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• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
  • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
  • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
  • A61K48/0058—Nucleic acids adapted for tissue specific expression, e.g. having tissue specific promoters as part of a contruct
• • A—HUMAN NECESSITIES
  • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
  • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
  • A61P25/00—Drugs for disorders of the nervous system
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  • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
  • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
  • C12N15/09—Recombinant DNA-technology
  • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
  • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
  • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
  • C12N15/86—Viral vectors
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
  • C12N9/0004—Oxidoreductases (1.)
  • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
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  • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
  • C12N2750/00011—Details
  • C12N2750/14011—Parvoviridae
  • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
  • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
  • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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  • C12N2830/00—Vector systems having a special element relevant for transcription
  • C12N2830/008—Vector systems having a special element relevant for transcription cell type or tissue specific enhancer/promoter combination

Definitions

• WWOX WW domain-containing oxidoreductase
• the present disclosure provides methods and compositions for the treatment of WWOX-associated CNS disease.
• the present invention involves expressing a heterologous WWOX gene in the brain of the subject, and in various embodiments involves expressing the heterologous WWOX gene in neurons to treat or ameliorate conditions such as WOREE syndrome and SCAR12.
• the WWOX gene comprises one or more regulatory elements including a promoter that directs expression of the WWOX gene in neurons.
• the promoter can be a universal promoter or a neuron- specific promoter.
• An exemplary neuron- specific promoter is synapsin I promoter.
• the WWOX gene is a wild type gene or functional derivative and comprises untranslated sequences (e.g., in a 3'-UTR) that enhance mRNA stability.
• the individual to be treated is a pediatric or neonatal patient (e.g., a patient with WOREE or SCAR12).
• early treatment prevents manifestation of some clinical parameters of disease.
• the individual is an adult patient (e.g., with WOREE or SCAR12), and treatment can ameliorate one or more clinical parameters, such as epileptic episodes.
• the treatment substantially reduces frequency and/or severity of epileptic episodes.
• the invention provides a method for the treatment of WOREE syndrome or SCAR12, the method comprising administering to the brain of a patient in need of such treatment, an AAV9 gene delivery system comprising a WWOX wild type gene under control of a synapsin I promoter.
• the AAV9 delivery system may comprise the nucleotide sequence substantially as set forth in SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, and/or SEQ ID NO: 5.
• the present disclosure provides an expression construct comprising a WWOX wild type gene, or a functional derivative thereof, under the expression control of a neuron- specific promotor.
• An exemplary neuron- specific promoter is a synapsin I promoter.
• the nucleotide sequence comprises a sequence substantially as set forth in SEQ ID NO: 1, 3, 4, and/or 5.
• the expression construct is a viral vector, such as an adeno-associated virus (AAV) delivery system.
• the expression construct is an AAV9 delivery system.
• FIGS. 1A-1M provide a summary of a study, showing the phenotypes of the conditional deletion of murine Wwox in brain cells.
• A A representative image of Wwox null (KO) and wild type (WT) mice at P18.
• FIGS. 2A-F provide a summary of a study showing neocortical hyperexcitability in the S-KO neocortex.
• A In vivo recordings (P13-P17) from S- Control, S-HT and S- KO indicating bursting activity in S-KO (shown in red) as compared to heterozygote (S- HT, shown in blue) and S-Control, (shown in black).
• Inset of whole brain shows the positioning of the in vivo recording electrodes.
• 23 S-HT and 42 S-KO slices from 7 S-Control, 14 S-HT and 24 S-KO animals 0 S-Control slices showed busting (0%), 4 slices from 3 S-HT animals showed bursting ( ⁇ 20%), and 36 slices from 20 S-KO animals showed bursting ( ⁇ 84%).
• C A second example of an in vivo recording and its time-frequency spectrogram.
• D Power spectral analysis for in vivo and in vitro datasets for S-Controls, S-HTs and S-KOs obtained from data clear of stimulation artifacts.
• Gray bars indicate regions of significance as identified frequency-by-frequency.
• In vivo 12-20Hz shows elevated power in S-KO as compared to S-HT and 7-15Hz for S- KO as compared to S-Control.
• In vitro 3-13Hz showed elevated power of S-KO as compared to S-HT and S-Control.
• In vitro data z-score normalized to mean and standard deviation of 320-400Hz. Box plots show normalized power with frequency bands indicated on the horizontal axis.
• FIGS. 3A-3E provide a summary of a study, showing that neuronal deletion of Wwox impairs myelination and oligodendrocyte maturation.
• B Representative images of brain sections immunostained with anti-CNP and anti-MBP are shown from cerebellum.
• C Quantification of fluorescence intensity of CNP and MBP display reduced intensity in S-KO compared to S-Control.
• D Sagittal section of the brain tissues immunostained for CC1 and anti-PDGFRa. Images showing reduced number of matured oligodendrocytes in corpus callosum (marked with dotted white line and the magnified area is shown with white square) of S-KO compared to S-Control at P17.
• FIGS. 4A-4D provide a summary of a study, showing that neuronal deletion of Wwox reduces the myelination and axonal conductivity.
• FIGS 6A-6G provide a summary of a study, showing that WWOX-deficient oligocortical spheroids exhibit hyperexcitability and hypomyelination.
• A Schematic illustration of oligocortical spheroids slice set up. An electrode is used for local field potential recordings (LFP) while a second one is used for whole-cell patch recordings. Electrodes are positioned 150pm from the edge of the slice and 10- 15pm apart.
• FIGS. 7A-7F provide a summary of a studying, showing that restoration of WWOX in Synapsin I-positive neurons improves growth of Wwox null mice and extends their life span.
• A Illustration of the plasmid vector construct containing murine Wwox gene under human Synapsin I promoter. The Wwox gene sequence is followed by an IRES promoter and EGFP gene sequence.
• B Physical appearance of wild type (WT), Wwox null injected either with AAV9-hSynI-GFP (the control virus) or AAV9-hSynI- mWwox-IRES-GFP virus at P17.
• Graphs showing body weight (C) and blood glucose levels (D) of the mice at indicated days.
• FIGS. 8 A and 8B provide a summary of a studying, showing that neuronal restoration of WWOX reduces epileptic activity in neocortex.
• A Representative traces of cell-attached recordings performed in WT, KO and KO-treated with AAV9-hSynI- mWwox [KO+A-Wwox] pups at P20-21 days. Traces represent spontaneous neocortical activity (action potentials shown). The panels represent 12 s recording with an inset presenting a zoom-in of an 0.5 s interval. A clear hyperactivity of the KO brain is observed in these representative traces with the KO showing bursts of action potentials.
• FIGS 9A-9C provide a summary of a study, showing that WWOX restoration in neurons improves myelination by promoting OPCs differentiation in Wwox null.
• B Sagittal section of the brain (Pl 7) tissues immunostained for CC1 and PDGFRa.
• FIG. 1 Images showing increased number of matured oligodendrocytes in corpus callosum of the Wwox null after treatment with AAV9-hSynI-mWwox compared to Wwox null injected with AAV9-hSynI-GFP virus.
• FIGS. 10A-10E provide a summary of a study, showing that WWOX restoration in neurons reverses the abnormal behavioral phenotypes of Wwox null mice.
• B and
• C Graphs represent the velocity and distance travelled (cm) from the open field tracking.
• D Mice tracking images of elevated plus maze test from WT and KO+AAV-Wwox mice (age 8-10 weeks).
• FIGS. 11A-11F provide a summary of a study relating to the generation and characterization of WWOX knockout cerebral organoids.
• B Quantification of markers that represent the different populations that compose the ventricular- like zone (VZ), subventricular zone (SVZ), and the cortical plate (CP).
• TBR2 the intermediate progenitors (IPs)
• SOX2 the ventricular radial glia (vRGs).
• the boxplot represents the 1st and 3rd quartile, with its whiskers showing the minimum and maximum points and a central band representing the median.
• C qPCR analysis for the assessment of expression levels of different neural markers in 15 weeks COs: SOX2 and PAX6 (progenitor cells), TUBB3 (pan- neuronal), SLC17A6 and SLC17A7 (VGLUT2 and VGLUT1; glutamatergic neurons), and GAD1 and GAD2 (GAD67 and GAD65; GABAergic neurons).
• FIGS. 12A-12C provide a summary of a study, showing that WWOX-KO cerebral organoids demonstrated hyperexcitability and epileptiform activity.
• A Sample traces show visible differences in local field potential, with WWOX-KO COs showing increased activity compared with WT in baseline condition (left) and in the presence of 100 ⁇ M 4-AP (right).
• B Mean spectral power of week 7 WT and KO COs in baseline conditions. The line marks 0.25- to 1-Hz frequency range.
• FIGS. 13A-13F provide the summary of a study, showing that WWOX-KO cerebral organoids exhibited impaired astrogenesis and DNA damage response.
• B qPCR analysis of astrocytic markers in COs at week 15.
• FIGS. 14A-14E provide a summary of a study, showing that cerebral organoid RNA sequencing revealed major differentiation defects.
• RNA sequencing RNA-seq
• WT transcriptome analysis
• WT transcriptome analysis
• WT transcriptome analysis
• the y-axis indicates relative expression fold change.
• Data are represented as mean _ SEM.
• C Heatmap showing the expression levels of markers of the six different layers of the human cortex in week 15 organoids from deepest to the most superficial: TBR1, BCL11B (CTIP2), SATB2, POU3F2 (BRN2), CUX1, and RELN.
• FIGS. 15A-15E provide a summary of a study, showing that WWOX-related epileptic encephalopathy cerebral organoids recapitulate neuronal abnormalities.
• Peripheral blood mononuclear cells PBMCs
• iPSCs iPSCs
• FIGS. 16A-16F provide a summary of a study, showing that WWOX-related epileptic encephalopathies depict molecular abnormalities similar to a complete WWOX loss.
• A Week 15 WSM COs stained for astrocytic markers GFAP and S100b.
• Scale 50 pm.
• B Impaired DNA damage response in WOREE-derived organoids.
• Scale 50 ⁇ m (left) and 25 ⁇ m (right).
• C Quantification of DNA damage foci, marked by cH2AX (left) and 53BP1 (right), in the nuclei of the cells in the VZs of week 6 WSM COs.
• the boxplot represents the 1st and 3rd quartile, with its whiskers showing the minimum and maximum points and a central band representing the median.
• the present disclosure provides methods and compositions for the treatment of WW domain-containing oxidoreductase (WWOX)-associated CNS disease.
• WWOX WW domain-containing oxidoreductase
• the present invention involves expressing a heterologous WWOX gene in the brain of the subject, and in various embodiments involves expressing the heterologous WWOX gene in neurons to treat or ameliorate conditions such as WOREE syndrome and SCAR12.
• WWOX-associated CNS disease refers to diseases resulting from or associated with a mutated WWOX gene or with abnormal WWOX expression. Mutation could lead to complete or partial genomic deletion leading to loss of protein or truncation (non-sense mutations) or in milder conditions missense mutation. These diseases are those that are manifested in the CNS. Examples of such diseases are: WWOX-related epileptic encephalopathy (WOREE) syndrome; spinocerebellar ataxia, autosomal recessive, 12 (SCAR12), multiple sclerosis, Alzheimer, ’s disease, West syndrome, autism, and disorder of sexual development (DSD).
• WOREE WWOX-related epileptic encephalopathy
• SCAR12 autosomal recessive, 12
• DSD disorder of sexual development
• the invention provides for a method for the treatment of WWOX-associated CNS disease.
