENw*VKhiiLRELKMLR-.KQLNV*LKLA
FRRRGK.Y.VFEYVFKNM.F. .PFMPWGVPPEKVKSY YQ. KA HWCHKNJ VHRD KPHN.
LISiWDV.K.CDTGFARN.STGNNANYTEYVATRWY RSPF.L.GAPYGKSV3MWSVGCTT.GF.
SDGQPLFPGESEIJQLFT:_QKVLGPLPSEQWKLFYSWPRF{GLRFPAVNHPQSLERRYLGILW
SVLLDLMKNLLKLDPADRYLTEQCLNHPTFQTQRLLDRSPSRSAKRKPYHVESSTLSNRNQAG
KSTALQS{{RSNSKJIQNLSVGLPRADEGLPAVESF.WGN.AGASTSP.HTKTYQASSQPGST
SKJ.TNNNTPALLSPKEAKSKTEFJFNIDPKPSEGPGTKYLKSNSRSQQNRASTMESSQSKAG
TLQTNEKQS?iSYIDTIPQSSQSPSYQTKAKSiGALSDSKSVSVLSEAQAQIAETSTSQYFPS
SPTSTTPTRiSDTRTLLSPSGRNWRNTGT.JSRRTTTQHSKTWEF.K.?EHWJSSHS
HSLSAPHESTSYGLGYTSPTSSQQRPflRHSMYVTRDKVRAKGLJGSLSIGQGMAARANSLQLL
SPQTGRQLTTTMTVARSSVKETSREGTSSFHTQQKSEGGVYHDTHSDDGTAPKTVRHLYNDPV
PRRVGSFYRVPSPRPDNSF{EVNVSTRVSSLPSESSSGTNHSKRQPAFDPWKSPEN:S{SEQL
KEKjKQGETRSMKKKKKKSQTVPNSDSPDLLTLQKSIHSASTPSSRPK:WRPEK-SDLQ1QSQ
PLKSLRKL.HLSSASWHPASSDPRTQTLTAQQTKNSTSEIR:HTLSQASGGSSW'RQTTAPKG
RPALQLPGQWJPGWHVSSVTRSAT.EGPSYS_EQLGAKSGPNGHPYNRTNRSRMPWLNJ.KTTA.
SRGSRADYKJdDGDYKDHDIDYKDJDDK
SEQ ID NO: 15 CDKL5 107 isoform polynucleotide. Sequence lacks the codon for the
initiator methionine.
aagattcctaacattggtaavgtgaLgaaLaaatLLgagaLccttggggttgtaggtgaagga
gcctatggagttgtacttaaatgcagacacaaggaaacacatgaaattgtggcgatcaagaaa
ttcaaggacagtgaagaaaatgaagaagtcaaagaaacgact:tacgagagc:taaaatgctt
ctcaagcaggaaaacattgtggagttgaaggaagcaVttcgvcggaggggaaagttg
tacttggtgtttgagtatgttgaaaaaaatatgctcgaattgctggaagaaatgccaaatgga
gttccacctgagaaagtaaaaagctacatCtatcagctaatcaaggC:attcactgg:gccat
aagaatgatattgtccatcgagatataaaaccagaaaatctcttaatcagccacaatgatgtc
ctaaaac:gtgtgactttggttttgctcgtaatctgtcagaaggcaataatgctaat:acaca
gagtacgttgccaccagatggtatcggtcoccagaactcttacttggcgctccctatggaaag
tccgtggacatgtggtcggtgggctgtattcttggggagcttagcgatggacagcctttattt
gaaagtgaaattgaccaacLLtLVaCLaLvcagaaggth:aggaccacttccatct
gagcagatgaagcttttctacagtaatcctcgcttccatgggctccggtttccagctgttaac
catcctcagtccttggaaagaagataccttggaatvvtgaaLagtgVLctanLgaCCLaatg
aagaatttactgaagttggacccagctgacagataettgacagaacagtgtttgaatcaCCC:
acatttcaaacccagagacttctggatcgttctccttcaaggtcagcaaaaagaaaaccttac
cavgvggaaagcagcacattgtctaatagaaaccaagccggcaaaagVaCLgCvttgcagtC:
caccacagatctaacagcaaggacatccagaacctgagtgtaggcctgccccgggctgacgaa
ggvcVCCCLgccaatgaaagcttcctaaatggaaaccttgctggagcvagtcvvachcactg
