Competitive Replacement of Glial Cells CROSS REFERENCE TO RELATED APPLICATIONS This application claims priority to U.S. Provisional Application No. 63/482,862 filed on February 2, 2023 and U.S. Provisional Application No.63/493,451 filed on March 31, 2023. The contents of the applications are incorporated herein by reference in their entireties. REFERENCE TO SEQUENCE LISTING The present application is being filed along with a Sequence Listing in electronic format. The Sequence Listing is provided as a file entitled SeqList-161118-04702.xml, created on January 29, 2024, which is 18,319 bytes in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety. FIELD The present application relates to competitive replacement of glial cells and its uses in treatment of oligodendrocyte loss, astrocyte loss, or white matter loss, including age-related oligodendrocyte loss, age-related astrocyte loss, or age-related white matter loss. BACKGROUND The central nervous system (CNS) is organized into gray matter, which generally contains the cell bodies and dendrite networks of neurons, and white matter, which consists of axon bundles encased by myelin produced by oligodendrocytes. Loss of white matter, oligodendrocyte, or astrocyte can lead to poor outcomes, including cognitive impairment, dementia, urinary incontinence, gait disturbances, depression, and increased risk of stroke and death. This loss involves partial loss of myelin, axons, and oligodendroglial cells; mild reactive astrocytic gliosis; sparsely distributed macrophages as well as stenosis resulting from hyaline fibrosis of arterioles and smaller vessels. There is a need for therapeutics and methods for treating disorders and conditions mediated by or characterized by loss of white matter, oligodendrocytes, or astrocytes. The present disclosure is directed to overcoming these and other deficiencies in the art. SUMMARY This disclosure addresses the need mentioned above in a number of aspects. In one aspect, this disclosure provides a method for rejuvenating, or enhancing the development potential of, a glial progenitor cell or a progeny thereof. The method comprises increasing in the glial progenitor cell or the progeny a level or activity of (i) a transcription
factor selected from the group consisting of CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 or (ii) a target of the transcription factor. In some embodiments, the transcription factor is selected from the group consisting of CTCF, E2F1, and ETV4. The target can be selected from the group (as listed Table 1 and Figure 5) consisting of RPL6, RPS27, RPS16, RPS21, DOHH, PCCB, UTP11, RPS8, RPL27A, EIF2A, UBLCP1, RPL32, GIN1, PATZ1, TNFRSF1A, MRPL10, RFXANK, BORCS8, ENOPH1, RPS16, SNHG11, SLC35A5, RAB1B, RPL23A, YBX1, TMEM129, DOHH, CCND1,MRPL24, RPL14, HMGA1, DCTPP1, ENOPH1, ZNF436, RPLP2, CCND1, TNFRSF1A, FBXL12, NTMT1, IMPDH2, MRPL18, LIMS1, CD82, POLR2H, LRRC8A, EXOSC5, RAN, DYNLT1, FDPS, ACTL6A, RPS5, DOLPP1, GGCT, RPS2, SYCE1L, MRPL17, ZDHHC16, YBX1, RPLP0, ELK1, RPSA, NME2, RPS15, TSPAN33, B3GNT9, DCLRE1B, CMC1, RPLP1, ACAT2, RPL6, RPL28, RPL18A, CCDC51, RACK1, RPS14, RPS19, RPL12, RPS5, RPL19, RPL27A, RPS19, RPS21, POLR2H, RPS14, CCDC51, EIF2A, UBLCP1, SNHG19, RPL32, ZNF579, RPS27, RPL6, GIN1, PATZ1, RACK1, LRRC8A, TNFRSF1A, RPL28, RPS18, MRPL10, RFXANK, BORCS8, FBXL12, PEF1, ENOPH1, PEX7, RPS16, SNHG11, RPL10, ZDHHC16, HMGA1, ZNF436, UTP11, DCLRE1B, RPS5, EXOSC5, MRPL17, RPL19, PRMT1, NME2, CCND1, NRN1, YBX1, LIMS1, RPL23A, CD82, NTMT1, RPL18A, DOLPP1, GGCT, ELK1, ACTL6A, FDPS, MRPL18, RPLP0, ACAT2, SLC35A5, RAB1B, RAN, DYNLT1, TMEM129, RPSA, RPS15, RPL13A, PCCB, DCTPP1, RPLP2, B3GNT9, IMPDH2, RPL14, MRPL24, RPS8, RPS2, SYCE1L, RPL12, CMC1, DOHH, RPLP1, BTBD17, TSPAN33, ACAT2, GGCT, FDPS, SNHG19, PRMT1, RPL13A, FBXL12, RPS19, RFXANK, NRN1, DCTPP1, ZNF579, YBX1, MRPL18, NTMT1, RPL14, PEF1, RPS21, PEX7, BTBD17, RPL10, and RPS18. In some embodiments, the glial progenitor cell is an aged glial progenitor cell. In some embodiments, the progeny is an oligodendrocyte or an astrocyte. In some embodiments, the increasing step comprises expressing or introducing in the glial progenitor cell or the progeny the transcription factor or the target. In some embodiments, the increasing step comprises contacting the glial progenitor cell or the progeny with an agent that increase the level or activity of the transcription factor or the target. In some embodiments, the method further comprises suppressing in the glial progenitor cell or the progeny a transcription repressor selected from the group consisting of E2F6, ZNF274, MAX, and IKZF3. In another aspect, the disclosure provides a cell prepared according to the method described herein or a progeny thereof.
In a further aspect, this disclosure provides a method of treating a condition mediated by white matter loss, oligodendrocyte loss, or astrocyte loss. The method comprises administering to a subject in need thereof (a) a therapeutically effective amount of an agent that increase the level or activity of (i) a transcription factor selected from the group consisting of CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 or (ii) a target of the transcription factor, or (b) a therapeutically effective amount of the cell prepared according to the method described herein or a progeny thereof. In some embodiments, the transcription factor is selected from the group consisting of CTCF, E2F1, and ETV4. The target is selected from the group mentioned above and listed Table 1 and Figure 5. In some embodiments, the method further comprises administering to the subject a therapeutically effective amount of a suppressor of a transcription repressor selected from the group consisting of E2F6, ZNF274, MAX, and IKZF3. In some embodiments, the subject is a human. In some embodiments, the agent comprises a small molecule compound, an oligonucleotide, a nucleic acid, a peptide, a polypeptide, a CRISPR/Cas system, or an antibody or an antigen-binding portion thereof. In some embodiments, the nucleic acid encodes the transcription factor or the target mentioned above. In some embodiments, the suppressor comprises a small molecule compound, an oligonucleotide, a nucleic acid, a peptide, a polypeptide, a CRISPR/Cas system, or an antibody or an antigen-binding portion thereof. In some embodiments, the agent, suppressor, or cell is administered by intraparenchymal, intracallosal, intraventricular, intrathecal, intracerebral, intracisternal, or intravenous administration. In some embodiments, the cell or progeny is administered to the forebrain, striatum, and/or cerebellum. In some embodiments, the condition is a lysosomal storage disease, an autoimmune demyelination condition (e.g., multiple sclerosis, neuromyelitis optica, transverse myelitis, and optic neuritis), a vascular leukoencephalopathy (e.g., subcortical stroke, diabetic leukoencephalopathy, hypertensive leukoencephalopathy, age-related white matter disease, and spinal cord injury), a radiation induced demyelination condition, a leukodystrophy (e.g., Pelizaeus-Merzbacher Disease, Tay-Sach Disease, Sandhoff’s gangliosidoses, Krabbe's disease, metachromatic leukodystrophy, mucopolysaccharidoses, Niemann-Pick A disease, adrenoleukodystrophy, Canavan's disease, Vanishing White Matter Disease, and Alexander Disease), or periventricular leukomalacia or cerebral palsy. In some embodiments, the
condition is Huntington’s disease or subcortical dementia. In some embodiments, the condition is Parkinson’s disease. In some embodiments, the glial progenitor cell is derived from a pluripotent stem cell. In some embodiments, the pluripotent stem cell is an embryonic stem cell or an induced pluripotent stem cell. In some embodiments, the cell or progeny is heterologous, xenogenic, allogeneic, isogenic, or autologous to the subject. In some embodiments, the white matter loss, oligodendrocyte loss, or astrocyte loss is age-related. BRIEF DESCRIPTION OF THE DRAWINGS The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. Figs.1A-1J show that adult-transplanted WT human GPCs outcompeted and replaced neonatally resident HD hGPCs. Fig. 1A shows an experimental design and analytical endpoints. STR, striatum (caudate-putamen); LV, lateral ventricle; CTX, cortex. Dashed rectangle (orange) represents inset (B’). Scale: B, 500 µm; C’, 100 µm; D, 50 µm; E, 10 µm; I: 100 μm; I’: 10 μm. Fig. 1B shows that engraftment of WT glia (mCherry
+, red) into the striatum of HD chimeras yielded progressive replacement of HD glia (EGFP
+, green) creating extensive exclusive domains in their advance. Dashed outlines (white) demarcate the striatal outlines within which human cells were mapped and quantified. Figs. 1C-D. show that the border between advancing WT and retreating HD hGPCs was typically well-delineated, such that exclusive domains are formed as WT GPCs (Olig2
+, white) displace their HD counterparts. Fig. 1E shows that GPC replacement preceded astrocytic replacement, as within regions colonized by WT hGPCs, stray HD astrocytes (hGFAP
+, white) could still be found. Fig. 1F shows mapped distributions of human glia in host striata. Human glia were mapped in 15 equidistant sections (5 are shown as example) and reconstructed in 3D. Their distribution was measured radially as a function of distance to the injection site. Fig.1G shows rendered examples of mapped striata. Fig. 1H shows volumetric quantification indicating that WT gradually replaced their HD counterparts as they expanded from their implantation site; H
1: WT vs. HD (Allograft; n=8 for 54 weeks, n=7 for 72 weeks). The advance of WT cells was accompanied by a progressive
elimination of HD glia from the tissue, relative to untransplanted HD chimeras (HD control); H
2: HD (Allograft; n=8 for 54 weeks, n=7 for 72 weeks) vs. HD Control (n=4 for both timepoints; 2-way ANOVA with Šidák’s multiple comparisons tests. ****P<0.0001, ***P<0.001, **P<0.01, *P<0.05; data are presented as means ± SEM). Fig.1I shows that at the boundary between WT and HD glia, a high incidence of Ki67
+ (white) cells can be seen exclusively within the WT glial population. I’. Higher magnification of two WT daughter cells at the edge of the competitive boundary. Fig.1J shows that quantification of Ki67
+ glia within each population as a function of time shows a significant proliferative advantage by WT glia, that is sustained throughout the experiment. HD control: 54 wks (n=4), 72 wks (n=4); WT control: 54 wks (n=5), 72 wks: n=3; WT vs. HD allograft: 54 wks (n=5), 72 wks (n=3). Comparisons by 2-way ANOVA with Šidák’s multiple comparisons tests; mean ± SEM. Figs.2A-2I show that WT glia acquired a dominant competitor transcriptional profile in the face of resident HD glia. Fig.2A. shows an experimental design. Figs. 2B and C show that uniform manifold approximation projection (UMAP) visualization of the integrated (B) and split by group (C) scRNA-seq data identified six major cell populations. Fig.2D shows tacked bar plot proportions of cell types in each group. Fig.2E shows cell cycle analysis notched box plots of cycling GPCs and GPCs in the G2/M phase. The box indicates the interquartile range, the notch indicates the 95% confidence interval with the median at the center of the notch, and the error bars represent the minimum and maximum non-outlier values. Fig.2F shows a Venn diagram of pairwise differentially expressed GPC genes (Log2 fold change > 0.15, adjusted p-value < 0.05). Fig. 2G shows curated ingenuity pathway analysis of genes differentially expressed between GPC groups. The size of circles represent p-value while the shading indicates activation Z-Score with red being more active in the upper group and green being more active in the lower group. Fig.2H shows heatmap of curated pairwise differentially expressed GPC genes. * = < 0.05, ** < 0.01, *** = < 0.001, **** = < 0.0001 adjusted p-value. Fig.2I shows violin plots of pairwise differentially expressed GPC ribosomal gene log2 fold changes. Comparisons between groups in (E) utilized Dunn tests following a Kruskal- Wallis test with multiple comparisons adjusted via the Benjamini-Hochberg method.
Figs. 3A-3I show that differences in cell age were sufficient to drive competitive repopulation of humanized striata. B-C. STR, striatum (caudate-putamen); LV, lateral ventricle; CTX, cortex.). Scale: B, 500 µm; C, 100 µm; E – 100 µm; G – 50 µm. Fig.3A shows an experimental design and analytical endpoints. Fig.3B shows that engraftment of younger WT glia (EGFP
+, green) into the striatum of WT chimeras yielded selective replacement of their aged counterparts (mCherry
+, red). Dashed outlines demarcate the striatal regions within which human cells were mapped and quantified. Fig.3C shows WT chimeric control, engrafted only at birth. Fig.3D shows rendered examples of mapped striata. Volumetric quantification shows that the younger WT glia replace their older isogenic counterparts as they expand from their injection site; Fig.3E shows Aged vs. Young (Isograft), n=3. Their advance tracked the progressive elimination of aged WT glia from the tissue, relative to control WT chimeras (Aged control); Fig. 3F shows Aged (Isograft) vs. Aged (Control) n=3 each; 2-way ANOVA with Šidák’s multiple comparisons test; Interactions or main effects are shown as numerical P values, while post-hoc comparisons are shown as: **** P<0.0001, *** P<0.001, **P<0.01, *P<0.05; data presented as means ± SEM. Fig.3G shows that at the interface between young and aged WT glia, a higher incidence of Ki67
+ (white) cells can be seen within the younger population. Fig.3H shows the inset color split represented in the dashed square in Fig.3G. Fig.3I shows that quantification of Ki67
+ cells indicating that younger WT glia were significantly more proliferative than their aged counterparts; n=3 for all experimental groups; One-way ANOVA with Šidák’s multiple comparisons test; data are shown as means ± SEM with individual data points. Figs. 4A-4I show that WT glia acquired a dominant transcriptional profile when confronting their aged counterparts. * = < 0.05, ** < 0.01, *** = < 0.001, **** = < 0.0001 adjusted p-value. Fig.4A shows an experimental design. Figs.4B-C show uniform manifold approximation projection (UMAP) visualization of the integrated (B) and split by group (C) scRNA-seq data identifies six major cell populations. Fig.4D shows stacked bar plot proportions of cell types in each group. Fig.4E shows cell cycle analysis notched box plots of cycling GPCs and GPCs in the G2/M phase. The box indicates the interquartile range, the notch indicates the 95% confidence
interval with the median at the center of the notch, and the error bars represent the minimum and maximum non-outlier values. Fig.4F shows a Venn diagram of pairwise differentially expressed GPC genes (Log2 fold change > 0.15, adjusted p-value < 0.05). Fig. 4G shows curated Ingenuity Pathway analysis of genes differentially expressed between GPC groups. The size of circles represent p-value while the shading indicates activation Z-Score with red being more active in the upper group and green being more active in the lower group. Fig.4H shows heatmap of curated pairwise differentially expressed GPC genes. Fig.4I shows violin plots of pairwise differentially expressed GPC ribosomal gene log2 fold changes. Comparisons between groups in E utilized Dunn tests, following a Kruskal- Wallis test with multiple comparisons adjusted via the Benjamini-Hochberg method. Figs.5A-5F show transcriptional signature of competitive advantage. Fig.5A shows schematic of a protocol for identifying transcription factors (TFs) linked specifically to competitive advantage. Fig.5B shows a box plot of identified WGCNA module eigengene of interest (blue) in competing and non-competing cells. Fig.5C shows that GSEA highlighted prioritized transcription factors whose regulons were enriched for upregulated genes in dominant young WT cells. Fig. 5D shows analysis of the relative contribution of each biological factor (age vs genotype) towards the composition of each module eigengene. Fig. 5E shows important transcription factors, as predicted by SCENIC to establish competitive advantage, and their relative activities across groups. Fig. 5F shows regulatory network including downstream targets and their functional signaling pathways. Target expressions are controlled by at least one other important transcription factor in (E). NES: Network Enrichment Score. Figs. 6A-6J show generation of human HD glial chimeric striata. C-D; G-H: Data presented as means ± s.e.m with individual data points (n=4) C-D. One-way ANOVA with Tukey’s multiple comparisons test; 12 weeks (n=3), 24 weeks (n=3), 36 weeks (n=4). Scale: B, 500 µm; H, 10 µm. Fig.6A shows an experimental design and analytical endpoints.
Fig.6B shows that neonatally engrafted HD glia (EGFP
+, green) expanded within the murine striatum yielding substantial humanization of the tissue over time. Dashed lines demarcate the striatal borders within which human cells were mapped and quantified. Figs.6C-D shows that their expansion was concomitant with an increase in the number of HD glia harbored in the murine striatum over time (C) at the cost of their Ki67
+ proliferative cell pool (D). Fig. 6E shows a strategy employed to assess the extent of striatal humanization 36 weeks following neonatal implantation of HD GPCs. HD cell distribution was mapped in 15 equidistant sagittal sections (5 are shown for example) and reconstructed in 3D for analysis. Fig. 6F shows a rendered example of a mapped and reconstructed striatum for volumetric analysis. Fig.6G shows volumetric quantification demonstrating that by 36 weeks HD glia had expanded throughout whole striatum assuming a uniform distribution; Data are shown as mean (line) and individual data points (n=4). Figs.6H-J show that as they colonized the murine striatum, HD glia either expanded and persisted as Olig2
+ GPCs (arrows point to Olig2
+/EGFP
+ (red/green) cells) or differentiated into hGFAP
+ (red) astrocytes. Proliferating (Ki67
+, red) HD glia can be found even after 36 weeks of expansion, albeit in decreased numbers (D). STR, neostriatum; LV, lateral ventricle; CTX, cortex. Figs.7A-7H show replacement of HD by WT glial progenitor cells yielded proportional phenotypic replacement. Scale: D-E, G-H, 50 µm. Fig. 7A shows an experimental design and analytical endpoints for the WT Control group. Fig.7B shows stereological estimations demonstrating that the total number of HD glia progressively decreased relatively to HD chimera controls as WT glia expanded within the humanized striatum; 2-way ANOVA with Šidák’s multiple comparisons test. HD Control: n=4 for both timepoints; WT Control: n=5 for 54 wks, n=3 for 72 wks; Allograft: n=5 for 54 wks, n=3 for 72 wks. Data shown as means ± SEMs with individual data points. Figs.7C–E show that WT glia expanded as Olig2
+ (white) GPCs displacing their HD counterparts. Figs.7F-H show within areas where they became dominant, they further differentiated into hGFAP
+ (white) astrocytes. The proportion of GPCs and astrocytes in both populations was maintained as they competed for striatal dominance. Orange arrows point to co-labelled cells.
Figs.8A-8D show that adult-engrafted hGPCs more rapidly dominated already-resident mouse than human hGPCs. Fig. 8A shows an experimental design and analytical endpoints for the WT Control group. Fig.8B shows that engraftment of WT glia (mCherry
+, red) into the adult striatum of Rag1
(-/-) mice yielded substantial humanization of the murine striatum over time. Scale: B, 500 µm Figs.8C-D show volumetric quantifications demonstrating that adult-transplanted WT glia infiltrated and dispersed throughout the murine striatum over time (C), and (D), and that they do so significantly more broadly than do those grafted into already HD chimeric mice. WT Allografts (into HD chimeras; data comparison to Figure 2): n=8 for 54 weeks, n=7 for 72 weeks; WT Controls: n=8 for 54 weeks, n=5 for 72 weeks. Two-way ANOVA with Šidák’s multiple comparisons test; Main effects are shown as P values. Figs.9A-9F show eexpression of fluorescent transgenes did not influence competitive dominance. Co-engrafted isogenic clones of tagged and untagged WT hGPCs admixed while displacing resident HD glia. Scale: B, 500 µm; C-D, 100 µm; E, 10 µm. Fig.9A shows an experimental design for mice that received a 1:1 mixture of mCherry- tagged (WT-mCherry) and untagged (WT-untagged) WT glia. Fig.9B shows iimmunolabeling against human nuclear antigen (hN) demonstrating that both WT-mCherry (mCherry
+ hN
+, red, white) and WT-untagged (mCherry- EGFP- hN
+, white) glia expanded within the previously humanized striatum, progressively displacing HD glia (EGFP
+ hN
+, green, white). Fig.9C shows that vast homotypic domains were formed as mixed WT glia expanded and displaced resident HD glia. Fig. 9D shows that in contrast, isogenic WT-mCherry and WT-untagged were found admixing. Fig.9E shows that as previously noted, within WT glia dominated domains, only more complex astrocyte-like HD glia could be found, typically within white matter tracts. Fig.9F shows quantification of the proportion of WT-mCherry and WT-untagged glia within the striatum demonstrating no significant difference between the two populations at either quantified timepoint (n=6 for each timepoint; samples were pooled from both experimental groups); Two-way ANOVA with Šidák’s multiple comparisons test; Data is shown as means ± SEM with individual data points.
Figs.10A-10D show human GPC chimeric mice were established by either a neonatal striatal injection of HD EGFP-tagged glial (Fig. 10A; G20 only), G19 mCherry-tagged wildtype glial transplanted into untreated 36 week old mice (Fig. 10B; G19 only) or into previously G20-EGFP chimerized 36 week old mice (Fig.10C). All mice were sacrificed at 72 week and human cells mapped in equidistant serial brain sections. In all groups, cells dispersed beyond the striatum where the cell were injected and colonized most of the forebrain. Fig.10D Stereological counts of human cell. Means ± SEM. ns: not significant; *p < 0.05 by 1-way ANOVA with Tukey’s post hoc test. Figs. 11A-11C show that aged human glia were eliminated by their younger counterparts through induced apoptosis. Scale: A –100 µm, B – 50 µm. Fig. 11A shows that at the border between young (EGFP
+, green) and aged WT glia (mCherry
+, red), a higher incidence of apoptotic TUNEL
+ (white) cells were apparent in the aged population. Fig.11B shows higher magnification of a competitive interface between these distinct populations demonstrating resident glia selectively undergoing apoptosis. Fig. 11C shows quantification of TUNEL
+ cells demonstrating significantly higher incidence of TUNEL
+ cells among aged resident WT glia, relative to both their younger isogenic counterparts, and to aged WT chimeric controls not challenged with younger cells. Quantification was performed on pooled samples from 60 and 80 weeks timepoints (n=5 for all experimental groups). One-way ANOVA with Šidák’s multiple comparisons test; data are shown as means ± SEM with individual data points. DETAILED DESCRIPTION The disclosure is based at least in part on unexpected discoveries that aged and diseased human glia may be broadly replaced in adult brain by younger healthy glial progenitor cells. Accordingly, this disclosure relates to compositions and methods for treating a condition mediated by oligodendrocyte loss, astrocyte loss, or white matter loss, including age-related oligodendrocyte loss, age-related astrocyte loss, or age-related white matter loss. This disclosure also relates to (a) rejuvenating a glial progenitor cell or a progeny thereof or (b) enhancing the development potential of a glial progenitor cell or a progeny thereof. As used herein, “glial progenitor cells” refers to cells having the potential to differentiate into cells of the glial lineage such as oligodendrocytes and astrocytes. Glia progenitor cells may be astrocyte-biased. Glial progenitor cells may be oligodendrocyte biased. Examples of glial progenitor cells include astrocyte progenitor cells and
oligodendrocyte progenitor cells. As used herein, the term “glial cells” refers to a population of non-neuronal cells that provide support and nutrition, maintain homeostasis, either form myelin or promote myelination, and participate in signal transmission in the nervous system. “Glial cells” as used herein encompasses fully differentiated cells of the glial lineage, such as oligodendrocytes or astrocytes, and well as glial progenitor cells, each of which can be referred to as macroglial cells. In some embodiments, glial progenitor cells are also known as oligodendrocyte progenitor cells or NG2 cells. Conditions Mediated by Loss of While Matter/Oligodendrocytes/Astrocytes and Related Disorders Certain aspects of this disclosure relate to compositions and methods for treating a condition or disorder mediated by oligodendrocyte loss, astrocyte loss, or white matter loss. Such a condition often entails a deficiency in myelin in central nerve system (“CNS”). Examples of such conditions or disorders include any diseases or conditions related to demyelination, insufficient myelination and remyelination, or dysmyelination in a subject. Such a condition or disorder can be inherited, acquired, or due to the ageing process, i.e., age- related. In some embodiments, the condition is that of age-related white matter disease defined as or characterized by oligodendrocyte loss, astrocyte loss, or white matter atrophy in the setting of normal otherwise healthy aging. In humans, ageing represents the accumulation of changes in a human being over time and can encompass physical, psychological, and social changes. Ageing increases the risk of human diseases such as cancer, diabetes, cardiovascular disease, stroke, and many more, including demyelination in the CNS, which are often seen in various neurodegenerative diseases. Accordingly, in some embodiments of this disclosure, the condition or disorder is mediated by age-related oligodendrocyte loss, age-related astrocyte loss, or age-related white matter loss. Demyelination in the CNS may occur in response to genetic mutation (leukodystrophies), autoimmune disease (e.g., multiple sclerosis), or trauma (e.g., traumatic brain injury, spinal cord injury, or ischemic stroke). Perturbation of myelin function may play a critical role in neurologic and psychiatric disorders such as Autism Spectrum Disorder (ASD), Alzheimer’s disease, Huntington’s disease, Multiple System Atrophy, Parkinson’s disease, Fragile X syndrome, schizophrenia, and various leukodystrophies. Leukodystrophies are a group of rare, primarily inherited neurological disorders that result from the abnormal production, processing, or development of myelin and are the result of genetic defects (mutations). Some forms are present at birth, while others may not produce
symptoms until a child becomes older. A few primarily affect adults. Leukodystrophies include Canavan disease, Pelizaeus-Merzbacher disease, Hypomyelination with Atrophy of the Basal Ganglia and Cerebellum, Krabbe disease (Globoid cell leukodystrophy), X-linked adrenoleukodystrophy, Metachromatic leukodystrophy, Pelizaeus-Merzbacher-like disease (or hypomyelinating leukodystrophy-2), Niemann-Pick disease type C (NPC), Autosomal dominant leukodystrophy with autonomic diseases (ADLD), 4H Leukodystrophy (Pol III- related leukodystrophy), Zellweger Spectrum Disorders (ZSD), Childhood ataxia with central nervous system hypomyelination or CACH (also called vanishing white matter disease or VWMD), Cerebrotendinous xanthomatosis (CTX), Alexander disease (AXD), SOX10- associated peripheral demyelinating neuropathy, central dysmyelinating leukodystrophy, Waardenburg syndrome, Hirschsprung disease (PCWH), Adult polyglucosan body disease (APBD), Hereditary diffuse leukoencephalopathy with spheroids (HDLS), Aicardi-Goutieres syndrome (AGS), and Adult Refsum disease. Suitable subjects for treatment in accordance with the methods described herein include any human subject having a condition mediated by a deficiency in myelin, which may be manifested by age-related oligodendrocyte loss, age-related astrocyte loss, or age-related white matter loss. In another embodiment, the condition mediated by a deficiency in myelin is selected from the group consisting of pediatric leukodystrophies, the lysosomal storage diseases, congenital dysmyelination, cerebral palsy, inflammatory demyelination, post-infectious and post-vaccinial leukoencephalitis, radiation- or chemotherapy induced demyelination, and vascular demyelination. In a further embodiment, the condition mediated by a deficiency in myelin requires myelination. In another embodiment, the condition mediated by a deficiency in myelin requires remyelination. In some embodiments, the condition requiring remyelination is selected from the group consisting of multiple sclerosis, neuromyelitis optica, transverse myelitis, optic neuritis, subcortical stroke, diabetic leukoencephalopathy, hypertensive leukoencephalopathy, age-related white matter disease, white matter dementia, Binswanger's disease, spinal cord injury, radiation- or chemotherapy induced demyelination, post-infectious and post-vaccinial leukoencephalitis, periventricular leukomalacia, and cerebral palsy. In a further embodiment, the condition mediated by a deficiency in myelin is neurodegenerative disease. In some embodiments, the neurodegenerative disease is Huntington’s disease. Huntington’s disease is an autosomal dominant neurodegenerative disease characterized by a relentlessly progressive movement disorder with devastating
psychiatric and cognitive deterioration. Huntington's disease is associated with a consistent and severe atrophy of the neostriatum which is related to a marked loss of the GABAergic medium-sized spiny projection neurons, the major output neurons of the striatum. Huntington's disease is characterized by abnormally long CAG repeat expansions in the first exon of the Huntingtin gene. The encoded polyglutamine expansions of mutant huntingtin protein disrupt its normal functions and protein-protein interactions, ultimately yielding widespread neuropathology, most rapidly evident in the neostriatum. Other neurodegenerative diseases treatable in accordance with the present application include frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, multisystem atrophy, and amyotrophic lateral sclerosis. In an embodiment, the condition mediated by a deficiency in myelin is a neuropsychiatric disease. In some embodiments, the neuropsychiatric disease is schizophrenia. Schizophrenia is a serious mental illness that affects how a person thinks, feels, and behaves. The symptoms of schizophrenia generally fall into the following three categories: (1) psychotic symptoms including altered perceptions, (2) negative symptoms including loss of motivation, disinterest and lack of enjoyment, and (3) cognitive symptoms including problems in attention, concentration, and memory. Other neuropsychiatric diseases treatable in accordance with the present application include autism spectrum disorder and bipolar disorder. The above-described myelin-related disorders, inherited or acquired or age-related, impact millions of people, levying a heavy burden on affected individuals and their families. The pathological processes underlying many of these disorders remain poorly understood and few disease-modifying therapies exist. There are unmet needs for therapeutics for treating these disorders. This disclosure address these needs in a number of ways, such as competitive replacement of aged or older glial progenitor cells in the brain and rejuvenation of glial progenitor cells or their progeny cells. Competitive Replacement of Glial Progenitor Cells in Adult Brain Some aspects of this disclosure relate to competitive replacement of glial progenitor cells. Competition among cell populations in development and oncogenesis is well- established, and yet competition among cells in the adult brain has remained little-studied. In particular, it is unknown whether allografted human glia can outcompete diseased cells to achieve therapeutic replacement in the adult human brain. As disclosed herein, healthy, fluorophore-tagged wild-type (WT) hGPCs produced from human embryonic stem cells (hESCs) were engrafted into the striata of adult mice that had been neonatally chimerized with spectrally-distinct mutant HTT-expressing hGPCs
produced from Huntington disease (HD)-derived hESCs. The WT hGPCs outcompeted and ultimately eliminated their human HD counterparts, repopulating the host striata with healthy glia. Single-cell RNA-Seq revealed that WT donor hGPCs acquired a YAP1/MYC/E2F- defined dominant competitor phenotype upon interaction with the resident HD-derived glia. Competitive success depended primarily upon the age difference between competing populations, in that adult-transplanted WT hGPCs outcompeted resident isogenic WT cells that had been transplanted neonatally, and were thus older. These data indicate that aged and diseased human glia may be broadly replaced in adult brain by younger healthy hGPCs, and suggest that the transplantation of newly-generated glial progenitors may be used as a broad therapeutic platform for the replacement of aged as well as diseased human glia. Glial dysfunction is a causal contributor to a broad spectrum of neurological conditions. Astrocytic and oligodendrocytic pathology have been associated with the genesis and progression of a number of both neurodegenerative and neuropsychiatric disorders, including conditions as varied as amyotrophic lateral sclerosis (ALS)
1-4, Huntington’s disease (HD)
5-10 and Parkinson’s disease
11, 12, as well as schizophrenia and bipolar disease
13-19. In such conditions, the replacement of diseased glia by healthy glial progenitor cells (hGPCs) might provide real therapeutic benefit
20, given their ability to disperse and colonize their hosts while giving rise to new astrocytes and oligodendrocytes. Yet, while human GPCs can outcompete and replace their murine counterparts in a variety of experimental therapeutic models
21-23, it has remained unclear if allografted human GPCs can replace other human cells, diseased or otherwise. As disclosed herein, human glial-chimeric mice
24 were used to model competition between healthy and diseased human glia in vivo, by engrafting healthy hGPCs into the striata of adult mice neonatally chimerized with hGPCs derived from subjects with HD. HD is a prototypic monogenic neurodegenerative disease, resulting from the expression of a mutant, CAG-repeat expanded, Huntingtin (mHTT) gene
25. Glial pathology is causally involved in the synaptic dysfunction of HD and that replacement of mHTT-expressing murine glia by implanted healthy hGPCs was sufficient to both delay disease progression and rescue important elements of function in transgenic HD mouse models
5. On that basis, in this study genetically-tagged wild-type (WT) and mHTT- expressing hGPCs, derived from sibling lines of human embryonic stem cells (hESCs), were used to examine if healthy WT hGPCs can replace diseased HD hGPCs in vivo. It was found that when healthy hGPCs were delivered into the striata of adult mice chimerized with HD hGPCs, that the healthy hGPCs outcompeted and displaced the already resident HD hGPCs.