• the method comprises administering to the brain of a patient in need of such treatment, a WWOX wild type gene, or a functional derivative thereof, under control of regulatory element(s) that result in expression of WWOX in the brain.
• the WWOX-associated CNS disease is selected from WOREE syndrome, SCAR12, Alzheimer’s disease, West syndrome, autism, multiple sclerosis and DSD.
• the WWOX-associated CNS disease is WOREE syndrome or SCAR12.
• the patient has compound heterozygous mutations of WWOX.
• treatment refers to improving at least one clinical parameter related to the disease, and further includes prevention of the disease (or one or more clinical parameters of the disease) from manifestation.
• treatment also refers to improving at least one symptom or aspect of the disease (as compared to non-treated subjects), such as: survival, growth, number or frequency of epileptic episodes, cognitive function, social function (e.g., in autism) fertility, ataxia, retinopathy, mental retardation, and microcephaly.
• WWOX wild type gene refers to a gene that comprises the WWOX coding sequence represented by SEQ ID NO:1, or which codes for the amino acid sequence of SEQ ID NO: 2.
• WWOX wild type gene further includes the cDNA sequence (as represented by SEQ ID NO: 1), or comprises the gene sequence with one or more introns.
• the full gene sequence with introns is represented by NCBI Reference Sequence: NC_000016.10.
• WWOX wild type gene further includes naturally occuring nucleotide polymorphisms or amino acid modifications (with respect to SEQ ID NO: 1 or SEQ ID NO: 2, respectively) in the human population that are not associated with disease or loss of WWOX function or expression.
• the WWOX gene can be a functional equivalent of the WWOX wild type gene, that is, the WWOX gene may encode one or more amino acid modifications (such as one, two, three, four, or five amino acid modifications) independently selected from insertions, deletions, or substitutions, and which do not significantly impact WWOX activity or expression (e.g., in neurons).
• a functional derivative will encode an amino acid sequence having at least 95% sequence identity, or at least 96% sequence identity, or at least 97% sequence identity, or at least 98% sequence identity, or at least 99% sequence identity with the amino acid sequence of SEQ ID NO: 2.
• a WWOX wild type gene may further comprise regulatory elements, including a promoter and 5'- and 3'- untranslated regions, although these regulatory elements are not restricted to the naturally occurring WWOX gene sequences, but instead can be selected to achieve the desired level of mRNA expression or turnover, and/or desired cell- specificity of gene expression.
• the WWOX wild type gene does not include substantial untranslated regions, that is, may consist essentially of or consist of the WWOX coding sequence.
• the WWOX wild type gene will comprise at least a heterologous promoter.
• a “heterologous promoter” is a promoter that is placed in a non-native location, such as in position to control expression of a coding sequence that it does not control in nature.
• the WWOX wild type gene encodes the amino acid sequence of SEQ ID NO: 2.
• the WWOX wild type gene is a cDNA sequence, which in some embodiments comprises the nucleotide sequence of SEQ ID NO: 1 or SEQ ID NO: 3.
• promoter refers to a DNA sequence capable of controlling the expression of an RNA, such as transcription of the WWOX wild type gene.
• Promoter sequences contain at least proximal elements for controlling gene expression, and may optionally further comprise more distal upstream elements, the latter elements often referred to as enhancers.
• an “enhancer” is a DNA sequence that can stimulate promoter activity, or is an innate element of the promoter or a heterologous element inserted to enhance the level or tissue specificity of a promoter. Promoters may be derived in their entirety from a native gene, or may be composed of different elements derived from different promoters found in nature, or even comprise synthetic DNA segments. It is further recognized that the exact boundaries of regulatory sequences may not be completely defined, and thus DNA fragments of some variation may have identical promoter activity.
• the regulatory element includes a promoter that directs expression of the WWOX gene in neurons.
• the promoter can be a universal promoter. Examples of universal promoters include CMV promoter, E2F1 promoter, and UlsnRNA promoter, or a derivative thereof.
• the promotor is a universal promoter, and the construct is delivered specifically or selectively to neurons.
• the regulatory element is a promoter (a neuron- specific promoter) that is expressed specifically in neurons. Exemplary neuron- specific promoters include synapsin I promoter, CamKII promoter, MeCP2 promoter, NSE promoter, and Hb9 promoter, or a derivative thereof.
• the promoter is not expressed or is expressed at a lower level in glial cells. In some embodiments, the promoter is not expressed or is expressed at a lower level in oligodendrocytes and/or astrocytes.
• the regulatory element is a synapsin I promoter, or functional derivative thereof for directing neuron- specific expression.
• the promoter is a synapsin I promoter, for example, represented by GeneBank accession number NM_006950 (SEQ ID NO: 4), which confers highly neuron- specific and long-term transgene expression.
• the structure of the synapsin I promoter is described in Schloch et al., Neutron-specific Gene Expression of Synapsin I, J. Biol. Chem. 271(6): 3317-3323 (1996).
• the synapsin I promoter is a functional derivative thereof that comprises (i.e., maintains) the NRSE/RE- 1 sequence, which imparts neuron- specific expression.
• the synapsin I promoter comprises a nucleotide sequence of at least about 250 nucleotides, or at least about 300 nucleotides, or at least about 350 nucleotides of the 3’ end of SEQ ID NO: 4.
• the synapsin I promoter (or portion thereof) may have up to about 20%, or up to about 10%, or up to about 5% nucleotide modifications, as long as the neuron- specific or neuron- selective expression of the promoter is maintained.
• the WWOX wild type gene, or a functional derivative thereof, under control of a regulatory element comprises the nucleotide sequence substantially as set forth in SEQ ID NO: 5.
• the regulatory element is a promoter that directs expression of the WWOX gene in oligodendrocytes.
• Exemplary promoters include MBP promoter, PLP1 promoter, and CNP promoter, or a derivative thereof.
• the regulatory element is a promoter that directs expression of the WWOX gene in astrocytes.
• Exemplary promoters include GFAP promoter or S 100b promoter, or a derivative thereof.
• the WWOX wild type gene or the promoter further comprises one or more enhancer sequences, which can comprise distal portions of the synapsin I promoter or other neuron- specific promoter.
• the promoter comprises one or more neuron- specific or neuron- selective enhancers, to increase expression levels in neurons. See, for example, Charron G. et al., Multiple Neuron-snecific Enhancers in the Gene Coding for the Human Neurofilament Light
• the WWOX wild type gene or functional derivative comprises untranslated sequences (e.g., a 3'-UTR) that enhance mRNA stability.
• the WWOX wild type gene may contain a ⁇ -globin mRNA 3'-UTR, or components of the ⁇ -globin mRNA 3'-UTR that confer mRNA stability.
• the WWOX wild type gene includes 3' untranslated sequences from mRNAs that exhibit low turnover in neurons.
• the transcribed WWOX nucleotide sequence comprises one or more woodchuck hepatitis post-transcriptional regulatory elements (WPRE), which can enhance stability.
• the WPRE in some embodiments is included in the 3' UTR of the WWOX gene.
• the WWOX wild type gene is delivered with one or more detectable labels, including but not limited to a fluorescent protein, such as a GFP or RFP, allowing for visualization of expression of the WWOX-containing expression construct.
• detectable labels including but not limited to a fluorescent protein, such as a GFP or RFP, allowing for visualization of expression of the WWOX-containing expression construct.
• the WWOX wild type gene or functional derivative thereof is delivered with a Cas endonuclease enzyme or polynucleotide encoding a Cas endonuclease enzyme, and guide RNA (gRNA) or polynucleotide encoding the gRNA, to direct or enhance insertion of the WWOX wild type gene or a portion thereof.
• the WWOX-associated CNS disease is characterized by a known mutation in WWOX.
• a gRNA complementary to the mutated region, or a DNA sequence coding for said gRNA are delivered along with a Cas endonuclease.
• the WWOX wild type gene may be a fragment of the WWOX wild type gene to replace the mutated sequence cleaved by the Cas endonuclease enzyme (e.g., Cas9).
• the individual is treated by administering to the brain of the individual a Cas endonuclease (e.g., Cas9) enzyme and a gRNA targeted to the mutated sequence, so that the mutated sequence can be edited to revert to the wild type form either by cleaving the mutated region and/or by replacing the sequence of the mutated region by the sequence of the wild type region.
• a Cas endonuclease e.g., Cas9
• a gRNA targeted to the mutated sequence e.g., Cas9
• a gRNA targeted to the mutated sequence e.g., gRNA targeted to the mutated sequence
• the mutated sequence can be edited to revert to the wild type form either by cleaving the mutated region and/or by replacing the sequence of the mutated region by the sequence of the wild type region.
• mere cleavage of the mutated sequence by the Cas endonuclease will result in
• the method comprises also the administration of a donor DNA sequence, corresponding to a fragment of the WWOX wild type gene; to replace the mutated sequence.
• the Cas endonuclease may be administered into the brain cells as a protein or may be administered as a polynucleotide encoding the enzyme and capable of being expressed in the brain cells (e.g., in neurons).
• the Cas endonuclease is expressed via a neuron- specific promoter (e.g., synapsin I promoter), as described herein.
• the Cas endonuclease is delivered as an mRNA, and thus does not require transcription in transfected cells.
• promotors and delivery vectors as described herein for the WWOX gene may be used, or deliver vectors may be used that are capable of delivering longer polynucleotides (which may be better suited for delivering Cas endonuclease-encoding polynucleotides) such as AAV6 and Lentivirus vectors.
• delivery particles, liposomes etc. may be used for its delivery to the brain (e.g., to neurons).
• the gRNA may be delivered as an RNA molecule or as a DNA molecule coding for the gRNA, using the delivery and promoter systems as described herein for the WWOX gene.
• the gRNA is expressed via a neuron- specific promoter.
• the WWOX polynucleotide to replace the mutated DNA, can be administered as a separate sequence or can be delivered as part of a vector containing a sequence coding for the Cas endonuclease and the gRNA.
• the donor DNA can be cleaved out of the vector, for example by use of “donor-specific” second set of guide RNA that with the aid of the Cas endonuclease, can cleave the donor out of the vector with blunt ends.
• Cas endonuclease e.g., Cas9 molecules of a variety of species can be used in the methods and compositions described herein, including S. pyogenes and S. thermophilus Cas9.
• Other Cas endonucleases are described in US Patent Publication No. 20160010076 (which is hereby incorporated by reference in its suney).
• the constructs and methods described herein can include the use of any Cas endonuclease, including Cas9 enzymes, and their corresponding gRNAs or other gRNAs that are compatible.
• the Cas9 from Streptococcus thermophilus LMD-9 CRISPR1 system has been shown to function in human cells. (See, Cong et al., Science 339, 819 (2013)).
• RNAs generally speaking come in two different systems: System 1, which uses separate crRNA and tracrRNAs that function together to guide cleavage by Cas9, and System 2, which uses a chimeric crRNA-tracrRNA hybrid that combines the two separate gRNAs in a single system (referred to as a single guide RNA or sgRNA, see also Jinek et al., Science 2012; 337:816-821).
• the tracrRNA can be variably truncated and a range of lengths has been shown to function in both the separate system (system 1) and the chimeric gRNA system (system 2).