cacaccaaaacctaccaagcaagcagccagcctgggtctaccagcaaagatC:caccaacaac
aacataccacaccttcttagcccaaaagaagccaagtcaaaaacagagtttgattttaatatt
aagccttcagaaggcccagggacaaagtacctcaagtcaaacagcagatctcagcag
aaccgccactcattcatggaaagctctcaaagcaaagctgggacactgcagcccaatgaaaag
cagagtcggcatagctatattgacacaattccccagvcctcvaggagtCCC:CctacaggaCC
aaggccaaaagccatggggcactgagtgac:ccaagtctgtgagcaaccttvcvgaagccagg
gcccaaattgcggagcccagtaccagtaggtacttcccatCtagctgcttagacttgaattct
cccaccagcccaacccccaccagacacagtgacacgagaaC:ttgctcagCCC:tctggaaga
aataaccgaaatgagggaacgctggactcacgtcgaaccacaaccagacattCtaagacgatg
gaggaattgaagctgccggagcacatggacagtagccattcccattcactgtC:gcacctcaC
gaaLcttvLLcttangacnggcLacaccagcccottttcttcccagcaacg:cctcatagg
3O atgtatgtgacccgtgacaaagtgagagCcaagggcttggatggaagcttgagcata
gggcaagggatggcagctagagccaacagcctgcaactcttg:cacoccagcc:ggagaacag
ctccctccagagatgactgtggcaagatcttcggtcaaagagacctccagagaaggcacctct
tccttccatacacgccagaagtctgagggtggagtgtatcatgacccacactC:gatgatggC
acagcccccaaagaaaatagacacctatacaatgatcctgtgccaaggagagt:ggtagcttZ
tacagagtgccatctccacgtccagacaattctttccatgaaaataatgtgtcaactagagtt
tcvvctcLaccaLcagagagcagttctggaaccaaccactcaaaaagacaaccagcattcga:
ccatggaaaagtcctgaaaatattagtcattcagagcaactcaaggaaaaagagaagcaagga
tLvVLcagchaavgaaaaagaaaaagaagaaatthaaacagtacccaattccgacagCCC:
gatcttctgacgttgcagaaatccavtcatLctgcvagcactccaagcagcagaccaaaggag
40 tggcgccccgagaagatctcagatC:gcagacccaaagccagccattaaaatcactgcgcaag
ttgttacatctctcttcggcctcaaatcacccggC:tcctcagatccccgcttccagccctta
acagctcaacaaaccaaaaattccttctcagaaattcggattcaccccctgagccaggcctct
ggcgggagcagcaacatccggcaggaacccgcaccgaagggcaggccagccctccagctgcca
ggtcagatggatcctggttggcatgtgtcctctgtgaccaggagtgccacagagggcccttcc
gaacagctgggtgccaaaagtgggccaaatgggcacccctataacagaacaaatcgc
atgccaaatctgaatgatttaaaagagacagccttg
SEQ ID NO: 16 CDKLS 107 isoform polypeptide. Sequence lacks the initiator nine.
KIPNIGNVMNKFE".GVVGTGAYGVVLKCRinlHfi"VAiKKiKDS£4NEHVK1£LLRfi4KM.
RTWKQFNTVP‘.KPAFRRRGKiYT.VFPYVPKWMVFWTPPMPWGVPPEKVKSYTYQU‘KATHWCH
KND_VHRD’KPEN..TSHWJVUK.CJFGFARNUSTGWNANYTEYVATRWYRSPwULLGAPYGK
SVJMWSVGCI4GE_JSDGQPHEPGHS_LiDQLbiiQKV_nGPLPSEQMKnFYSNPRidGLRiPAVN
HPQSiPRRY.GTLWSVT.LDWWKNWWKTDPADRYLTEQCLNHPTPQTQQLLDRSPSRSAKQKPY
HVESSTLSNRVQAGKSTAJQSHHRSWSKDIQNLSVG.PRAJPGLPAWPSFTWGWLAGAS:SP.