However, since the WT donor cells were effectively younger than the resident host glia that they were replacing, study was carried out to find if differences in cell age might also contribute to competitive outcome. It was found this to be so, in that healthy young hGPCs implanted into adult mice that had been neonatally engrafted with separately-tagged glia derived from the same healthy line, inexorably replaced their older isogenic counterparts. Single cell RNA sequence analysis (scRNA-seq) of the younger winning and older losing hGPC populations revealed a set of differentially-expressed pathways that overlapped those of winning WT and losing HD hGPCs, suggesting a common transcriptional signature of competitively dominant GPCS. These data indicate that dynamic competition among clonally-distinct glial populations may occur in the mature adult brain, and that the replacement of both existing and diseased glia may thereby be achieved by the introduction of young healthy hGPCs. In light of the contribution of glial pathology to a broad variety of neurodegenerative and neuropsychiatric disorders
36, 37, it was sought here to establish the relative fitness of wild- type and both diseased and aged human GPCs in vivo, so as to assess the potential for allogeneic glial replacement as a therapeutic strategy. Some parts of this disclosure focused on Huntington’s disease, given the well-described role of glial pathology in HD
5, 8, 10, 38, 39. It was found that when WT hGPCs were introduced into brains already chimerized with HD hGPCs, that the WT cells out-competed and ultimately replaced the already-resident HD glial progenitors. The selective expansion of the healthy cells was associated with the active elimination of the resident HD glia, and was further supported by the proliferative advantage of the healthy donor cells relative to their already-resident diseased counterparts. Single-cell RNA sequencing revealed that the dominance of healthy WT hGPCs encountering HD glia in these adult chimeric mouse brains was linked to their expression of a transcriptional signature characteristic of competitively dominant cells in invertebrate systems. Surprisingly though, when controlled for the relative ages of the already-resident (older) and newly-introduced (younger) donor hGPCs, it was found that WT hGPCs transplanted into adult neostriata, which had been neonatally chimerized with separately-tagged but otherwise isogenic WT hGPCs, similarly out-competed and replaced their older, already-resident counterparts. This observation suggested that cellular youth was a critical determinant of competitive success, and of the ability of a donor hGPC population to replace that of the host. Accordingly, transplanted young WT hGPCs acquired the gene expression signature of a dominant competitor phenotype in vivo, whether challenged by already-resident older HD or isogenic WT hGPCs; indeed, the analysis described herein suggested that cellular youth was an even stronger determinant of competitive fitness than was disease genotype.
These observations suggest that cell replacement was driven by a recapitulation of developmental cell competition, an evolutionarily conserved selection process by which less fit clones are sensed and eliminated from a tissue by their fitter neighbors
40-43, but as manifested here dynamically in the adult brain. This process has been shown in a variety of systems to comprise the active elimination of relatively slowly growing cells by their faster growing, more competitively fit neighbors
44-48. It was noted that in the adult brain, WT hGPCs typically expanded from their implantation sites in an advancing proliferative wave. These younger hGPCs largely eliminated their hitherto stably resident – and hence older - counterparts, whether the latter were mHTT-expressing HD cells, or isogenic WT cells that had been transplanted months earlier. In both cases, the younger cells ultimately recolonized their host brains with healthy new hGPCs (Figs.1 and 3), and in both cases the younger donor cells differentially expressed gene sets associated with competitive dominance (Figs.2, 4 and 5). In particular, the competitive dominance of younger, adult-transplanted hGPCs was associated with their increased levels of predicted YAP1, E2F, MYC and MYCN pathway activity. These data provided a striking parallel to cell-cell competition in the mouse embryo, in which defective cells are eliminated by their neighbors following the acquisition of differential MYC expression during competitive challenge
44, 49, 50, and in which YAP1 and MYC interact to determine competitive outcomes during cell-cell competition
51, 52. Indeed, the concurrent enrichment for YAP1 pathway members in “winner” WT hGPCs, including transcripts both upstream and downstream of YAP1, suggests that the Hippo pathway might be an especially promising target for the regulation of glial replacement in the adult human brain. Indeed, these observations parallel the results of liver repopulation studies, in which mouse fetal liver progenitors were found to drive faster and more extensive replacement when allografted into older than into younger hosts
53, and for which MYC and YAP1 activities were predominant determinants of competitive success
54. As such, the identification of YAP1 and MYC as important regulators of competition among hGPCs may enable strategies by which to further enhance the competitive advantage, speed and extent of donor cell colonization following the delivery of these cells to the brain. The competitive replacement of resident glia by younger hGPCs observed resembles that of mouse glial replacement by implanted human GPCs, as their expansion within the murine brain is also sustained by a relative proliferative advantage, and progresses with the elimination of their murine counterparts upon contact
22. As in the xenograft setting, the winning population of young WT hGPCs appears to trigger the apoptotic death and local elimination of the resident losing population, whether comprised of older isogenic WT or
sibling HD cells. The relative localization of dying host cells to the advancing wavefronts of younger WT cells suggests that the latter trigger the death of already-resident hGPCs, likely via contact-dependent means. Potential mechanisms for such contact-dependent expression of relative cell fitness have been described in a variety of models
40, and include selective expression of Fwr isoforms
55, 56, as well as mechanical signals, potentially transduced through Piezo1-dependent modulation of YAP
57. In addition, the selective elimination of both HD and isogenic hGPCs when confronted with younger hGPCs was paralleled by their depletion of ribosomal encoding transcripts, consistent with the loss of ribosomal transcripts by ‘loser’ cells during cell competition
58-59, and highlighting the contribution of ribosomal protein transcription to the regulation of cell fitness
60-63. Together, these data suggest that the transcriptional control of translational machinery is as important in cell-cell competition in the adult brain as it is in development. These observations suggest that the brain may be a far more dynamic structural environment than previously recognized, with cell-cell competition among glial progenitor cells - and potentially their derived astrocytes - playing as critical a role in adult brain maintenance as in development. Indeed, the competitive advantage of young over older resident cells seems to largely mimic development, where successive waves of GPCs compete amongst each other, with the oldest largely eradicated from the brain by birth, replaced by younger successors
64. In adulthood, one may similarly envision that somatic mutation among dividing glial progenitors may yield selective clonal advantage to one daughter lineage or the other, resulting in the inexorable replacement of the population by descendants of the dominant daughter. This scenario, while typifying the onset of carcinogenesis, may also be involved in tumor suppression, via the competitive elimination of neoplastic cells by more fit non- neoplastic neighbors
65. It is especially intriguing to consider whether such a process of dynamic competition among differentially fit hGPCs may be involved in the development of non-neoplastic adult-onset brain disorders in which glia are involved, such as some schizophrenias
13, 14, 16, 17, and HD itself
5-10. Indeed, such a mechanism may contribute to the late-stage acceleration in disease progression often noted among those neurodegenerative and neuropsychiatric disorders in which glial pathology is involved. These data also have strong therapeutic implications, as they suggest that in the adult human brain, resident glia – whether diseased or simply aged - may be replaced following the introduction of younger and healthier GPCs. Given the many neurodegenerative and neuropsychiatric diseases in which causally contributory glial pathology is now recognized
1- 19, the clinical implications of this observation is profound: It suggests that the dysfunctional
glia of diseased brains, across a variety of disease etiologies and phenotypes, might be effectively eliminated and replaced by the intracerebral delivery of newly generated allogeneic hGPCs. The results suggest that glial progenitor cell delivery and glial replacement offers a viable and broadly applicable strategy towards the cell-based treatment of those diseases of the brain in which glial cells are causally involved. Rejuvenation of Glial Progenitor Cells or Progenies Thereof Some aspects of this disclosure relate to rejuvenation of glial progenitor cells or their progeny cells. Human glial progenitor cells emerge during the 2
nd trimester to colonize the brain, in which a parenchymal pool remains throughout adulthood. While fetal hGPCs are highly migratory and proliferative, their expansion competence diminishes with age, as well as following demyelination-associated turnover. Rejuvenation via Upregulation In one aspect, the present disclosure provides a method of rejuvenating a glial progenitor cell or a progeny thereof. Also provided is a method of enhancing the development potential of, a glial progenitor cell or a progeny thereof. Each of the methods comprises upregulating or increasing in the glial progenitor cell or the progeny a level or activity of (i) a transcription factor selected from the group consisting of CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 or (ii) a target of the transcription factor. Shown below are some examples of human CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 proteins. sp|P01106|MYC_HUMAN Myc proto-oncogene protein OS=Homo sapiens OX=9606 GN=MYC PE=1 SV=2 (SEQ ID NO: 1) MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAP SEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTEL LGGDMVNQSFICDPDDETFIKNIIIQDCMWSGFSAAAKLVSEKLASYQAARKDSGSPNPA RGHSVCSTSSLYLQDLSAAASECIDPSVVFPYPLNDSSSPKSCASQDSSAFSPSSDSLLS STESSPQGSPEPLVLHEETPPTTSSDSEEEQEDEEEIDVVSVEKRQAPGKRSESGSPSAG GHSKPPHSPLVLKRCHVSTHQHNYAAPPSTRKDYPAAKRVKLDSVRVLRQISNNRKCTSP RSSDTEENVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILS VQAEEQKLISEEDLLRKRREQLKHKLEQLRNSCA sp|P01106-1|MYC_HUMAN Isoform 1 of Myc proto-oncogene protein OS=Homo sapiens OX=9606 GN=MYC (SEQ ID NO: 2) MPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPP LSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD DETFIKNIIIQDCMWSGFSAAAKLVSEKLASYQAARKDSGSPNPARGHSVCSTSSLYLQD LSAAASECIDPSVVFPYPLNDSSSPKSCASQDSSAFSPSSDSLLSSTESSPQGSPEPLVL HEETPPTTSSDSEEEQEDEEEIDVVSVEKRQAPGKRSESGSPSAGGHSKPPHSPLVLKRC HVSTHQHNYAAPPSTRKDYPAAKRVKLDSVRVLRQISNNRKCTSPRSSDTEENVKRRTHN VLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSVQAEEQKLISEEDLL RKRREQLKHKLEQLRNSCA
sp|P01106-3|MYC_HUMAN Isoform 3 of Myc proto-oncogene protein OS=Homo sapiens OX=9606 GN=MYC (SEQ ID NO: 3) MDFFRVVENQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPS EDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELL GGDMVNQSFICDPDDETFIKNIIIQDCMWSGFSAAAKLVSEKLASYQAARKDSGSPNPAR GHSVCSTSSLYLQDLSAAASECIDPSVVFPYPLNDSSSPKSCASQDSSAFSPSSDSLLSS TESSPQGSPEPLVLHEETPPTTSSDSEEEQEDEEEIDVVSVEKRQAPGKRSESGSPSAGG HSKPPHSPLVLKRCHVSTHQHNYAAPPSTRKDYPAAKRVKLDSVRVLRQISNNRKCTSPR SSDTEENVKRRTHNVLERQRRNELKRSFFALRDQIPELENNEKAPKVVILKKATAYILSV QAEEQKLISEEDLLRKRREQLKHKLEQLRNSCA sp|P43268|ETV4_HUMAN ETS translocation variant 4 OS=Homo sapiens OX=9606 GN=ETV4 PE=1 SV=3 (SEQ ID NO: 4) MERRMKAGYLDQQVPYTFSSKSPGNGSLREALIGPLGKLMDPGSLPPLDSEDLFQDLSHF QETWLAEAQVPDSDEQFVPDFHSENLAFHSPTTRIKKEPQSPRTDPALSCSRKPPLPYHH GEQCLYSSAYDPPRQIAIKSPAPGALGQSPLQPFPRAEQRNFLRSSGTSQPHPGHGYLGE HSSVFQQPLDICHSFTSQGGGREPLPAPYQHQLSEPCPPYPQQSFKQEYHDPLYEQAGQP AVDQGGVNGHRYPGAGVVIKQEQTDFAYDSDVTGCASMYLHTEGFSGPSPGDGAMGYGYE KPLRPFPDDVCVVPEKFEGDIKQEGVGAFREGPPYQRRGALQLWQFLVALLDDPTNAHFI AWTGRGMEFKLIEPEEVARLWGIQKNRPAMNYDKLSRSLRYYYEKGIMQKVAGERYVYKF VCEPEALFSLAFPDNQRPALKAEFDRPVSEEDTVPLSHLDESPAYLPELAGPAQPFGPKG GYSY sp|P43268-2|ETV4_HUMAN Isoform 2 of ETS translocation variant 4 OS=Homo sapiens OX=9606 GN=ETV4 (SEQ ID NO: 5) MDPGSLPPLDSEDLFQDLSHFQETWLAEAQVPDSDEQFVPDFHSENLAFHSPTTRIKKEP QSPRTDPALSCSRKPPLPYHHGEQCLYSSAYDPPRQIAIKSPAPGALGQSPLQPFPRAEQ RNFLRSSGTSQPHPGHGYLGEHSSVFQQPLDICHSFTSQGGGREPLPAPYQHQLSEPCPP YPQQSFKQEYHDPLYEQAGQPAVDQGGVNGHRYPGAGVVIKQEQTDFAYDSDVTGCASMY LHTEGFSGPSPGDGAMGYGYEKPLRPFPDDVCVVPEKFEGDIKQEGVGAFREGPPYQRRG ALQLWQFLVALLDDPTNAHFIAWTGRGMEFKLIEPEEVARLWGIQKNRPAMNYDKLSRSL RYYYEKGIMQKVAGERYVYKFVCEPEALFSLAFPDNQRPALKAEFDRPVSEEDTVPLSHL DESPAYLPELAGPAQPFGPKGGYSY sp|P43268-3|ETV4_HUMAN Isoform 3 of ETS translocation variant 4 OS=Homo sapiens OX=9606 GN=ETV4 (SEQ ID NO: 6) MYLHTEGFSGPSPGDGAMGYGYEKPLRPFPDDVCVVPEKFEGDIKQEGVGAFREGPPYQR RGALQLWQFLVALLDDPTNAHFIAWTGRGMEFKLIEPEEVARLWGIQKNRPAMNYDKLSR SLRYYYEKGIMQKVAGERYVYKFVCEPEALFSLAFPDNQRPALKAEFDRPVSEEDTVPLS HLDESPAYLPELAGPAQPFGPKGGYSY sp|P25208|NFYB_HUMAN Nuclear transcription factor Y subunit beta OS=Homo sapiens OX=9606 GN=NFYB PE=1 SV=2 (SEQ ID NO: 7) MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLP IANVARIMKNAIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILF AMSTLGFDSYVEPLKLYLQKFREAMKGEKGIGGAVTATDGLSEELTEEAFTNQLPAGLIT TDGQQQNVMVYTTSYQQISGVQQIQFS sp|Q01094|E2F1_HUMAN Transcription factor E2F1 OS=Homo sapiens OX=9606 GN=E2F1 PE=1 SV=1 (SEQ ID NO: 8) MALAGAPAGGPCAPALEALLGAGALRLLDSSQIVIISAAQDASAPPAPTGPAAPAAGPCD PDLLLFATPQAPRPTPSAPRPALGRPPVKRRLDLETDHQYLAESSGPARGRGRHPGKGVK SPGEKSRYETSLNLTTKRFLELLSHSADGVVDLNWAAEVLKVQKRRIYDITNVLEGIQLI AKKSKNHIQWLGSHTTVGVGGRLEGLTQDLRQLQESEQQLDHLMNICTTQLRLLSEDTDS QRLAYVTCQDLRSIADPAEQMVMVIKAPPETQLQAVDSSENFQISLKSKQGPIDVFLCPE ETVGGISPGKTPSQEVTSEEENRATDSATIVSPPPSSPPSSLTTDPSQSLLSLEQEPLLS
RMGSLRAPVDEDRLSPLVAADSLLEHVREDFSGLLPEEFISLSPPHEALDYHFGLEEGEG IRDLFDCDFGDLTPLDF sp|P49711|CTCF_HUMAN Transcriptional repressor CTCF OS=Homo sapiens OX=9606 GN=CTCF PE=1 SV=1 (SEQ ID NO: 9) MEGDAVEAIVEESETFIKGKERKTYQRRREGGQEEDACHLPQNQTDGGEVVQDVNSSVQM VMMEQLDPTLLQMKTEVMEGTVAPEAEAAVDDTQIITLQVVNMEEQPINIGELQLVQVPV PVTVPVATTSVEELQGAYENEVSKEGLAESEPMICHTLPLPEGFQVVKVGANGEVETLEQ GELPPQEDPSWQKDPDYQPPAKKTKKTKKSKLRYTEEGKDVDVSVYDFEEEQQEGLLSEV NAEKVVGNMKPPKPTKIKKKGVKKTFQCELCSYTCPRRSNLDRHMKSHTDERPHKCHLCG RAFRTVTLLRNHLNTHTGTRPHKCPDCDMAFVTSGELVRHRRYKHTHEKPFKCSMCDYAS VEVSKLKRHIRSHTGERPFQCSLCSYASRDTYKLKRHMRTHSGEKPYECYICHARFTQSG TMKMHILQKHTENVAKFHCPHCDTVIARKSDLGVHLRKQHSYIEQGKKCRYCDAVFHERY ALIQHQKSHKNEKRFKCDQCDYACRQERHMIMHKRTHTGEKPYACSHCDKTFRQKQLLDM HFKRYHDPNFVPAAFVCSKCGKTFTRRNTMARHADNCAGPDGVEGENGGETKKSKRGRKR KMRSKKEDSSDSENAEPDLDDNEDEEEPAVEIEPEPEPQPVTPAPPPAKKRRGRPPGRTN QPKQNQPTAIIQVEDQNTGAIENIIVEVKKEPDAEPAEGEEEEAQPAATDAPNGDLTPEM ILSMMDR sp|P49711-2|CTCF_HUMAN Isoform 2 of Transcriptional repressor CTCF OS=Homo sapiens OX=9606 GN=CTCF (SEQ ID NO: 10) MAFVTSGELVRHRRYKHTHEKPFKCSMCDYASVEVSKLKRHIRSHTGERPFQCSLCSYAS RDTYKLKRHMRTHSGEKPYECYICHARFTQSGTMKMHILQKHTENVAKFHCPHCDTVIAR KSDLGVHLRKQHSYIEQGKKCRYCDAVFHERYALIQHQKSHKNEKRFKCDQCDYACRQER HMIMHKRTHTGEKPYACSHCDKTFRQKQLLDMHFKRYHDPNFVPAAFVCSKCGKTFTRRN TMARHADNCAGPDGVEGENGGETKKSKRGRKRKMRSKKEDSSDSENAEPDLDDNEDEEEP AVEIEPEPEPQPVTPAPPPAKKRRGRPPGRTNQPKQNQPTAIIQVEDQNTGAIENIIVEV KKEPDAEPAEGEEEEAQPAATDAPNGDLTPEMILSMMDR sp|Q03701|CEBPZ_HUMAN CCAAT/enhancer-binding protein zeta OS=Homo sapiens OX=9606 GN=CEBPZ PE=1 SV=3 (SEQ ID NO: 11) MAAVKEPLEFHAKRPWRPEEAVEDPDEEDEDNTSEAENGFSLEEVLRLGGTKQDYLMLAT LDENEEVIDGGKKGAIDDLQQGELEAFIQNLNLAKYTKASLVEEDEPAEKENSSKKEVKI PKINNKNTAESQRTSVNKVKNKNRPEPHSDENGSTTPKVKKDKQNIFEFFERQTLLLRPG GKWYDLEYSNEYSLKPQPQDVVSKYKTLAQKLYQHEINLFKSKTNSQKGASSTWMKAIVS SGTLGDRMAAMILLIQDDAVHTLQFVETLVNLVKKKGSKQQCLMALDTFKELLITDLLPD NRKLRIFSQRPFDKLEQLSSGNKDSRDRRLILWYFEHQLKHLVAEFVQVLETLSHDTLVT TKTRALTVAHELLCNKPEEEKALLVQVVNKLGDPQNRIATKASHLLETLLCKHPNMKGVV SGEVERLLFRSNISSKAQYYAICFLNQMALSHEESELANKLITVYFCFFRTCVKKKDVES KMLSALLTGVNRAYPYSQTGDDKVREQIDTLFKVLHIVNFNTSVQALMLLFQVMNSQQTI SDRYYTALYRKMLDPGLMTCSKQAMFLNLVYKSLKADIVLRRVKAFVKRLLQVTCQQMPP FICGALYLVSEILKAKPGLRSQLDDHPESDDEENFIDANDDEDMEKFTDADKETEIVKKL ETEETVPETDVETKKPEVASWVHFDNLKGGKQLNKYDPFSRNPLFCGAENTSLWELKKLS VHFHPSVALFAKTILQGNYIQYSGDPLQDFTLMRFLDRFVYRNPKPHKGKENTDSVVMQP KRKHFIKDIRHLPVNSKEFLAKEESQIPVDEVFFHRYYKKVAVKEKQKRDADEESIEDVD DEEFEELIDTFEDDNCFSSGKDDMDFAGNVKKRTKGAKDNTLDEDSEGSDDELGNLDDDE VSLGSMDDEEFAEVDEDGGTFMDVLDDESESVPELEVHSKVSTKKSKRKGTDDFDFAGSF QGPRKKKRNLNDSSLFVSAEEFGHLLDENMGSKFDNIGMNAMANKDNASLKQLRWEAERD DWLHNRDAKSIIKKKKHFKKKRIKTTQKTKKQRK Each of the transcription factors described here has highly conserved protein domains, conserved in several species including human, mouse, rat, chicken, fish and Drosophila. Accordingly, CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 of non-human species can also be
used in the expression cassette, genetic construct, vector, composition, or method disclosed herein. The term CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 also encompasses all the alternatively spliced variants, isoforms, functional fragments, or derivatives that substantially retain transcription factor activity of the CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 described herein. Typically, a functional fragment or derivative retains at least 50%, 60%, 70%, 80%, 90%, 95%, 99% or 100% of its transcription factor activity. It is also intended that a CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 transcription factor can include conservative amino acid substitutions that do not substantially alter its activity. Suitable conservative substitutions of amino acids are known to those of skill in this art and may be made generally without altering the biological activity of the resulting molecule. Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity. Conservative and non-conservative amino acid substitutions have been described herein. As used herein, the term "conservative sequence modifications" refers to amino acid modifications that do not significantly affect or alter the activity of one of the above-described protein. Conservative amino acid substitutions are ones in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been known in the art. A conservative modification or functional equivalent of a peptide, polypeptide, or protein disclosed herein refers to a polypeptide derivative of the peptide, polypeptide, or protein, e.g., a protein having one or more substitutions, point mutations, insertions, deletions, truncations, a fusion protein, or a combination thereof. It retains substantially the activity to of the parent peptide, polypeptide, or protein (such as those disclosed herein). In general, a conservative modification or functional equivalent is at least 60% (e.g., any number between 60% and 100%, inclusive, e.g., 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, and 99%) identical to a parent (e.g., one of the human or non-human CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 sequences or the targets disclosed herein). Amino acid substitutions can be made, in some cases, by selecting substitutions that do not differ significantly in their effect on maintaining (a) the structure of the peptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the molecule at the target sit; or (c) the bulk of the side chain. For example, naturally occurring residues can be divided into groups based on side-chain properties; (1) hydrophobic amino acids (norleucine, methionine, alanine, valine, leucine, and isoleucine); (2) neutral hydrophilic amino acids (cysteine, serine,
threonine, asparagine, and glutamine,); (3) acidic amino acids (aspartic acid and glutamic acid); (4) basic amino acids (histidine, lysine, and arginine); (5) amino acids that influence chain orientation (glycine and proline); and (6) aromatic amino acids (tryptophan, tyrosine, and phenylalanine). Substitutions made within these groups can be considered conservative substitutions. Examples of substitutions include, without limitation, substitution of valine for alanine, lysine for arginine, glutamine for asparagine, glutamic acid for aspartic acid, serine for cysteine, asparagine for glutamine, aspartic acid for glutamic acid, proline for glycine, arginine for histidine, leucine for isoleucine, isoleucine for leucine, arginine for lysine, leucine for methionine, leucine for phenylalanine, glycine for proline, threonine for serine, serine for threonine, tyrosine for tryptophan, phenylalanine for tyrosine, and/or leucine for valine. Exemplary substitutions are shown in the table below. Amino acid substitutions may be introduced into a human CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4 and the products screened for retention of the biological activity of the parent protein.