• Cas endonuclease can be guided to specific 17-20 nt genomic targets bearing an additional proximal protospacer adjacent motif (PAM), e.g., of sequence NGG, using a gRNA, e.g., a sgRNA or a tracrRNA/crRNA, bearing 17-20 nts at its 5' end that are complementary to the complementary strand of the genomic DNA target site.
• PAM proximal protospacer adjacent motif
• a single guide RNA comprising a crRNA fused to a normally trans-encoded tracrRNA, e.g., a single Cas9 guide RNA as described in Mali et al., Science 2013 Feb.
• nts nucleotides
• PAM protospacer adjacent motif
• the gRNAs can include X.N which can be any sequence, wherein N (in the RNA) can be 0-200, e.g., 0-100, 0-50, or 0-20, that does not interfere with the binding of the ribonucleic acid to Cas9.
• the gRNA includes one or more Adenine (A) or Uracil (U) nucleotides on the 3' end. In some embodiments the gRNA includes one or more U, e.g., 1 to 8 or more Us at the 3' end of the molecule, as a result of the optional presence of one or more Ts used as a termination signal to terminate RNA PolIII transcription.
• A Adenine
• U Uracil
• the gRNA is targeted to a site that is at least three or more mismatches different from any sequence in the rest of the genome in order to minimize off-target effects.
• Modified RNA oligonucleotides such as locked nucleic acids (LNAs) have been demonstrated to increase the specificity of RNA-DNA hybridization by locking the modified oligonucleotides in a more favorable (stable) conformation.
• the gRNAs disclosed herein may comprise one or more modified RNA oligonucleotides.
• the truncated guide RNAs molecules described herein can have one, some or all of the region of the guide RNA complementary to the target sequence are modified, e.g., locked (2'-O-4'-C methylene bridge), 5'-methylcytidine, 2'-O-methyl- pseudouridine, or in which the ribose phosphate backbone has been replaced by a polyamide chain (peptide nucleic acid), e.g., a synthetic ribonucleic acid.
• a polyamide chain peptide nucleic acid
• the gRNA may be provided per se or in an expression vector.
• the vectors for expressing the gRNAs can include RNA Pol III promoters to drive expression of the gRNAs, e.g., the Hl, U6 or 7SK promoters. These human promoters allow for expression of gRNAs in mammalian cells following plasmid transfection. Alternatively, a T7 promoter may be used, e.g., for in vitro transcription, and the RNA can be transcribed in vitro and purified. Vectors suitable for the expression of short RNAs, e.g., siRNAs, shRNAs, or other small RNAs, can be used.
• the delivery of the sequences can be done by any delivery system suitable for delivery to the CNS, either by direct delivery to the CNS or by systemic delivery.
• the WWOX wild type gene or functional derivative thereof is delivered using a viral vector, polymeric nanoparticles, inorganic nanoparticles, lipid nanoparticles, or exosomes.
• the WWOX wild type gene or functional derivative thereof is delivered by a viral vector.
• the viral vector can be an adeno- associated virus (AAV) delivery system.
• the AAV delivery system is AAV9, which crosses the blood-brain barrier better than other AAV serotypes. Additional viral delivery systems that may be used include Lentivirus and Herpes Simplex Virus delivery systems.
• Another suitable delivery vehicle for the CNS comprises nanoparticles, typically having a size of less than 200 nm, or less than about 150 nm, or less than about 100 nm. These may include lipid-based nanoparticles, polymer nanoparticles, dendrimers and inorganic nanoparticles, some of which may be tailored to pass through the blood brain barrier (BBB).
• BBB blood brain barrier
• the delivery system actively targets delivery by using ligands of transporters or receptors to enhance nanoparticle uptake across the BBB.
• the preferred pathway for this approach is receptor (or transporter) -mediated transcytosis by which a cargo (e.g., nanoparticles) transports between the apical and basolateral surface in the brain ECs.
• low-density lipoproteins undergo transcytosis through the ECs by a receptor-mediated process, bypassing the lysosomal compartment and releasing at the basolateral surface of the brain side.
• BBB contains transporters to amino acids
• using the naturally present arginine transporter for the delivery is one approach for delivery to the brain.
• exosomes Another vehicle for brain delivery is exosomes which are small extracellular vesicles secreted by cells.
• exosomes Another vehicle for brain delivery is exosomes which are small extracellular vesicles secreted by cells.
• the major advantage of exosomes versus other synthetic nanoparticles is their non-immunogenic nature, leading to a long and stable circulation.
• delivery to the brain employs compounds or electric stimulation to transiently open the BBB and allow high concentrations of systemically administered polynucleotides to reach the brain.
• An example of such a compound is cereport (a bradykinin analog) or regadenoson (an adenosine receptor agonist).
• Another manner to increase penetration is via Ultrasound, which is an attractive technique to facilitate drugs to cross the BBB.
• Microbubble-enhanced diagnostic ultrasound (MEUS) a non-invasive technique, effectively helps drugs cross the BBB.
• Another approach is transcranial magnetic stimulation (TMS), which stimulates neuronal activity and increases glutamate release, facilitating delivery across the BBB. (Review by Xiaowei Don. 2018; 8(6): 1481-149- incorporated in its entirely herein by reference).
• Routes of administration of the desired delivery vehicles may be systemic delivery without further manipulations (using particles or viral vector, that inherently enter the BBB); or may be systemic in connection with various manipulations (such as microbubble-enhanced diagnostic ultrasound (MEUS), transcranial magnetic stimulation (TMS)) to transiently open the BBB.
• delivery is by nasal administration.
• delivery to the brain is by delivery to the cerebrospinal fluid via intracerebroventricular route.
• Another option is delivery to the cisterna magna route of injection, which is an alternative method for delivery into cerebrospinal fluid (CSF) which results in wide-spread gene delivery throughout the CNS.
• the administration is by direct injection into the parenchyma or injection into the cerebrospinal fluid via the intracerebroventricular, and by intrathecal (cisternal or lumbar) route.
• the individual to be treated is a pediatric or neonatal patient (e.g., a patient with WOREE or SCAR12).
• early treatment prevents manifestation of some clinical parameters of disease, such as growth impairments, epileptic episodes, impairment of cognitive function, and mental retardation.
• the individual is an adult patient (e.g., with WOREE or SCAR12), and treatment can ameliorate one or more clinical parameters, such as epileptic episodes.
• the individual or patient exhibits one or more symptoms selected from growth impairment, epileptic episodes, impairment of cognitive function, impairment of social function, impairment of fertility, ataxia, retinopathy, mental retardation, and microcephaly.
• the treatment substantially reduces frequency and/or severity of epileptic episodes for patients with WOREE or SCAR12.
• the invention provides a method for the treatment of WOREE syndrome or SCAR12, the method comprising administering to the brain of a patient in need of such treatment, an AAV9 gene delivery system comprising a WWOX wild type gene (i.e., encoding the polypeptide of SEQ ID NO: 2) under control of a synapsin I promoter.
• the AAV9 delivery system may comprise the nucleotide sequence substantially as set forth in SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, and/or SEQ ID NO: 5.
• the present disclosure provides an expression construct comprising a WWOX wild type gene, or a functional derivative thereof, under the expression control of a neuron- specific promotor.
• exemplary neuron- specific promoters include synapsin I promoter, CamKII promoter, MeCP2 promoter, NSE promoter, and Hb9 promoter, or a derivative thereof.
• the promoter is synapsin I or derivative thereof as already described.
• the nucleotide sequence comprises a sequence substantially as set forth in SEQ ID NO: 1, 3, 5, and/or 5.
• the expression construct is a viral vector, such as an adeno-associated virus (AAV) delivery system.
• AAV adeno-associated virus
• the expression construct is an AAV9 delivery system. A specific example for such a vector is depicted in FIG. 7A.
• the expression construct is contained in a pharmaceutical composition for administration into the brain.
• the composition will further comprise a pharmaceutically acceptable carrier suitable for injection, including direct injection to the brain or CNS, or systemic administration.
• the invention provides a method for treating WOREE syndrome or SCAR12, comprising, administering the pharmaceutical composition to a patient in need.
• the present invention provides for a use of the pharmaceutical composition in the treatment of WOREE or SCAR12. Definitions
• sequence identity in the context of two or more nucleic acid or polypeptide sequences, refers to two or more sequences or subsequences that have a specified percentage of nucleotides or amino acid residues that are the same, when compared and aligned for maximum correspondence, as measured using one of the sequence comparison algorithms described below (e.g., BLAST? and BLASTN or other algorithms available to persons of skill) or by visual inspection.
• Example 1 Neuronal deletion of Wwox, associated with WQREE syndrome, causes epilepsy and myelin defects
• WWOX oxidoreductase
• WiBR3 hES cells were maintained in 5% CO 2 conditions on irradiated DR4 mouse embryonic fibroblasts (MEF) feeder plates in FGF/KOSR conditions: DMEM- F12 (Gibco; 21331-020 or Biological Industries; 01-170-1A) supplemented with 15% Knockout Serum Replacement (KOSR, Gibco; 10828-028), 1% GlutaMax (Gibco; 35050-038), 1% MEM non-essential amino acids (NEAA, Biological Industries; 01-340- 1B), 1% Sodium-pyruvate (Biological Industries; 03-042- IB), 1% Penicillin- Streptomycin (P/S, Biological Industries; 03-031-113), and 8ng/mE bFGF (Peprotech; 100-18B).
• hESCs were treated with Rho-associated kinase inhibitor (ROCKi, also known as Y27632) (Cayman; 10005583) at a 10 ⁇ M concentration.
• ROCKi Rho-associated kinase inhibitor
• transfection of hESCs cells were cultured in 10 ⁇ M ROCKi 24h before electroporation.
• Cells were detached using Trypsin C solution and resuspended in PBS (with Ca 2+ and Mg 2+ ) mixed with a total of 100 ⁇ g DNA constructs (px330 plasmid containing the sgRNA targeting exon 1 mixed in a 1:5 ratio with pNTK-GFP), and electroporated in Gene Pulser Xcell System (Bio-Rad; 250 V, 500pF, 0.4cm cuvettes). Cells were subsequently plated on MEF feeder layers in the above-mentioned conditions. 48hr-later, GFP -positive cells were sorted and subsequently plated sparsely (2,000 cells per 10cm plate) on MEF feeder plates for colonies isolation, ⁇ 10 days later.
• mice were maintained in FVB background.
• Mice carrying two loxp sites (W wox flox/flox ) flanking Exon 1 of the Wwox genomic locus was previously documented 22 .
• Mice carrying transgenic Cre recombinase under the promoter of Nestin original Jax line stock: 003771, B6.Cg-Tg(Nes-cre)lKln/J) is a generous gift from Dr. Tai Burstyn-Cohen at the Hebrew University- Hadassah Dental School of Medicine.
• mice lines were purchased from Jackson laboratory, USA.
• DRG neurons were isolated from mouse embryos at El 3.5. Embryos were genotyped and the DRGs were collected in cold L-15 medium. Tissues were dissociated in 0.25% trypsin, triturated, centrifuged, and re- suspended in NB medium (Neurobasal, B27 supplement, 0.5 mM L-glutamine, and penicillin-streptomycin). Pre-cleaned 13mm diameter glass coverslips were placed in 4- well dishes and coated with Matrigel (1 hr at RT) then poly-D-lysine (30 min at RT) prior to dissection.