HTKTYQASSQPGSTSKDLT-NNIP{4LSPK1AKSKiiEDENI PKPSEGPGTKYJKSNSRSQQ
NRHSPMESSQSKAGT"QPWTKQSRHSYIDT:PQSSQSPSYRTKAKSHGALSDSKSVS LSEAR
AQAPPSTSRYFPSSCLD_JW PTSPTPTRiSDTRT..SPSGRWNRNEGTLDSRRTTTR{SKTW
EELKAPEHMJSSHSHSLSAP.&ESFSYGLGYTSPFSSQQRPHRjSMYVTRDKVRAKGLJGSLSI
GQGWAARAWSLQLLSPQPGPQUPPTMTVARSSVKETSREGTSSPHTQQKSEGGVYHDPHSDDG
TAPKHNRi.YNDPVP RRVGSFYRVPSPRPDNS:'H_LWWV81RVSSLPSESSSGTWHSKRQPAPJ
PWKSPENIS_{SEQLK;KLKQG:bRSMKKKKKKSQTVPNSDSPDJLTHQKSIHSASTPSSRPKE
WRPTKISD QTQSQP.KSLRK.LH.SSASWHPASSJPRFQPLTAQQTKNSFSmTR'HP.SQAS
GGSSWIRQEPAPKGRPALQHPGQMDPGWHVSSVTRSATEGPSYSEQJGAKSGPWGHPYWRTNR
SRMPNLNDGKETAL
2017/039692
Claims (56)
1. A fusion protein for use in treating a CDKL5 deficiency or a Rett syndrome variant, wherein the fusion protein is administered systemically and the fusion protein comprises: a CDKL5 polypeptide sequence, wherein the CDKL5 polypeptide sequence has about 98% to 100% sequence identity to SEQ ID NO:2 or SEQ ID NO: 16; and a TATK polypeptide sequence, wherein the TATK polypeptide sequence has about 90% to about 100% ce identity to SEQ ID NO: 4, wherein the TATK polypeptide is operatively coupled to the CDKL5 polypeptide. 10
2. The fusion protein for use according to claim 1, r comprising an in leader sequence polypeptide, wherein the ng-chain leader sequence is operatively coupled to the CDKL5 polypeptide.
3. The fusion protein for use according to claim 1 or 2, further comprising a reporter 15 protein polypeptide, wherein the reporter protein polypeptide is operatively coupled to the CDKL5 polypeptide.
4. The fusion protein for use according to any one of claims 1-3, further comprising a protein tag polypeptide, wherein the n tag polypeptide is operatively coupled to the 20 CDKL5 polypeptide.
5. The fusion protein for use according to any one of claims 1-4, wherein the fusion protein has a polypeptide sequence according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
6. The fusion n for use according to any one of claims 1-5, wherein the fusion protein ses neurite growth, elongation, tic spine number, branch number, or branch density in a brain of a subject as compared to a control. 30
7. The fusion protein for use ing to any one of claims 1-6, wherein the fusion protein s neuronal apoptosis in the brain of a subject as compared to a control.
8. The fusion protein for use according to any one of claims l-7, wherein the fusion n is administered intravenously.
9. A pharmaceutical formulation for use in treating a CDKL5 deficiency or a Rett syndrome variant, wherein the pharmaceutical formulation comprises a pharmaceutically acceptable carrier and an effective amount of the fusion protein for use according to any one of claims 1—8.
10. A fusion n for use in sing neural activity in the visual cortex of a patient 10 having a CDKL5 deficiency, wherein the fusion protein is stered systemically and the fusion protein comprises: a CDKL5 ptide sequence, wherein the CDKL5 polypeptide sequence has about 98% to 100% sequence identity to SEQ ID N012 or SEQ ID NO: 16; and a TATK polypeptide sequence, wherein the TATK polypeptide sequence has about 90% 15 to about 100% sequence identity to SEQ ID NO: 4, wherein the TATK polypeptide is operatively coupled to the CDKL5 polypeptide.
11. The fusion protein for use according to claim 10, further sing an ng-chain leader sequence ptide, wherein the ng-chain leader sequence is operatively coupled to 20 the CDKL5 polypeptide.
12. The fusion protein for use according to claim 10 or 11, further comprising a reporter protein polypeptide, wherein the er protein polypeptide is operatively coupled to the CDKL5 polypeptide.
13. The fusion protein for use according to any one of claims 10-12, further comprising a protein tag polypeptide, wherein the protein tag polypeptide is operatively d to the CDKL5 polypeptide. 30
14. The fusion protein for use according to any one of claims 10-13, wherein the fusion protein has a polypeptide sequence according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
15. The fusion protein for use ing to any one of claims 10-14, wherein the fusion protein increases neurite growth, elongation, dendritic spine number, branch number, or branch density in a brain of a subject as ed to a control.