The methods described herein can also achieved by upregulating or increasing in a glial progenitor cell or the progeny a level or activity of one or more of targets of one or more of the transcription factors described above. Examples of the targets include those listed in Table 1 and Figure 5, including but not limited to: RPL6, RPS27, RPS16, RPS21, DOHH, PCCB, UTP11, RPS8, RPL27A, EIF2A, UBLCP1, RPL32, GIN1, PATZ1, TNFRSF1A, MRPL10,
RFXANK, BORCS8, ENOPH1, RPS16, SNHG11, SLC35A5, RAB1B, RPL23A, YBX1, TMEM129, DOHH, CCND1,MRPL24, RPL14, HMGA1, DCTPP1, ENOPH1, ZNF436, RPLP2, CCND1, TNFRSF1A, FBXL12, NTMT1, IMPDH2, MRPL18, LIMS1, CD82, POLR2H, LRRC8A, EXOSC5, RAN, DYNLT1, FDPS, ACTL6A, RPS5, DOLPP1, GGCT, RPS2, SYCE1L, MRPL17, ZDHHC16, YBX1, RPLP0, ELK1, RPSA, NME2, RPS15, TSPAN33, B3GNT9, DCLRE1B, CMC1, RPLP1, ACAT2, RPL6, RPL28, RPL18A, CCDC51, RACK1, RPS14, RPS19, RPL12, RPS5, RPL19, RPL27A, RPS19, RPS21, POLR2H, RPS14, CCDC51, EIF2A, UBLCP1, SNHG19, RPL32, ZNF579, RPS27, RPL6, GIN1, PATZ1, RACK1, LRRC8A, TNFRSF1A, RPL28, RPS18, MRPL10, RFXANK, BORCS8, FBXL12, PEF1, ENOPH1, PEX7, RPS16, SNHG11, RPL10, ZDHHC16, HMGA1, ZNF436, UTP11, DCLRE1B, RPS5, EXOSC5, MRPL17, RPL19, PRMT1, NME2, CCND1, NRN1, YBX1, LIMS1, RPL23A, CD82, NTMT1, RPL18A, DOLPP1, GGCT, ELK1, ACTL6A, FDPS, MRPL18, RPLP0, ACAT2, SLC35A5, RAB1B, RAN, DYNLT1, TMEM129, RPSA, RPS15, RPL13A, PCCB, DCTPP1, RPLP2, B3GNT9, IMPDH2, RPL14, MRPL24, RPS8, RPS2, SYCE1L, RPL12, CMC1, DOHH, RPLP1, BTBD17, TSPAN33, ACAT2, GGCT, FDPS, SNHG19, PRMT1, RPL13A, FBXL12, RPS19, RFXANK, NRN1, DCTPP1, ZNF579, YBX1, MRPL18, NTMT1, RPL14, PEF1, RPS21, PEX7, BTBD17, RPL10, and RPS18. Like the transcription factors described above, one or more of the targets may also have highly conserved protein domains, conserved in several species including human, mouse, rat, chicken, fish and Drosophila. Accordingly, a homologue of non-human species can also be used in the expression cassette, genetic construct, vector, composition, or method disclosed herein. Accordingly, each of the target also encompasses functional fragments or derivatives that substantially retain the respective activity of the target described herein. Typically, a functional fragment or derivative retains at least 50% of 60%, 70%, 80%, 90%, 95%, 99% or 100% of its parent’s activity. It is also intended that a target may include conservative amino acid substitutions that do not substantially alter its activity. As described herein, suitable conservative substitutions of amino acids are known to those of skill in this art and may be made generally without altering the biological activity of the resulting molecule. Those of skill in this art recognize that, in general, single amino acid substitutions in non-essential regions of a polypeptide do not substantially alter biological activity.
Rejuvenation via Suppression In some embodiments, a method disclosed herein can further comprise suppressing in the glial progenitor cell or the progeny a transcription repressor selected from the group consisting of E2F6, ZNF274, MAX, and IKZF3. Exemplary nucleic acid sequences and amino acid sequences of these repressors include those described in PCT/US22/78344 and PCT/US22/78356, the contents of which are incorporated by references. In some examples, this suppressing can be achieved by administering to a subject in need thereof or a target cell in need thereof a suppressor or inhibitor of one or more of the transcription repressor. Such a suppressor or inhibitor can comprise or be a small molecule compound, an oligonucleotide, a nucleic acid, a peptide, a polypeptide, a CRISPR/Cas system, or an antibody or an antigen-binding portion thereof. Examples of the suppressor/inhibitor include activators, agonists, or potentiators of the related YAP or MYC pathway signaling pathways (e.g., the Hippo signaling pathway). Various activators for this signaling pathway are known in the art. In some embodiments, the suppressor is an inhibitory nucleic acid or interfering nucleic acid, such as siRNA, shRNA, miRNA, antisense oligonucleotides (ASOs), and/or a nucleic acid comprising one or more modified nucleic acid residues. Examples include those described in PCT/US22/78344 and PCT/US22/78356, the contents of which are incorporated by references. In one aspect, suppressing or knocking down of one or more of the repressor genes described herein can also be achieved via a CRISPR-Cas guided nuclease using a CRISPR/Cas system and related methods known in the art. Examples include those described in PCT/US22/78344 and PCT/US22/78356, the contents of which are incorporated by references. Expression Cassettes and Expression Vectors The disclosure also provides an expression cassette, comprising or consisting of a recombinant nucleic acid encoding a transcription factor or a target thereof described above. Where such recombinant nucleic acid may not already comprise a promoter, the expression cassette may additionally comprise a promoter. Thus, an expression cassette according to the present disclosure comprises, in 5' to 3' direction, a promoter, a coding sequence, and optionally a terminator or other elements. The expression cassette allows an easy transfer of a nucleic acid sequence of interest into an organism, preferably a cell and preferably a disease cell. The expression cassette of the present disclosure is preferably comprised in a vector. Thus, the vector of the present disclosure allows to transform, transfect, transduce, infect, or introduce into a cell with a nucleic acid sequence of interest. Correspondingly the disclosure
provides a host cell comprising an expression cassette according to the present disclosure or a recombinant nucleic acid according to the present disclosure. The recombinant nucleic acid may also comprise a promoter or enhancer such as to allow for the expression of the nucleic acid sequence of interest. Exogenous genetic material (e.g., a nucleic acid, an expression cassette, or an expression vector encoding one or more therapeutic or inhibitory proteins or RNAs) can be introduced into a target cells of interest in vivo by genetic transfer methods, such as transfection or transduction, to provide a genetically modified cell. Various expression vectors (i.e., vehicles for facilitating delivery of exogenous genetic material into a target cell) are known to one of ordinary skill in the art. As used herein, "exogenous genetic material" refers to a nucleic acid or an oligonucleotide, either natural or synthetic, that is not naturally found in the cells; or if it is naturally found in the cells, it is not transcribed or expressed at biologically significant levels by the cells. Thus, "exogenous genetic material" includes, for example, a non-naturally occurring nucleic acid that can be transcribed into an RNA. As used herein, "transfection of cells" refers to the acquisition by a cell of new genetic material by incorporation of added nucleic acid (DNA, RNA, or a hybrid thereof) without use of a viral delivery vehicle. Thus, transfection refers to the introducing of nucleic acid into a cell using physical or chemical methods. Several transfection techniques are known to those of ordinary skill in the art including: calcium phosphate nucleic acid co-precipitation, strontium phosphate nucleic acid co-precipitation, DEAE-dextran, electroporation, cationic liposome- mediated transfection, and tungsten particle-facilitated microparticle bombardment. In contrast, "transduction of cells" refers to the process of transferring nucleic acid into a cell using a DNA or RNA virus. An RNA virus (e.g., a retrovirus) for transferring a nucleic acid into a cell is referred to herein as a transducing chimeric virus. Exogenous genetic material contained within the virus can be incorporated into the genome of the transduced cell. A cell that has been transduced with a chimeric DNA virus (e.g., an adenovirus carrying a DNA encoding a therapeutic agent), may not have the exogenous genetic material incorporated into its genome but may be capable of expressing the exogenous genetic material that is retained extrachromosomally within the cell. Typically, the exogenous genetic material may include a heterologous gene (coding for a therapeutic RNA or protein) together with a promoter to control transcription of the new gene. The promoter characteristically has a specific nucleotide sequence necessary to initiate transcription. Optionally, the exogenous genetic material further includes additional sequences (i.e., enhancers) required to obtain the desired gene transcription activity. The exogenous
genetic material may introduced into the cell genome immediately downstream from the promoter so that the promoter and coding sequence are operatively linked so as to permit transcription of the coding sequence. A retroviral expression vector may include an exogenous promoter element to control transcription of the inserted exogenous gene. Such exogenous promoters include both constitutive and inducible promoters. Naturally-occurring constitutive promoters control the expression of essential cell functions. As a result, a gene under the control of a constitutive promoter is expressed under all conditions of cell growth. Exemplary constitutive promoters include the promoters for the following genes that encode certain constitutive or "housekeeping" functions: hypoxanthine phosphoribosyl transferase, dihydrofolate reductase, adenosine deaminase, phosphoglycerol kinase, pyruvate kinase, phosphoglycerol mutase, the actin promoter, ubiquitin, elongation factor-1 and other constitutive promoters known to those of skill in the art. In addition, many viral promoters function constitutively in eucaryotic cells. These include the early and late promoters of SV40; the long terminal repeats (LTRs) of Moloney Leukemia Virus and other retroviruses; and the thymidine kinase promoter of Herpes Simplex Virus, among many others. Accordingly, any of the above-referenced constitutive promoters can be used to control transcription of a heterologous gene insert. Genes that are under the control of inducible promoters are expressed only in, or largely controlled by, the presence of an inducing agent, (e.g., transcription under control of the metallothionein promoter is greatly increased in presence of certain metal ions). Inducible promoters include responsive elements (REs) which stimulate transcription when their inducing factors are bound. For example, there are REs for serum factors, steroid hormones, retinoic acid and cyclic AMP. Promoters containing a particular RE can be chosen in order to obtain an inducible response and in some cases, the RE itself may be attached to a different promoter, thereby conferring inducibility to the recombinant gene. Thus, by selecting the appropriate promoter (constitutive versus inducible; strong versus weak), it is possible to control both the existence and level of expression of a therapeutic agent in the genetically modified cell. If the gene encoding the therapeutic agent is under the control of an inducible promoter, delivery of the therapeutic agent in situ is triggered by exposing the genetically modified cell in situ to conditions for permitting transcription of the therapeutic agent, e.g., by injection of specific inducers of the inducible promoters which control transcription of the agent. For example, in situ expression by genetically modified cells of a therapeutic agent encoded by a gene under the control of the metallothionein promoter, is enhanced by contacting
the genetically modified cells with a solution containing the appropriate (i.e., inducing) metal ions in situ. Accordingly, the amount of therapeutic agent that is delivered in situ is regulated by controlling such factors as: (1) the nature of the promoter used to direct transcription of the inserted gene, (i.e., whether the promoter is constitutive or inducible, strong or weak); (2) the number of copies of the exogenous gene that are inserted into the cell; (3) the number of transduced/transfected cells that are administered (e.g., implanted) to the patient; (4) the size of the implant (e.g., graft or encapsulated expression system); (5) the number of implants; (6) the length of time the transduced/transfected cells or implants are left in place; and (7) the production rate of the therapeutic agent by the genetically modified cell. Selection and optimization of these factors for delivery of a therapeutically effective dose of a particular therapeutic agent is deemed to be within the scope of one of ordinary skill in the art without undue experimentation, taking into account the above-disclosed factors and the clinical profile of the patient. In addition to at least one promoter and at least one heterologous nucleic acid encoding the therapeutic agent, the expression vector may include a selection gene, for example, a neomycin resistance gene or a fluorescent protein gene, for facilitating selection of cells that have been transfected or transduced with the expression vector. Alternatively, the cells are transfected with two or more expression vectors, at least one vector containing the gene(s) encoding the therapeutic agent(s), the other vector containing a selection gene. The selection of a suitable promoter, enhancer, selection gene, and/or signal sequence is deemed to be within the scope of one of ordinary skill in the art without undue experimentation. A coding sequence of the present disclosure can be inserted into any type of target or host cell. In the context of an expression vector, the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art. For example, the expression vector can be transferred into a host cell by physical, chemical, or biological means. Carrier/Delivery of polynucleotides As disclosed herein, the polynucleotides or nucleic acid molecules described above can be used for treating a disorder in a subject. Accordingly, this disclosure provides systems and methods for delivery of the polynucleotides to a target cell or a subject. Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids
are well-known in the art. See, for example, Sambrook et al. (2012, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York). Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors. Viral vectors, and especially retroviral vectors, have become the most widely used method for inserting genes into mammalian, e.g., human cells. Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like. See, for example, U.S. Pat. Nos. 5,350,674 and 5,585,362. Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle). The polynucleotides or nucleic acids described herein (e.g., protein-coding nucleic acids, inhibitory nucleic acids, those encoding a CRISPR-Cas system, expression cassettes, and expression vectors) can be added directly, or can be complexed with cationic lipids, packaged within liposomes, or as a recombinant plasmid or viral vectors, or otherwise delivered to target cells or tissues. Methods for the delivery of nucleic acid molecules are known in the art. See, e.g., U.S. Pat. No. 6,395,713, WO 94/02595, Akhtar et al., 1992, Trends Cell Bio., 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol., 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137, 165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074; WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (see, e.g., WO 00/53722). In one aspect, the present application provides carrier systems containing the nucleic acid molecules described herein. In some embodiments, the carrier system is a lipid-based carrier system, cationic lipid, or liposome nucleic acid complexes, a liposome, a micelle, a virosome, a lipid nanoparticle or a mixture thereof. In other embodiments, the carrier system
is a polymer-based carrier system such as a cationic polymer-nucleic acid complex. In additional embodiments, the carrier system is a cyclodextrin-based carrier system such as a cyclodextrin polymer-nucleic acid complex. In further embodiments, the carrier system is a protein-based carrier system such as a cationic peptide-nucleic acid complex. Preferably, the carrier system in a lipid nanoparticle formulation. Lipid nanoparticle (“LNP”) formulations described herein can be applied to any nucleic acid molecules (e.g., an RNA molecule) or combination of nucleic acid molecules described herein. In certain embodiment, the nucleic acid molecules described herein are formulated as a lipid nanoparticle composition such as is described in U.S. Patent Nos.7514099 and 7404969. In some embodiments, this application features a composition comprising a nucleic acid molecule formulated as any of formulation as described in US 20120029054, such as LNP- 051; LNP-053; LNP-054; LNP-069; LNP-073; LNP-077; LNP-080; LNP-082; LNP-083; LNP-060; LNP-061; LNP-086; LNP-097; LNP-098; LNP-099; LNP-100; LNP-101; LNP-102; LNP-103; or LNP-104. In other embodiments, this disclosure features conjugates and/or complexes of nucleic acid molecules described herein. Such conjugates and/or complexes can be used to facilitate delivery of nucleic acid molecules into a biological system, such as a cell. The conjugates and complexes provided by hereon can impart therapeutic activity by transferring therapeutic compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of nucleic acid molecules of the disclosure. Non-limiting, examples of such conjugates are described in e.g., U.S. Pat. Nos.7,833,992; 6,528,631; 6,335,434; 6, 235,886; 6,153,737; 5,214,136; 5,138,045. In various embodiments, polyethylene glycol (PEG) can be covalently attached to nucleic acid molecules described herein. The attached PEG can be any molecular weight, preferably from about 100 to about 50,000 daltons (Da). Accordingly, the disclosure features compositions or formulations comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes) and nucleic acid molecules described herein. See, e.g., WO 96/10391, WO 96/10390, and WO 96/10392). In some embodiments, the nucleic acid molecules can also be formulated or complexed with polyethyleneimine and derivatives thereof, such as polyethyleneimine- polyethyleneglycol-N-acetylgalactosamine (PEI-PEG-GAL) or polyethyleneimine- polyethyleneglycol-tri-N-acetylgalactosamine (PEI-PEG-triGAL) derivatives. In one
embodiment, the nucleic acid molecules can be formulated in the manner described in U.S. 20030077829. In other embodiments, nucleic acid molecules described herein can be complexed with membrane disruptive agents such as those described in U.S. 20010007666. In still other embodiments, the membrane disruptive agent or agents and the molecule can be complexed with a cationic lipid or helper lipid molecule, such as those lipids described in U.S. Pat. No. 6,235,310. In certain embodiments, nucleic acid molecules described herein can be complexed with delivery systems as described in U.S. Patent Application Publication Nos.2003077829; 20050287551; 20050164220; 20050191627; 20050118594; 20050153919; 20050085486; and 20030158133; and IWO 00/03683 and WO 02/087541. In some embodiments, a liposomal formulation described herein can comprise a nucleic acid molecule described herein formulated or complexed with compounds and compositions described in U.S. Pat. Nos.6,858,224; 6,534,484; 6,287,591; 6,835,395; 6,586,410; 6,858,225; 6,815,432; 6,586,001; 6,120,798; 6,977,223; 6,998,115; 5,981,501; 5,976,567; 5,705,385; and U.S. Patent Application Publication Nos. 2006/0019912; 2006/0019258; 2006/0008909; 2005/0255153; 2005/0079212; 2005/0008689; 2003/0077829, 2005/0064595, 2005/0175682, 2005/0118253; 2004/0071654; 2005/0244504; 2005/0265961 and 2003/0077829. As disclosed herein, the nucleic acid molecules described above can be used for treating a disorder in a subject. Vectors (such as recombinant plasmids and viral vectors) as discussed above can be used to deliver a therapeutical agent described herein. Delivery of the vectors can be systemic, such as by intravenous or intra-muscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell. Such recombinant vectors can also be administered directly or in conjunction with a suitable delivery reagents, including, for example, the Mirus Transit LT1 lipophilic reagent; lipofectin; lipofectamine; cellfectin; polycations (e.g., polylysine) or liposomes lipid-based carrier system, cationic lipid, or liposome nucleic acid complexes, a micelle, a virosome, a lipid nanoparticle. Viral Vectors In some embodiments, a polynucleotide encoding the RNA molecule or protein can be inserted into, or encoded by, vectors such as plasmids or viral vectors. Preferably, the polynucleotide is inserted into, or encoded by, viral vectors. Viral vectors may be Herpesvirus (HSV) vectors, retroviral vectors, adenoviral vectors, AAV vectors, lentiviral vectors, and the
like. In some specific embodiments, the viral vectors are AAV vectors. In some embodiments, the RNA may be encoded by a retroviral vector (See, e.g., U.S. Pat. Nos.5,399,346; 5,124,263; 4,650,764 and 4,980,289; the content of each of which is incorporated herein by reference in their entirety). Lentiviral vectors Lentiviruses, such as HIV, are “slow viruses.” Vectors derived from lentiviruses can be expressed long-term in the host cells after a few administrations to the patients, e.g., via ex vivo transduced stem cells or progenitor cells. For most diseases and disorders, including genetic diseases, cancer, and neurological disease, long-term expression is crucial to successful treatment. Regarding safety with lentiviral vectors, a number of strategies for eliminating the ability of lentiviral vectors to replicate have now been known in the art. See e.g., US 20210401868 and 20210403517, each of which is incorporated herein by reference in its entirety. For example, the deletion of promoter and enhancer elements from the U3 region of the long terminal repeat (LTR) are thought to have no LTR-directed transcription. The resulting vectors are called “self-inactivating” (SIN). Lentiviral vectors are particularly suitable to achieving long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells. Lentiviral vectors have the added advantage over vectors derived from onco-retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as CNS cells. They also have the added advantage of low immunogenicity. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e.g., WO01/96584 and WO01/29058; and U.S. Pat. No. 6,326,193). Several vector promoter sequences are available for expression of the transgenes. One example of a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto. Another example of a suitable promoter is EF1a. However, other constitutive promoter sequences can also be used, including, but not limited to the simian virus 40 (SV40) early promoter, mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the hemoglobin promoter, and the creatine kinase
promoter. Inducible promoters include, but are not limited to a metallothionein promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline promoter. The present disclosure provides a recombinant lentivirus capable of infecting dividing and non-dividing cells, such oligodendrocytes, astrocytes, or glial progenitor cells. The virus is useful for the in vivo and ex vivo transfer and expression of nucleic acid sequences. Lentiviral vectors of the present disclosure may be lentiviral transfer plasmids or infectious lentiviral particles. Construction of lentiviral vectors, helper constructs, envelope constructs, etc., for use in lentiviral transfer systems has been described in, e.g., US 20210401868 and 20210403517, each of which is incorporated herein by reference in its entirety. Adenoviruses Adenoviruses are eukaryotic DNA viruses that can be modified to efficiently deliver a nucleic acid to a variety of cell types in vivo, and have been used extensively in gene therapy protocols, including for targeting genes to neural cells and glial cells. Various replication defective adenovirus and minimum adenovirus vectors have been described for nucleic acid therapeutics (See, e.g., PCT Patent Publication Nos. WO199426914, WO 199502697, WO199428152, WO199412649, WO199502697 and WO199622378; the content of each of which is incorporated by reference in their entirety). Such adenoviral vectors may also be used to deliver therapeutic molecules of the present disclosure to cells. Adeno-Associated Virus The adeno-associated virus is a widely used gene therapy vector due to its clinical safety record, non-pathogenic nature, ability to infect non-dividing cells (like neurons), and ability to provide long-term gene expression after a single administration. Currently, many human and non-human primate AAV serotypes have been identified. AAV vectors have demonstrated safety in hundreds of clinical trials worldwide, and clinical efficacy has been shown in trials of hemophilia B, spinal muscular atrophy, alpha 1 antitrypson, and Leber congenital amaurosis. Because of their safety, nonpathogenic nature, and ability to infect neurons, AAVs such as AAV1, AAV2, AAV4, AAV5, AAV6, AAV8, and AAV9 are commonly used gene therapy vectors for CNS applications. However, after direct CNS infusion, these serotypes exhibit a dominant neuronal tropism and expression in oligodendrocytes is low, especially when gene expression is driven by a constitutive promoter, which restricts their potential for use in treating white matter diseases. AAV1/2, AAV2, and AAV8 have been shown transduce oligodendrocytes. Reliance on cell-specific promoters for expression specificity allows for the
possibility of nonselective cellular uptake and leaky transgene expression through cryptic promoter activity in non–oligodendrocyte lineage cells. The approach described herein to alleviate these issues includes using AAV serotypes with high tropism for oligodendrocytes or astrocytes or glial progenitor cells. Recently, using DNA shuffling and directed evolution, a chimeric AAV capsid with strong selectivity for oligodendrocytes, AAV/Olig001, has been described (Powell et al., 2016, Gene Ther 23:807– 814). Subsequently, AAV/Olig001 was shown to transduce neonatal oligodendrocytes in a mouse model of Canavan disease (Francis et al., 2021. Mol Ther Methods Clin Dev 20:520– 534). Other approaches such as random mutagenesis and peptide library insertion can be used to generate capsid libraries that can be screened for tropism and selectivity for oligodendrocytes or astrocytes or glial progenitor cells. As discussed above, the terms “adeno-associated virus” and/or “AAV” refer to parvoviruses with a linear single-stranded DNA genome and variants thereof. The term covers all subtypes and both naturally occurring and recombinant forms, except where required otherwise. Parvoviruses, including AAV, are useful as gene therapy vectors as they can penetrate a cell and introduce a nucleic acid (e.g., transgene) into the nucleus. In some embodiments, the introduced nucleic acid (e.g., rAAV vector genome) forms circular concatemers that persist as episomes in the nucleus of transduced cells. In some embodiments, a transgene is inserted in specific sites in the host cell genome. Site-specific integration, as opposed to random integration, is believed to likely result in a predictable long-term expression profile. The insertion site of AAV into the human genome is referred to as AAVS1. Once introduced into a cell, RNAs or polypeptides encoded by the nucleic acid can be expressed by the cell. Because AAV is not associated with any pathogenic disease in humans, a nucleic acid delivered by AAV can be used to express a therapeutic RNA or polypeptide for the treatment of a disease, disorder and/or condition in a human subject. Multiple serotypes of AAV exist in nature with at least fifteen wild type serotypes having been identified from humans thus far (i.e., AAV1-AAV15). Naturally occurring and variant serotypes are distinguished by having a protein capsid that is serologically distinct from other AAV serotypes. Examples include AAV1, AAV2, AAV, AAV3 (including AAV3A and AAV3B), AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV12, AAVrh10, AAVrh74 (see WO 2016/210170), avian AAV, bovine AAV, canine AAV, equine AAV, primate AAV, non-primate AAV, and ovine AAV, and recombinantly produced variants (e.g., capsid variants with insertions, deletions and substitutions, etc.), such as variants referred to as AAV2i8, NP4, NP22, NP66, DJ, DJ/8, DJ/9, LK3, RHM4-1, among many others. “Primate
AAV” refers to AAV that infect primates, “non-primate AAV” refers to AAV that infect non- primate mammals, “bovine AAV” refers to AAV that infect bovine mammals, and so on. Serotype distinctiveness is determined on the basis of the lack of cross-reactivity between antibodies to one AAV as compared to another AAV. Such cross-reactivity differences are usually due to differences in capsid protein sequences and antigenic determinants (e.g., due to VP1, VP2, and/or VP3 sequence differences of AAV serotypes). However, some naturally occurring AAV or man-made AAV mutants (e.g., recombinant AAV) may not exhibit serological difference with any of the currently known serotypes. These viruses may then be considered a subgroup of the corresponding type, or more simply a variant AAV. Thus, as used herein, the term “serotype” refers to both serologically distinct viruses, as well as viruses that are not serologically distinct but that may be within a subgroup or a variant of a given serotype. A comprehensive list and alignment of amino acid sequences of capsids of known AAV serotypes is provided by Marsic et al. (2014) Molecular Therapy 22(11):1900-1909. Genomic sequences of various serotypes of AAV, as well as sequences of the native ITRs, rep proteins, and capsid subunits are known in the art. Such sequences may be found in the literature or in public databases such as GenBank. See, e.g., GenBank Accession Numbers NC_002077 (AAV1), AF063497 (AAV1), NC_001401 (AAV2), AF043303 (AAV2), NC_001729 (AAV3), NC_001863 (AAV3B), NC_001829 (AAV4), U89790 (AAV4), NC_006152 (AAV5), NC_001862 (AAV6), AF513851 (AAV7), AF513852 (AAV8), and NC_006261 (AAV8); the disclosures of which are incorporated by reference herein. See also, e.g., Srivistava et al. (1983) J. Virology 45:555; Chiorini et al. (1998) J. Virology 71:6823; Chiorini et al. (1999) J. Virology 73: 1309; Bantel-Schaal et al. (1999) J. Virology 73:939; Xiao et al. (1999) J. Virology 73:3994; Muramatsu et al. (1996) Virology 221:208; Shade et al. (1986) J. Virol. 58:921; Gao et al. (2002) Proc. Nat. Acad. Sci. USA 99: 11854; Moris et al. (2004) Virology 33:375-383; international patent publications WO 00/28061, WO 99/61601, WO 98/11244; WO 2013/063379; WO 2014/194132; WO 2015/121501, and U.S. Patent No. 6,156,303 and U.S. Patent No.7,906,111. As discussed herein, a “recombinant adeno-associated virus” or “rAAV” is distinguished from a wild-type AAV by replacement of all or part of the endogenous viral genome with a non-native sequence. Incorporation of a non-native sequence within the virus defines the viral vector as a “recombinant” vector, and hence a “rAAV vector.” An rAAV vector can include a heterologous polynucleotide encoding a desired RNA or protein or polypeptide (e.g., an RNA molecule disclosed herein). A recombinant vector sequence may be
encapsidated or packaged into an AAV capsid and referred to as an “rAAV vector,” an “rAAV vector particle,” “rAAV viral particle” or simply a “rAAV.” The present disclosure provides for an rAAV vector comprising a polynucleotide sequence not of AAV origin (e.g., a polynucleotide heterologous to AAV). The heterologous polynucleotide may be flanked by at least one, and sometimes by two, AAV terminal repeat sequences (e.g., inverted terminal repeats). The heterologous polynucleotide flanked by ITRs, also referred to herein as a “vector genome,” typically encodes an RNA or a polypeptide of interest, or a gene of interest, such as a target for therapeutic treatment. Delivery or administration of an rAAV vector to a subject (e.g. a patient) provides encoded RNAs/proteins/peptides to the subject. Thus, an rAAV vector can be used to transfer/deliver a heterologous polynucleotide for expression for, e.g., treating a variety of diseases, disorders and conditions. rAAV vector genomes generally retain 145 base ITRs in cis to the heterologous nucleic acid sequence that replaced the viral rep and cap genes. Such ITRs are useful to produce a recombinant AAV vector; however, modified AAV ITRs and non-AAV terminal repeats including partially or completely synthetic sequences can also serve this purpose. ITRs form hairpin structures and function to, for example, serve as primers for host-cell-mediated synthesis of the complementary DNA strand after infection. ITRs also play a role in viral packaging, integration, etc. ITRs are the only AAV viral elements which are required in cis for AAV genome replication and packaging into rAAV vectors. An rAAV vector genome optionally comprises two ITRs which are generally at the 5’ and 3’ ends of the vector genome comprising a heterologous sequence (e.g., a transgene encoding a gene of interest, or a nucleic acid sequence of interest including, but not limited to, an antisense, and siRNA, a CRISPR molecule, among many others). A 5’ and a 3’ ITR may both comprise the same sequence, or each may comprise a different sequence. An AAV ITR may be from any AAV including by not limited to serotypes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or 11 or any other AAV. An rAAV vector of the disclosure may comprise an ITR from an AAV serotype (e.g., wild-type AAV2, a fragment or variant thereof) that differs from the serotype of the capsid (e.g., AAV8, Olig001). Such an rAAV vector comprising at least one ITR from one serotype, but comprising a capsid from a different serotype, may be referred to as a hybrid viral vector (see U.S. Patent No.7,172,893). An AAV ITR may include the entire wild type ITR sequence, or be a variant, fragment, or modification thereof, but will retain functionality. In some embodiments, an rAAV vector genome is linear, single-stranded and flanked by AAV ITRs. Prior to transcription and translation of the heterologous gene, a single stranded
DNA genome of approximately 4700 nucleotides must be converted to a double-stranded form by DNA polymerases (e.g., DNA polymerases within the transduced cell) using the free 3’-OH of one of the self-priming ITRs to initiate second-strand synthesis. In some embodiments, full length-single stranded vector genomes (i.e., sense and anti-sense) anneal to generate a full length-double stranded vector genome. This may occur when multiple rAAV vectors carrying genomes of opposite polarity (i.e., sense or anti-sense) simultaneously transduce the same cell. Regardless of how they are produced, once double-stranded vector genomes are formed, the cell can transcribe and translate the double-stranded DNA and express the heterologous gene. The efficiency of transgene expression from an rAAV vector can be hindered by the need to convert a single stranded rAAV genome (ssAAV) into double-stranded DNA prior to expression. This step can be circumvented by using a self-complementary AAV genome (scAAV) that can package an inverted repeat genome that can fold into double-stranded DNA without the need for DNA synthesis or base-pairing between multiple vector genomes. See, e.g., U.S. Patent No. 8,784,799; McCarty, (2008) Molec. Therapy 16(10):1648-1656; and McCarty et al., (2001) Gene Therapy 8:1248-1254; McCarty et al., (2003) Gene Therapy 10:2112-2118. A viral capsid of an rAAV vector may be from a wild type AAV or a variant AAV such as AAV1, AAV2, AAV3, AAV3A, AAV3B, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAVrh10, AAVrh74 (see WO2016/210170), AAV12, AAV2i8, AAV1.1, AAV2.5, AAV6.1, AAV6.3.1, AAV9.45, RHM4-1 (WO 2015/013313), RHM15-1, RHM15-2, RHM15- 3/RHM15-5, RHM15-4, RHM15-6, AAV hu.26, AAV1.1, AAV2.5, AAV6.1, AAV6.3.1, AAV9,45, AAV2i8, AAV29G, AAV2,8G9, AVV-LK03, AAV2-TT, AAV2-TT-S312N, AAV3B-S312N, AAV avian AAV, bovine AAV, canine AAV, equine AAV, primate AAV, non-primate AAV, snake AAV, goat AAV, shrimp AAV, ovine AAV and variants thereof (see, e.g., Fields et al., VIROLOGY, volume 2, chapter 69 (4
th ed., Lippincott-Raven Publishers). Capsids may be derived from a number of AAV serotypes disclosed in U.S. Patent No. 7,906,111; Gao et al. (2004) J. Virol. 78:6381; Morris et al. (2004) Virol. 33:375; WO 2013/063379; WO 2014/194132; and include true type AAV (AAV-TT) variants disclosed in WO 2015/121501, and RHM4-1, RHM15-1 through RHM15-6, and variants thereof, disclosed in WO 2015/013313. A full complement of AAV cap proteins includes VP1, VP2, and VP3. The ORF comprising nucleotide sequences encoding AAV VP capsid proteins may comprise less than a full complement AAV Cap proteins or the full complement of AAV cap proteins may be provided.