• Cells were plated at a density of 40,000 cells/13mm coverslips in NB medium and maintained in a humidified incubator at 37 °C and 5% CO 2 . Cultures were treated with fluorodeoxyuridine at DIV2, 4 and 6 to eliminate non-neuronal cells. Fifty percent of cell media was replaced every third day and OPCs were added on DIV15. OPCs were isolated from mouse pups aged P0-P2, respectively.
• Cortices were isolated in ice-cold L-15 medium and dissociated using syringe (19G followed by 21G for mouse tissue), triturated, centrifuged, and re-suspended in glial plating medium (DMEM containing 10% fetal bovine serum, penicillin streptomycin) on PDL-coated flasks. Glial cells were maintained in a humidified incubator at 37 °C and 5% CO 2 , and fifty percent of cell medium was changed every third day.
• DMEM fetal bovine serum, penicillin streptomycin
• OPCs were isolated by shaking the flasks vigorously, followed by depletion of astrocytes by fast adhesion to culture dishes (10 min at 37°C x3) or purified OPCs (200,000/coverslip) were seeded on DRG neuronal cultures and maintained in co-culture medium (DMEM containing B27 and N2 supplements, 5mg/ml N-Acetyl-Cysteine, 5mM forskolin, penicillin-streptomycin). The medium was changed every other day for 9-11 days, then cultures were fixed and stained for analysis. Oligocortical Spheroids Generation and Culture
• Cerebral organoids were generated from hESCs as previously described. 24 Briefly, Human WiBR3 cells were maintained on mitotically inactivated MEFs. 4-7 days before protocol initiation, cells were passaged onto MEF-coated 60mm plates and grown until 70-80% confluency was reached. On day 0, hESCs colonies were detached from MEFs with 0.7mg/ml collagenase D solution (Sigma; 11088858001) and dissociated to single cell suspension with Trypsin type C for 2 minutes.
• hESCs medium composed of DMEM/F12 supplemented 20% KOSR, 1% GlutaMax, 1% NEAA, 1% P/S and 100 ⁇ M 2-mercaptoethanol (Sigma; M3 148), supplemented with 10 ⁇ M Dorsomorphin (Sigma; P5499) or 100nm LDN- 193189 (Axon medchem; Axonl509), and 10 ⁇ M SB-431542 (Sigma; S4317) and 10 ⁇ M Rocki, sterilized through 0.22pm filter.
• NM Neural Medium
• Neurobasal medium Gibco; 21103049 or Biological Industries; 06-1055- 110-1A
• B27 supplement Gibco; 17504044
• GlutaMax GlutaMax
• P/S 1% P/S
• Matrigel Cornning; 356231
• EBX EB -expansion
• spheroids Over-grew the 96-well plate, and therefore were transferred to a 24-well ULA (Corning; 3473), with half-medium changes every other day up to day 26.
• spheroids were moved to 90mm sterile, non-treated, culture dishes (Miniplast; 825-090-15-017) and the medium was changed to Neuro-differentiation medium (NDM), composed of NM supplemented with 20ng/ml BDNF (Peprotech; 450-02) and 20ng/ml NT-3 (Peprotech; 450-03).
• NDM Neuro-differentiation medium
• OMM Oligo Maturation Medium
• OMM Oligo Maturation Medium
• spheroids were cultured at static conditions at 37°C and 5% CO 2 , growth factor and cytokines were added freshly before medium changes, and the spheroids were transferred into a fresh plate at least once every 30 days.
• organoids from the same batch were used, unless stated otherwise.
• mice from different genotypes were euthanized by CO 2 and transcardially perfused with 2% PFA/PBS. Dissected brains were post fixed on ice for 30min. For immunofluorescence brains were incubated in 30% sucrose at 4°C overnight then embedded in OCT and sectioned (12- 14 ⁇ m) using cryostat. Sagittal sections were washed with PBS and blocked with 5% goat serum containing 0.5% of Triton X-100 then incubated for Ih at room temperature followed by incubation with primary antibodies for overnight at 4°C. Then, sections were washed with PBS and incubated with corresponding secondary antibodies tagged with Alexa fluorophore for 1 hr at room temperature followed by washing with PBS and mounted with mounting medium.
• Oligocortical spheroids fixation and immunostaining were performed as previously described 25 . Briefly, organoids were washed three times in PBS, then transferred for fixation in 4% ice-cold paraformaldehyde for 45 min, washed three times in cold PBS, and cryoprotected by over-night equilibration in 30% sucrose solution. The next day, spheroids were embedded in OCT, snap frozen on dry ice, and sectioned at 10 ⁇ m by Leica CM 1950 cryostats.
• LFB staining was preformed following previously published protocol 23 using Nova Ultra luxol fast blue stain kit. Briefly, paraffin embedded brain sections (6 pm) from at least three mice of each genotype were dewaxed followed and rehydrated to 95% ethanol after which sections were incubated in LFB solution (0.1% LFB in 95% ethanol/0.5% acetic acid) overnight at 56°C. Sections were then washed in 95% ethanol and ddH 2 O followed by 0.05% lithium carbonate for 30s, and then with 70% ethanol until the gray matter was colorless and white matter appeared blue. Sections were then rinsed in ddH 2 O before counterstaining with preheated 0.1% Cresyl Violet acetate solution for 30-40s. Finally, sections were rinsed in ddH 2 O , dehydrated with 100% ethanol and xylene and mounted with resinous medium.
• LFB solution 0.1% LFB in 95% ethanol/0.5% acetic acid
• mice were anesthetized and perfused with a fixative containing 4% PFA, 2.5% glutaraldehyde, and 0.1 M cacodylate buffer. Brains were isolated and incubated in the fixative overnight at room temperature and processed as previously described. 26 Samples were examined using a FEI Tecnai T12 transmission electron microscope or Tecnai F20 S/TEM equipped with a XF416 TVIP camera or a US4000 Gatan camera, respectively. EM micrographs were analyzed using computer-assisted ImageJ analysis software.
• LFB stained sections were imaged using panoramic digital slide scanner (3DHISTECH). Immuno stained sections were imaged using panoramic digital slide scanner or Olympus FV1000 confocal laser scanning microscope or Nikon A1R+ confocal microscope. Fluorescence sum intensity of CNP and MBP staining in cortex and cerebellum was calculated using NIS elements software. The acquired images are processed using the associated microscope software programs namely CaseViewer, F- 10-ASW viewer, NIS elements. Images were analyzed using ImageJ software. Images were analyzed while blinded to the genotype and the processing include the global changes of brightness and contrast. Spontaneous seizure recordings
• Electrophysiological recordings were performed in mice with conditional deletion of Wwox in neurons using synapsin-Cre recombinase.
• S- Control Wwox +/+ Synapsin-Cre +
• S-HT Wwox +/flox -, Synapsin-Cre +
• S-KO W ox flox/flox Synapsin-Cre +
• mice were injected intraperitoneally with ketamine - xylazine (100mg/kg ketamine with 10mg/kg xylazine) dissolved in phosphate-buffered saline (PBS).
• PBS phosphate-buffered saline
• the pedal reflex was used to determine the depth of anesthesia. Once the mouse was deeply anaesthetized, it was positioned into a stereotaxic frame.
• a local anesthetic (lidocane) was injected just above the skull at the site of incision, then, after a brief period ( ⁇ 5min), the skin was removed, and the skull exposed.
• a drill was used to score the skull, then a set of forceps was used to peel it back to reveal the cortical tissue.
• Thin walled glass electrodes (1.5 diameter, World Precision Instruments) were pulled using a vertical puller. These were filled with PBS. The electrode was positioned at 1.6- 2mm posterior to the bregma and 4mm lateral to the midline. The electrode was positioned at multiple depths, for 3 min at each depth, to record neocortical subcortical brain and hippocampi activity.
• mice were anesthetized with pentobarbital (50mg/kg). Depth of anesthesia was tested using the pedal reflex. Once the mice were deeply anaesthetized, they were swiftly decapitated and the brain was removed. The cerebellum and olfactory bulbs were removed and the remainder of the tissue was placed caudal-side down onto a platform in a solution of ice-cold sucrose containing (in mM): 248 sucrose, 26 NaHCO 3 , 10 glucose, 2 KC1, 3 MgSO 4 -7H 2 O, 1.25NaH 2 PO 4 , lCaCl 2 -2H 2 O.
• the neocortex was sectioned coronally 400-500 um thick (0.6mm/s speed, 1mm amplitude) using a Leica 1200 vibratome. After this, slices were incubated in artificial cerebral spinal fluid (ACSF) containing (in mM): 123 NaCl, 25 NaHCO 3 , 10 glucose, 3.5 KC1, 1.3 MgSO 4 -7H 2 O, 1.2 NaH 2 PO 4 , 1.5 CaCl 2 -2H 2 O, pH 7.3-7.4. Slices were kept at 34°C for 30min, after which they were removed to room temperature for at least 60min prior to experimentation.
• ACSF artificial cerebral spinal fluid
• LFP glass electrodes 1.5mm, World Precision Instruments
• ACSF Central field potential
• a vertical puller Narishige, Japan PP-83
• An Olympus BX51 microscope Olympus BX51 microscope (OLY-150IR camera-video monitor unit) was used as guidance for proper electrode placement.
• layer V cortex or dentate gyrus stimulation was performed using a bipolar concentric tungsten electrode positioned along the same vertical column as the recordings from layers U/III.
• Current pulses of 0.1ms duration with varying strengths were applied every 30s using a GRASS S88 stimulator connected to a photoelectric stimulus isolation unit.
• the amplitude of the maximal steady state response for S -Control, S-HT and S-KO mice 100 ⁇ A were compared.
• the data was decimated so that the final sampling frequency was 1000Hz.
• the data was notch filtered at 60Hz and its harmonics.
• the spectral power was analyzed using a fast Fourier transform and bin sizes of 1Hz in MATLAB. For each animal, we averaged the power spectrum over 2.5 min at 300 ⁇ m depth using 10s windows with 5s overlap. The power spectrum was plotted as the average across all subjects.
• Organoids at indicated time points were embedded in 3% low temperature gelling agarose (at ⁇ 36°C) and incubated on ice for 5 minutes, after which they were sliced to 400pm using a Leica 1200S Vibratome in sucrose solution (in mM: 87 NaCl, 25 NaHCO 3 , 2.5 KC1, 25 Glucose, 0.5 CaCl 2 , 7 MgCl 2 , 1.25 NaHPO 4 , 75 Sucrose) at 4°C.
• sucrose solution in mM: 87 NaCl, 25 NaHCO 3 , 2.5 KC1, 25 Glucose, 0.5 CaCl 2 , 7 MgCl 2 , 1.25 NaHPO 4 , 75 Sucrose
• LFP electrodes were filled with ACSF, while patch electrodes were filled with internal solution. Data was recorded using MultiClamp software at a sampling rate of 25,000 Hz. Data was analyzed using MATLAB software. Traces were filtered using (1) 60 notch filter (with 5 harmonics) to eliminate noise and (2) 0.1 Hz high-pass IIR filter to eliminate fluctuations from the recording setup.
• Wwox-null mice are born with Mendelian ratio and are indistinguishable from wild type littermates. 19, 20 Within a few days after birth, mice start to show signs of growth retardation and seizures until they succumb by 3-4 weeks of age (Fig. 1A-C). These phenotypes very much resemble what is observed in WOREE/EIEE28 patients who mostly die between ages 2-4 years. 10 To better understand the precise function of WWOX in CNS, we generated conditional mouse models of the brain considering the high expression of WWOX during embryonic brain development in different regions.
