Compositions and methods for xi chromosome reactivation

Abstract

In some aspects, the disclosure relates to the reactivation of inactive X chromosomes (Xi). In some embodiments, the disclosure provides compositions and methods for the reactivation of inactive X chromosomes. In some embodiments, the compositions and methods described by the disclosure may be useful for the treatment of dominant X-linked diseases.

1 . A method of inducing expression of an X-linked gene in a cell having an inactive X chromosome, the method comprising
 delivering to the cell an X chromosome inactivation factor (XCIF) inhibitor in an amount effective for inducing expression of the X-linked gene,   optionally wherein the cell is of a subject having a dominant X-linked disease.   
     
     
         2 . (canceled) 
     
     
         3 . The method of  claim 1 , wherein the X-linked gene is MECP2. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , wherein the dominant X-linked disease is selected from the group consisting of Rett Syndrome, X-linked hypophosphatemia, incontinentia pigmenti type 2, Aicardi syndrome, CDK5L syndrome, focal dermal hypoplasia, CHILD syndrome, Lujan-Fryns syndrome, orofaciodigital syndrome 1, hereditary nephritis (Alport syndrome), Giuffre-Tsukahara syndrome, Goltz syndrome, Fragile X syndrome, Bazex-Dupre-Christol syndrome, Charcot-Marie-Tooth disease, chondrodysplasia punctate, erythropoietic protoporphyria, scapuloperoneal myopathy, and craniofrontonasal dysplasia. 
     
     
         6 . The method of  claim 1 , wherein the XCIF inhibitor selectively inhibits activity of an X chromosome inactivation factor selected from the group consisting of: ACVR1, AURKA, DNMT1, FBXO8, LAYN, NF1, PI3K, PDPK1, PYGO1, RNF165, SGK1/2, SOX5, STC1, ZNF426 and C17orf98. 
     
     
         7 . The method of  claim 6 , wherein:
 (i) the X chromosome inactivation factor is PI3K and the XCIF inhibitor is GNE-317 or LY29400, or   (ii) the X chromosome inactivation factor is PDPK1 and the XCIF inhibitor is OSU-03012 or BX912; or,   (iii) the X chromosome inactivation factor is AURKA and the XCIF inhibitor is VX680, CD532, or MLN8237; or,   (iv) the X chromosome inactivation factor is SGK1/2 and the XCIF inhibitor is GSK650394; or,   (v) the X chromosome inactivation factor is ACVR1 and the XCIF inhibitor is K02288, dorsomorphin, or LDN193189.   
     
     
         8 - 11 . (canceled) 
     
     
         12 . The method of  claim 1 , wherein the XCIF inhibitor selectively inhibits activity of mTOR, optionally wherein the inhibitor is rapamycin, KU-0063794, or everolimus. 
     
     
         13 . (canceled) 
     
     
         14 . The method of  claim 1 , wherein the XCIF inhibitor is an inhibitory oligonucleotide having a region of complementarity that is complementary with at least 8 nucleotides of an mRNA encoded by an XCIF gene, optionally wherein:
 (i) the inhibitory oligonucleotide is selected from the group consisting of: antisense oligonucleotide, siRNA, shRNA and miRNA; or,   (ii) the inhibitory oligonucleotide comprises one or more modified nucleotides, wherein the one or more of the modified nucleotides is an LNA nucleotide; or,   (iii) inhibitory oligonucleotide comprises one or more modified internucleoside linkages.   
     
     
         15 - 18 . (canceled) 
     
     
         19 . The method of  claim 1  further comprising determining that the cell has a mutant allele of the X-linked gene. 
     
     
         20 . The method of  claim 1  further comprising determining that delivery of the XCIF inhibitor to the cell results in
 (i) induced expression of the X-linked gene, or a wild-type allele of the X-linked gene; or, 
 (ii) determining that an X-chromosome is reactivated; or 
 (iii) determining that there is decreased expression or activity of XIST. 
 