In some embodiments, an rAAV vector comprising a capsid protein encoded by a nucleotide sequence derived from more than one AAV serotype (e.g., wild type AAV serotypes, variant AAV serotypes) is referred to as a “chimeric vector” or “chimeric capsid” (See U.S. Patent No. 6,491,907, the entire disclosure of which is incorporated herein by reference). In some embodiments, a chimeric capsid protein is encoded by a nucleic acid sequence derived from 2, 3, 4, 5, 6, 7, 8, 9, 10 or more AAV serotypes. In some embodiments, a recombinant AAV vector includes a capsid sequence derived from e.g., AAV1, AAV2, AAV3, AAV3A, AAV3B, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, AAVrh74, AAVrh10, AAV2i8, or variant thereof, resulting in a chimeric capsid protein comprising a combination of amino acids from any of the foregoing AAV serotypes (see, Rabinowitz et al. (2002) J. Virology 76(2):791-801). Alternatively, a chimeric capsid can comprise a mixture of a VP1 from one serotype, a VP2 from a different serotype, a VP3 from yet a different serotype, and a combination thereof. For example a chimeric virus capsid may include an AAV1 cap protein or subunit and at least one AAV2 cap protein or subunit. A chimeric capsid can, for example include an AAV capsid with one or more B19 cap subunits, e.g., an AAV cap protein or subunit can be replaced by a B19 cap protein or subunit. For example, in one embodiment, a VP3 subunit of an AAV capsid can be replaced by a VP2 subunit of B19. In some embodiments, a chimeric capsid is an Olig001 capsid as described in WO2021221995 and WO2014052789, which are incorporated herein by reference. In some embodiments, chimeric vectors have been engineered to exhibit altered tropism or tropism for a particular tissue or cell type. The term “tropism” refers to preferential entry of the virus into certain cell (e.g., oligodendrocytes) or tissue types and/or preferential interaction with the cell surface that facilitates entry into certain cell or tissue types. AAV tropism is generally determined by the specific interaction between distinct viral capsid proteins and their cognate cellular receptors (Lykken et al. (2018) J. Neurodev. Disord.10:16). Preferably, once a virus or viral vector has entered a cell, sequences (e.g., heterologous sequences such as a transgene) carried by the vector genome (e.g., an rAAV vector genome) are expressed. A “tropism profile” refers to a pattern of transduction of one or more target cells in various tissues and/or organs. For example, a chimeric AAV capsid may have a tropism profile characterized by efficient transduction of oligodendrocytes or astrocytes or oligodendrocyte progenitor cells with only low transduction of neurons and other CNS cells. See WO2014/052789, incorporated herein by reference. Such a chimeric capsid may be considered specific for oligodendrocytes or astrocytes or glial progenitor cells exhibiting tropism for oligodendrocytes or astrocytes or glial progenitor cells, and referred to herein as “glialtropism,”
if when administered directly into the CNS, preferentially transduces oligodendrocytes or astrocytes or oligodendrocyte progenitor cells over neurons and other CNS cell types. In some embodiments, at least about 80% of cells that are transduced by a capsid specific for oligodendrocytes or oligodendrocyte progenitor cells are oligodendrocytes or oligodendrocyte progenitor cells, e.g., at least about 85%, 90%, 95%, 96%, 97%, 98% 99% or more of the transduced cells are oligodendrocytes or oligodendrocyte progenitor cells. Gene and Cell Therapies The nucleic acids, genetic constructs, expression cassettes, expression vectors, and cells described herein may be used for gene therapy treatment and/or prevention of a disease, disorder or condition. In particular, it can be used for treating or preventing a disease, disorder or condition associated with deficiency or dysfunction of oligodendrocyte or myelin by increasing the expression of a transcription factor or a target thereof, and of any other condition and or illness in which increasing the expression of the protein may produce a therapeutic benefit or improvement, e.g., a disease, disorder or condition mediated by, or associated with, a decrease in the level or function of the protein compared with the level or function of the protein in an otherwise healthy individual. As used herein a disorder of myelin, a disease of myelin, a myelin-related disorder, a myelin-related disease, a myelin disorder, a disorder mediated by a deficiency in myelin, and a myelin disease are used interchangeably. They include a condition mediated by loss of while matter/oligodendrocytes/astrocytes and any disease, condition (e.g., those occurring from traumatic spinal cord injury and cerebral infarction), or disorder related to demyelination, insufficient myelination and remyelination, or dysmyelination in a subject. Such a disorder can be inherited or acquired or both. It can arise from a myelination related disorder or demyelination resulting from a variety of neurotoxic insults. "Demyelination" as used herein, refers to the act of demyelinating, or the loss of the myelin sheath insulating the nerves, and is the hallmark of some neurodegenerative autoimmune diseases, including multiple sclerosis, transverse myelitis, chronic inflammatory demyelinating polyneuropathy, and Guillain-Barre Syndrome. Leukodystrophies are caused by inherited enzyme deficiencies, which cause abnormal formation, destruction, and/or abnormal turnover of myelin sheaths within the CNS white matter. Both acquired and inherited myelin disorders share a poor prognosis leading to major disability. Thus, some embodiments of the present disclosure can include methods for the treatment of neurodegenerative autoimmune diseases in a subject. Remyelination of neurons requires oligodendrocytes. The term "remyelination", as used herein, refers to the re-
generation of the nerve's myelin sheath by replacing myelin producing cells or restoring their function. Myelin related diseases or disorders which may be treated or ameliorated by the methods of the present disclosure include diseases, disorders or injuries which relate to dysmyelination or demyelination in a subject's brain cells, e.g., CNS neurons. Such diseases include, but are not limited to, diseases and disorders in which the myelin which surrounds the neuron is either absent, incomplete, not formed properly, or is deteriorating. Such disease include, but are not limited to, multiple sclerosis (MS), neuromyelitis optica (NMO), progressive multifocal leukoencephalopathy (PML), encephalomyelitis (EPL), central pontine myelolysis (CPM), adrenoleukodystrophy, Alexander's disease, Pelizaeus Merzbacher disease (PMD), Wallerian Degeneration, optic neuritis, transverse myelitis, amyotrophic lateral sclerosis (ALS), Huntington's disease, Alzheimer's disease, Parkinson's disease, spinal cord injury, traumatic brain injury, post radiation injury, neurologic complications of chemotherapy, stroke, acute ischemic optic neuropathy, vitamin E deficiency, isolated vitamin E deficiency syndrome, Bassen-Kornzweig syndrome, Marchiafava-Bignami syndrome, metachromatic leukodystrophy, trigeminal neuralgia, acute disseminated encephalitis, Guillian-Barre syndrome, Marie-Charcot-Tooth disease and Bell's palsy. Myelin related diseases or disorders which may be treated or ameliorated by the methods of the present disclosure include a disease or disorder characterized by a myelin deficiency. Insufficient myelination in the central nervous system has been implicated in a wide array of neurological disorders. Among these are forms of cerebral palsy in which a congenital deficit in forebrain myelination in children with periventricular leukomalacia, contributes to neurological morbidity (Goldman et al., 2008) Goldman, S. A., Schanz, S., and Windrem, M. S. (2008). Stem cell-based strategies for treating pediatric disorders of myelin. Hum Mol Genet.17, R76-83. At the other end of the age spectrum, myelin loss and ineffective repair may contribute to the decline in cognitive function associated with senescence (Kohama et al., 2011) Kohama, S. G., Rosene, D. L., and Sherman, L. S. (2011) Age (Dordr). Age- related changes in human and non-human primate white matter: from myelination disturbances to cognitive decline. Therefore, it is contemplated that effective compositions and methods of enhancing myelination and/or remyelination may have substantial therapeutic benefits in halting disease progression and restoring function in a wide array of myelin-related disorders. Accordingly, one aspect of this disclosure provides a method of treating a condition mediated by white matter loss, oligodendrocyte loss, or astrocyte loss. The method comprises administering to a subject in need thereof (a) a therapeutically effective amount of an agent
that increase the level or activity of (i) a transcription factor selected from the group consisting of CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 or (ii) a target of the transcription factor, or (b) a therapeutically effective amount of the cell prepared according to the method described herein or a progeny thereof. The target is selected from the group mentioned above and listed Table 1 and Figure 5. Such an agent may comprise or be a small molecule compound, an oligonucleotide, a nucleic acid, a genetic construct, a peptide, a polypeptide, a CRISPR/Cas system, or an antibody or an antigen-binding portion thereof. Examples of the agent include activators, agonists, or potentiators of the related CEBPZ, CTCF, E2F1, MYC, NFYB, and ETV4 signaling pathways. Various activators for this signaling pathway are known in the art. In one embodiment, the agent comprises or is (i) the polypeptide of CEBPZ, CTCF, E2F1, MYC, NFYB, or ETV4, or target thereof (e.g., those listed Table 1 and Figure 5) or (ii) a nucleic acid, a genetic construct, or vector encoding the polypeptide. In some embodiments, the agent may be or comprise (i) a suppressor of a transcription repressor selected from the group consisting of E2F6, ZNF274, MAX, and IKZF3, or (ii) a nucleic acid, a genetic construct, or vector encoding the suppressor. In one embodiment, the one or more genetic constructs may activate transcription of one or more of the genes described herein via a CRISPR-Cas9 guided nuclease (Gimenez et al., “CRISPR-on System for the Activation of the Endogenous human INS gene,” Gene Therapy 23: 543-547 (2016); Wiedenheft et al., “RNA-Guided Genetic Silencing Systems in Bacteria and Archaea,” Nature 482:331-338 (2012); Zhang et al., “Multiplex Genome Engineering Using CRISPR/Cas Systems,” Science 339(6121):819-23 (2013); and Gaj et al., “ZFN, TALEN, and CRISPR/Cas-based Methods for Genome Engineering,” Cell 31(7):397- 405 (2013), which are hereby incorporated by reference in their entirety). CRISPR-Cas9 is a genetic technique which allows for sequence- specific control of gene expression in prokaryotic and eukaryotic cells by guided nuclease double-stranded DNA cleavage. It is based on the bacterial immune system-derived CRISPR (clustered regularly interspaced palindromic repeats) pathway. In the embodiments described supra, the one or more genetic constructs may be packaged in a suitable delivery vehicle or carrier for delivery to the subject. Suitable delivery vehicles include, but are not limited to viruses, virus-like particles, bacteria, bacteriophages, biodegradable microspheres, microparticles, nanoparticles, exosomes, liposomes, collagen minipellets, and cochleates. These and other biological gene delivery vehicles are well known to those of skill in the art (see, e.g., Seow and Wood, “Biological Gene Delivery Vehicles:
Beyond Viral Vectors,” Mol. Therapy 17(5):767- 777 (2009), which is hereby incorporated by reference in its entirety). In one embodiment, the genetic construct is packaged into a therapeutic expression vector to facilitate delivery. Suitable expression vectors are well known in the art and include, without limitation, viral vectors such as adenovirus vectors, adeno- associated virus vectors, retrovirus vectors, lentivirus vectors, or herpes virus vectors. The viral vectors or other suitable expression vectors comprise sequences encoding the genetic constructs of the present application and any suitable promoter and/or enhancer for expressing the genetic construct. Suitable promoters include, for example, and without limitation, the U6 or HI RNA pol III promoter sequences and the cytomegalovirus promoter. Selection of other suitable promoters is within the skill in the art. The expression vectors may also comprise inducible or regulatable promoters for expression of the inhibitory nucleic acid molecules in a tissue or cell-specific manner. Gene therapy vectors carrying the therapeutic genetic construct or nucleic acid molecule are administered to a subject by, for example, intravenous injection, local administration (U.S. Patent No. 5,328,470 to Nabel et al., which is hereby incorporated by reference in its entirety) or by stereotactic injection (see, e.g., Chen et al., “Gene Therapy for Brain Tumors: Regression of Experimental Gliomas by Adenovirus Mediated Gene Transfer In vivo,” Proc. Nat’l. Acad. Sci. USA 91:3054-3057 (1994), which is hereby incorporated by reference in its entirety). The pharmaceutical preparation of the therapeutic vector can include the therapeutic vector in an acceptable diluent, or can comprise a slow release matrix in which the therapeutic delivery vehicle is imbedded. Alternatively, where the complete therapeutic delivery vector can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can include one or more cells which produce the therapeutic delivery system. Gene therapy vectors typically utilize constitutive regulatory elements which are responsive to endogenous transcriptions factors. Another suitable approach for the delivery of the genetic construct of the present disclosure, involves the use of liposome delivery vehicles or nanoparticle delivery vehicles. In another embodiment of the present application, the delivery vehicle is a nanoparticle. A variety of nanoparticle delivery vehicles are known in the art and are suitable for delivery of the genetic constructs of the present application (see, e.g., van Vlerken et al., “Multi-functional Polymeric Nanoparticles for Tumour-Targeted Drug Delivery,” Expert Opin. Drug Deliv. 3(2):205–216 (2006), which is hereby incorporated by reference in its entirety). Suitable nanoparticles include, without limitation, poly(beta-amino esters) (Sawicki et al.,
“Nanoparticle Delivery of Suicide DNA for Epithelial Ovarian Cancer Cell Therapy,” Adv. Exp. Med. Biol.622:209–219 (2008), which is hereby incorporated by reference in its entirety), polyethylenimine-alt-poly(ethylene glycol) copolymers (Park et al., “Degradable Polyethylenimine-alt-Poly(ethylene glycol) Copolymers As Novel Gene Carriers,” J. Control Release 105(3):367–80 (2005) and Park et al., “Intratumoral Administration of Anti-KITENIN shRNA-Loaded PEI-alt-PEG Nanoparticles Suppressed Colon Carcinoma Established Subcutaneously in Mice,” J Nanosci. Nanotechnology 10(5):3280–3 (2010), which are hereby incorporated by reference in their entirety), poly(d,l-lactide-coglycolide) (Chan et al., “Antisense Oligonucleotides: From Design to Therapeutic Application,” Clin. Exp. Pharm. Physiol. 33: 533-540 (2006), which is hereby incorporated by reference in its entirety), and liposome- entrapped siRNA nanoparticles (Kenny et al., “Novel Multifunctional Nanoparticle Mediates siRNA Tumor Delivery, Visualization and Therapeutic Tumor Reduction In vivo,” J. Control Release 149(2):111–116 (2011), which is hereby incorporated by reference in its entirety). Other nanoparticle vehicles suitable for use in the present application include microcapsule nanotube devices disclosed in U.S. Patent Publication No. 2010/0215724 to Prakash et al., which is hereby incorporated by reference in its entirety. In another embodiment, the genetic construct is contained in a liposome delivery vehicle. The term "liposome" means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers. Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo. Several advantages of liposomes include: their biocompatibility and biodegradability, incorporation of a wide range of water and lipid soluble drugs; and they afford protection to encapsulated molecules from metabolism and degradation. Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes. Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes and as the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.
Methods for preparing liposomes include those disclosed in Bangham et al., “Diffusion of Univalent Ions Across the Lamellae of Swollen Phospholipids,” J. Mol. Biol. 13:238–52 (1965); U.S. Patent No.5,653,996 to Hsu; U.S. Patent No.5,643,599 to Lee et al.; U.S. Patent No.5,885,613 to Holland et al.; U.S. Patent No.5,631,237 to Dzau et al.; and U.S. Patent No. 5,059,421 to Loughrey et al., which are hereby incorporated by reference in their entirety. As disclosed herein, in another embodiment, the genetic construct, expression cassette, or expression vector can be administered in association with a glial progenitor cell-targeted fusogen or a glial progenitor cell-selective surface-binding moiety. For example, the genetic construct, expression cassette, or expression vector can be in or associated with a fusosome. As used herein, "fusogen" refers to an agent or molecule that creates an interaction between two membrane enclosed lumens. In embodiments, the fusogen facilitates fusion of the membranes. In other embodiments, the fusogen creates a connection, e.g., a pore, between two lumens (e.g., a lumen of a liposome and a cytoplasm of a target cell, or a lumen of a viral vector and a cytoplasm of a target cell). In some embodiments, the fusogen comprises a protein or a complex of two or more proteins having a targeting domain or binding moiety. In some examples, the targeting domain or binding moiety specifically targets or binds to a molecule on glial progenitor cell or a glial progenitor cell. Examples of the molecule include, but not limited to, CD140a, NG2/CSPG4, A2B5 gangliosides, O4 sulfatides, or CD133. A targeting domain or binding moiety can be a receptor ligand, a peptide/polypeptide, an antibody, or an antigen-binding portion thereof that specifically binds to a molecule or marker on a glial progenitor cell or a glial progenitor cell. Non-limiting examples of human and non-human fusogens are described in, e.g., US 20210198698 and US 20210137839, which are incorporated by reference in their entireties. As used herein, "fusosome" refers to a bilayer of amphipathic lipids enclosing a lumen or cavity and a fusogen that interacts with the amphipathic lipid bilayer. In some embodiments, the fusosome comprises a nucleic acid. In some embodiments, the fusosome is a membrane enclosed preparation. In some embodiments, the fusosome is derived from a source cell. Fusosomes can take various forms. For example, in some embodiments, a fusosome described herein is derived from a source cell. A fusosome may be or comprise, e.g., an extracellular vesicle, a microvesicle, a nanovesicle, an exosome, a microparticle, or any combination thereof. In some embodiments, a fusosome is released naturally from a source cell, and in some embodiments, the source cell is treated to enhance formation of fusosomes. In some embodiments, the fusosome is between about 10-10,000 nm in diameter, e.g., about
30-100 nm in diameter. In some embodiments, the fusosome comprises one or more synthetic lipids. In some embodiments, the fusosome is or comprises a virus, e.g., a retrovirus, e.g., a lentivirus. For instance, in some embodiments, the fusosome's bilayer of amphipathic lipids is or comprises the viral envelope. The viral envelope may comprise a fusogen, e.g., a fusogen that is endogenous to the virus or a pseudotyped fusogen. In some embodiments, the fusosome's lumen or cavity comprises a viral nucleic acid, e.g., a retroviral nucleic acid, e.g., a lentiviral nucleic acid. The viral nucleic acid may be a viral genome. In some embodiments, the fusosome further comprises one or more viral non-structural proteins, e.g., in its cavity or lumen. Fusosomes may have various structures or properties that facilitate delivery of a payload to a target cell. For instance, in some embodiments, the fusosome and the source cell together comprise nucleic acid(s) sufficient to make a particle that can fuse with a target cell. In embodiments, these nucleic acid(s) encode proteins having one or more of (e.g., all of) the following activities: gag polyprotein activity, polymerase activity, integrase activity, protease activity, and fusogen activity. In some embodiments, the compositions of the present disclosure can be administered to a subject that does not have, and/or is not suspected of having, a myelin related disorder in order to enhance or promote a myelin dependent process. In some embodiments, compositions described herein can be administered to a subject to promote myelination of CNS neurons in order to enhance cognition, which is known to be a myelin dependent process, in cognitive healthy subjects. In certain embodiments, compositions described herein can be administered in combination with cognitive enhancing (nootropic) agents. Exemplary agents include any drugs, supplements, or other substances that improve cognitive function, particularly executive functions, memory, creativity, or motivation, in healthy individuals. Non limiting examples include racetams (e.g., piracetam, oxiracetam, and aniracetam), nutraceuticals (e.g., bacopa monnieri, panax ginseng, ginko biloba, and GABA), stimulants (e.g., amphetamine pharmaceuticals, methylphenidate, eugeroics, xanthines, and nicotine), L-Theanine, Tolcapone, Levodopa, Atomoxetine, and Desipramine. The overall dosage of a therapeutic agent (e.g., a protein, a polynucleotide encoding the protein, or a vector, such as an rAAV vector, or a cell) will be a therapeutically effective amount depending on several factors including the overall health of a subject, the subject's disease state, severity of the condition, the observation of improvements and the formulation and route of
administration of the selected agent(s). Determination of a therapeutically effective amount is within the capability of those skilled in the art. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the subject's condition. Cell Replacement Therapy Also within scope of this disclosure is a host cell comprising the genetic construct, cassette, or expression vector described above, or a progeny cell of the host cell. The host cell can be a stem cell or a progenitor cell. Example of the stem cell include embryonic stem cells, ES-like stem cells, fetal stem cells, adult stem cells, pluripotent stem cells, induced pluripotent stem cells, multipotent stem cells, oligopotent stem cells, unipotent stem cells and others. In some embodiments, the host cell is a glial progenitor cell, such as an oligodendrocyte progenitor cell. The glial progenitor cells described herein may be derived from any suitable source of pluripotent stem cells, such as, for example and without limitation, human induced pluripotent stem cells (iPSCs) and embryonic stem cells, as described in more detail below. In one example, glial progenitor cells can be cells rejuvenated from glial progenitor cells or progenies thereof as described herein. The host cell or a progeny thereof can be used as a therapeutic cell or agent for treating the disorders or conditions described herein. One aspect of the present application relates to a method of alleviating adverse effects of oligodendrocyte loss, astrocyte loss, or white matter loss in the CNS (e.g., brain) of an adult subject. The loss can be an age-related loss. This method includes identifying a subject, e.g., an adult subject, undergoing adverse effects of oligodendrocyte loss, astrocyte loss, or white matter loss in the CNS (e.g., brain) and providing a population of isolated glial progenitor cells. The population of isolated glial progenitor cells is then introduced into CNS (such as the brain and/or brain stem) of the selected subject to at least partially replace cells in the subject’s brain in the location undergoing the adverse effects of oligodendrocyte loss, astrocyte loss, or white matter loss. Glial cells are a population of non-neuronal cells that provide support and nutrition, maintain homeostasis, either form myelin or promote myelination, and participate in signal transmission in the nervous system. “Glial cells” as used herein encompasses fully differentiated cells of the glial lineage, such as oligodendrocytes or astrocytes, and as well as glial progenitor cells. Glial progenitor cells are cells having the potential to differentiate into cells of the glial lineage such as oligodendrocytes and astrocytes. In some embodiments, to treat a subject in need thereof, glial progenitor cells or rejuvenated cells are young glial or glial progenitor cells, or are younger than the counterparts in the subject to be treated.