• N-KO mice showed tremors/seizures and ataxia (lack of coordination in hind limb clasping test) as observed in Wwox null mice. All (100%) of the N-KO mice died postnatally by 4 weeks of age (Fig. IF). Mice carrying one intact allele of Wwox (Wwox +/fl , Nestin-Cre+) did not show any visible abnormal phenotype which is in accordance with absence of neurological symptoms in heterozygous carriers in human individuals. These phenotypes indicate a crucial role for WWOX in the CNS and imply that its ablation in Nestin-positive cells and their progenies is responsible for the complex phenotype observed in WWOX-rodent models and human patients.
• Phenotypic analysis of conditional ablation of WWOX in neuronal cells revealed growth retardation (Fig. 1G, H), and premature death (Fig. II) by the age of 3-4 weeks, phenocopying the N-KO and Wwox null mice.
• the heterozygote ( Wwox +/fl , Synapsin Cre+) carrying one intact allele of Wwox did not show any abnormal phenotypes and were behaviorally indistinguishable from control mice.
• the phenotypes of the S-KO model strongly indicate that WWOX plays an essential role in neurons and its deficiency leads to a dramatic neurological phenotype.
• RNA-seq and single-nucleus RNA-seq revealed transcriptomic changes of myelination and cellular alternations in Wwox mutant models
• RNA-seq single-nucleus RNA-seq
• RNA-seq data from the cortex and hippocampus of the S-KO mice showed significant downregulation of genes involved in maturation (Gjbl, Gjc2 and Oligl) myelin development, maintenance and functionality of oligodendrocytes (OLs) 31, 33-36 (Ermn, Ugt8a, Plpl, Otud7b, Mai, Emil, Mobp, Histlh2be, Cldnll, Mbp, Gal3stl, Fa2h, Gsn, Adamts4, Crip, Mog, Oplalin, Enpp, Mag and Myrf.
• the top 25 DEGs indeed showed downregulation of transcripts associated with myelination including Cnp, Ugt8a, Plpl, Ermn, Otud7b, Metl7al, Prrl8, Adamts4, Klhdc7a, Mobp, Cldnll and Mbp.
• GSEA and GO term analysis showed significant negative FDR values associated with myelination, ensheathment of neurons and axon ensheathment.
• RNA-seq single-nucleus RNA-seq
• snRNA-seq single-nucleus RNA-seq
• Different cell population clusters were identified based on the expression levels of gene-sets specific to each cell type or the subtype 37-41 .
• Uniform Manifold Approximation and Projection (UMAP) analysis revealed reduced number of matured myelinating oligodendrocyte cells (15%), COPs (committed oligodendrocyte progenitors) (68%) and a greater number of oligodendrocytes progenitor cells (OPCs) (150%) in S-KO compared to S-Control.
• UMAP Uniform Manifold Approximation and Projection
• Neuronal WWOX ablation results in hypomyelination, reduced oligodendrocyte maturation and impaired axonal conductivity
• Electron micrograph images demonstrate substantial reduction ( ⁇ 3.5-4 folds) in number of myelinated axons in the corpus callosum and significantly a greater number ( ⁇ 6 folds) of unmyelinated axons in optic nerves of S-KO as compared to age-matched S-Control (Fig. 4A).
• Neuronal WWOX promotes the differentiation of OPCs to mature oligodendrocytes
• oligodendrocyte status we followed the timeline for oligodendrocyte and myelin development and maturation as previously described. 24 First, we immunostained for CC1 and anti-PDGFRa in week 14 OS, the first time point in which mature OLs are observed. Although staining revealed similar proportions of OPCs, the number of CC1 + was decreased in OS-WWOX-KO compared to OS-WT. We next examined OLs and OPCs at week 20, the first time point in which myelin is expected by staining for the myelin protein CNP and the OPCs marker NG2.
• WWOX expression is found in neurons, oligodendrocytes and astrocytes in the CNS. 46 To identify the type of cells contributing to the defects in the Wwox null mice we decided to systematically mutate the gene in different neural populations. Conditional deletion of WWOX in either neural stem cells and progenitors or matured neurons reproduced the Wwox null phenotypes including growth retardation, epileptic seizures, ataxia and premature death. Consistent with the documented EEG recording from WWOX patients 10, 13 18 , we found that neuronal deletion of WWOX is associated with hyperexcitability and spontaneous epileptic activity in the neocortex.
• oligodendrocytes from OPCs is orchestrated by a multitude of intrinsic and extrinsic factors in the CNS. 49-51 Increasing evidence shows that neuronal activity and glutamate signaling can promote OPC migration, proliferation, differentiation, and myelination during development. 52, 53 It remains to be seen if neuronal WWOX impacts oligodendrocytes differentiation by neuronal activity or by an alternative mechanism. WWOX was found to regulate many signaling pathways including Wnt/ ⁇ -catenin 54-56 , TGF ⁇ /SMAD 57, 58 and DNA damage response 6, 59 through its physical interactions with key proteins so whether WWOX loss of function could deregulate these critical pathways and affect CNS homeostasis remains to be explored.
• WWOX deficient brain organoids also reproduced the hypomyelination defect observed in Wwox -mutant mice.
• the phenotype was found to be progressive, and eventually resulted in apparent diminished myelin staining and more unmyelinated axons, suggestive of hypomyelination.
• our results in this system further support the function of WWOX in OL and myelination in humans.
• Emery B Agalliu D, Cahoy JD, et al.
• Myelin gene regulatory factor is a critical transcriptional regulator required for CNS myelination. Cell. Jul 102009;138(l):172-85. doi: 10.1016/j.cell.2009.04.031
• Habib N Li Y, Heidenreich M, et al. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science. Aug 26 2016;353(6302):925-8. doi: 10.1126/science.aad7038 38.
• Habib N Avraham-Davidi I, Basu A, et al. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. Oct 2017;14(10):955-958. doi : 10.1038/nmeth .4407
• Cicciarelli J Terasaki PI. DR phenotype matching and transfusion in patients treated with cyclosporine. Transplant Proc. Dec 1988;20(6): 1082-3.
• Emery B Regulation of oligodendrocyte differentiation and myelination. Science. Nov 5 2010;330(6005):779-82. doi: 10.1126/science.1190927
• WOREE The clinical spectrum of WOREE includes severe developmental delay, early-onset of severe epilepsy with variable seizure manifestations (tonic, clonic, tonic-clonic, myoclonic, infantile spasms and absence). Most of the affected patients make no eye contact and are not able to sit, speak, or walk. 9 WOREE syndrome is refractory to current anticonvulsant drugs, hence there is an urgent need to develop alternative treatments to help children with WOREE syndrome. Children with SCAR12, mostly due to missense mutations in WWOX, display a milder phenotype including ataxia and epilepsy. 12 Epilepsy in SCAR12 can be treated with anticonvulsant drugs, though children still display ataxia and are intellectually disabled.
• WWOX mutations have been documented in patients with West Syndrome, which is characterized by epileptic spasms with hypsarrhythmia. 13 Brains of the children carrying WWOX gene mutations are found to be abnormal, as assessed by magnetic resonance imaging (MRI). Brain abnormalities such as hypoplasia of the corpus callosum, progressive cerebral atrophy, delayed myelination and optic nerve atrophy have been documented in most cases. It is largely unknown how mutations in WWOX or loss of WWOX function could lead to these CNS-associated abnormalities.
• MRI magnetic resonance imaging
• hWWOX human WWOX
• mWwox murine Wwox
• human WWOX protein sequence is 93% identical and 95% similar to the murine WWOX protein sequence.
• targeted loss of Wwox function in rodent models phenocopies the complex human neurological phenotypes, including severe epileptic seizures, growth retardation, ataxia and premature death. 12,14,15 Wwox null mice also exhibit phenotypes associated with impaired bone metabolism and steroidogenesis.
• Example 1 of this disclosure shows that conditional ablation of murine Wwox in either neural stem cells and progenitors (N-KO) or neuronal cells (S-KO mice) resulted in severe epilepsy, ataxia and premature death at 3-4 weeks, recapitulating the phenotypes observed in the Wwox-null mice.
• N-KO neural stem cells and progenitors
• S-KO mice neuronal cells
• Wwox-null mice could rescue lethality of these mice and their associated phenotypes.
• AAV adeno-associated viral
• AAV9-hSynI-mWwox -IRES-EGFP AAV9-hSynI-mWwox
• AAV9-hSynI-mWwox AAV9-hSynI-mWwox
• aAV9-hSynI-EGFP was used as control.
• Expression of WWOX and GFP was initially validated by infecting primary Wwox-null dorsal root ganglion (DRGs) neurons with the viral particles in vitro.
• DRGs primary Wwox-null dorsal root ganglion
• Viral particles (2x10 lo /hemisphere) of AAV9-hSynI- mWwox or AAV9-hSynI-EGFP were injected into the intracerebroventricular region of Wwox null mice at birth (P0), to achieve widespread transduction of neurons throughout the brain.
• 25,26 Successful expression of the transgene in neurons, but not in oligodendrocytes (CC1 -positive cells), was validated by immunofluorescence using anti-NeuN and anti-WWOX antibodies.
• mice injected with AAV9- hSynl-mWwox grew normally (Fig. 7B), gradually gained weight (Fig. 7C) and were indistinguishable from wild type by the age of 6-8 weeks.
• AAV9-hSynI-EGFP-injected mice exhibited similar phenotypes of Wwox null mice (Fig. 7C).
• Wwox null and AAV9-hSynI-EGFP-injected mice were hypoglycemic from the second week until they died, while AAV9-hSynI-mWwox-injected mice had normal blood glucose levels when compared to the wild type mice (Fig. 7D).
• mice lived longer with a median survival of 240 days compared to the Wwox null or AAV9-hSynI-EGFP- injected Wwox null mice (p value ⁇ 0.0001) (Fig. 7E). Similar results and outcomes were obtained when replacing mWwox with hWWOX cDNA, though we have only followed these mice for up to 100 days so far (Fig. 7F). Notably, the rescued mice were active and both males and females were fertile.
• Wwox null mice were previously shown to lack testicular Leydig cells, 16 we next determined if WWOX neuronal restoration rescues this phenotype and indeed found intact Leydig cells in P17 AAV9-hSynI-m Wwox- treated mice. Bone growth defects were also formerly documented in Wwox mutant mice 17,27-30 , and hence we examined bones of rescued mice and observed that cortical bones were of comparable size and thickness to WT mice. These results imply that neuronal restoration of WWOX could be sufficient to rescue the abnormal phenotypes of Wwox null mice.
• Wwox null mutants display spontaneous recurrent seizures. 12,14,18 ’ 31
• WT Wwox null
• KO Wwox null
• Fig. 8A Representative traces with spontaneous firing of action potentials are shown in Fig. 8A. A clear hyperexcitability can be noted from the representative traces (WT, KO+AAV9- Wwox, and KO).
• the activity of the KO brains usually resulted in bursts of action potentials and overall there was a drastic increase in the firing rate.
• Example 1 linked WWOX loss with hypomyelination.
• neuronal WWOX ablation results in a non-cell autonomous function impairing differentiation of oligodendrocyte progenitors (OPCs).