16. The fusion protein for use according to any one of claims 10-15, wherein the fusion protein reduces neuronal apoptosis in the brain of a subject as compared to a control.
17. The fusion protein for use according to any one of claims 10-16, wherein the fusion protein is stered intravenously.
18. A pharmaceutical ation for use in increasing neural activity in the visual cortex of a patient having a CDKL5 deficiency or a Rett syndrome variant, wherein the pharmaceutical formulation comprises a pharmaceutically acceptable r and an effective amount of the fusion protein for use according to any one of claims 10-17.
19. A method of treating a CDKL5 deficiency or a Rett syndrome variant, the method comprising systemically administering to a patient in need thereof a fusion protein sing: a CDKL5 polypeptide sequence, wherein the CDKL5 polypeptide sequence has about 98% to 100% sequence ty to SEQ ID NO:2 or SEQ ID NO: 16; and 20 a TATK polypeptide sequence, wherein the TATK polypeptide sequence has about 90% to about 100% sequence ty to SEQ ID NO: 4, wherein the TATK polypeptide is operatively coupled to the CDKL5 polypeptide.
20. The method according to claim 19, wherein the fusion protein further comprises an ng- 25 chain leader sequence polypeptide, wherein the ng-chain leader sequence is operatively coupled to the CDKL5 polypeptide.
21. The method according to claim 19 or claim 20, wherein the fusion n r comprises a reporter protein polypeptide, wherein the reporter protein polypeptide is 30 operatively coupled to the CDKL5 polypeptide.
22. The method according to any one of claims 19-21, wherein the fusion protein further comprises a protein tag polypeptide, wherein the protein tag polypeptide is ively coupled to the CDKL5 polypeptide.
23. The method according to any one of claims 19-22, wherein the fusion protein has a ptide sequence according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
24. The method according to any one of claims 19-23, wherein systemic administration of 10 the fusion protein increases e growth, elongation, dendritic spine number, branch number, or branch density in a brain of a subject as compared to a control.
25. The method according to any one of claims 19-24, wherein systemic administration of the fusion protein reduces neuronal apoptosis in the brain of a subject as compared to a control.
26. The method according to any one of claims 19-25, wherein the fusion protein is administered intravenously.
27. A method of increasing neural activity in the visual cortex of a patient having a CDKL5 20 deficiency or a Rett syndrome variant, the method comprising systemically administering to a patient in need thereof a fusion protein comprising: a CDKL5 polypeptide sequence, wherein the CDKL5 polypeptide sequence has about 98% to 100% ce identity to SEQ ID N022 or SEQ ID NO: 16; and a TATK polypeptide ce, wherein the TATK polypeptide ce has about 90% 25 to about 100% sequence identity to SEQ ID NO: 4, wherein the TATK polypeptide is ively coupled to the CDKL5 ptide.
28. The method according to claim 27, wherein the fusion protein further comprises an ng- chain leader sequence polypeptide, wherein the in leader sequence is operatively 30 coupled to the CDKL5 polypeptide.
29. The method according to claim 27 or claim 28, wherein the fusion protein further comprises a reporter protein polypeptide, n the reporter protein polypeptide is operatively coupled to the CDKL5 polypeptide.
30. The method according to any one of claims 27-29, wherein the fusion protein further comprises a protein tag polypeptide, wherein the protein tag polypeptide is operatively d to the CDKL5 polypeptide.
31. The method according to any one of claims 27-30, wherein the fusion protein has a 10 polypeptide sequence according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
32. The method according to any one of claims 27-31, n systemic administration of the fusion protein increases neurite growth, elongation, dendritic spine number, branch 15 number, or branch density in a brain of a subject as compared to a control.
33. The method according to any one of claims 27—32, wherein systemic stration of the fusion protein reduces neuronal apoptosis in the brain of a t as compared to a control. 20
34. The method according to any one of claims 27-33, wherein the fusion protein is administered intravenously.
35. A method of increasing neurite growth, elongation, dendritic spine number, branch number, or branch density in a brain of a patient having a CDKL5 ency or a Rett 25 syndrome variant, the method comprising systemically administering to a patient in need thereof a fusion protein comprising: a CDKL5 polypeptide ce, wherein the CDKL5 polypeptide sequence has about 98% to 100% sequence identity to SEQ ID N02 or SEQ ID NO: 16; and a TATK polypeptide sequence, wherein the TATK polypeptide sequence has about 90% 30 to about 100% sequence identity to SEQ ID NO: 4, n the TATK ptide is operatively d to the CDKL5 polypeptide.