As used herein the term “young” glial or glial progenitor cells refers to cells that are induced to start differentiation into glial progenitor cell in an in vitro setting (about 105 days from cell isolation from fetal donor tissue). In some embodiments, the term “young glial cells” refers to differentiated glial progenitor cells that are ready for transplantation into an animal (about 160 days from cell isolation from fetal donor tissue). In some embodiments, the term “young glial cells” refers to glial progenitor cells or their progeny that are within 1-20 weeks of transplantation. The term “older glial cells” is used in relative to the term “young glial cells”. Compared with older glial cells, young glial cells may have one or more of the following characteristics: (i) growing or proliferating or dividing faster, (ii) having lower levels than old of senescence-associated transcripts encoding CDKN1A (p21Cip1) and CDKN2/p16(INK4) and p14(ARF), and (iii) longer telomeres or higher telomerase activity or both. In some embodiments, older glial cells are glial cells that are derived from glial progenitor cells that have been transplanted into a host for 5, 10, 20, 30 or 40 weeks. In some embodiments, the older glial cells are glial cells that have been cultured for an additional 5, 10, 20, 30 or 40 weeks from differentiated glial progenitor cells (e.g., about 160 days from the initial tissue harvest). In some embodiments, the older glial cells are glial cells that have been cultured for an additional 5, 10, 20, 30 or 40 weeks from the introduction of differentiation (e.g., about 105 days from the initial tissue harvest). The glial progenitor cells described herein may be derived from any suitable source of pluripotent stem cells, including iPSCs. iPSCs are pluripotent cells that are derived from non- pluripotent cells, such as somatic cells. For example, and without limitation, iPSCs can be derived from tissue, peripheral blood, umbilical cord blood, and bone marrow (see e.g., Cai et al., J. Biol. Chem.285(15):112227-11234 (2110); Giorgetti et al., Nat. Protocol.5(4):811-820 (2010); Streckfuss-Bomeke et al., Eur. Heart J. doi:10.1093/eurheartj/ehs203 (July 12, 2012); Hu et al., Blood doi:10.1182/blood-2010-07-298331 (Feb.4, 2011); Sommer et al., J. Vis. Exp. 68:e4327 doi:10.3791/4327 (2012), which are hereby incorporated by reference in their entirety). The somatic cells can be reprogrammed to an embryonic stem cell-like state using genetic manipulation. Exemplary somatic cells suitable for the formation of iPSCs include fibroblasts (see e.g., Streckfuss-Bomeke et al., Eur. Heart J. doi:10.1093/eurheartj/ehs203 (2012), which is hereby incorporated by reference in its entirety), such as dermal fibroblasts obtained by a skin sample or biopsy, synoviocytes from synovial tissue, keratinocytes, mature B cells, mature T cells, pancreatic β cells, melanocytes, hepatocytes, foreskin cells, cheek cells, or lung fibroblasts.
Methods of producing induced pluripotent stem cells are known in the art and typically involve expressing a combination of reprogramming factors in a somatic cell. Suitable reprogramming factors that promote and induce iPSC generation include one or more of Oct4, Klf4, Sox2, c-Myc, Nanog, C/EBPα, Esrrb, Lin28, and Nr5a2. In certain embodiments, at least two reprogramming factors are expressed in a somatic cell to successfully reprogram the somatic cell. In other embodiments, at least three reprogramming factors are expressed in a somatic cell to successfully reprogram the somatic cell. iPSCs may be derived by methods known in the art, including the use integrating viral vectors (e.g., lentiviral vectors, inducible lentiviral vectors, and retroviral vectors), excisable vectors (e.g., transposon and floxed lentiviral vectors), and non-integrating vectors (e.g., adenoviral and plasmid vectors) to deliver the genes that promote cell reprogramming (see e.g., Takahashi and Yamanaka, Cell 126:663-676 (2006); Okita. et al., Nature 448:313-317 (2007); Nakagawa et al., Nat. Biotechnol.26:101-106 (2007); Takahashi et al., Cell 131:1-12 (2007); Meissner et al. Nat. Biotech. 25:1177-1181 (2007); Yu et al. Science 318:1917-1920 (2007); Park et al. Nature 451:141-146 (2008); and U.S. Patent Application Publication No. 2008/0233610, which are hereby incorporated by reference in their entirety). Other methods for generating IPS cells include those disclosed in WO2007/069666, WO2009/006930, WO2009/006997, WO2009/007852, WO2008/118820, U.S. Patent Application Publication No. 2011/0200568 to Ikeda et al., U.S. Patent Application Publication No 2010/0156778 to Egusa et al., U.S. Patent Application Publication No 2012/0276070 to Musick, and U.S. Patent Application Publication No 2012/0276636 to Nakagawa, Shi et al., Cell Stem Cell 3(5):568- 574 (2008), Kim et al., Nature 454:646-650 (2008), Kim et al., Cell 136(3):411-419 (2009), Huangfu et al., Nat. Biotechnol.26:1269-1275 (2008), Zhao et al., Cell Stem Cell 3:475-479 (2008), Feng et al., Nat. Cell Biol.11:197-203 (2009), and Hanna et al., Cell 133(2):250-264 (2008) which are hereby incorporated by reference in their entirety. The methods of iPSC generation described above can be modified to include small molecules that enhance reprogramming efficiency or even substitute for a reprogramming factor. These small molecules include, without limitation, epigenetic modulators such as, the DNA methyltransferase inhibitor 5’-azacytidine, the histone deacetylase inhibitor VPA, and the G9a histone methyltransferase inhibitor BIX-01294 together with BayK8644, an L-type calcium channel agonist. Other small molecule reprogramming factors include those that target signal transduction pathways, such as TGF-β inhibitors and kinase inhibitors (e.g., kenpaullone) (see review by Sommer and Mostoslavsky, Stem Cell Res. Ther. 1:26
doi:10.1186/scrt26 (August 10, 2010), which is hereby incorporated by reference in its entirety). Methods of obtaining highly enriched preparations of glial progenitor cells from the iPSCs that are suitable for making the non-human mammal models described herein are disclosed in WO2014/124087 to Goldman and Wang, and Wang et al., Cell Stem Cell 12(2):252-264 (2013), which are hereby incorporated by reference in their entirety. In another embodiment of the present application, the glial progenitor cells are derived from embryonic stem cells. Embryonic stem cells are derived from totipotent cells of the early mammalian embryo and are capable of unlimited, undifferentiated proliferation in vitro. As used herein, the term “embryonic stem cells” refer to a cells isolated from an embryo, placenta, or umbilical cord, or an immortalized version of such a cells, i.e., an embryonic stem cell line. Suitable embryonic stem cell lines include, without limitation, lines WA-01 (H1), WA-07, WA-09 (H9), WA-13, and WA-14 (H14) (Thomson et al., Science 282 (5391): 1145-47 (1998) and U.S. Patent No.7,029,913 to Thomson et al., which are hereby incorporated by reference in their entirety). Other suitable embryonic stem cell lines includes the HAD-C100 cell line (Tannenbaum et al., PLoS One 7(6):e35325 (2012), which is hereby incorporated by reference in its entirety, the WIBR4, WIBR5, WIBR6 cel lines (Lengner et al., Cell 141(5):872-83 (2010), which is hereby incorporated by reference in its entirety), and the human embryonic stem cell lines (HUES) lines 1-17 (Cowan et al., N. Engl. J. Med.350:1353-56 (2004), which is hereby incorporated by reference in its entirety). Human embryonic stem cells provide a virtually unlimited source of clonal/genetically modified cells potentially useful for tissue replacement therapies. Methods of obtaining highly enriched preparations of glial progenitor cells from embryonic cells that are suitable for making the non-human mammal model of the present disclosure are described herein as disclosed in Wang et al., Cell Stem Cell 12:252-264 (2013), which is hereby incorporated by reference in its entirety. Briefly, glial progenitor cells are derived from a pluripotent population of cells, i.e., iPSCs or embryonic stem cells, using a protocol that directs the pluripotent cells through serial stages of neural and glial progenitor cell differentiation. Each stage of lineage restriction is characterized and identified by the expression of certain cell proteins. Stage 1 of this process involves culturing the pluripotent cell population under conditions effective to induce embryoid body formation. As described herein, the pluripotent cell population may be maintained in co-culture with other cells, such as embryonic fibroblasts, in an embryonic stem cell (ESC) media (e.g., DMEM/F12 containing a suitable serum replacement and bFGF). The
pluripotent cells are passaged before reaching 100% confluence, e.g., 80% confluence, when colonies are approximately 250-300μm in diameter. The pluripotential state of the cells is readily assessed using markers to SSEA4, TRA-1-60, OCT-4, NANOG, and/or SOX2. To generate embryoid bodies (EBs) (Stage 2), which are complex three-dimensional cell aggregates of pluripotent stem cells, pluripotent cell cultures are dissociated once they achieved ~80% confluence with colony diameters at or around 250-300μm. The EBs are initially cultured in suspension in ESC media without bFGF, and then switched to neural induction medium supplemented with bFGF and heparin. To induce neuroepithelial differentiation (Stage 3) EBs are plated and cultured in neural induction medium supplemented with bFGF, heparin, laminin, then switched to neural induction media supplemented with retinoic acid. Neuroepithelial differentiation is assessed by the co-expression of PAX6 and SOX1, which characterize central neural stem and progenitor cells. To induce pre-oligodendrocyte progenitor cell (“pre-OPCs”) differentiation, neuroepithelial cell colonies can be cultured in the presence of additional factors including retinoic acid, B27 supplement, and a sonic hedgehog (shh) agonist (e.g., purmophamine). The appearance of pre-OPC colonies is assessed by the presence of OLIG2 and/or NKX2.2 expression. While both OLIG2 and NKX2.2 are expressed by central oligodendrocyte progenitor cells, NKX2.2 is a more specific indicator of oligodendroglial differentiation. Accordingly, an early pre-oligodendrocyte progenitor cell stage is marked by OLIG
+/NKX2.2- cell colonies. OLIG
+/NKX2.2- early pre-OPCs are differentiated into later-stage OLIG
+/NKX2.2
+ pre-OPCs by replacing retinoic acid with bFGF. At the end of Stage 5, a significant percentage of the cells are pre-OPCs as indicated by OLIG2
+/NKX2.2
+ expression profile. Pre-OPCs can be further differentiated into bipotential glial progenitor cells by culture in glial induction media supplemented with growth factors such as triiodothyronine (T3), neurotrophin 3 (NT3), insulin growth factor (IGF-1), and platelet-derived growth factor-AA (PDGF-AA) (Stage 6). These culture conditions can be extended for 3-4 months or longer to maximize the production of myelinogenic glial progenitor cells when desired. Cell preparations suitable for transplantation into an appropriate subject are identified as containing PDGFRα
+ glial progenitor cells. The population of glial progenitor cells used in carrying out the method of the present application may comprise at least about 80% glial progenitor cells, including, for example, about 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100% glial cells. The selected preparation of glial progenitor cells can be relatively devoid (e.g., containing less than 20, 15, 10, 9, 8, 7,
6, 5, 4, 3, 2, or 1%) of other cells types such as neurons and neuronal progenitor cells. Optionally, the cell population can be a substantially pure populations of glial progenitor cells. The subject being treated in accordance with the method of the present application can be an adult afflicted with age-related white matter/oligodendrocyte/astrocyte loss in the brain. This method alleviates the adverse effects of this condition which can arise as part of the normal aging process. As used herein, “treating” or “treatment” refers to any indication of success in amelioration of an injury, pathology, or condition, including any objective or subjective parameter such as abatement; remission; diminishing of symptoms or making the injury, pathology, or condition more tolerable to the patient; slowing the rate of degeneration or decline; making the final point of degeneration less debilitating; or improving a subject’s physical or mental well-being. The treatment or amelioration of symptoms can be based on objective or subjective parameters; including the results of a physical examination, neurological examination, and/or psychiatric evaluation. “Treating” may include the administration of glial progenitor cells or/and other agent(s) to prevent or delay, to alleviate, or to arrest or inhibit development of the symptoms or conditions associated with the disease, condition or disorder. “Therapeutic effect” refers to the reduction, elimination, or prevention of the disease, symptoms of the disease, or side effects of a disease, condition or disorder in the subject. Treatment may be prophylactic (to prevent or delay the onset or worsening of the disease, condition or disorder, or to prevent the manifestation of clinical or subclinical symptoms thereof) or therapeutic suppression or alleviation of symptoms after the manifestation of the disease, condition or disorder. One of the conditions resulting from age-related white matter loss, oligodendrocyte loss, or astrocyte loss in the brain which can be treated by the method of the present application is subcortical dimentia. As used herein, the term “white matter” relates to a component of the central nervous system, in the brain and superficial spinal cord, which consists mostly of glial cells and myelinated axons that transmit signals from one region of the cerebrum to another and between the cerebrum and lower brain centers. The glial progenitor cells may be introduced into the subject needing alleviation of the adverse effects by a variety of know techniques. These include, but are not limited to, injection, deposition, and grafting as described herein. In one embodiment, the glial progenitor cells can be transplanted bilaterally into multiple sites of the subject, as described U.S. Patent No.7,524,491 to Goldman, Windrem et
al., Cell Stem Cell 2:553-565 (2008), Han et al., Cell Stem Cell 12:342-353 (2013), and Wang et al., Cell Stem Cell 12:252-264 (2013), which are hereby incorporated by reference in their entirety). Methods for transplanting nerve tissues and cells into host brains are described by Bjorklund and Stenevi (eds), Neural Grafting in the Mammalian CNS, Ch. 3-8, Elsevier, Amsterdam (1985); U.S. Patent No. 5,082,670 to Gage et al.; and U.S. Patent No.6,497,872 to Weiss et al., which are hereby incorporated by reference in their entirety. Typical procedures include intraparenchymal, intracallosal, intraventricular, intrathecal, and intravenous transplantation. Intraparenchymal transplantation can be achieved by injection or deposition of tissue within the host brain so as to be apposed to the brain parenchyma at the time of transplantation. The two main procedures for intraparenchymal transplantation are: (1) injecting the donor cells within the host brain parenchyma or (2) preparing a cavity by surgical means to expose the host brain parenchyma and then depositing the graft into the cavity (Bjorklund and Stenevi (eds), Neural Grafting in the Mammalian CNS, Ch.3, Elsevier, Amsterdam (1985), which is hereby incorporated by reference in its entirety). Both methods provide parenchymal apposition between the donor cells and host brain tissue at the time of grafting, and both facilitate anatomical integration between the graft and host brain tissue. This is of importance if it is required that the donor cells become an integral part of the host brain and survive for the life of the host. Glial progenitor cells can also be delivered intracallosally as described in U.S. Patent Application Publication No. 20030223972 to Goldman, which is hereby incorporated by reference in its entirety. The glial progenitor cells can also be delivered directly to the forebrain subcortex, specifically into the anterior and posterior anlagen of the corpus callosum. Glial progenitor cells can also be delivered to the cerebellar peduncle white matter to gain access to the major cerebellar and brainstem tracts. Glial progenitor cells can also be delivered to the spinal cord. Alternatively, the cells may be placed in a ventricle, e.g., a cerebral ventricle. Grafting cells in the ventricle may be accomplished by injection of the donor cells or by growing the cells in a substrate such as 30% collagen to form a plug of solid tissue which may then be implanted into the ventricle to prevent dislocation of the graft cells. For subdural grafting, the cells may be injected around the surface of the brain after making a slit in the dura.. Suitable techniques for cell delivery are described supra. In one embodiment, said preparation of glial progenitor cells is administered to the striatum, forebrain, brain stem, and/or cerebellum of the subject.
Delivery of the cells to the subject can include either a single step or a multiple step injection directly into the nervous system. For localized disorders such as demyelination of the optic nerve, a single injection can be used. Although adult and fetal oligodendrocyte precursor cells disperse widely within a transplant recipient’s brain, for widespread disorders, multiple injections sites can be performed to optimize treatment. Injection is optionally directed into areas of the central nervous system such as white matter tracts like the corpus callosum (e.g., into the anterior and posterior anlagen), dorsal columns, cerebellar peduncles, cerebral peduncles. Such injections can be made unilaterally or bilaterally using precise localization methods such as stereotaxic surgery, optionally with accompanying imaging methods (e.g., high resolution MRI imaging). One of skill in the art recognizes that brain regions vary across species; however, one of skill in the art also recognizes comparable brain regions across mammalian species. The cellular transplants can be optionally injected as dissociated cells but can also be provided by local placement of non-dissociated cells. In either case, the cellular transplants optionally comprise an acceptable solution. Such acceptable solutions include solutions that avoid undesirable biological activities and contamination. Suitable solutions include an appropriate amount of a pharmaceutically-acceptable salt to render the formulation isotonic. Examples of the pharmaceutically-acceptable solutions include, but are not limited to, saline, Ringer’s solution, dextrose solution, and culture media. The pH of the solution is preferably from about 5 to about 8, and more preferably from about 7 to about 7.5. The injection of the dissociated cellular transplant can be a streaming injection made across the entry path, the exit path, or both the entry and exit paths of the injection device (e.g., a cannula, a needle, or a tube). Automation can be used to provide a uniform entry and exit speed and an injection speed and volume. The number of glial progenitor cells administered to the subject can range from about 10
2-10
8 at each administration (e.g., injection site), depending on the size and species of the recipient, and the volume of tissue requiring cell replacement. Single administration (e.g., injection) doses can span ranges of 10
3-10
5, 10
4-10
7, and 10
5-10
8 cells, or any amount in total for a transplant recipient patient. Since the CNS is an immunologically privileged site, administered cells, including xenogeneic, can survive and, optionally, no immunosuppressant drugs or a typical regimen of immunosuppressant agents are used in the treatment methods. However, optionally, an immunosuppressant agent may also be administered to the subject. Immunosuppressant agents and their dosing regimens are known to one of skill in the art and include such agents as
Azathioprine, Azathioprine Sodium, Cyclosporine, Daltroban, Gusperimus Trihydrochloride, Sirolimus, and Tacrolimus. Dosages ranges and duration of the regimen can be varied with the disorder being treated; the extent of rejection; the activity of the specific immunosuppressant employed; the age, body weight, general health, sex and diet of the subject; the time of administration; the route of administration; the rate of excretion of the specific immunosuppressant employed; the duration and frequency of the treatment; and drugs used in combination. One of skill in the art can determine acceptable dosages for and duration of immunosuppression. The dosage regimen can be adjusted by the individual physician in the event of any contraindications or change in the subject’s status. In one embodiment, one or more immunosuppressant agents can be administered to the subject starting at 10 weeks prior to cell administration. In one embodiment, the one or more immunosuppressant agents are administered to the subject starting at 9 weeks, 8 weeks, 7 weeks, 6 weeks, 5 weeks, 4 weeks, 3 weeks, 2 weeks, 1 week, 7 days, 6 days, 5 days, 4 days, 3 days, 2 days, 1 day, < 24 hours prior to cell administration. In one embodiment, one or more immunosuppressant agents are administered to the subject starting on the day of cell administration and continuing for 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 months post administration. In one embodiment, the one or more immunosuppressant agents are administered to the subject for > 1 year following administration. Suitable subjects for treatment in accordance with the methods described herein include any mammalian subject afflicted with age-related white matter loss. Exemplary mammalian subjects include humans, mice, rats, guinea pigs, and other small rodents, dogs, cats, sheep, goats, and monkeys. In one embodiment, the subject is human. The above-described rejuvenation therapy and cell therapy can be used together. For example, the nucleic acid molecules, the inhibitory molecules, CRISPR/Cas systems, expression cassettes, or expression vectors described above can be used as therapeutic reagents in ex vivo applications. To that end, the reagents can be introduced into tissue or cells that are transplanted into a subject for therapeutic effect. The cells and/or tissue can be derived from an organism or subject that later receives the explant (e.g., isogenic or autologous), or can be derived from another organism or subject (e.g., a relative, a sibling, or a HLA matching donor) prior to transplantation (e.g., heterologous, xenogenic, allogeneic, or isogenic). The reagents can be used to modulate the expression of one or more genes in the cells or tissue, such that the cells or tissue obtain a desired phenotype or are able to perform a function when transplanted in vivo. In one embodiment, certain target cells from a patient are extracted or isolated. These isolated cells are contacted with the reagent targeting a specific nucleotide sequence within the
cells under conditions suitable for uptake of the reagent by these cells (e.g., using delivery reagents such as cationic lipids, liposomes and the like or using techniques such as electroporation to facilitate the delivery of reagent into cells). The cells are then reintroduced back into the same patient or other patients. For therapeutic applications, a pharmaceutically effective dose of the therapeutic reagent or pharmaceutical composition can be administered to the subject. A pharmaceutically effective dose is a dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. One skilled in the art can readily determine a therapeutically effective dose of the reagent to be administer to a given subject, by taking into account factors, such as the size and weight of the subject, the extent of the disease progression or penetration, the age, health, and sex of the subject, the route of administration m and whether the administration is regional or systemic. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer. The therapeutic reagent or pharmaceutical composition can be administered in a single dose or in multiple doses. In certain embodiments, the cell, protein, or nucleotide compositions described herein may be administered in an amount effective to enhance myelin production in the CNS of a subject by an increase in the amount of one or more myelin proteins (e.g., MBP, MAG, MOG, MOBP, PLP1, GPR37, ASPA, CNP, MYRF, BCAS1, PLP1, UGT8, TF, LPAR1, and FA2H) of at least 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, or 1000% as compared to the level of myelin proteins of an untreated subject. In other embodiments, the compositions may be administered in an amount effective to promote survival of CNS neurons in a subject by an increase in the number of surviving neurons of at least 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, or 1000% as compared to the number of surviving neurons in an untreated CNS neurons or subject. Another strategy for treating a subject suffering from myelin-related disorder is to administer a therapeutically effective amount of a cell or nucleotide composition described herein along with a therapeutically effective amount of an oligodendrocyte differentiation and/or proliferation inducing agent(s) and/or anti-neurodegenerative disease agent. Examples
of anti-neurodegenerative disease agents include L-dopa, cholinesterase inhibitors, anticholinergics, dopamine agonists, steroids, and immunomodulators including interferons, monoclonal antibodies, and glatiramer acetate. Therefore, in a further aspect of the disclosure, the compositions described herein can be administered as part of a combination therapy with adjunctive therapies for treating neurodegenerative and myelin related disorders. The phrase "combination therapy" embraces the administration of oligodendrocyte precursor differentiation inducing compositions described herein and a therapeutic agent as part of a specific treatment regimen intended to provide a beneficial effect from the co-action of these therapeutic agents. When administered as a combination, the oligodendrocyte precursor differentiation inducing compound and a therapeutic agent can be formulated as separate compositions. Administration of these therapeutic agents in combination typically is carried out over a defined time period (usually minutes, hours, days, or weeks depending upon the combination selected). The genetic nucleic acids, genetic constructs, expression cassettes, expression vectors, and cells of the present application may be administered by intracerebral delivery, intrathecal delivery, intranasal delivery, or via direct infusion into the brain ventricles. Pharmaceutical Compositions The present disclosure provides a pharmaceutical composition, or medicament, for preventing or treating an inherited or acquired disorder of myelin. In some embodiments, a pharmaceutical composition comprises one or more of the above-described protein molecule, polynucleotide, expression cassette, expression vector (e.g., viral vector genome, expression vector, rAAV vector), system (e.g., a CRISPR/Cas system or nucleic acid(s) encoding components of the system), and host cell or a progeny thereof. The pharmaceutical composition further comprises a pharmaceutically-acceptable carrier, adjuvant, diluent, excipient and/or other medicinal agents. A pharmaceutically acceptable carrier, adjuvant, diluent, excipient or other medicinal agent is one that is not biologically or otherwise undesirable, e.g., the material may be administered to a subject without causing undesirable biological effects which outweigh the advantageous biological effects of the material. Any suitable pharmaceutically acceptable carrier or excipient can be used in the preparation of a pharmaceutical composition according to the disclosure (See e.g., Remington The Science and Practice of Pharmacy, Adeboye Adejare (Editor) Academic Press, November 2020).