• OPCs oligodendrocyte progenitors
• AAV oligodendrocyte progenitors
• WWOX neuronal restoration decreases anxiety and improves motor functions
• WWOX The role of WWOX in regulating CNS homeostasis is emerging as a key function of the WWOX gene. Deficiency of WWOX has been linked to a number of neurological disorders. 9 10 Of particular interest is WOREE syndrome, a devastating complex neurological disease causing premature death with a median survival of 1-4 years. 9,10 WOREE children are refractory to the current antiepileptic drugs (AEDs) hence challenging the medical and scientific communities to develop new therapeutic strategies. We believe that delivering AAV9-WWOX into the brain of WOREE syndrome patients could be a novel gene therapy approach that would help these patients.
• AEDs antiepileptic drugs
• WWOX is ubiquitously expressed in all brain regions. 10,43,44 Our current observations do not imply that WWOX expression in other brain cell types, such as astrocytes and oligodendrocyte, are dispensable. Evidence linking WWOX function with oligodendrocyte pathology is starting to emerge 45-49 , however less is known about the cell-autonomous functions of WWOX in oligodendrocytes. The fact that WWOX expression in neurons regulates oligodendrocyte maturation and antagonizes astrogliosis 50 suggests a complex function of WWOX in CNS physiology and pathophysiology that warrants further in-depth analysis.
• Wwox-null mice should be explored in the future.
• Our current findings indicate that WWOX restoration in neonatal mice using an AAV vector could reverse the phenotypes associated with WWOX deficiency.
• this proof-of-concept will lay down the groundwork for a possible gene therapy clinical trial on children suffering from the devastating and often refractory WOREE syndrome.
• Murine Wwox or human WWOX cDNA was cloned under the promoter of human Synapsin I in pAAV and this vector was packaged into AAV9 serotype (Vector Biolabs, Philadelphia, USA).
• Custom-made AAV9-hSynI-mWwox-IRES-EGFP, AAV9-hSynI- hWWOX-2A-EGFP and AAV9-hSynI-EGFP viral particles were obtained either from Vector Biolabs or from the Vector Core Facility at Hebrew University of Jerusalem.
• Wwox null mice (-/- ) mice (KO) was previously reported 16 and these mice were maintained in an FVB background. Heterozygote (+/- ) mice were used for breeding to get the Wwox null mice. Animals were maintained in a SPF unit in a 12 h-light/dark cycle with ad libitum access to the food and water. All animal-related experiments were performed in accordance and with prior approval of the Hebrew University-Institutional Animal Care Use Committee (HU-IACUC). Intracerebroventricular (ICV) injection of AAV particles in to P0 Wwox null mice
• Free-hand intracranial injections of either AAV9-hSynI-mWwox-IRES-EGFP (AAV9-WW0X) or AAV9-hSynI-EGFP (AAV9-GFP) into the Wwox null mice were done following a published protocol. 25 Briefly, when neonates were bom, they were PCR genotyped to identify Wwox null mice. Wwox null neonates were anesthetized by placing on a dry, flat, cold surface. The anesthetized pup head was gently wiped with a cotton swab soaked in 70% ethanol. Trypan blue 0.1% was added to the virus to enable visualization of the dispensed liquid.
• An injection site was located at 2/5 of the distance from the lambda suture to each eye. Holding the syringe (preloaded with virus) perpendicular to the surface of the skull, the needle was inserted to a depth of approximately 3 mm. Approximately 1 ⁇ l (2 x IO 10 GC/hemi sphere) virus was dispensed using a NanoFil syringe with a 33G beveled needle (World Precision Instruments). The other hemisphere was injected in the same way. Injected pups were placed on the warming pad until they were awake, then transferred to the mother’s cage. Each injected mouse was carefully monitored for growth, mobility, seizures, ataxia and general condition to assess phenotypes.
• mice were weighed regularly as indicated in the Figures. To monitor the blood glucose, the tip of the mouse tail was ruptured with scissors and a tiny drop of blood collected for measurement (mg/dL) using an Accu-Check glucometer (Roche Diagnostics, Mannheim, Germany).
• mice from different genotypes and treatment groups were euthanized by CO 2 and transcardially perfused with 2% PFA/PBS.
• Dissected brains were postfixed on ice for 30 min then incubated in 30% sucrose at 4°C overnight. They were then embedded in OCT and sectioned (12-14 pm) using a cryostat. Sagittal sections were washed with PBS and blocked with 5% goat serum containing 0.5% Triton X-100 then incubated for 1 h at room temperature followed by incubation with primary antibodies overnight at 4°C. Then, sections were washed with PBS and incubated with corresponding secondary antibodies tagged with Alexa fluorophore for 1 h at room temperature followed by washing with PBS and mounting with mounting medium.
• Surgical procedures for electrophysiology Mice were anesthetized using ketamine/medetomidine (i.p; 100 and 83 mg/kg, respectively). The effectiveness of anesthesia was confirmed by the absence of toe-pinch reflexes. Supplemental doses were administered every ⁇ 1 h with a quarter of the initial dosage to maintain anesthesia during the electrophysiology procedures.
• body temperature was maintained using a heating pad (37°C).
• the skin was removed to expose the skull.
• a custom-made metal pin was affixed to the skull using dental cement and connected to a custom stage.
• a small hole (3 mm diameter craniotomy) was made in the skull using a biopsy punch (Miltex, PA).
• Electrodes were pulled from filamented, thin-walled, borosilicate glass (outer diameter, 1.5 mm; inner diameter, 0.86 mm; Hilgenberg GmbH, Malsfeld, Germany) on a vertical two-stage puller (PC- 12, Narishige, EastMeadow, NY).
• the electrodes were filled with internal solution containing the following: 140 mM K- gluconate, 10 mM KC1, 10 mM HEPES, 10 mM Na2-phosphocreatine, and 0.5 mM EGTA, adjusted to pH 7.25 with KOH.
• the electrode was inserted at a 45 degrees angle and reached a depth of 300 pm.
• the electrode positioning was targeted on the brain surface, positioned at 1.6-2 mm posterior to the bregma and 4 mm lateral to the midline. While positioning the electrode, an increase of the pipette resistance to 10-200 MOhm resulted in most cases in the appearance of action potentials (spikes). The detection of a single spike was the criteria to start the recording. All recordings were acquired with an intracellular amplifier in current clamp mode (Multiclamp 700B, Molecular Devices), acquired at 10 kHz (CED Micro 1401-3, Cambridge Electronic Design Limited) and filtered with a high pass filter. For calculation of the average firing rate, the firing rate over a 4 min recording period was calculated for each of the recorded cells. A two-sample t-test was used to assess statistical significance between the recorded groups.
• mice were anesthetized and perfused with a fixative containing 2% paraformaldehyde and 2.5% glutaraldehyde (EM grade) in 0.1 M sodium cacodylate buffer, pH 7.3. Brains were isolated and incubated in the same fixative for 2 h at room temperature then stored in 4°C until they were processed. Collected tissues (corpus callosum, optic nerve) were washed four times with sodium cacodylate and postfixed for 1 h with 1% osmium tetroxide, 1.5% potassium ferricyanide in sodium cacodylate, and washed four times with the same buffer.
• tissue samples were dehydrated with graded series of ethanol solutions (30, 50, 70, 80, 90, 95%) for 10 min each and then 100% ethanol three times for 20 min each, followed by two changes of propylene oxide.
• Tissue samples were then infiltrated with series of epoxy resin (25, 50, 75, 100%) for 24 h each and polymerized in the oven at 60°C for 48 h.
• the blocks were sectioned by an ultramicrotome (Ultracut E, Riechert-Jung), and sections of 80 nm were obtained and stained with uranyl acetate and lead citrate. Sections were observed using a Jeol JEM 1400 Plus transmission electron microscope and pictures were taken using a Gatan Orius CCD camera.
• mice were placed in the comer of a 50 x 50 x 33 cm arena, and allowed to freely explore for 6 min.
• the center of the arena was defined as a 25 x 25 cm square in the middle of the arena. Velocity and time spent in the center and arena circumference were measured. Mice tested in the open field were recorded using a video camera connected to a computer having tracking software (Ethovision 12).
• the test apparatus consisted of two open arms (30 x 5 cm) bordered by a 1 cm high rim across from each other and perpendicular to two closed arms bordered by a rim of 16 cm, all elevated 75 cm from the floor. Mice were put into the maze and were allowed to explore it for 5 min. Duration of visits in both the open and closed arms were recorded. 60
• Immunostained sections were imaged using a panoramic digital slide scanner or an Olympus FV1000 confocal laser scanning microscope or Nikon A1R+ confocal microscope.
• the acquired images were processed using the associated microscope software programs, namely CaseViewer, F-10-ASW viewer, and NIS elements respectively. Images were analyzed using ImageJ software. Images were analyzed while blinded to the genotype and the processing included the global changes of brightness and contrast.
• tumour suppressor gene WWOX is mutated in autosomal recessive cerebellar ataxia with epilepsy and mental retardation. Brain 137, 411-419. 10.1093/brain/awt338awt338 [pii].
• mice carrying a conditional allele of the Wwox tumor suppressor gene PLoS One 4, e7775. 10.1371/journal.pone.0007775.
• AAV9 Vector a Novel modality in gene therapy for spinal muscular atrophy. Gene Ther 26, 287-295. 10.1038/s41434-019-0085- 4.
• Example 3 Modeling genetic epileptic encephalopathies using brain organoids
• Epilepsy is a neurological disorder characterized by a chronic predisposition for the development of recurrent seizures (Fisher et al, 2014; Aaberg et al, 2017). Epilepsy affects around 50 million people worldwide and is considered the most frequent chronic neurological condition in children (Aaberg et al, 2017; Blumcke et al, 2017). Approximately 40% of seizures in the early years of life are accounted for by developmental and epileptic encephalopathy (DEE), previously known as early infantile epileptic encephalopathies (EIEEs) (Howell et al, 2021).
• DEE developmental and epileptic encephalopathy
• EIEEs early infantile epileptic encephalopathies
• WWOX a tumor suppressor that spans the chromosomal fragile site FRA16D, is highly expressed in the brain, suggesting an important role in central nervous system (CNS) homeostasis (Abu-Remaileh et al, 2015).
• CNS central nervous system
• WWOX was implicated in the autosomal recessive spinocerebellar ataxia- 12 (SCAR 12) (Gribaa et al, 2007; Mallaret et al, 2014) and in the WWOX- related epileptic encephalopathy (WOREE syndrome, also termed DEE28) (Abdel-Salam et al, 2014; Ben-Salem et al, 2015; Mignot et al, 2015).
• SCAR 12 autosomal recessive spinocerebellar ataxia- 12
• WOREE syndrome also termed DEE28
• Both disorders are associated with a wide variety of neurological symptoms, including seizures, intellectual disability, growth retardation, and spasticity, but differ by severity, onset, and underlying types of mutations.
• the WOREE syndrome is considered more aggressive, appearing as early as 1.5 months and associating with more extreme genetic changes (Banne et al, 2021). This observation may imply that both syndromes can be considered as a continuum.
• patients with WOREE syndrome may present with global developmental delay, progressive microcephaly, atrophy of specific CNS components, and premature death.
• the phenotypic spectrum of WOREE syndrome is wide, with different patients exhibiting different symptoms. For example, although microcephaly is seen in some patients, many other do not exhibit this condition (Piard et al, 2018).
• WWOX knockout (KO) clones of the WiBR3 hESC line using the CRISPR/Cas9 system (Abdeen et al, 2018). Immunoblot analysis was used to assess WWOX expression in these lines. Two clones that showed consistent undetectable protein levels of WWOX throughout our validations were picked for the continuation of the study — WWOX-KO line IB (WK0-1B, from here on KOI) and WK0-A2 (from here on KO2).
