{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:28:03Z","timestamp":1785407283207,"version":"3.56.0"},"posted":{"date-parts":[[2026,3,1]]},"group-title":"Genomics","reference-count":67,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T00:00:00Z","timestamp":1772323200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nd\/4.0\/"}],"funder":[{"award":["R01AA023797"],"award-info":[{"award-number":["R01AA023797"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01MH125528"],"award-info":[{"award-number":["R01MH125528"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01MH106575"],"award-info":[{"award-number":["R01MH106575"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01MH116281"],"award-info":[{"award-number":["R01MH116281"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R01AG063175"],"award-info":[{"award-number":["R01AG063175"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"award":["RM1MH133065"],"award-info":[{"award-number":["RM1MH133065"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,3,1]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                <jats:p>\n                  Human induced pluripotent stem cells (hiPSC) and iPSC-differentiated neural cells, in combination with CRISPR editing, are commonly used for studying neurodevelopmental and other brain disorders. Female iPSCs undergo random X-chromosome inactivation (XCI) via epigenetic silencing by noncoding\n                  <jats:italic>X inactive specific transcript<\/jats:italic>\n                  (\n                  <jats:italic>XIST<\/jats:italic>\n                  ). It is known that female iPSCs may lose\n                  <jats:italic>XIST<\/jats:italic>\n                  expression, leading to XCI erosion that affects both X-linked and autosomal gene expression. However, the effects of CRSIPR editing and neural differentiation on XCI erosion in iPSC-derived neurons and how this may confound a real-world transcriptomic analysis of differentially expressed genes (DEGs) are poorly understood. Here, leveraging bulk RNA-seq of hundreds of CRISPR-edited female iPSC lines from four donor lines for 66 genes and single-cell RNA-seq of iPSC-derived neurons of a subset of 42 edited genes, we investigated the effects of XCI erosion during CRISPR editing and in iPSC-derived neurons. We found that XCI erosion was variable in CRISPR-edited female iPSCs and largely preserved in iPSC-derived neurons. Like in iPSCs,\n                  <jats:italic>XIST<\/jats:italic>\n                  in neurons predominately influenced the expression of X-linked genes; however, its effect on autosomal genes was more pronounced in single neurons. Mechanistically,\n                  <jats:italic>XIST<\/jats:italic>\n                  epigenetically causes allelic imbalance of both X-linked and autosomal genes, with the former showing stronger allele-specific expression (ASE) bias. Notably,\n                  <jats:italic>XIST-<\/jats:italic>\n                  induced ASE bias exhibited a conserved positional pattern at loci affecting neurodevelopmental genes across different female lines and cell types. Finally, we demonstrated a confounding effect of XCI erosion on DEG analyses in iPSC-derived neurons. These results have significant implications in hiPSC modeling of neurodevelopmental and other brain disorders.\n                <\/jats:p>","DOI":"10.64898\/2026.02.27.708613","type":"posted-content","created":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T03:10:13Z","timestamp":1772421013000},"source":"Crossref","is-referenced-by-count":1,"title":["Female iPSC X-chromosome inactivation (XCI) erosion and its transcriptomic effects during CRISPR gene editing and neural differentiation"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0822-2911","authenticated-orcid":false,"given":"Christina","family":"Thapa","sequence":"first","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"},{"name":"Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-6317-4473","authenticated-orcid":false,"given":"Emily K.","family":"Oh","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-9985-1052","authenticated-orcid":false,"given":"David","family":"Sirkin","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Lahey","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1457-8204","authenticated-orcid":false,"given":"Sol","family":"D\u00edaz de Le\u00f3n Guerrerro","sequence":"additional","affiliation":[{"name":"Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"},{"name":"Center for NeuroMetabolism, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-3592-4463","authenticated-orcid":false,"given":"Ada","family":"McCarroll","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Prarthana","family":"Gowda","sequence":"additional","affiliation":[{"name":"Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"},{"name":"Center for NeuroMetabolism, Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8490-918X","authenticated-orcid":false,"given":"Hanwen","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2801-290X","authenticated-orcid":false,"given":"Alexandra","family":"Barishman","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7860-0096","authenticated-orcid":false,"given":"Lilia","family":"Peyton","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1646-063X","authenticated-orcid":false,"given":"Siwei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center for Psychiatric Genetics, Endeavor Health, Evanston, IL, USA"},{"name":"Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0428-240X","authenticated-orcid":false,"given":"Rebecca M.","family":"Pollak","sequence":"additional","affiliation":[{"name":"Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA"},{"name":"Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4836-8712","authenticated-orcid":false,"given":"Ronald 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