A pharmaceutical composition is typically sterile, pyrogen-free and stable under the conditions of manufacture and storage. A pharmaceutical composition may be formulated as a solution (e.g., water, saline, dextrose solution, buffered solution, or other pharmaceutically sterile fluid), microemulsion, liposome, or other ordered structure suitable to accommodate a high product (e.g., viral vector particles, microparticles or nanoparticles) concentration. In some embodiments, a pharmaceutical composition comprising the above-described protein, polynucleotide, expression cassette, expression vector, vector genome, cell, or rAAV vector of the disclosure is formulated in water or a buffered saline solution. A carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. Proper fluidity can be maintained, for example, by use of a coating such as lecithin, by maintenance of a required particle size, in the case of dispersion, and by the use of surfactants. In some embodiments, it may be preferable to include isotonic agents, for example, a sugar, a polyalcohol such as mannitol, sorbitol, or sodium chloride in the composition. Prolonged adsorption of an injectable composition can be brought about by including, in the composition, an agent which delays absorption, e.g., a monostearate salt and gelatin. In some embodiments, a nucleic acid, vector and/or host cell of the disclosure may be administered in a controlled release formulation, for example, in a composition which includes a slow-release polymer or other carrier that protects the product against rapid release, including an implant and microencapsulated delivery system. In some embodiments, a pharmaceutical composition of the disclosure is a parenteral pharmaceutical composition, including a composition suitable for intravenous, intraarterial, subcutaneous, intradermal, intraperitoneal, intramuscular, intraarticular, intraparenchymal (IP), intrathecal (IT), intracerebroventricular (ICV) and/or intracisternal magna (ICM) administration. In some embodiments, a pharmaceutical composition of this disclosure is formulated for administration by ICV injection. In some embodiments, a vector (e.g., a viral vector such as AAV) may be formulated in 350 mM NaCl and 5% D-sorbitol in PBS. Administrations The above-described molecule, or polynucleotide, or vector (e.g., vector genome, rAAV vector), or system (e.g., a CRISPR/Cas systems or nucleic acid(s) encoding components of the system), or a cell may be administered to a subject (e.g., a patient) or a target cell in order to treat the subject. Administration of a vector to a human subject, or an animal in need thereof, can be by any means known in the art for administering a vector. Examples of a target
cell include cells of the CNS, preferably oligodendrocytes, astrocytes, or the progenitor cells thereof. A vector can be administered in addition to, and as an adjunct to, the standard of care treatment. That is, the vector can be co-administered with another agent, compound, drug, treatment or therapeutic regimen, either simultaneously, contemporaneously, or at a determined dosing interval as would be determined by one skilled in the art using routine methods. Uses disclosed herein include administration of an rAAV vector of the disclosure at the same time, in addition to and/or on a dosing schedule concurrent with, the standard of care for the disease as known in the art. In some embodiments, a combination composition includes one or more immunosuppressive agents. In some embodiments, a combination composition includes an rAAV vector comprising a transgene (e.g., a polynucleotide encoding an RNA molecule disclosed herein) and one or more immunosuppressive agents. In some embodiments, a method includes administering or delivering an rAAV vector comprising the transgene to a subject and administering an immunosuppressive agent to the subject either prophylactically prior to administration of the vector, or after administration of the vector (i.e., either before or after symptoms of a response against the vector and/or the protein provided thereby are evident). In one embodiment, a vector of the disclosure (e.g., an rAAV vector) is administered systemically. Exemplary methods of systemic administration include, but are not limited to, intravenous (e.g., portal vein), intraarterial (e.g., femoral artery, hepatic artery), intravascular, subcutaneous, intradermal, intraperitoneal, transmucosal, intrapulmonary, intralymphatic and intramuscular administration, and the like, as well as direct tissue or organ injection. One skilled in the art would appreciate that systemic administration can deliver a nucleic acid to all tissues. In some embodiments, direct tissue or organ administration includes administration to areas directly affected by oligodendrocyte deficiency (e.g., brain and/or central nervous system). In some embodiments, vectors of the disclosure, and pharmaceutical compositions thereof, are administered to the brain parenchyma (i.e., by intraparenchymal administration), to the spinal canal or the subarachnoid space so that it reaches the cerebrospinal fluid (CSF) (i.e., by intrathecal administration), to a ventricle of the brain (i.e., by intracerebroventricular administration) and/or to the cisterna magna of the brain (i.e., by intracisternal magna administration). Accordingly, in some embodiments, a vector of the present disclosure is administered by direct injection into the brain (e.g., into the parenchyma, ventricle, cisterna magna, etc.) and/or into the CSF (e.g., into the spinal canal or subarachnoid space) to treat a disorder of
myelin. A target cell of a vector of the present disclosure includes a cell located in the cortex, subcortical white matter of the corpus callosum, striatum and/or cerebellum. In some embodiments, a target cell of a vector of the present disclosure is an oligodendrocyte or a progenitor cell thereof. Additional routes of administration may also comprise local application of a vector under direct visualization, e.g., superficial cortical application, or other stereotaxic application. In some embodiments, a vector of the disclosure is administered by at least two routes. For example, a vector is administered systemically and also directly into the brain. If administered via at least two routes, the administration of a vector can be, but need not be, simultaneous or contemporaneous. Instead, administration via different routes can be performed separately with an interval of time between each administration. The above-described protein, or polynucleotide encoding the protein, or a vector genome, or a vector (e.g., an rAAV vector) comprising the polynucleotide may be used for transduction of a cell ex vivo or for administration directly to a subject (e.g., directly to the CNS of a patient with a disease). In some embodiments, a transduced cell (e.g., a host cell) is administered to a subject to treat or prevent a disease, disorder or condition (e.g., cell therapy for the disease). For example, an rAAV vector comprising a therapeutic nucleic acid (e.g., encoding a protein) can be preferably administered to an oligodendrocyte, an astrocyte, or a progenitor cell thereof in a biologically-effective amount. The dosage amount of a vector depends upon, e.g., the mode of administration, disease or condition to be treated, the stage and/or aggressiveness of the disease, individual subject's condition (age, sex, weight, etc.), particular viral vector, stability of protein to be expressed, host immune response to the vector, and/or gene to be delivered. Generally, doses range from at least 1 x 10
8, or more, e.g., 1 x 10
9, 1 x 10
10, 1 x 10
11, 1 x 10
12, 1 x 10
13, 1 x 10
14, 1 x 10
15 or more vector genomes (vg) per kilogram (kg) of body weight of the subject to achieve a therapeutic effect. In some embodiments, a polynucleotide encoding a protein described herein may be administered as a component of a DNA molecule (e.g., a recombinant nucleic acid) having a regulatory element (e.g., a promoter) appropriate for expression in a target cell (e.g., an oligodendrocyte, an astrocyte, or a progenitor cell thereof). The polynucleotide may be administered as a component of a plasmid or a viral vector, such as an rAAV vector. An rAAV vector may be administered in vivo by direct delivery of the vector (e.g., directly to the CNS) to a patient in need of treatment. An rAAV vector may be administered to a patient ex vivo by
administration of the vector in vitro to a cell from a donor patient in need of treatment, followed by introduction of the transduced cell back into the donor (e.g., cell therapy). Kit The present disclosure provides a kit with packaging material and one or more components described therein. A kit typically includes a label or packaging insert including a description of the components or instructions for use in vitro, in vivo or ex vivo, of the components therein. A kit can contain a collection of such components, e.g., the above- described polynucleotide, nucleic acid, expression cassette, expression vector (e.g., viral vector genome, expression vector, rAAV vector), and cell, and optionally a second active agent such as a compound, therapeutic agent, drug or composition. A kit refers to a physical structure that contains one or more components of the kit. Packaging material can maintain the components in a sterile manner and can be made of material commonly used for such purposes (e.g., paper, glass, plastic, foil, ampules, vials, tubes, etc). A label or insert can include identifying information of one or more components therein, dose amounts, clinical pharmacology of the active ingredients(s) including mechanism of action, pharmacokinetics and pharmacodynamics. A label or insert can include information identifying manufacture, lot numbers, manufacture location and date, expiration dates. A label or insert can include information on a disease (e.g., an inherited or acquired or age-related disorder of myelin such as HD) for which a kit component may be used. A label or insert can include instructions for a clinician or subject for using one or more of the kit components in a method, use or treatment protocol or therapeutic regimen. Instructions can include dosage amounts, frequency of duration and instructions for practicing any of the methods, uses, treatment protocols or prophylactic or therapeutic regimens described herein. A label or insert can include information on potential adverse side effects, complications or reaction, such as a warning to a subject or clinician regarding situations where it would not be appropriate to use a particular composition. Definitions Unless otherwise defined, all technical and scientific terms used herein have the meaning commonly understood by one of ordinary skill in the art to which this disclosure belongs. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the disclosure. As used in the description of the disclosure and the appended claims, the singular forms “a,” “an” and “the” are intended to
include the plural forms as well, unless the context clearly indicates otherwise. The following terms have the meanings given: As used herein, the term “about,” or “approximately” refers to a measurable value such as an amount of the biological activity, homology or length of a polynucleotide or polypeptide sequence, dose, time, temperature, and the like, and is meant to encompass variations of 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% 1%, 0.5% or even 0.1%, in either direction (greater than or less than) of the specified amount unless otherwise stated, otherwise evident from the context, or except where such number would exceed 100% of a possible value. The term "transgene" refers to a heterologous polynucleotide that is introduced into a cell and is capable of being transcribed into RNA and optionally, translated and/or expressed under appropriate conditions. In aspects, it confers a desired property to a cell into which it was introduced, or otherwise leads to a desired therapeutic or diagnostic outcome. In another aspect, it may be transcribed into a molecule that mediates RNA interference, such as miRNA, siRNA, or shRNA. As used herein, the term “homologous,” or “homology,” refers to two or more reference entities (e.g., a nucleic acid or polypeptide sequence) that share at least partial identity over a given region or portion. For example, when an amino acid position in two peptides is occupied by identical amino acids, the peptides are homologous at that position. Notably, a homologous peptide will retain activity or function associated with the unmodified or reference peptide and the modified peptide will generally have an amino acid sequence “substantially homologous” with the amino acid sequence of the unmodified sequence. When referring to a polypeptide, nucleic acid or fragment thereof, “substantial homology” or “substantial similarity,” means that when optimally aligned with appropriate insertions or deletions with another polypeptide, nucleic acid (or its complementary strand) or fragment thereof, there is sequence identity in at least about 70% to 99% of the sequence. The extent of homology (identity) between two sequences can be ascertained using computer program or mathematical algorithm known in the art. Such algorithms that calculate percent sequence homology (or identity) generally account for sequence gaps and mismatches over the comparison region or area. A nucleic acid or polynucleotide refers to a DNA molecule (e.g., a cDNA or genomic DNA), an RNA molecule (e.g., an mRNA), or a DNA or RNA analog. A DNA or RNA analog can be synthesized from nucleotide analogs. The nucleic acid molecule can be single-stranded or double-stranded, but preferably is double-stranded DNA.
An isolated or recombinant nucleic acid refers to a nucleic acid the structure of which is not identical to that of any naturally occurring nucleic acid or to that of any fragment of a naturally occurring genomic nucleic acid. The term therefore covers, for example, (a) a DNA which has the sequence of part of a naturally occurring genomic DNA molecule but is not flanked by both of the sequences that flank that part of the molecule in the genome of the organism in which it naturally occurs; (b) a nucleic acid incorporated into a vector or into the genomic DNA of a prokaryote or eukaryote in a manner such that the resulting molecule is not identical to any naturally occurring vector or genomic DNA; (c) a separate molecule such as a cDNA, a genomic fragment, a fragment produced by polymerase chain reaction (PCR), or a restriction fragment; and (d) a recombinant nucleotide sequence that is part of a hybrid gene, i.e., a gene encoding a fusion protein. The nucleic acid described above can be used to express the protein of this disclosure. For this purpose, one can operatively linked the nucleic acid to suitable regulatory sequences to generate an expression vector. A "recombinant nucleic acid” is a combination of nucleic acid sequences that are joined together using recombinant technology and procedures used to join together nucleic acid sequences. The terms “heterologous” DNA molecule and “heterologous” nucleic acid, as used herein, each refer to a molecule that originates from a source foreign to the particular host cell or, if from the same source, is modified from its original form. Thus, a heterologous gene in a host cell includes a gene that is endogenous to the particular host cell but has been modified through, for example, the use of shuffling or recombination. When used to describe two nucleic acid segments, the terms mean that the two nucleic acid segments are not from the same gene or, if form the same gene, one or both of them are modified from the original forms. The terms also include non-naturally occurring multiple copies of a naturally occurring DNA molecule. Thus, the terms refer to a nucleic acid segment that is foreign or heterologous to the cell, or homologous to the cell but in a position within the host cell nucleic acid in which the element is not ordinarily found. Exogenous DNA segments are expressed to yield exogenous RNAs or polypeptides. A "homologous DNA molecule" is a DNA molecule that is naturally associated with a host cell into which it is introduced. A "regulatory sequence" includes promoters, enhancers, and other expression control elements (e.g., polyadenylation signals). Regulatory sequences include those that direct constitutive expression of a nucleotide sequence, as well as tissue-specific regulatory and/or inducible sequences. The design of the expression vector can depend on such factors as the choice of the host cell to be transformed, the level of expression of protein or RNA desired,
and the like. The expression vector can be introduced into host cells to produce an RNA or a polypeptide of interest. A promoter is defined as a DNA sequence that directs RNA polymerase to bind to DNA and initiate RNA synthesis. A strong promoter is one which causes RNAs to be initiated at high frequency. A "promoter" is a nucleotide sequence which initiates and regulates transcription of a polynucleotide. Promoters can include inducible promoters (where expression of a polynucleotide sequence operably linked to the promoter is induced by an analyte, cofactor, regulatory protein, etc.), repressible promoters (where expression of a polynucleotide sequence operably linked to the promoter is repressed by an analyte, cofactor, regulatory protein, etc.), and constitutive promoters. It is intended that the term "promoter" or "control element" includes full-length promoter regions and functional (e.g., controls transcription or translation) segments of these regions. "Operably linked" refers to an arrangement of elements wherein the components so described are configured so as to perform their usual function. Thus, a given promoter operably linked to a nucleic acid sequence is capable of effecting the expression of that sequence when the proper enzymes are present. The promoter need not be contiguous with the sequence, so long as it functions to direct the expression thereof. Thus, for example, intervening untranslated yet transcribed sequences can be present between the promoter sequence and the nucleic acid sequence and the promoter sequence can still be considered "operably linked" to the coding sequence. Thus, the term "operably linked" is intended to encompass any spacing or orientation of the promoter element and the DNA sequence of interest which allows for initiation of transcription of the DNA sequence of interest upon recognition of the promoter element by a transcription complex. As used here, the term “genetic construct” or “nucleic acid construct,” refers to a non- naturally occurring nucleic acid molecule resulting from the use of recombinant DNA technology (e.g., a recombinant nucleic acid). A genetic or nucleic acid construct is a nucleic acid molecule, either single or double stranded, which has been modified to contain segments of nucleic acid sequences, which are combined and arranged in a manner not found in nature. A nucleic acid construct may be a “cassette” or a “vector” (e.g., a plasmid, an rAAV vector genome, an expression vector, etc.), that is, a nucleic acid molecule designed to deliver exogenously created DNA into a host cell. "Expression cassette" as used herein means a nucleic acid sequence capable of directing expression of a particular nucleotide sequence in an appropriate host cell, which may include a promoter operably linked to the nucleotide sequence of interest that may be operably linked
to termination signals. It also may include sequences required for proper translation of the nucleotide sequence. The coding region usually codes for an RNA or protein of interest. The expression cassette including the nucleotide sequence of interest may be chimeric. The expression cassette may also be one that is naturally occurring but has been obtained in a recombinant form useful for heterologous expression. The expression of the nucleotide sequence in the expression cassette may be under the control of a constitutive promoter or of a regulatable promoter that initiates transcription only when the host cell is exposed to some particular stimulus. In the case of a multicellular organism, the promoter can also be specific to a particular tissue or organ or stage of development. A vector refers to a nucleic acid molecule capable of transporting another nucleic acid to which it has been linked. The vector may or may not be capable of autonomous replication or integrate into a host DNA. Examples include a plasmid, virus (e.g., an rAAV), cosmid, or other vehicle that can be manipulated by insertion or incorporation of a nucleic acid (e.g., a recombinant nucleic acid). A vector can be used for various purposes including, e.g., genetic manipulation (e.g., cloning vector), to introduce/transfer a nucleic acid into a cell, to transcribe or translate an inserted nucleic acid in a cell. In some embodiments a vector nucleic acid sequence contains at least an origin of replication for propagation in a cell. In some embodiments, a vector nucleic acid includes a heterologous nucleic acid sequence, an expression control element(s) (e.g., promoter, enhancer), a selectable marker (e.g., antibiotic resistance), a poly-adenosine (polyA) sequence and/or an ITR. In some embodiments, when delivered to a host cell, the nucleic acid sequence is propagated. In some embodiments, when delivered to a host cell, either in vitro or in vivo, the cell expresses the polypeptide encoded by the heterologous nucleic acid sequence. In some embodiments, when delivered to a host cell, the nucleic acid sequence, or a portion of the nucleic acid sequence is packaged into a capsid. A host cell may be an isolated cell or a cell within a host organism. In addition to a nucleic acid sequence (e.g., transgene) which encodes an RNA, or a polypeptide or a protein, additional sequences (e.g., regulatory sequences) may be present within the same vector (i.e., in cis to the gene) and flank the gene. In some embodiments, regulatory sequences may be present on a separate (e.g., a second) vector which acts in trans to regulate the expression of the gene. Plasmid vectors may be referred to herein as “expression vectors.” As used herein, the term “vector genome” refers to a recombinant nucleic acid sequence that is packaged or encapsidated to form an rAAV vector. Typically, a vector genome includes a heterologous polynucleotide sequence, e.g., a transgene, regulatory elements, ITRs not originally present in the capsid. In cases where a recombinant plasmid is used to construct or
manufacture a recombinant vector (e.g., rAAV vector), the vector genome does not include the entire plasmid but rather only the sequence intended for delivery by the viral vector. This non- vector genome portion of the recombinant plasmid is typically referred to as the “plasmid backbone,” which is important for cloning. selection and amplification of the plasmid, a process that is needed for propagation of recombinant viral vector production, but which is not itself packaged or encapsidated into an rAAV vector. As used herein, the term “viral vector” generally refers to a viral particle that functions as a nucleic acid delivery vehicle and which comprises a vector genome (e.g., comprising a transgene instead of a nucleic acid encoding an AAV rep and cap) packaged within the viral particle (i.e., capsid) and includes, for example, lenti- and parvo- viruses, including AAV serotypes and variants (e.g., rAAV vectors). A recombinant viral vector does not comprise a vector genome comprising a rep and/or a cap gene. As used herein, the term "overexpressing," "overexpress," "overexpressed," or "overexpression," when referring to the production of a nucleic acid or a protein in a host cell means that the nucleic acid or protein is produced in greater amounts than it is produced in its naturally occurring environment. It is intended that the term encompass overexpression of endogenous, as well as exogenous or heterologous nucleic acids and proteins. As such, the terms and the like are intended to encompass increasing the expression of a nucleic acid or a protein in a cell to a level greater than that the cell naturally contains. In certain embodiments, the expression level or amount of the nucleic acid or protein in a cell is increased by at least 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, or 1000% as compared to the level or amount that the cell naturally contains. In the context of a mutant or diseased cell, the terms "overexpressing," "overexpress," "overexpressed," and "overexpression," and the like are intended to encompass increasing the expression of a nucleic acid or a protein to a level greater than that a mutant cell, a diseased cell, a wildtype cell, or a non-diseased cell contains. In certain embodiments, the expression level or amount of the nucleic acid or protein in a mutant or diseased cell is increased by at least 5%, 10%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 100%, 110%, 120%, 130%, 140%, 150%, 160%, 170%, 180%, 190%, 200%, 250%, 300%, 350%, 400%, 450%, 500%, 550%, 600%, 650%, 700%, 750%, 800%, 850%, 900%, 950%, or 1000% as compared to the level or amount that a mutant cell, a diseased cell, a wildtype cell, or a non- diseased cell contains.
“Anti-sense" refers to a nucleic acid sequence, regardless of length, that is complementary to the coding strand or mRNA of a nucleic acid sequence. Antisense RNA can be introduced to an individual cell, tissue or organanoid. An anti-sense nucleic acid can contain a modified backbone, for example, phosphorothioate, phosphorodithioate, or other modified backbones known in the art, or may contain non-natural internucleoside linkages. As referred to herein, a "complementary nucleic acid sequence" is a nucleic acid sequence capable of hybridizing with another nucleic acid sequence comprised of complementary nucleotide base pairs. By "hybridize" is meant pair to form a double-stranded molecule between complementary nucleotide bases (e.g., adenine (A) forms a base pair with thymine (T), as does guanine (G) with cytosine (C) in DNA) under suitable conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol.152:507). A “suppressor” or an "inhibitor" refers to an agent that causes a decrease in the expression or activity of a target gene or protein, respectively. The terms “inhibit”, “down-regulate”, or “reduce”, refer to the reduction in the expression of a gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, below that observed in the absence of an inhibitor, suppressor or repressor, such as the inhibitory nucleic acid molecules (e.g., siRNA) described herein. Down-regulation can be associated with post-transcriptional silencing, such as, RNAi mediated cleavage or by alteration in DNA methylation patterns or DNA chromatin structure. As used herein, an "inhibitory nucleic acid" is a double-stranded RNA, RNA interference, miRNA, siRNA, shRNA, or antisense RNA, or a portion thereof, or a mimetic thereof, that when administered to a mammalian cell results in a decrease in the expression of a target gene. Typically, a nucleic acid inhibitor comprises at least a portion of a target nucleic acid molecule, or an ortholog thereof, or comprises at least a portion of the complementary strand of a target nucleic acid molecule. Typically, expression of a target gene is reduced by 10%, 25%, 50%, 75%, or even 90-100%. As used herein, the term "siRNA" intends a double-stranded RNA molecule that interferes with the expression of a specific gene or genes post-transcription. In some embodiments, the siRNA functions to interfere with or inhibit gene expression using the RNA interference pathway. Similar interfering or inhibiting effects may be achieved with one or more of short hairpin RNA (shRNA), microRNA (mRNA) and/or nucleic acids (such as siRNA, shRNA, or miRNA) comprising one or more modified nucleic acid residue--e.g.