36. The method according to claim 35, wherein the fusion protein further comprises an ng- chain leader sequence polypeptide, wherein the ng—chain leader sequence is operatively coupled to the CDKL5 ptide.
37. The method according to claim 35 or claim 36, wherein the fusion protein further comprises a reporter protein polypeptide, wherein the reporter protein polypeptide is operatively coupled to the CDKL5 ptide.
38. The method according to any one of claims 35-37, wherein the fusion protein further 10 comprises a protein tag polypeptide, wherein the n tag polypeptide is ively coupled to the CDKL5 polypeptide.
39. The method ing to any one of claims 35-38, wherein the fusion protein has a polypeptide sequence according to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ 15 ID NO: 14.
40. The method according to any one of claims 35-39, wherein the fusion protein is administered intravenously. 20
41. A method of reducing neuronal apoptosis in the brain of a patient having a CDKL5 deficiency or a Rett syndrome variant, the method comprising systemically administering to a patient in need thereof a fusion protein comprising: a CDKL5 polypeptide sequence, wherein the CDKL5 polypeptide sequence has about 98% to 100% sequence ty to SEQ ID NO:2 or SEQ ID NO: 16; and 25 a TATK polypeptide sequence, n the TATK ptide sequence has about 90% to about 100% sequence ty to SEQ ID NO: 4, wherein the TATK polypeptide is operatively coupled to the CDKL5 polypeptide.
42. The method according to claim 41, wherein the fusion protein further comprises an ng- 30 chain leader sequence polypeptide, wherein the ng-chain leader sequence is operatively coupled to the CDKL5 polypeptide.
43. The method according to claim 41 or claim 42, wherein the fusion protein further comprises a reporter n polypeptide, wherein the reporter protein polypeptide is operatively coupled to the CDKL5 ptide.
44. The method according to any one of claims 41-43, wherein the fusion protein further comprises a protein tag polypeptide, wherein the protein tag polypeptide is operatively coupled to the CDKL5 polypeptide.
45. The method according to any one of claims 41-44, wherein the fusion protein has a 10 polypeptide sequence ing to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
46. The method according to any one of claims 41—45, n the fusion protein is administered intravenously.
47. A method of improving motor function of a patient having a CDKL5 deficiency or a Rett syndrome variant, the method comprising systemically administering to a patient in need thereof a fusion protein comprising: a CDKL5 polypeptide sequence, wherein the CDKL5 ptide sequence has about 20 98% to 100% sequence identity to SEQ ID NO:2 or SEQ ID NO: 16; and a TATK polypeptide ce, wherein the TATK polypeptide sequence has about 90% to about 100% sequence identity to SEQ ID NO: 4, wherein the TATK polypeptide is ively coupled to the CDKL5 polypeptide. 25
48. The method according to claim 47, wherein the fusion protein further ses an ng- chain leader sequence polypeptide, wherein the ng-chain leader sequence is operatively coupled to the CDKL5 polypeptide.
49. The method ing to claim 47 or claim 48, wherein the fusion protein further 30 comprises a reporter protein polypeptide, wherein the reporter protein polypeptide is ively coupled to the CDKL5 polypeptide.
50. The method according to any one of claims 47-49, n the fusion protein further comprises a protein tag polypeptide, wherein the n tag polypeptide is operatively coupled to the CDKL5 polypeptide.
51. The method according to any one of claims 47-50, wherein the fusion protein has a polypeptide sequence ing to SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, or SEQ ID NO: 14.
52. The method according to any one of claims 47-51, wherein the fusion protein is 10 administered intravenously.
53. A polynucleotide as substantially described herein.
54. A polypeptide as substantially described .
55. A vector as substantially described herein.
56. A pharmaceutical formulation as substantially described herein.
Applications Claiming Priority (2)
Application Number | Priority Date | Filing Date | Title |
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US62/355,579 | 2016-06-28 | ||
US62/381,886 | 2016-08-31 |
Publications (1)
Publication Number | Publication Date |
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NZ749459A true NZ749459A (en) |
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