• VZ ventricular-like zone
• WWOX expression was not seen in COs generated from the WWOX-KO lines, although similar levels of expression of the other markers such as SOX2 and neuron -specific class III P- tubulin (TUBB3 or TUJ1) were observed (Fig. 11B).
• the W-AAV COs in which WWOX expression is driven by human ubiquitin promoter (UBP), exhibited high WWOX levels in the VZ, as expected, though other cellular populations also showed prominent WWOX expression.
• RNA levels of SLC17A6 (VGLUT2), SLC17A7 (VGLUT1), GAD1 (GAD67) and GAD2 (GAD65) followed the same trend.
• WWOX-depleted cerebral organoids exhibited hyperexcitability and epileptiform activity
• the oscillatory power (OP) was quantified by the area under the curve, which was significantly higher than the WT line, under baseline conditions (Fig. 12C). Over time, the OP of the KO lines decreased significantly, while the WT line’ s OP stayed the same, suggesting a developmental delay in the KO line.
• WWOX-depleted cerebral organoids exhibited impaired astrogenesis and DNA damage response It is widely accepted that an imbalance between excitatory and inhibitory activity in the brain is a leading mechanism for seizures, but this does not necessarily mean neurons are the only population involved. It is well known that brain samples from epileptic patients show signs of inflammation, astrocytic activation, and gliosis (Cohen- Gadol et al, 2004; Thom, 2009), which can be a sole histopathological finding in some instances (Blumcke et al, 2017).
• GFAP glial fibrillary acidic protein
• S100 ⁇ S100 calcium-binding protein B
• Astrocytes arise from two distinct populations of cells in the brain: the RG cells, switching from neurogenesis to astrogenesis, or the astrocyte progenitor cells (APCs) (Zhang et al, 2016; Blair et al, 2018).
• APCs astrocyte progenitor cells
• WWOX-KO COs present with a progressive increase in astrocytic number, likely due to enhanced differentiating RGs, and with increased DNA damage in neural progenitor cells.
• RNA-sequencing of WWOX-depleted cerebral organoids revealed major differentiation defects
• RNA-seq whole-transcriptome RNA-sequencing
• PCA principal component analysis
• GABAergic neurons GAD1 , GRM7, LHX5
• astrocytes AAT, S100A1, GJ Al, OTX2
• PDGFRA calcium signaling
• GATA3, DRGX, ATOH1, NTN1, SHH, RELN, OTX2, SLIT3, GBX2, LHX5 GABAergic neurons
• GABA receptors GBRB3, GABRB2
• autophagy IF116, MDM2, RBI, PLAT, RB1CC1
• GSEA Gene set enrichment analysis
• GO gene ontology
• Wnt pathway e.g., WNT1, WNT2B, WNT3, WNT3A, WNT5A, WNT8B, LEF1, AXIN2, GBX2, ROR2, LRP4, NKD1, IRX3, CDH1
• Shh pathway e.g., SHH, GLI1, LRP2, PTCHI, HHIP, PAX1, PAX2.
• RNA-seq data we used our RNA-seq data to inspect the expression of different members of the WNT signaling pathway (such as WNT1, WNT3, WNT5A, WNT8B), of canonical targets (such as Axin2, TCF7L2, LEF1, TCF7L1), of brain-specific targets (IRX3, ITGA9, GATA2, FRAS1, SP5), and of receptors (ROR2, FZD2, FZD10, FZD1).
• WNT1, WNT3, WNT5A, WNT8B canonical targets
• Axin2, TCF7L2, LEF1, TCF7L1 IRX3, ITGA9, GATA2, FRAS1, SP5
• receptors receptors
• RNA-seq revealed impaired spatial patterning, axis formation, and cortical layering in WWOX-KO COs, which is correlated with disruption of cellular pathways and activation of Wnt signaling.
• the reintroduction of WWOX prevents these changes to some extent, further supporting its possible implication in gene therapy.
• PBMCs peripheral blood mononuclear cells
• WWOX was mainly expressed in the VZ in WSM Fl and WSM M2. Although ⁇ 3- Tubulin + -positive cells and SOX2 + -positive cells were comparable in numbers, WSM S COs showed no detectable levels of WWOX, and WSM S W-AAV COs expressed WWOX globally.
• RNA levels of Wnt genes did show a pattern suggestive of the Wnt pathway activation, which raises a question regarding its role in the pathogenesis of the milder disease.
• DEEs are a group of severe neurological syndromes whose underlying molecular pathology is unknown (Howell et al, 2021). Together with the lack of accessibility of human samples, it is not surprising that the current medical treatment is lacking.
• Our study set out to utilize the major technological advances in developmental biology, together with the role of WWOX in the severe WOREE syndrome, to model human refractory DEEs in a tissue-relevant context.
• We By utilizing genetic manipulations and reprogramming, along with electro-physiology, we observed hyperexcitability in both WWOX CRISPR-edited and patient-derived brain organoids, therefore successfully demonstrating epileptiform activity.
• Seizure dynamics in developmental epilepsies are known to be dependent on depolarizing GABA responses, particularly due to an accumulation of intracellular chloride resulting in a depolarized chloride reversal potential, thereby causing increased excitability, instead of hyperpolarization upon activation of GABAA receptors (Khalilov et al, 2005; Ben-Ari et al, 2007).
• the evidence of increased mean spectral power in WWOX-depleted COs and WSM FOs, and its recovery in the presence of lentivirus containing WWOX, further strengthens the idea that depolarizing GABA plays a key role in seizure susceptibility.
• Fig 12A-C shows a decrease in higher frequency activity — beta (12-30 Hz) and gamma (> 30 Hz) oscillations.
• higher frequency activity particularly gamma oscillations — is known to increase prior to seizure onset at specific focal zones and has been studied as a possible determinant of epileptogenesis (Medvedev et al, 2011), our data do not support this for WWOX-related seizures.
• One possible explanation for this is the maturity of the 7-week-old COs.
• Gamma oscillations are associated with functional connectivity and integrate neural networks within and across brain structures (Kheiri et al, 2013; Ahnaou et al, 2017).
• physiological DNA breaks can be formed by replicative stress (mainly in dividing progenitor cells), by oxidative and metabolic stress as a result of accumulation of reactive oxygen species (ROS), and even by neuronal activity (as part of developmental processes and learning) (Suberbielle et al, 2013; Madabhushi et al, 2014; Madabhushi et al, 2015). Impaired repair of these breaks is linked with CNS pathology and neurode-generation (Suberbielle et al, 2013; Madabhushi et al, 2014; Shanbhag et al, 2019).
• ROS reactive oxygen species
• Samarasinghe et al took advantage of the organoid fusion method and generated organoids enriched with inhibitory interneurons from Rett syndrome patient’s iPSCs. In the disease-bearing organoids, they observed susceptibility to hyperexcitability, reductions in the microcircuit clusters, recurring epileptiform spikes, and altered frequency oscillations, which were traced back to dysfunctional inhibitory neurons (preprint: Samarasinghe et al, 2019).
• the model was used to test treatment options by treating the mutated organoids with valproic acid (VPA) or with the TP53 inhibitor, pifithrin-a (PFT), showing improved neuronal activity compared with the treatment with vehicle, with better results using PFT rather than VPA.
• VPA valproic acid
• PFT pifithrin-a
• WWOX was found to bind the Dishevelled proteins Dvll and Dvl2, with the latter being inhibited by WWOX, therefore attenuating the Wnt pathway (Bouteille et al, 2009; Abu-Odeh et al, 2014a).
• Our study further highlights a possible crosstalk between Wnt activation and DNA damage, a phenomenon that was previously described (Elyada et al, 2011). This is very much in line with the previously described pleiotropic functions of WWOX (Abu-Remaileh et al, 2015) and with the reduced negative regulation of cell cycle and MDM2 levels seen in our RNA-seq.
• WiBR3 hES cell line and the generated iPS cell lines were maintained in 5% CO 2 conditions on irradiated DR4 mouse embryonic fibroblast (MEF) feeder layers in FGF/KOSR conditions: DMEM/F12 (Gibco; 21331-020 or Biological Industries; 01- 170-1A) supplemented with 15% knockout serum replacement (KOSR, Gibco; 10828- 028), 1% GlutaMAX (Gibco; 35050-038), 1% MEM nonessential amino acids (NEAA, Biological Industries; 01-340-1B), 1% sodium pyruvate (Biological Industries; 03-042- 1B), 1% penicillin-streptomycin (Biological Industries; 03-031-113), and 8 ng/ml bFGF (PeproTech; 100-18B).
• Rho-associated kinase inhibitor (ROCKi, also known as Y27632) (Cayman; 10005583) was added for the first 24-48 h after passaging at a 10 ⁇ M concentration.
• hESCs For transfection of hESCs, cells were cultured in 10 ⁇ M ROCKi 24h before electroporation. Cells were detached using trypsin C solution and resuspended in PBS (with Ca 2+ and Mg 2+ ) mixed with a total of 100 ⁇ g DNA constructs, and electroporated in Gene Pulser Xcell System (Bio-Rad; 250 V, 500 pF, 0.4-cm cuvettes). Cells were subsequently plated on MEF feeder layers in FGF/KOSR medium supplemented with ROCKi.
• px33O plasmid containing the sgRNA targeting exon 1 was co-electroporated in 1:5 ratio with pNTK-GFP, and 48hr later, GFP-positive cells were sorted and subsequently plated sparsely (2,000 cells per 10-cm plate) on MEF feeder plates for colony isolation, ⁇ 10 days later.
• pAAVS-2aNeo- UBp-IRES-GFP plasmid cloned to carry the WWOX coding sequence was co- electroporated with px33O targeting the AAVS1 locus (Guemet el al, 2016), sorted for GFP, and selected with 0.5 ⁇ g/ml puromycin for colony isolation.
• Gene editing was validated via Western blot. sgRNA sequences are noted in Table EV3.
• hPSCs were passaged onto Matrigel-coated plates (Coming; 356231) as indicated above and were cultured in NutriStem hPSC XF Medium (Biological Industries; 05-100-1A).
• Cerebral organoid generation, culture, and lentiviral infection Cerebral organoids were generated from hESCs as previously described (Lancaster et al, 2013; Lancaster & Knowalker, 2014; Bagley et al, 2017; Lancaster et al, 2018), with the following changes:
• Human WiBR3 cells and WSM iPSCs were maintained on mitotically inactivated MEFs. 4-7 days before protocol initiation, cells were passaged onto 60-mm plates coated with either MEFs or Matrigel (Corning; FAL356231) and grown until 70-80% confluency was reached. On day 0, hESC colonies were detached from MEFs with 0.7 mg/ml collagenase D solution (Sigma; 11088858001) and dissociated to single-cell suspension using a quick 2-min treatment with trypsin type C. For cells cultured on Matrigel, collagenase D treatment was skipped, and cells were immediately dissociated with trypsin type C, with no other variations in protocols from this point forward. Although only empirically observed, no major differences were seen in final outcome; however, MEF-cultured hPSCs seemed to have better success rates of neural induction and therefore were preferentially used.
• hESC medium composed of DMEM/F 12- supplemented 20% KOSR, 3% USDA-certified hESC-quality FBS (Biological Industries), 1% GlutaMAX, 1% NEAA, 100 ⁇ M 2-mercaptoethanol (Sigma; M3148), 4 ng/ml bFGF, and 10 ⁇ M Rocki.