peptide nucleic acids (PNA), locked nucleic acids (LNA), unlocked nucleic acids (UNA), or triazole-linked DNA. Optimally, a siRNA is 18, 19, 20, 21, 22, 23 or 24 nucleotides in length and has a 2-base overhang at its 3′ end. These dsRNAs can be introduced to an individual cell or culture system. Such siRNAs are used to downregulate mRNA levels or promoter activity. As used herein, the terms “treat,” “treating” or “treatment” refer to administration of a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and/or reduces incidence of one or more symptoms, features, and/or causes of a particular disease, disorder, and/or condition. As used herein, the term “ameliorate” means a detectable or measurable improvement in a subject’s disease, disorder or condition, or symptom thereof, or an underlying cellular response. A detectable or measurable improvement includes a subjective or objective decrease, reduction, inhibition, suppression, limit or control in the occurrence, frequency, severity, progression or duration of, complication cause by or associated with, improvement in a symptom of, or a reversal of a disease, disorder or condition. As used herein, the term “associated with” refers to with one another, if the presence, level and/or form of one is correlated with that of the other. For example, a particular entity (e.g., polypeptide, genetic signature, metabolite, microbe, etc.) is considered to be associated with a particular disease, disorder, or condition, if its presence, level and/or form correlates with incidence of and/or susceptibility to the disease, disorder, or condition (e.g., across a relevant population). As used herein, the term “prevent” or “prevention” refers to delay of onset, and/or reduction in frequency and/or severity of one or more sign or symptom of a particular disease, disorder or condition (e.g., a myelin disease). In some embodiments, prevention is assessed on a population basis such that an agent is considered to “prevent” a particular disease, disorder or condition if a statistically significant decrease in the development, frequency and/or intensity of one or more sign or symptom of the disease, disorder or condition is observed in a population susceptible to the disease, disorder or condition. Prevention may be considered complete when onset of disease, disorder or condition has been delayed for a predefined period of time. As used herein, the term “therapeutically effective amount” refers to an amount that produces the desired therapeutic effect for which it is administered. In some embodiments, the term refers to an amount that is sufficient, when administered to a population suffering from or susceptible to a disease, disorder or condition in accordance with a therapeutic dosing regimen, to treat the disease, disorder or condition. In some embodiments, a therapeutically effective amount is one that reduces the incidence and/or severity of, and/or delays onset of,
one or more symptoms of the disease, disorder, and/or condition. Those of ordinary skill in the art will appreciate that the term “therapeutically effective amount” does not in fact require successful treatment be achieved in a particular individual. Rather, a therapeutically effective amount may be that amount that provides a particular desired pharmacological response in a significant number of subjects when administered to patients in need of such treatment. “Population” of cells refers to any number of cells greater than 1, but is at least 1×10
3 cells, at least 1×10
4 cells, at least at least 1×10
5 cells, at least 1×10
6 cells, at least 1×10
7 cells, at least 1×10
8 cells, at least 1×10
9 cells, or at least 1×10
10 cells. As used herein, the term "stem cells" refers to cells with the ability to both replace themselves and to differentiate into more specialized cells. Their self-renewal capacity generally endures for the lifespan of the organism. A pluripotent stem cell can give rise to all the various cell types of the body. A multipotent stem cell can give rise to a limited subset of cell types. For example, a hematopoietic stem cell can give rise to the various types of cells found in blood, but not to other types of cells. Multipotent stem cells can also be referred to as somatic stem cells, tissue stem cells, lineage-specific stem cells, and adult stem cells. The non- stem cell progeny of multipotent stem cells are progenitor cells (also referred to as restricted- progenitor cells). Progenitor cells give rise to fully differentiated cells, but a more restricted set of cell types than stem cells. Progenitor cells also have comparatively limited self-renewal capacity; as they divide and differentiate they are eventually exhausted and replaced by new progenitor cells derived from their upstream multipotent stem cell. "Induced pluripotent stem cells," commonly abbreviated as iPS cells or iPSCs, refer to a type of pluripotent stem cell artificially prepared from a non-pluripotent cell, typically an adult somatic cell, or terminally differentiated cell, such as fibroblast, a hematopoietic cell, a myocyte, a neuron, an epidermal cell, or the like, by introducing certain factors, referred to as reprogramming factors. "Pluripotency" refers to a stem cell that has the potential to differentiate into all cells constituting one or more tissues or organs, or particularly, any of the three germ layers: endoderm (interior stomach lining, gastrointestinal tract, the lungs), mesoderm (muscle, bone, blood, urogenital), or ectoderm (epidermal tissues and nervous system). "Pluripotent stem cells" used herein refer to cells that can differentiate into cells derived from any of the three germ layers, for example, direct descendants of totipotent cells or induced pluripotent cells. As used herein, "therapeutic cells" refers to a cell population that ameliorates a condition, disease, and/or injury in a patient. Therapeutic cells may be autologous (i.e., derived from the patient), allogeneic (i.e., derived from an individual of the same species that is
different from the patient) or xenogeneic (i.e., derived from a different species than the patient). Therapeutic cells may be homogenous (i.e., consisting of a single cell type) or heterogeneous (i.e., consisting of multiple cell types). The term "therapeutic cell" includes both therapeutically active cells as well as progenitor cells capable of differentiating into a therapeutically active cell. The term "autologous" refers to any material derived from the same subject or individual to which it is later to be re-introduced. For example, the autologous cell therapy method described herein involves collection of glial cells, or progenitors thereof from a donor, e.g., a patient, which are then engineered to express, e.g., a transgene, and then administered back to the same donor, e.g., patient. The term "heterologous" refers to any material (e.g., cells or tissue scaffold) derived from a different subject or individual. As used herein, "heterologous" or "non-endogenous" or "exogenous" also refers to any material (e.g., gene, protein, compound, molecule, cell, or tissue or tissue component) or activity that is not native to a host cell or a host subject, or is any gene, protein, compound, molecule, cell, tissue or tissue component, or activity native to a host or host cell but has been altered or mutated such that the structure, activity or both is different as between the native and mutated versions. The term "allogeneic" refers to any material (e.g., cells or tissue) derived from one individual which is then introduced to another individual of the same species, e.g., allogeneic cell transplantation. For example, cells may be obtained from a first subject, modified ex vivo according to the methods described herein and then administered to a second subject in order to treat a disease. In such embodiments, the cells administered to the subject are allogeneic and heterologous cells. The term “xenogenic” refers to any material (e.g., cells or tissue) derived from an individual of a different species. The term “isogenic” refers to any materials (e.g., cells or tissue) characterized by essentially identical genes. As used herein, the term “subject” refers to an organism, for example, a mammal (e.g., a human, a non-human mammal, a non-human primate, a primate, a laboratory animal, a mouse, a rat, a hamster, a gerbil, a cat, a dog). In some embodiments, a subject is a non-human disease model. In some embodiments, a human subject is an adult, adolescent, or pediatric subject. In some embodiments, a subject is suffering from a disease, disorder or condition, e.g., a disease, disorder or condition that can be treated as provided herein. In some embodiments, a subject is suffering from a disease, disorder or condition associated with deficient or dysfunctional myelin. In some embodiments, a subject is susceptible to a disease, disorder, or condition. In some embodiments, a susceptible subject is predisposed to and/or shows an
increased risk (as compared to the average risk observed in a reference subject or population) of developing a disease, disorder or condition. In some embodiments, a subject displays one or more symptoms of a disease, disorder or condition. In some embodiments, a subject does not display a particular symptom (e.g., clinical manifestation of disease) or characteristic of a disease, disorder, or condition. In some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition. In some embodiments, a subject is a human patient. In some embodiments, a subject is an individual to whom diagnosis and/or therapy is and/or has been administered. As used herein, the term “therapeutically effective amount” refers to an amount that produces the desired therapeutic effect for which it is administered. In some embodiments, the term refers to an amount that is sufficient, when administered to a population suffering from or susceptible to a disease, disorder or condition in accordance with a therapeutic dosing regimen, to treat the disease, disorder or condition. In some embodiments, a therapeutically effective amount is one that reduces the incidence and/or severity of, and/or delays onset of, one or more symptoms of the disease, disorder, and/or condition. Those of ordinary skill in the art will appreciate that the term “therapeutically effective amount” does not in fact require successful treatment be achieved in a particular individual. Rather, a therapeutically effective amount may be that amount that provides a particular desired pharmacological response in a significant number of subjects when administered to patients in need of such treatment. The examples below are intended to exemplify the practice of embodiments of the disclosure but are by no means intended to limit the scope thereof. EXAMPLES Example 1 Materials and Methods This example descibes material and methods used in Examples 2-10 bellow. Human embryonic stem cell lines and culture conditions Sibling human embryonic stem cells (hESCs) lines GENEA019 (WT: 18;15 CAG) and GENEA020 (HD: 48;17 CAG), both female, were obtained from GENEA, Inc. (Sydney, Australia). hESCs were regularly cultured under feeder-free conditions on 0.55 ug/cm
2 human recombinant laminin 521 (Biolamina, cat. no. LN521) coated cell culture flasks with mTeSR1 medium (StemCell Technologies, cat. no. 85850). Daily medium changes were performed. hESCs were routinely passaged at 80% confluency onto freshly coated flasks. Passaging was performed using ReLeSR (StemCell Technologies, cat. no. 05872). All hESCs and differentiated cultures were maintained in a 5% CO2 incubator at 37 °C and routinely checked
for contamination and mycoplasma free status. The karyotypes of the source lines, both before and after reporter insertion (see below), were analyzed on metaphase spreads by G-banding (Institut für Medizinishche Genetik und Angewandte Genomik, Universitätsklinikum Tübingen). All hESC lines had a normal karyotype. Additionally, acquired copy number variants (CNVs) and loss-of-heterozygosity regions (LOH) were assessed by array CGH (Cell Line Genetics). No CNVs were noted that were either known or might be expected to influence the outcome of competitive interactions between the clones. Generation of fluorescent reporter hESCs For ubiquitous and distinct fluorescent labeling of WT and HD cells, reporter constructs driving expression of either mCherry or EGFP were inserted into the AAVS1 safe-harbor locus of WT GENEA019 and HD GENEA020 hESCs using a modified version of the CRISPR-Cas9 mediated strategy previously described in
26. To prepare hESCs for plasmid delivery by electroporation, hESC were harvested as single cell suspension following dissociation with Accutase (StemCell Technologies, cat. no. 07920), washed in culture medium, and counted with the automated cell counter NucleoCounter NC-200 (ChemoMetec). Per electroporation, a total of 1.5 × 10
6 cells were mixed with 5 µg of the AAVS1 targeting CRISPR-Cas9 plasmid (pXAT2) and 5 µg of reporter donor plasmid (pAAVS1-P-CAG-mCherry or pAAVS1-P- CAG-EGFP). pXAT2 (Addgene plasmid no. 80494), pAAVS1-P-CAG-mCherry (Addgene plasmid no. 80491) and pAAVS1-P-CAG-EGFP (Addgene plasmid no. 80492) were a gift from Knut Woltjen. Electroporation was performed using an Amaxa 4D-Nucleofector (Lonza) with the P3 primary cell kit (Lonza, cat. no. V4XP-3024) according to manufacturer’s guidelines. After nucleofection, the electroporated hESC suspensions were transferred to 10 cm cell culture dishes and cultured with mTeSR1 supplemented with 10 µM Y-27632 (Tocris, cat. no.1254) for the first 24h. Electroporated hESCs were grown for 48-72h, then treated with 0,5 µg/µL puromycin (ThermoFisher, cat. A1113803). Electroporated hESC cultures were kept under puromycin until individual colonies were large enough to be picked manually. Colonies were assessed by fluorescence microscopy and transferred to a 96-well plate based on uniformity of reporter expression. Following expansion, each clone was split for further expansion and genotyping. For genotyping, DNA was extracted using the prepGEM Tissue DNA extraction kit (Zygem). Correctly targeted transgenic integrations in the AAVS1 locus were detected by PCR using the following primers: dna803: 5’- TCGACTTCCCCTCTTCCGATG-3’ (SEQ ID NO: 12) and dna804: 5’- CTCAGGTTCTGGGAGAGGGTAG-3’ (SEQ ID NO: 13); while the zygosity of the
integrations was determined by the presence or absence of a WT allele using an additional primer: (dna803 and dna183: 5’-GAGCCTAGGGCCGGGATTCTC-3’, SEQ ID NO: 14). hESCs with correctly targeted insertions were cryopreserved with Pro-Freeze CDM (Lonza, cat. BEBP12-769E), then expanded for karyotype and array comparative genomic hybridization (aCGH) prior to hGPC production. Derivation of hGPCs from reporter WT and HD hESCs Human GPCs were derived from both reporter WT and HD hESCs using the protocol described in Wang et al., Cell Stem Cell 12, 252--264 (2013) with minor modifications to the embryoid body (EB) generation step. Cells were collected for transplant between 150 and 200 DIV, at which time the cultures derived from both WT-mCherry/EGFP and HD-EGFP hESCs were comprised predominantly of PDGFRα
+/CD44
+ bipotential GPCs. Xenotransplantation Cell preparation To prepare cells for transplant, glial cultures were collected in Ca
2+/Mg
2+-free Hanks’ balanced salt solution (HBSS
(-/-); ThermoFisher, cat. no. 14170112), then mechanically dissociated to small clusters by gentle , and counted with a hemocytometer. The cell suspension was then spun and resuspended in cold HBSS
(-/-) at 10
5 cells/µl, and kept on ice until transplanted. Neonatal grafts To generate human-mouse chimeras harboring mHTT-expressing human glia (HD chimeras), newborn immunocompromised Rag1
(-/-) pups
66 were cryoanesthetized, secured in a custom baked clay stage, and injected bilaterally with 100,000 HD glia (50,000 per hemisphere) into the presumptive striatum within 48h of birth. Cells were delivered using a 10 μl syringe (Hamilton, cat. no. 7653-01) with pulled glass pipettes at a depth of 1.2-1.4 mm. The pups were then returned to their mother until weaned. Adult grafts To assess the capacity of implanted healthy human glia to replace their diseased counterparts, 36 week-old HD glial chimeras were anesthetized by ketamine/xylazine and secured in a stereotaxic frame.200,000 WT glia were delivered bilaterally using a 10 μl syringe and metal needle into the striatum (AP: + 0.8 mm; ML: ± 1.8 mm; DV: -2.5 to -2.8 mm, all from Bregma). To minimize damage, cells were infused at a controlled rate of 175 nl/min using a controlled micropump system (World Precision Instruments). Backflow was minimized by leaving the needle in place for an additional 5 min. Experimental animals were compared to HD chimeric littermates that did not receive WT glia and to naïve rag1
(-/-) mice that received WT glia at 36 weeks of age following this exact procedure.
Human glial striatal isografts To evaluate the effects of cell age as a determinant of competitive dominance between human glia, newborn Rag1
(-/-) mice were injected following the same perinatal transplant protocol described above, but instead glia derived from WT- mCherry was delivered to generate human-mouse chimeras harboring WT human glia (WT chimeras). At 40 weeks of age, WT chimeras were then injected following the same adult transplant above described, but instead isogenic WT-EGFP glia was delivered. Likewise, experimental animals were compared to WT chimeric littermates that did not receive WT- EGFP glia and to naïve rag1
(-/-) mice that received WT-EGFP glia at 40 weeks of age following this exact procedure. Aseptic technique was used for all xenotransplants. All mice were housed in a pathogen-free environment, with ad libitum access to food and water, and all procedures were performed in agreement with protocols approved by the University of Rochester Committee on Animal Resources. Tissue processing and immunostaining Experimental animals were perfused with HBSS (ThermoFisher, cat. no. 24020117) followed by 4% PFA. The brains were removed, post-fixed for 2h in 4% PFA and rinsed 3x with PBS. They were then incubated in 30% sucrose solution (Sigma-Aldrich, cat. no. S9378) until equilibrated at which point, they were embedded in OCT in a sagittal orientation (Sakura, cat. no.4583), frozen in 2-methylbutane (Fisher Scientific, cat. no.11914421) between -60 ºC and -70ºC, and transferred to a -80ºC freezer. The blocks were then cut as 20 µm sections on a CM1950 cryostat (Leica), serially collected on adhesion slides and stored at -20ºC until further use. Identification and phenotyping of human cells was accomplished by immunostaining for their respective fluorescent reporter, together with a phenotypic marker, including Olig2 (GPCs and oligodendroglia), GFAP (astrocytes), or Ki67 (proliferating cells). Genetically- expressed fluorescent reporters were used as markers for human cells, as their expression remained stable throughout the animal’s life. In mice that received a 1:1 mixture of WT- mCherry and WT-untagged human glia, the latter were identified by the expression of human nuclear antigen (hN), and the lack of fluorescent reporter expression. Immunolabeled sections were rehydrated with PBS, then incubated in permeabilization/blocking buffer (PBS + 0.1% Triton-X (Sigma-Aldrich cat. no. T8787) + 10% Normal Goat Serum (ThermoFisher, cat. no.16210072)) for 2h. Sections were then incubated overnight with primary antibodies at 4ºC. The following day, the sections were rinsed with
PBS, and secondary antibodies applied for 1h. After again rinsing with PBS, a second round of primary antibodies, this time against fluorescent reporters, were applied to the sections overnight at 4ºC. These were rinsed with PBS the following day and the sections incubated with secondary antibodies for 1h. The slides were again thoroughly washed with PBS, and mounted with Vectashield Vibrance (Vector Labs, cat. no. H-1800). Apoptosis assay Identification of apoptotic cells within human cell populations was accomplished by terminal deoxynucleotidyl transferase-dUTP nick end labeling (TUNEL) together with immunostaining for their respective fluorescent reporters. TUNEL was performed using the Click-iT TUNEL Alexa Fluor 647 Imaging Assay (Invitrogen, cat. no. C10247) following manufacturer’s instructions with the exception that samples were incubated in Proteinase K solution for 20 minutes at room temperature. To confirm efficient TUNEL staining in fixed- frozen brain cryosections, positive control sections were treated with DNase I following manufacturer’s instructions. Following TUNEL, sections were immunolabeled for fluorescent reporters following the previously described immunostaining protocol. Quantitative histology Transplant mapping and 3D reconstruction: To map human cell distribution, whole brain montages of 15 equidistantly spaced, 160 µm apart, sagittal sections spanning the entire striatum were captured using a Nikon Ni-E Eclipse microscope equipped with a DS-Fi3 camera at 10x magnification and stitched in the NIS-Elements imaging software (Nikon). The striatum within each section was outlined and immunolabeled human cells were identified and mapped within the outlined striatum using Stereo Investigator (MicroBrightField Bioscience). When applicable, the site of adult injection was mapped as a reference point for volumetric quantification of human cell distribution. Mapped sections were then aligned using the lateral ventricle as a reference to produce a 3D reconstructed model of the humanized murine striatum. After 3D reconstruction, the cartesian coordinates for each human cell marker, injection site and striatal outlines were exported for further analysis. To map the distribution and proportion of mitotically-active cells within each human donor cell population, human cells expressing Ki67-immunoreactivity were mapped in every third section of the 15 equidistant sections used to perform the 3D reconstructions. Ki67 sampling was thus done every (160 µm x 3=) 480 µm. Volumetric distribution analysis: To quantify the spatial distribution of HD glia in HD chimeras (Fig. 6), the volumes of each mapped striatal section were calculated by
multiplying the section thickness (20 µm) by the section area. The cell density for each section was then calculated by dividing the number of mapped cells in each section by their respective volume. To quantify the spatial-temporal dynamics of competing human glia, a program was developed to calculate the volumetric distribution of each cell population as a function of distance to the WT glia delivery site in 3D reconstructed datasets (Figs.1 and 3; Figs.6 and 8). To that end, each quantified section was given an upper and lower boundary ^^^^
^^^^, ^^^^
^^^^, by representing the striatal outline as two identical polygons separated from each other by the section thickness (20 µm). Then, since the depth-wise location of each cell marker within each individual section is unknown, mapped cells within each section were represented as uniform point probability functions with constant probability across the section. I.e., each cell marker in a section from ^^^^
^^^^ to ^^^^
^^^^ has a probability function:
The spatial distribution of each cell population was then measured by counting the number of mapped cells within concentric spherical shells radiating from the WT glia delivery site in radial increments of 125 µm (For control HD or WT chimeras, an average of the coordinates of the adult WT glia delivery site was used). Mapped cells were counted as 1 if their respective representative line segments were fully inside, 0 if fully outside, and partially if intersecting the spherical shell at either the upper or lower boundary of its corresponding section. The density of each cell population ^^^^
^^^^, ^^^^ – where a,b represent the minimum and maximum radii of the spherical shell – was then calculated by dividing the number of mapped cells within the spherical shell by the combined section volume in the shell: ^
^^^ ^^^^, ^^^^ = ^^^^ ^^^^, ^^^ � ^ ^
^^^ ^^^^, ^^^^ where ^^^^
^^^^, ^^^^ is the sum of integrated point probability functions over each section for each point and ^^^^
^^^^, ^^^^ is the combined section volume within the spherical shell. Subsequent analyses were restricted to a 2 mm spherical radius. The code was implemented in Python 3.8 and the package overlap (https://github.com/severinstrobl/overlap) was used to calculate the exact section volume within which the cells were counted. Human cell phenotyping Quantification of each human cell phenotype (except for Ki67 and TUNEL) was performed using the optical fractionator method
67 in 5 equidistant sagittal sections, separated 480µm apart, spanning the entire striatum. First, whole striatum z-
stacked montages were captured using a Nikon Ni-E Eclipse microscope equipped with a DS- Fi3 camera at 20x magnification and stitched together in NIS-Elements imaging software. Each z-stack tile was captured using a 0.9 µm step size. The montages were then loaded onto Stereo Investigator and outlines of the striatum were defined. A set of 200 × 200 µm counting frames was placed by the software in a systematic random fashion within a 400 × 400 µm grid covering the outlined striatum of each section. Counting was performed in the entire section height (without guard zones), and cells were counted based on their immunolabelling in the optical section in which they first came into focus. Representative images showing whole striata were generated from whole brain montages using the ‘crop’ function, and by adjusting the ‘min/max’ levels in NIS-Elements imaging software. Quantification of TUNEL
+ human cells To assess the distribution and proportion of apoptotic cells within each human cell pool, whole striatal montages of 5 equidistantly spaced, 480 μm apart, sagittal sections spanning the entire striatum were captured using a Nikon Ni-E Eclipse microscope equipped with a DS-Fi3 camera, at 10x magnification and stitched in the NIS-Elements imaging software. The striatum was outlined within each section, and immunolabeled human cells identified and mapped based on their TUNEL labelling within the outlined striatum using Stereo Investigator. Representative images showing whole humanized striata were generated from previously acquired whole brain montages using the ‘crop’ function and adjusting the ‘min/max’ levels in NIS-Elements imaging software. Representative images of human glial competitive interfaces were then captured as large field z-stacked montages, using a Nikon Ti- E C2+ confocal microscope equipped with 488nm, 561nm and 640nm laser lines, and a standard PMT detector. Images were captured at 40x or 60x magnification with oil-immersion objectives and stitched in NIS-Elements. Maximum intensity projections were then generated, and the ‘min/max’ levels adjusted in NIS-Elements. Similarly, representative images of human cell phenotype were captured, imaged, and processed as z-stacks using the Nikon Ti-E C2+ confocal and the same laser lines. Fluorescence activated cell sorting (FACS) of human glia from chimeric mice To isolate human cells for scRNA-seq, experimental chimeras were perfused intracardially with HBSS, their striata dissected and tissue dissociated as previously described
68. Briefly, mice were euthanized with euthasol, transcardially perfused with sterile Hank’s Balanced Salt Solution (HBSS) containing magnesium chloride and calcium chloride, and their brains removed. The brains were immersed in ice-cold sterile HBSS for about 5 minutes to
facilitate the microdissection. Under a dissecting microscope, the striata from each mouse was dissected and placed in sterile HBSS on ice. The striatal tissues were transferred to a Petri dish containing sterile HBSS without magnesium chloride and calcium chloride, chopped into small pieces using sterile disposable scalpels, transferred into a sterile tube, and then incubated in a papain/DNase dissociation solution at 37°C for 50 minutes. Ovomucoid dissolved in EBSS was then added to inactivate the papain. The tissue was triturated by repeated pipetting in order to achieve a single cell suspension. The cells were then pelleted, resuspended into MEM, and filtered for flow cytometry. Single cell preparations were isolated based on their expression of mCherry, EGFP, or their absence, using a BD FACSAria Fusion (BD Biosciences). To exclude dead cells, 4′,6-diamidino-2-phenylindole (DAPI; ThermoFisher cat. no. D1306) was added at 1 µg/ml. Single-cell RNA sequencing analysis Primary data acquisition Isolated cells were captured for scRNA-seq on a 10X Genomics chromium controller (v3.1 chemistry). Libraries were generated according to manufacturer’s instructions and sequenced on an Illumina NovaSeq 6000 at the University of Rochester Genomics Center. scRNA-seq libraries were aligned with STARsolo
69, 70 using a custom two-pass strategy. First, an annotated chimeric GRCh38 and GRCm38 reference was generated using Ensembl 102 human and mouse annotations, with the addition of mCherry and EGFP. STARsolo was then run with parameters: twopassMode=basic, limitSjdbInsertNsj=3000000, and soloUMIfiltering= MultiGeneUMI. BAM files were then split by species, and cross-species multimapping reads were assigned to both human or mouse BAMs. FASTQ files were re-generated from either the mouse or human BAM files and re- aligned to a single species reference. STARsolo was run again with the following parameters: twopassMode=basic, limitSjdbInsertNsj=2000000, and soloUMIfiltering= MultiGeneUMI. Differential expression analysis Human data were imported into R
71 using Seurat
72. Cells were filtered (Unique genes >250 and percent mitochondrial genes <15). Cells were then further filtered for expression of mCherry or EGFP. Counts were imported into Python for integration using scvi where the 4,000 most variable features were used
73. The model was trained for integration using the mouse sample and cell line in addition to the number of unique genes and percent mitochondrial gene expression. The latent representation was then used for dimensionality reduction via UMAP and Louvain community detection. Smaller populations of cells were classified into six major types of glia based on marker expression. Data were then re-imported into Seurat, and differential expression was carried out using MAST
74. Genes
were considered for differential expression if their expression was detected in at least 3% of all GPCs. The model design for differential expression utilized the number of unique genes in a cell and the experimental group (cell line/age of the cell, and if the cell was in the presence or absence of an opposing clone). Significance for differential expression was P<0.05, with a log2-fold change of at least 0.15. Ingenuity Pathway Analysis (QIAGEN) was using for functional analysis of each differentially expressed gene list. Cell cycle analysis G2M scores of each experimental group were calculated using Seurat’s CellCycleScoring function. Statistical comparisons between each model’s experimental groups were then calculated using Dunn tests with Benjamini-Hochberg multiple comparison adjustments. Identification of transcription factor-associated regulons Genes were first filtered to retain only those that expressed at least 3 counts in at least 1% of the cells. All 10,410 cells were used in this analysis. The filtered raw matrix was then used as input for the standard pipeline of pySCENIC
75 to identify each transcription factor and its putative downstream targets in the data set. These gene sets are referred to as regulons and are assigned “Area Under the Curve” (AUC) values to represent their activities in each cell, with higher values indicating a stronger enrichment of such regulon. The resulting AUC matrix was then used to look for important transcription factors. Within the GPC subpopulation in both isograft and allograft models, 1 was assigned to cells from the young WT samples, and 0 was assigned to cells from the aged WT or aged HD samples. Lasso logistic regression was then performed on predetermined 0/1 outcome with all TF’s AUCs as predictor using glmnet. Lambda for logistic regression was automatically defined with cv.glmnet. Inventors isolated TFs with positive coefficients, and further filtered based on their mean activity per group, such that TF mean activity in the young WT should be higher than that in the aged counterpart. The final step was to perform gene set enrichment analysis (GSEA)
76 on regulons identified thus far, to determine if they were enriched for differentially upregulated genes in young WT cells compared to aged HD and WT cells (adjusted p <x10
-3, NES > 0). Identification of co-expressed gene sets with competitive advantage Inventors filtered to exclude genes with fewer than 1 count across all cells, and used the resulting matrix to denoise data with DCA
77. Weighted gene co-expression network analysis (WGCNA)
35 was performed on denoised data of the GPC subset. A signed network adjacency was calculated with soft thresholding power of 19. Modules were detected after hierarchical clustering of genes on topological overlap matrix-based dissimilarity and dynamic tree cut. Inventors then
identified modules whose gene members represented a significant overlap with the important TF targets identified above, using GeneOverlap (adjusted p<10
-2)
78. The relative contribution of the linearly-independent covariates age (young, aged) and genotype (HD, WT) towards the additive explanation for each module eigengene (e.g., ME ~ age + genotype) was calculated by the lmg method, implemented in the relaimpo package
79. Network representation: Functional annotation of transcription factors’ gene targets was performed with IPA
80. To create a representative network, Inventors focused on the MYC regulon and its shared targets with other important TFs. Networks were constructed with Cytoscape
81. Statistical analysis and reproducibility Samples exhibiting artifacts related to technical issues from experimental procedures – such as mistargeted injections, or overt surgical damage – were excluded from this study. Statistical tests were performed using GraphPad Prism 9, and all tests used are indicated in each figure caption. For comparisons between more than two groups, one-way analysis of variance with Tukey’s or Šidák’s tests for multiple comparisons were applied. For comparisons between two groups with more than two factors, two-way analysis of variance with Šidák’s multiple comparison test was applied. When comparing two unmatched groups, unpaired two- tailed t-tests were applied. Significance was defined as P<0.05. Respective P values are stated in the figures whenever possible; otherwise, ****P<0.0001, ***P<0.001, **P<0.01, and *P<0.05. The number of replicates is indicated in the figure legends, with n denoting the number of independent experiments. Data are represented as the mean ± standard error of mean (SEM). Data Availability The sequencing datasets reported in this paper can be accessed at GEO, via accession number GSE206322. Code Availability The program for the quantification of mapped cell populations in 3D-reconstructed tissues is publicly available through the following link: QIM / Tools / Thick Section Point Density GitLab (dtu.dk). All codes used to analyze and generate Figures for the genomics dataset are accessible on Github, at: https://github.com/CTNGoldmanLab/HD_Competition_2022.