     
     
         21 - 23 . (canceled) 
     
     
         24 . The method of  claim 1 , wherein in the cell is in vitro or in a subject. 
     
     
         25 . (canceled) 
     
     
         26 . A method of treating a subject having a dominant X-linked disease, the method comprising:
 administering to the subject an X chromosome inactivation factor (XCIF) inhibitor in an amount effective for inducing expression a target X-linked gene.   
     
     
         27 . The method of  claim 26 , wherein the dominant X-linked disease results from a mutated allele of the X-linked gene, and wherein the inhibitor is administered in an amount effective for inducing expression of a wild-type allele of the X-linked gene. 
     
     
         28 . The method of  claim 26 , wherein the X-linked gene is MECP2. 
     
     
         29 . (canceled) 
     
     
         30 . The method of  claim 28 , wherein the dominant X-linked disease is selected from the group consisting of: Rett Syndrome, X-linked hypophosphatemia, incontinentia pigmenti type 2, Aicardi syndrome, CDK5L syndrome, focal dermal hypoplasia, CHILD syndrome, Lujan-Fryns syndrome, orofaciodigital syndrome 1, hereditary nephritis (Alport syndrome), Giuffre-Tsukahara syndrome, Goltz syndrome, Fragile X syndrome, Bazex-Dupre-Christol syndrome, Charcot-Marie-Tooth disease, chondrodysplasia punctate, erythropoietic protoporphyria, scapuloperoneal myopathy, and craniofrontonasal dysplasia. 
     
     
         31 . The method of  claim 26 , wherein the XCIF inhibitor selectively inhibits activity of an X chromosome inactivation factor selected from the group consisting of: ACVR1, AURKA, DNMT1, FBXO8, LAYN, NF1, PI3K, PDPK1, PYGO1, RNF165, SGK1/2, SOX5, STC1, ZNF426 and C17orf98. 
     
     
         32 . The method of  claim 31 , wherein:
 (i) the X chromosome inactivation factor is PI3K and the XCIF inhibitor is GNE-317 or LY29400, or   (ii) the X chromosome inactivation factor is PDPK1 and the XCIF inhibitor is OSU-03012 or BX912; or,   (iii) the X chromosome inactivation factor is AURKA and the XCIF inhibitor is VX680, CD532, or MLN8237; or,   (iv) the X chromosome inactivation factor is SGK1/2 and the XCIF inhibitor is GSK650394; or   (v) the X chromosome inactivation factor is ACVR1 and the XCIF inhibitor is K02288, dorsomorphin, or LDN193189.   
     
     
         33 - 36 . (canceled) 
     
     
         37 . The method of  claim 26 , wherein the XCIF inhibitor selectively inhibits activity of mTOR, optionally wherein the inhibitor is rapamycin, KU-0063794, or everolimus. 
     
     
         38 . (canceled) 
     
     
         39 . The method of  claim 26 , wherein the XCIF inhibitor is an inhibitory oligonucleotide having a region of complementarity that is complementary with at least 8 nucleotides of an mRNA encoded by an XCIF gene, optionally wherein
 (i) the inhibitory oligonucleotide is selected from the group consisting of: antisense oligonucleotide, siRNA, shRNA and miRNA; or,   (ii) the inhibitory oligonucleotide comprises one or more modified nucleotides, wherein the one or more modified nucleotides is an LNA nucleotide; or,   (iii) inhibitory oligonucleotide comprises one or more modified internucleoside linkages.   
     
     
         40 - 43 . (canceled) 
     
     
         44 . The method of  claim 26  further comprising determining that the subject has a mutant allele of the X-linked gene. 
     
     
         45 . The method of  claim 26  further comprising determining that delivery of the XCIF inhibitor to the cell results in
 (i) induced expression of the X-linked gene, or a wild-type allele of the X-linked gene; or, 
 (ii) determining that an X-chromosome is reactivated; or, 
 (iii) determining that there is decreased expression or activity of XIST. 
 
     
     
         46 - 48 . (canceled)