• EB embryoid body
• 9,000 cells were seeded in each well of an ultra-low attachment V-bottom 96-well plates (S-Bio Prime; MS-9096VZ). EBs were fed every other day for another 5 days, in which fresh bFGF and ROCKi were added in the first change.
• NI medium Neural Induction (NI) medium (Bagley et al, 2017), composed of DMEM/F12, 1% N2 supplement (Gibco; 17502048), 1% GlutaMAX, 1% MEM-NEAA, and 1 ⁇ g/ml heparin solution (Sigma; H3149).
• NI medium was changed every other day until establishment of neuroepithelium (usually on days 11-12), where quality control was performed as indicated (Lancaster & Knowalker, 2014; Bagley et al, 2017), and well- developed EBs were embedded in Matrigel droplets (Lancaster & Knowalker, 2014; Bagley et al, 2017).
• CMM Cerebral Maturation Medium
• B27 supplement changed to B27 supplement containing vitamin A (Gibco; 17504044), without CHIR-99021, and containing 400 ⁇ M vitamin C (Sigma; A4403) and 12.5 mM HEPES buffer (Biological Industries; 03-025- 1B).
• Medium was changed every 2-4 days. From week 6, 1% Matrigel was added to the medium. To reduce chances of contamination, every 30 days the organoids were moved to fresh sterile plates. All of the described media were filtered through a 0.22-pm filter and stored at 4°C until usage. For all analyses, organoids from the same batch were used, unless stated otherwise.
• iPSCs directly from PBMCs was conducted by infection with the Yamanaka factors and Sendai virus CytoTune-iPS 2.0 Kit according to the manufacturer’s instructions. Briefly, blood samples from PBMCs were isolated by Ficoll gradient and were cultured with StemPro-34TM medium (Gibco; 10639-011) supplemented with StemPro-34 Nutrient Supplement (Gibco; 10639-011), 100 ng/ml human SCF (PeproTech; 300-07), 100 ng/ml human FLT-3 ligand (R&D Systems; 308- FKE), 20 ng/ml human IL-3 (PeproTech; 200-03), and 10 ng/ml Human IL-6 (PeproTech; 200-06).
• StemPro-34TM medium Gibco; 10639-011
• StemPro-34 Nutrient Supplement Gibco; 10639-011
• 100 ng/ml human SCF PeproTech; 300-07
• iPSC cells were maintained on mitotically inactivated MEFs. 4-7 days before protocol initiation, cells were passaged onto MEF-coated 60 mm plates and were cultured up to 70-80% confluency. On day 0, iPSC colonies were detached, dissociated, and counted the same as for COs, and resuspended in hPSC medium containing DMEM/F12, 20% KOSR, 1% GlutaMax, 1% MEM-NEAA, 1% penicillin/streptomycin, and 100 ⁇ M 2-mercaptoethanol.
• NEM Neuroectoderm Medium
• NIM Neural Induction Medium
• DMEM/F12 fetal calf serum
• GlutaMax 1% penicillin/streptomycin
• NEAA 1% NEAA
• 10 ⁇ g/ml heparin 1 ⁇ M CHIR-99021 (Axon Medchem; 1386)
• SB- 431542 1 ⁇ M SB- 431542 (Sigma; S4317).
• quality control and Matrigel embedding were performed as indicated (Qian et al, 2018), and EBs were continued to be cultured in NIM with medium changes every other day.
• FDM Forebrain Differentiation Medium
• FMM Forebrain Maturation Medium
• Neurobasal medium 1% B27 supplement with vitamin A, 1% GlutaMax, 1% penicillin/streptomycin, 50 ⁇ M 2-mercaptoethanol, 200 ⁇ M vitamin C, 20 ng/ml human recombinant BDNF (Pepro-Tech; 450-02), 20 ng/ml human recombinant GDNF (PeproTech; 450-10), 1 ⁇ M dibutyryl-cAMP (Sigma; D0627), and 1 ng/mL TGF- ⁇ 1 (PeproTech; 100-21C).
• FMM Forebrain Maturation Medium
• Organoid fixation and immunostaining were performed as previously described (Mansour et al, 2018). Briefly, organoids were washed three times in PBS, then transferred for fixation in 4% ice-cold paraformaldehyde for 45 min, washed three times in cold PBS, and cryoprotected by overnight equilibration in 30% sucrose solution. The next day, organoids were embedded in OCT, snap-frozen on dry ice, and sectioned at 10 pm by Leica CM 1950 cryostats.
• sections were warmed to room temperature and washed in PBS for rehydration, permeabilized in 0.1% Triton X-100 in PBS (PBT), and then blocked for 1 hr in a blocking buffer containing 5% normal goat serum (NGS) and 0.5% BSA in PBT. The sections were then incubated at 4°C overnight with primary antibodies diluted in the blocking solution. The day after, sections were then washed in three times while shaking in PBS containing 0.05% Tween-20 (PBST) and incubated with secondary antibodies and Hoechst 33258 solution diluted in blocking buffer for 1.5 h at RT.
• PBS normal goat serum
• BSA normal goat serum
• Organoids were embedded in 3% low -temperature gelling agarose (at ⁇ 36°C) and incubated on ice for 5 min, after which they were sliced to 400 ⁇ m using a Leica 1200S Vibratome in sucrose solution (in mM: 87 NaCl, 25 NaHCO 3 , 2.5 KC1, 25 glucose, 0.5 CaCl 2 , 7 MgCl 2 , 1.25 NaHPO 4 , and 75 sucrose) at 4°C.
• sucrose solution in mM: 87 NaCl, 25 NaHCO 3 , 2.5 KC1, 25 glucose, 0.5 CaCl 2 , 7 MgCl 2 , 1.25 NaHPO 4 , and 75 sucrose
• LFP electrodes were filled with ACSF, while patch electrodes were filled with internal solution.
• Data were recorded using MultiClamp software at a sampling rate of 25,000 Hz.
• Data were analyzed using MATLAB software. Traces were filtered using (i) 60 notch filter (with 5 harmonics) to eliminate noise and (ii) 0.1 -Hz high-pass HR filter to eliminate fluctuations from the recording setup.
• the detrended feature (using the hamming window) was then used to eliminate large variations in the signal, and the normalized spectral power was calculated using the fast Fourier transform.
• the area under the curve of the power spectral density plots was calculated by taking the sum of binned frequencies over specific frequency ranges.
• Electrodes were pulled from filamented, thin-walled, borosilicate glass (outer diameter, 1.5 mm; inner diameter, 0.86 mm; Hilgenberg GmbH) on a vertical two- stage puller (PC-12, Narishige). The electrodes were filled with an internal solution that contained the following (in mM): 140 K-gluconate, 10 KC1, 10 HEPES, 10 Na2- phosphocreatine, and 0.5 EGTA, and adjusted to pH 7.25 with KOH.
• the electrodes were inserted at 45° to the organoid’s surface. During the recordings, the organoids were kept in CMM without Matrigel at 35°C. An increase in the pipette resistance to 10-200 MOhm resulted in most cases in the appearance of spikes. The detection of a single spike was the criteria to start the recording. All recordings were acquired with an intracellular amplifier in current-clamp mode (MultiClamp 700B, Molecular Devices), acquired at a sampling rate of 10 kHz (CED Micro 1401-3, Cambridge Electronic Design Limited), and filtered with a high -pass filter to eliminate field potentials and retain neuronal spikes.
• MultiClamp 700B Current-clamp mode
• organoids were homogenized in lysis buffer containing 50 mM Tris (pH 7.5), 150 mM NaCl, 10% glycerol, and 0.5% Nonidet P-40 (NP-40) that was supplemented with protease and phosphatase inhibitors.
• organoids were grinded in a hypotonic lysis buffer [10 mmol/1 HEPES (pH 7.9), 10 mmol/1 KC1, 0.1 mmol/1 EDTA] supplemented with 1 mmol/1 DTT and protease and phosphatase inhibitors. The cells were allowed to swell on ice for 15 min, then 0.5% NP- 40 was added, and cells were lysed by vortex.
• cytoplasmic fraction was collected. Afterwards, nuclear fraction was obtained by incubating remaining pellet in a hypertonic nuclear extraction buffer [20 mmol/1 HEPES (pH 7.9), 0.42 mol/1 KC1, 1 mmol/1 EDTA] supplemented with 1 mmol/1 DTT for 15 min at 4°C while shaking. The samples were centrifuged, and liquid phase was collected.
• a hypertonic nuclear extraction buffer [20 mmol/1 HEPES (pH 7.9), 0.42 mol/1 KC1, 1 mmol/1 EDTA] supplemented with 1 mmol/1 DTT for 15 min at 4°C while shaking. The samples were centrifuged, and liquid phase was collected.
• RNA extraction RNA extraction, reverse transcription-PCR, and qPCR
• RNA ScreenTape Kit Agilent Technologies; 5067-5576
• D1000 ScreenTape Kit Agilent Technologies; 5067-5582
• Qubit(r) RNA HS Assay Kit Invitrogen; Q32852
• Qubit(r) DNA HS Assay Kit Invitrogen; 32854
• 1 ⁇ g of RNA per sample was processed using KAPA Stranded mRNA-Seq Kit with mRNA Capture Beads (Kapa Biosystems; KK8421).
• the list of differentially expressed genes was separated to upregulated (WWOX-KO expression was higher than WT expression) and downregulated sublists. Each sublist was sorted by fold change values, and top 100 genes were selected from each sublist. For each of the selected genes, log2 -normalized counts were scaled and presented in a heatmap using heatmap.2 from R package gplots (ver.3.0.3). For the heatmap seen in Fig. 14F, log2-normalized counts for each of the six cortical layer gene markers were scaled and presented in a heatmap form using heatmap.2 from R package gplots. Gene set enrichment analysis was performed with Broad Institute GSEA software (ver.4.0.3).
• GO sets are Broad Institute set c5.all.v7.0.
• Permissible sets are those with at least 15 genes and no more than 500 genes.
• Gene sets are GO biological processes.
• Permissible sets in this analysis are those with at least 10 genes and no more than 500 genes.
• PCA plot of first two components was calculated and plotted with base R functions. Calculation is based on log2-transformed and log2 -normalized counts adding pseudo count of 1.
• Results of the experiments were expressed either as mean ⁇ SEM or in a boxplot indicating the 1 st and 3 rd quartiles, minimum and maximum values, and the median.
• Wilk-Shapiro test was used to determine normality: For normally distributed samples, a two-tailed unpaired Student’s t-test with Welch’s correction was used to compare the values of the test and control samples. For non-normally distributed samples, the non-parametric Mann-Whitney test was used. For comparisons between more than two samples, one-way ANOVA was used, correcting for the multiple comparisons with Tukey ’ s multiple comparisons test. For samples that were not normally distributed, the Kruskal-Wallis test was used with Dunn’s multiple comparisons test.
• tumour suppressor gene WWOX is mutated in autosomal recessive cerebellar ataxia with epilepsy and mental retardation. Brain 137: 411-419
• Neonatal seizures characteristics of EEG ictal activity in preterm and full-term infants. Brain Dev 25: 427-437
• SEQ ID No 5 Synapsin 1 / WWOX cDNA construct (bold font-minimal Synl promoter ; underline - human WWOX cDNA; regular font - AAV9 vector)

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