Example 2 Generation of distinctly color-tagged human glia from WT and HD hESCs To assess the ability of healthy glia to replace their diseased counterparts in vivo, fluorophore-tagged reporter lines of WT and HD human embryonic stem cells (hESC) were first generated so as to enable the production of spectrally-distinct GPCs of each genotype, whose growth in vivo could then be independently monitored. A CRISPR-Cas9-mediated knock-in strategy
26 was first used to integrate EGFP and mCherry reporter cassettes into the AAVS1 locus of matched, female sibling wild-type (WT, GENEA019) and mHtt-expressing (HD, GENEA020) hESCs
27, 28. It was then verified that the reporter cassettes stably integrated into each of these clones, and that editing did not influence the self-renewal, pluripotency, or karyotypic stability of the tagged hESCs. From these tagged and spectrally-distinct lines, a previously described differentiation protocol
5 was used to produce color-coded human glial progenitor cells (hGPCs) from each line, whose behaviors in vivo could be compared, both alone and in competition. Inventors validated the ability of each line to maintain EGFP or mCherry expression after maturation as astrocytes or oligodendrocytes, and their lack of any significant differentially-expressed oncogenic mutations, or copy number variants (CNVs) that could bias growth; it was also verified that both the WT and mHTT-expressing hGPCs, when injected alone, colonized the murine host brains (Figs.6A-6B and Figs.7a-7B). Both WT-mCherry and HD-EGFP hESCs were then differentiated using a protocol for generating hGPCs
21 and assays were carried out to assess both their capacity to differentiate into glia and the stability of their reporter expression upon acquisition of glial fate. By 150 days in vitro (DIV), glial cultures derived from both WT-mCherry and HD-EGFP were equally enriched for PDGFRα
+/CD44
+ bipotential GPCs
29 (P=0.78), comprising around half of the cells in the cultures, with the rest being immature A2B5
+ GPCs
30 and PDGFRα-/CD44
+ astrocytes and their progenitors
31. Importantly, virtually all immuno-phenotyped cells derived from WT-mCherry and HD-EGFP hESCs – including mature astrocytes as well as hGPCs – continued to express their respective fluorescent reporter, indicating that transgene expression remained stable upon acquisition of terminal glial identity, both in vitro and after subsequent transplantation in vivo. Example 3 Establishment of human HD glial chimeric mice Using these spectrally-distinct WT and HD hGPCs, it was examined if resident, mHTT- expressing HD glia were less fit, and hence potentially replaceable, by their healthy counterparts. To this end, mice whose striata were substantially chimerized by tagged mHTT- expressing glia were generated by neonatally injecting hGPCs derived from EGFP-tagged HD hESCs into the neostriata of immunodeficient Rag1
(-/-) mice (Figs. 6A). Following
implantation, the HD glia rapidly infiltrated the striata of these mice, migrating and expanding first within the striatal white matter tracts, and then progressively displacing their murine counterparts from the striatal neuropil (Figs.6B). As a result, by 36 weeks the murine striatum was substantially humanized by HD glia ( Figs.6B, 6F, and 6G). The colonization of the host striatum by human HD GPCs was driven by the mitotic expansion of the HD hGPCs, the total number of which typically more than doubled between 12 and 36 weeks ( Figs.6C; P=0.0032). In contrast, as these cells achieved their terminal densities in their hosts, their proliferative cell pool (Ki67
+) progressively declined ( Figs.6D; P=0.0036), resulting in their slowed expansion rate over time. Most HD glia expanded as Olig2
+ GPCs (72.7 ± 1.9%), which persisted as the new resident pool after replacing their murine counterparts. A fraction of these (4.8 ± 0.9%) further differentiated into GFAP
+ astrocytes ( Figs. 6I-6J). Astrocytic differentiation was mostly observed within striatal white matter tracts. These sick astrocytes lacked the structural complexity typically observed in healthy counterparts and displayed abnormal fiber architecture as previously reported
8 (Figs.6J). Example 4 Healthy WT hGPCs infiltrate the HD chimeric adult striatum and outcompete resident glia With established chimeras whose striatal glia were largely mHTT-expressing and human, assays were carried out to examine how these resident HD human glia might respond to the introduction of healthy hGPCs. To that end, hGPCs derived from WT hESCs engineered to express mCherry were engrafted into the striata of 36 week-old HD chimeras, and monitored their expansion histologically as they competed with the already-resident HD glia (Fig.1A and Figs.7A-B). Following engraftment, the WT glia pervaded the previously humanized striatum, gradually displacing their HD counterparts as they expanded from their implantation site (Fig. 1B). This process was slow but sustained, over time yielding substantial repopulation of the HD striatum with WT glia (Fig. 1B, G and H
1; 54 weeks: P<0.0001; 72 weeks, P<0.0001). Remarkably, the expansion of WT glia was paralleled by a concurrent elimination of HD glia from the tissue (Fig. 1B, G and H2; 54 weeks: P<0.0001, 72 weeks: P<0.0001). This was typically characterized by a discrete advancing front, behind which few HD glia could be found (Fig.1C). As a result, mutually exclusive domains were formed in the wake of this competition between HD and WT GPCs (Fig.1D). Of note, within regions dominated by WT glia, GFAP- defined HD astrocytes were found to often linger, primarily within white matter tracts (Fig. 1E). Astrocytic replacement progressed more slowly than did that of hGPCs, so that when
assessed at 72 weeks, most WT donor cells still expressed Olig2
+ (80.1 ± 4.7%), while only a fraction (4.0 ± 1.5%) had differentiated as GFAP
+ astrocytes (Figs.7A-H). As such, astrocytic replacement appeared to depend upon astrocytic turnover with replacement from the locally dominant parenchymal hGPCs, rather than from competition among mature astrocytes; dynamic competition within the time frame studied appeared to be primarily a feature of hGPCs. Of note, the allogeneic replacement of hGPCs by other hGPCs proceeded at a slower rate than the xenogeneic replacement of mouse by hGPCs, as WT hGPCs implanted into naïve adult Rag1
(-/-) mice expanded throughout the host striatum more rapidly and broadly than did WT hGPCs transplanted into adult HD chimeras (Figs.8A-D; 54 weeks: P=0.006; 72 weeks: P=0.0009). These results indicate that competitive glial replacement develops with kinetics that differ between xenogeneic and allogeneic grafts, with greater – but readily surmountable - competitive resistance posed by same-species cells. In parallel control studies, it was established that these diverse observations were not an artifact of off-target effects of either gene editing or fluorescent reporter toxicity. Co- engrafted hGPCs derived from WT-mCherry and their unmodified counterparts (WT- untagged) expanded equally within the striata of both naïve adult Rag1
(-/-) and HD chimeric mice; the tagged and untagged WT cells, otherwise isogenic, admixed freely and yielded analogous glial repopulation in each (Figs.9A-D, F; 54 weeks: P=0.50; 72 weeks: P=0.15). Example 5 Human WT glia enjoy a proliferative advantage relative to resident HD glia Since striatal humanization by HD glia decelerated with time as the fraction of proliferative HD hGPCs fell (Fig. 6D), assays were carried out to examine if the selective expansion of younger WT glia within the HD striatum was sustained by a difference in proliferative capacity between the two populations. To do so, the expression of Ki67 in both WT and HD glial populations was assessed as competitive striatal repopulation unfolded. At both 54 and 72 weeks of age, the mitotic fraction of implanted WT human glia was significantly larger than that of resident HD-derived human glia (Figs.1I, J; 54 weeks: P<0.0001; 72 weeks: P=0.009). These data suggest that the repopulation of the HD glial chimeric host striatum by WT glia was mediated in part via the selective expansion of a differentially proliferative donor pool. Of note, while the proliferative advantage of the adult-engrafted WT glia over the already-resident HD glia became less pronounced as the mice – and hence the cells - aged, it was maintained through at least 72 weeks of age, suggesting the persistence of WT glial competitive dominance beyond the observed experimental timepoints. Interestingly, it was found that throughout that 72-week period of observation, the leading edge of the neonatally-
implanted human HD glia continued to slowly expand well beyond the striatum into the basal forebrain, even as the leading edge of the adult-transplanted WT hGPCs replaced that striatal population, effectively from behind (Fig.10). Example 6 Human WT glia assume a dominant competitor profile when encountering HD glia As implanted WT hGPCs effectively colonize the HD glial chimeric striata at the expense of the resident mHTT-expressing glia, assays were carried out to define the molecular signals underlying their competitive dominance. To that end, inventors analyzed the transcriptional profiles of WT and HD human glia isolated from the striata of chimeras in which the two cell populations were co-resident and competing, as well as from their respective controls in which one or the other was transplanted without the other, using single cell RNA- sequencing (scRNA-seq; 10X Genomics, v3.1 chemistry) (Fig.2A). Following integration of all captures and aligning against human and mouse mixed species genome, Leiden community detection revealed six major populations of human glia; these included hGPCs, cycling hGPCs, immature oligodendrocytes (iOL), neural progenitor cells (NPCs), astrocytes, and their intermediate progenitors (astrocyte progenitor cells, APCs) (Figs. 2B-D). Within these populations, cell cycle analysis predicted higher G2/M scores in competing WT hGPCs compared to their HD counterparts (Fig.2E), aligning with histological observations (Fig.1J). To proceed, inventors focused on hGPCs as the primary competing population in the model. Pairwise differential expression revealed discrete sets of differentially expressed genes across groups (Fig. 2F), and subsequent functional analysis with Ingenuity pathway analysis (IPA) within the hGPC population revealed numerous salient terms pertaining to their competition (Fig.2G). It was found that during competition, WT GPCs activate pathways driving protein synthesis, whereas HD GPCs were predicted to downregulate them. Predicted upstream transcription factor activation identified YAP1, MYC, and MYCN – conserved master regulators of cell growth and proliferation
32-34 – as significantly modulated across experimental groups. Importantly, it was found YAP1 and MYC targets to be selectively down-regulated in competing HD GPCs relatively to their controls (Fig.2G). Notably, this down-regulation was attended by a marked repression of ribosomal encoding genes (Fig.2I). Conversely, competing WT hGPCs showed an upregulation of both YAP1 and MYC targets, as well as in the expression of ribosomal encoding genes, relative to controls (Figs.2G-H). As such, these data suggest that the implanted WT hGPCs actively assumed a competitively dominant phenotype
upon contact with their HD counterparts, to drive the latter’s local elimination while promoting their own expansion and colonization. Example 7 Age differences drive competitive human glial repopulation Since WT cells transplanted into adult hosts were fundamentally younger than the resident host cells that they displaced and replaced, assays were carried out to examine if differences in cell age, besides disease status, might have contributed to the competitive success of the late donor cells. To that end, hGPCs newly produced from WT hESCs engineered to express EGFP were engrafted into the striata of 40 week-old adult glial chimeras, which had been perinatally engrafted with hGPCs derived from mCherry-tagged, otherwise isogenic WT hESCs (Fig. 3A). Then the expansion of the transplanted cells histologically was monitored, so as to map the relative fitness and competitive performance of these isogenic, but otherwise distinctly aged pools of hGPCs. It was noted that the expansion of implanted WT glia within the striatum of WT chimeras was strikingly similar to their expansion in the striata of HD chimeras (Fig. 1). Following engraftment, the younger WT glia rapidly infiltrated the previously humanized striatum, progressively displacing their aged counterparts as they expanded from their implantation site, ultimately yielding substantial recolonization of the tissue (Figs.3B-D and E; P<0.0001). Their expansion was paralleled by the local elimination of aged WT glia (Figs. 3B-D and F; P<0.0001), which was also marked by a discrete advancing front, behind which few already-resident WT glia could be found (Fig.3C). Accordingly, it was also noted that the mitotic fraction of implanted WT glia was significantly larger than that of their resident aged counterparts (Figs.3G-I; P=0.018). Together, these data indicated that the repopulation of the human WT glial chimeric striatum by younger isogenic hGPCs was attended by the replacement of the older cells by their younger counterparts, fueled in part by the relative expansion of the younger, more mitotically active cell population. Example 8 Young cells replace their older counterparts via the induction of apoptosis Since younger glia appeared to exert clear competitive dominance over their older counterparts, assays were carried out to examine whether the elimination of the older glia by younger cells occurred passively, as a result of the higher proliferation rate of the younger cells leading to the relative attrition of the older residents during normal turnover, or whether replacement was actively driven by the induction of programmed cell death in the older cells by the more fit younger cells. To address this question, the TUNEL assay was used to compare the rates of apoptosis in aged and young WT glial populations as they competed in the host striatum, as well as at their respective baselines in singly-transplanted controls. It was found
that as competitive repopulation unfolded, that aged WT glia underwent apoptosis at a markedly higher rate than their younger counterparts (Figs.11A-C; P<0.0001). Critically, the increased apoptosis of older, resident glia appeared to be driven by their interaction with younger cells, since a significantly higher proportion of aged glia was found to be apoptotic in chimeras transplanted as adults with younger cells, than in controls that did not receive the later adult injection (Fig.11C; P=0.0013). These data suggest that aged resident glia confronted by their younger counterparts are actively eliminated, at least in part via apoptosis triggered by their encounter with the younger hGPCs, whose greater relative fitness permitted their repopulation of the chimeric host striatum. Example 9 Young hGPCs acquire a signature of dominance when challenged with older isogenic cells To ascertain if the molecular signals underlying the competitive dominance of younger WT glia over aged WT glia are similar to those underlying their dominance over HD glia, scRNA-seq was used to analyze the transcriptional signatures of competing young and aged WT glia and their respective controls, using (Fig.4A). Within the sequenced hGPC populations (Figs. 4B-D), it was noted that the G2/M scores in competing aged WT cells were markedly lower than those of their younger counterparts (Fig.4E), in accord with histological data (Figs. 3I). Differential expression analysis revealed discrete sets of genes differentially expressed between competing young and aged WT GPCs (Fig.4F and H), and subsequent IPA analysis of those gene sets revealed a signature similar to that observed between donor (young) WT and already-resident (aged) HD GPCs in the competitive allograft model (Fig. 4G). In particular, genes functionally associated with protein synthesis, including ribosomal genes and E2F family members, as well as upstream MYC and MYCN signaling, were all activated in competing young WT GPCs relative to their aged counterparts (Fig.4G). Yet despite these similarities, in other respects aged WT GPCs responded differently than did HD GPCs to newly implanted WT GPCs. In contrast to HD GPCs, aged WT cells confronted with younger isogenic competitors upregulated both MYC and MYCN targets relative to their non-competing controls (Fig.4G) with a concomitant upregulation of ribosomal genes (Fig.4I). This difference in their profiles may represent an intrinsic capacity to respond competitively when challenged, which mHTT-expressing HD hGPCs lack. Nonetheless, this upregulation was insufficient to match the greater fitness of their younger counterparts, which similarly – but to a relatively greater degree - manifested the selective upregulation of MYC targets, as well as ribosomal genes, relative to their non-competing controls (Figs. 4G-H). Together, these data indicate that the determinants of relative cell fitness may be conserved across different scenarios of challenge,
and that the outcomes of the resultant competition are heavily influenced by the relative ages of the competing populations. Example 10 Competitive advantage is linked to a discrete set of transcription factors Assays were carried out to examine what gene signatures would define the competitive advantage of newly-transplanted human GPCs over resident cells. To that end, a multi-stepped analysis was applied using lasso-regulated logistic regression (Fig.5A), that pinpointed 6 TFs (CEBPZ, CTCF, E2F1, MYC, NFYB, ETV4) whose activities could significantly explain the dominance of young WT GPCs over both aged HD and aged WT GPCs (Fig.5E). These 6 TFs and their putative targets established gene sets (regulons) that were upregulated (normalized enrichment score NES>0, adjusted p<10
-3) in the young WT cells, in either allograft or isograft models (Fig.5C and Table 1). It was also noticed that while their activities varied when not in a competitive environment (aged HD, aged WT, young WT alone), they were higher in the dominant young WT cells in both allograft (vs HD) and isograft (vs older isogenic self) paradigms, especially so for MYC (Fig.5E). Table 1
Next, assays were carried out to identify cohorts of genes with defined expression patterns as well as significant overlaps to the six prioritized regulons above. Weighted gene co- expression network analysis (WGCNA) was first employed
35 to detect a total of 25 modules in a GPC dataset (Fig.5A). Only one module (blue) harbored genes with significant overlap to the targets of the TF cohort. It was also noticed that genes of module blue were driven by competition, as their expression was upregulated in the competing versus non-competing environments (Fig.5B).
Then, assays were carried out to examine if the expression pattern of prioritized modules could be explained by the age of cells (young vs. old), by their genotype (HD vs. WT), or both. WGCNA defines module eigengene as the first principal component of a gene cohort, representing thereby the general expression pattern of all genes within that module. As such, inventors built linear models where module eigengene was a response that was described by both age and genotype. It was observed that module blue was primarily influenced by age (Fig. 5D), in contrast to other modules identified from WGCNA. MYC, whose regulated pathway activation had already been inferred as conferring competitive advantage (Figs. 2 and 4), was also one of the six prioritized TFs. Thus further analysis was carried out to characterize the MYC regulon and its downstream targets, and it was noticed how these downstream targets were also regulated by other prioritized TFs (Fig. 5F). Interestingly, MYC was part of module blue and regulated these blue modular genes, whose expression levels were higher in the competing versus non-competing paradigms (Fig. 5B), a pattern suggesting that the blue signature was not activated unless cells were in a competing environment. Furthermore, inventors noted lower TF activity of MYC in the aged HD relative to the aged WT hGPCs (Figs. 5E), which may highlight the intrinsically greater capacity of WT cells to compete; this was congruent with earlier observation that aged WT hGPCs respond differently than HD hGPCs when challenged with newly-engrafted WT GPCs. Importantly, the blue module eigengene could be described by age, demonstrating that the competitive advantage associated with MYC signaling was driven by mostly the age of the cells. Accordingly, the targets in this network were enriched for pathways regulating cell proliferation (TP53, YAP1, RICTOR), transcription (MYCN, MLXIPL), and protein synthesis (LARP1), each of which had been previously noted as differentially-expressed in each competitive scenario (Figs. 2 and 4). The output of this competition-triggered regulatory network thus appeared to confer competitive advantage upon young WT hGPCs when introduced into the adult brain, whether confronted by older, HD-derived or isogenic hGPCs. References 1. Giorgio, F.P.D., Boulting, G.L., Bobrowicz, S. & Eggan, K.C. Human Embryonic Stem Cell- Derived Motor Neurons Are Sensitive to the Toxic Effect of Glial Cells Carrying an ALS-Causing Mutation. Cell Stem Cell 3, 637--648 (2008). 2. Giorgio, F.P.D., Carrasco, M.A., Siao, M.C., Maniatis, T. & Eggan, K. Non–cell autonomous effect of glia on motor neurons in an embryonic stem cell–based ALS model. Nature Neuroscience 10, 608--614 (2007). 3. Meyer, K. et al. Direct conversion of patient fibroblasts demonstrates non-cell autonomous toxicity of astrocytes to motor neurons in familial and sporadic ALS. Proceedings of the National Academy of Sciences 111, 829--832 (2014).
4. Yamanaka, K. et al. Astrocytes as determinants of disease progression in inherited amyotrophic lateral sclerosis. Nature Neuroscience 11, 251--253 (2008). 5. Benraiss, A. et al. Human glia can both induce and rescue aspects of disease phenotype in Huntington disease. Nature Communications 7, 11758 (2016). 6. Diaz-Castro, B., Gangwani, M.R., Yu, X., Coppola, G. & Khakh, B.S. Astrocyte molecular signatures in Huntington’s disease. Science Translational Medicine 11, 8546 (2019). 7. Faideau, M. et al. In vivo expression of polyglutamine-expanded huntingtin by mouse striatal astrocytes impairs glutamate transport: a correlation with Huntington's disease subjects. Human Molecular Genetics 19, 3053--3067 (2010). 8. Osipovitch, M. et al. Human ESC-Derived Chimeric Mouse Models of Huntington’s Disease Reveal Cell-Intrinsic Defects in Glial Progenitor Cell Differentiation. Cell Stem Cell 24, 107--122.e107 (2019). 9. Shin, J.-Y. et al. Expression of mutant huntingtin in glial cells contributes to neuronal excitotoxicity. The Journal of Cell Biology 171, 1001--1012 (2005). 10. Tong, X. et al. Astrocyte Kir4.1 ion channel deficits contribute to neuronal dysfunction in Huntington's disease model mice. Nature Neuroscience 17, 694--703 (2014). 11. di Domenico, A. et al. Patient-Specific iPSC-Derived Astrocytes Contribute to Non-Cell- Autonomous Neurodegeneration in Parkinson's Disease. Stem cell reports 12, 213-229 (2019). 12. Sonninen, T.M. et al. Metabolic alterations in Parkinson's disease astrocytes. Scientific reports 10, 14474 (2020). 13. Hakak, Y. et al. Genome-wide expression analysis reveals dysregulation of myelination-related genes in chronic schizophrenia. Proceedings of the National Academy of Sciences 98, 4746--4751 (2001). 14. Katsel, P. et al. Astrocyte and Glutamate Markers in the Superficial, Deep, and White Matter Layers of the Anterior Cingulate Gyrus in Schizophrenia. Neuropsychopharmacology 36, 1171--1177 (2011). 15. Tkachev, D. et al. Oligodendrocyte dysfunction in schizophrenia and bipolar disorder. The Lancet 362, 798--805 (2003). 16. Voineskos, A.N. et al. Oligodendrocyte Genes, White Matter Tract Integrity, and Cognition in Schizophrenia. Cerebral Cortex 23, 2044--2057 (2013). 17. Windrem, M.S. et al. Human iPSC glial mouse chimeras reveal glial contributions to schizophrenia. Cell Stem Cell 21, 195--208.e196 (2017). 18. Dietz, A.G., Goldman, S.A. & Nedergaard, M. Glial cells in schizophrenia: a unified hypothesis. The Lancet Psychiatry 7, 272--281 (2020). 19. Koskuvi, M. et al. Contribution of astrocytes to familial risk and clinical manifestation of schizophrenia. Glia 70, 650-660 (2022). 20. Goldman, S.A. in Progress in Brain Research, Vol. 231. (eds. S.B. Dunnett & A. Björklund) 165--189 (Elsevier, 2017). 21. Wang, S. et al. Human iPSC-Derived Oligodendrocyte Progenitor Cells Can Myelinate and Rescue a Mouse Model of Congenital Hypomyelination. Cell Stem Cell 12, 252--264 (2013). 22. Windrem, M.S. et al. A Competitive Advantage by Neonatally Engrafted Human Glial Progenitors Yields Mice Whose Brains Are Chimeric for Human Glia. The Journal of Neuroscience 34, 16153--16161 (2014). 23. Windrem, M.S. et al. Human Glial Progenitor Cells Effectively Remyelinate the Demyelinated Adult Brain. Cell Reports 31, 107658 (2020). 24. Goldman, S.A., Nedergaard, M. & Windrem, M.S. Modeling cognition and disease using human glial chimeric mice. Glia 63, 1483--1493 (2015). 25. Bates, G.P. et al. Huntington disease. Nature Reviews Disease Primers 1, 15005 (2015). 26. Oceguera-Yanez, F. et al. Engineering the AAVS1 locus for consistent and scalable transgene expression in human iPSCs and their differentiated derivatives. Methods 101, 43--55 (2016). 27. Dumevska, B., Peura, T., McKernan, R., Goel, D. & Schmidt, U. Derivation of Huntington disease affected Genea020 human embryonic stem cell line. Stem Cell Research 16, 430--433 (2016). 28. Dumevska, B., Peura, T., McKernan, R., Goel, D. & Schmidt, U. Derivation of human embryonic stem cell line Genea019. Stem Cell Research 16, 397--400 (2016).
29. Sim, F.J. et al. CD140a identifies a population of highly myelinogenic, migration-competent and efficiently engrafting human oligodendrocyte progenitor cells. Nature Biotechnol. 29, 934--941 (2011). 30. Roy, N.S. et al. Identification, Isolation, and Promoter-Defined Separation of Mitotic Oligodendrocyte Progenitor Cells from the Adult Human Subcortical White Matter. Journal of Neuroscience 19, 9986--9995 (1999). 31. Liu, Y. et al. CD44 expression identifies astrocyte-restricted precursor cells. Developmental Biology 276, 31--46 (2004). 32. Harvey, K.F., Zhang, X. & Thomas, D.M. The Hippo pathway and human cancer. Nature Reviews Cancer 13, 246--257 (2013). 33. Pelengaris, S., Khan, M. & Evan, G. c-MYC: more than just a matter of life and death. Nature Reviews Cancer 2, 764--776 (2002). 34. Riggelen, J.v., Yetil, A. & Felsher, D.W. MYC as a regulator of ribosome biogenesis and protein synthesis. Nature Reviews Cancer 10, 301--309 (2010). 35. Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008). 36. Goldman, S.A. Glial evolution as a determinant of human behavior and its disorders. Ann N Y Acad Sci 1471, 72-85 (2020). 37. Verkhratsky, A. & Parpura, V. Astrogliopathology in neurological, neurodevelopmental and psychiatric disorders. Neurobiology of Disease 85, 254--261 (2016). 38. Khakh, B.S. et al. Unravelling and exploiting astrocyte dysfunction in Huntington’s Disease. Trends in Neurosciences 40, 422--437 (2017). 39. Octeau, J.C. et al. An Optical Neuron-Astrocyte Proximity Assay at Synaptic Distance Scales. Neuron 98, 49--66.e49 (2018). 40. Baker, N.E. Emerging mechanisms of cell competition. Nature Reviews Genetics 21, 683--697 (2020). 41. Bowling, S., Lawlor, K. & Rodríguez, T.A. Cell competition: the winners and losers of fitness selection. Development 146, dev167486 (2019). 42. Clavería, C. & Torres, M. Cell Competition: Mechanisms and Physiological Roles. Annual Review of Cell and Developmental Biology 32, 1--29 (2015). 43. Madan, E., Gogna, R. & Moreno, E. Cell competition in development: information from flies and vertebrates. Current Opinion in Cell Biology 55, 150--157 (2018). 44. Clavería, C., Giovinazzo, G., Sierra, R. & Torres, M. Myc-driven endogenous cell competition in the early mammalian embryo. Nature 500, 39--44 (2013). 45. Cova, C.d.l., Abril, M., Bellosta, P., Gallant, P. & Johnston, L.A. Drosophila Myc Regulates Organ Size by Inducing Cell Competition. Cell 117, 107--116 (2004). 46. Morata, G. & Ripoll, P. Minutes: Mutants of Drosophila autonomously affecting cell division rate. Developmental Biology 42, 211--221 (1975). 47. Moreno, E. & Basler, K. dMyc Transforms Cells into Super-Competitors. Cell 117, 117--129 (2004). 48. Simpson, P. & Morata, G. Differential mitotic rates and patterns of growth in compartments in the Drosophila wing. Developmental Biology 85, 299--308 (1981). 49. Díaz-Díaz, C. et al. Pluripotency Surveillance by Myc-Driven Competitive Elimination of Differentiating Cells. Developmental Cell 42, 585--599.e584 (2017). 50. Sancho, M. et al. Competitive Interactions Eliminate Unfit Embryonic Stem Cells at the Onset of Differentiation. Developmental Cell 26, 19--30 (2013). 51. Neto-Silva, R.M., Beco, S.d. & Johnston, L.A. Evidence for a Growth-Stabilizing Regulatory Feedback Mechanism between Myc and Yorkie, the Drosophila Homolog of Yap. Developmental Cell 19, 507--520 (2010). 52. Ziosi, M. et al. dMyc Functions Downstream of Yorkie to Promote the Supercompetitive Behavior of Hippo Pathway Mutant Cells. PLoS Genetics 6, e1001140 (2010). 53. Menthena, A. et al. Activin A, p15INK4b Signaling, and Cell Competition Promote Stem/Progenitor Cell Repopulation of Livers in Aging Rats. Gastroenterology 140, 1009--1020.e1008 (2011).
54. Nishina, H. Physiological and pathological roles of the Hippo-YAP/TAZ signaling pathway in liver formation, homeostasis, and tumorigenesis. Cancer Sci 113, 1900-1908 (2022). 55. Merino, M.M. et al. Elimination of unfit cells maintains tissue health and prolongs lifespan. Cell 160, 461--476 (2015). 56. Rhiner, C. et al. Flower forms an extracellular code that reveals the fitness of a cell to its neighbors in Drosophila. Developmental Cell 18, 985--998 (2010). 57. Matamoro-Vidal, A. & Levayer, R. Multiple influences of mechanical forces on cell competition. Current Biology 29, R762--R774 (2019). 58. Lima, A. et al. Cell competition acts as a purifying selection to eliminate cells with mitochondrial defects during early mouse development. Nature Metabolism, 1--18 (2021). 59. Ellis, S.J. et al. Distinct modes of cell competition shape mammalian tissue morphogenesis. Nature 569, 497--502 (2019). 60. Deisenroth, C. & Zhang, Y. Ribosome biogenesis surveillance: probing the ribosomal protein- Mdm2-p53 pathway. Oncogene 29, 4253-4260 (2010). 61. Baker, N.E., Kiparaki, M. & Khan, C. A potential link between p53, cell competition and ribosomopathy in mammals and in Drosophila. Dev Biol 446, 17-19 (2019). 62. Kale, A. et al. Ribosomal Protein S12e Has a Distinct Function in Cell Competition. Dev Cell 44, 42-55 e44 (2018). 63. Lee, C.-H. et al. A regulatory response to ribosomal protein mutations controls translation, growth, and cell competition. Developmental Cell 46, 456--469.e454 (2018). 64. Kessaris, N. et al. Competing waves of oligodendrocytes in the forebrain and postnatal elimination of an embryonic lineage. Nature Neuroscience 9, 173--179 (2006). 65. Colom, B. et al. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature 598, 510--514 (2021). 66. Mombaerts, P. et al. RAG-1-deficient mice have no mature B and T lymphocytes. Cell 68, 869- -877 (1992). 67. West, M.J. Stereological methods for estimating the total number of neurons and synapses: issues of precision and bias. Trends in Neurosciences 22, 51--61 (1999). 68. Mariani, J.N., Zou, L. & Goldman, S.A. in Oligodendrocytes. Methods in Molecular Biology, Vol.1936. (eds. D. Lyons & L. Kegel) 311--331 (Humana Press, New York, NY; 2019). 69. Kaminow, B., Yunusov, D. & Dobin, A. STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. bioRxiv, 2021.2005.2005.442755 (2021). 70. Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15-21 (2013). 71. R Core Team R: A language and environment for statistical computing. (2013). 72. Butler, A., Hoffman, P., Smibert, P., Papalexi, E. & Satija, R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nature Biotechnology 36, 411--420 (2018). 73. Lopez, R., Regier, J., Cole, M.B., Jordan, M.I. & Yosef, N. Deep generative modeling for single-cell transcriptomics. Nature Methods 15, 1053--1058 (2018). 74. Finak, G. et al. MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. Genome Biology 16, 278 (2015). 75. Aibar, S. et al. SCENIC: single-cell regulatory network inference and clustering. Nature Methods 14, 1083--1086 (2017). 76. Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences 102, 15545--15550 (2005). 77. Eraslan, G., Simon, L.M., Mircea, M., Mueller, N.S. & Theis, F.J. Single-cell RNA-seq denoising using a deep count autoencoder. Nat Commun 10, 390 (2019). 78. Shen, L. GeneOverlap: An R package to test and visualize gene overlaps. (2016). 79. Grömping, U. Relative Importance for Linear Regression in R : The Package relaimpo. Journal of Statistical Software 17 (2006). 80. Krämer, A., Green, J., Pollard, J. & Tugendreich, S. Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 30, 523--530 (2014).
81. Shannon, P. et al. Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Genome Research 13, 2498--2504 (2003). The foregoing examples and description of the preferred embodiments should be taken as illustrating, rather than as limiting the present disclosure as defined by the claims. As will be readily appreciated, numerous variations and combinations of the features set forth above can be utilized without departing from the present disclosure as set forth in the claims. Such variations are not regarded as a departure from the scope of the disclosure, and all such variations are intended to be included within the scope of the following claims. All references cited herein are incorporated by reference in their entireties.