{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:51:09Z","timestamp":1792061469358,"version":"4.4.0"},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T00:00:00Z","timestamp":1792022400000},"content-version":"vor","delay-in-days":287,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["K99 EY33833"],"award-info":[{"award-number":["K99 EY33833"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["F32 EY031242"],"award-info":[{"award-number":["F32 EY031242"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01 EY025779"],"award-info":[{"award-number":["R01 EY025779"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["P30 EY010572"],"award-info":[{"award-number":["P30 EY010572"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["T32 GM008629"],"award-info":[{"award-number":["T32 GM008629"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["T32 GM139776"],"award-info":[{"award-number":["T32 GM139776"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["F30 EY034009"],"award-info":[{"award-number":["F30 EY034009"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Malcolm M. Marquis, MD Endowed Fund for Innovation"},{"DOI":"10.13039\/100001818","name":"RPB","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100001818","id-type":"DOI","asserted-by":"publisher"}]},{"name":"The Claire Giannini Foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Variants in the transcription factor CRX cause a spectrum of retinal degenerative disorders including Leber congenital amaurosis 7 (LCA7). LCA7-associated variants exert a dominant effect in developing photoreceptor cells, leading to cellular dysfunction and poor to absent visual acuity in patients. Here, we dissect the allelic heterogeneity of LCA7 using multimodal single-cell gene expression and chromatin accessibility analysis of retinal organoids. We generated mature (240\u00a0day) retinal organoids from patient-derived iPSCs carrying missense (K88Q) and nonsense (T155fs) variants, as well as from CRISPR-corrected control lines. We show that these variants, while both causing LCA7, produce unique transcriptional changes in human photoreceptors. Furthermore, the K88Q variant causes aberrant chromatin accessibility at sites typically bound by non-photoreceptor retinal transcription factors, indicating a partial derangement of normal retinal cell fate programming. This work demonstrates the gene regulatory mechanisms of pathogenicity of two disease-causing CRX variants in human retinal cells.<\/jats:p>","DOI":"10.1093\/hmg\/ddag107","type":"journal-article","created":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T11:47:25Z","timestamp":1791546445000},"source":"Crossref","is-referenced-by-count":0,"title":["Gene regulatory behaviors of mutant CRX proteins demonstrated with late-stage human retinal organoids"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4320-2852","authenticated-orcid":false,"given":"Nathaniel K","family":"Mullin","sequence":"first","affiliation":[{"name":"Institute for Vision Research, Carver College of Medicine, University of Iowa , 200 Hawkins Dr, Iowa City, IA , 52242,","place":["United States"]},{"name":"Department of Ophthalmology and Visual Sciences, Carver College of Medicine University of Iowa , 200 Hawkins Dr, Iowa City, IA , 52242,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8107-8317","authenticated-orcid":false,"given":"Andrew P","family":"Voigt","sequence":"additional","affiliation":[{"name":"Institute for Vision Research, Carver College of Medicine, University of Iowa , 200 Hawkins Dr, Iowa City, IA , 52242,","place":["United States"]},{"name":"Department of Ophthalmology and Visual Sciences, Carver College of Medicine University of Iowa , 200 Hawkins Dr, Iowa City, IA , 52242,","place":["United States"]},{"name":"Department of Ophthalmology, Feinberg School of Medicine, Northwestern Medicine , 303 E Chicago Ave, Chicago, IL , 60611,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deepak A","family":"Lamba","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, University of California San Francisco , 505 Parnassus Ave, San Francisco, CA , 94143,","place":["United States"]},{"name":"Immunology and Regenerative Medicine, Genentech (Roche) , 1 DNA Way, South San Francisco, CA , 94080,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kathleen R","family":"Chirco","sequence":"additional","affiliation":[{"name":"Department of Ophthalmology, University of California San Francisco , 505 Parnassus Ave, San Francisco, CA , 94143,","place":["United States"]},{"name":"Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University , 515 SW Campus Dr, Portland, OR , 97239,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,15]]},"reference":[{"key":"2026101506243165200_ref1","doi-asserted-by":"publisher","first-page":"1314","DOI":"10.1016\/j.ophtha.2017.04.008","article-title":"Clinically focused molecular investigation of 1000 consecutive families with inherited retinal disease","volume":"124","author":"Stone","year":"2017","journal-title":"Ophthalmology"},{"key":"2026101506243165200_ref2","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1016\/j.preteyeres.2008.05.003","article-title":"Leber congenital amaurosis: genes, proteins and disease mechanisms","volume":"27","author":"Hollander","year":"2008","journal-title":"Prog Retin Eye Res"},{"key":"2026101506243165200_ref3","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1080\/13816810.2025.2458086","article-title":"Cone rod homeobox (CRX): literature review and new insights","volume":"46","author":"Leigh","year":"2025","journal-title":"Ophthalmic Genet"},{"key":"2026101506243165200_ref4","doi-asserted-by":"publisher","first-page":"1347436","DOI":"10.3389\/fncel.2024.1347436","article-title":"Transcriptional precision in photoreceptor development and diseases - lessons from 25 years of CRX research","volume":"18","author":"Zheng","year":"2024","journal-title":"Front Cell Neurosci"},{"key":"2026101506243165200_ref5","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1016\/j.brainres.2007.06.036","article-title":"Regulation of photoreceptor gene expression by Crx-associated transcription factor network","volume":"1192","author":"Hennig","year":"2008","journal-title":"Brain Res"},{"key":"2026101506243165200_ref6","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1016\/j.devcel.2017.10.029","article-title":"Molecular anatomy of the developing human retina","volume":"43","author":"Hoshino","year":"2017","journal-title":"Dev Cell"},{"key":"2026101506243165200_ref7","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.1038\/s41591-022-01755-w","article-title":"Intravitreal antisense oligonucleotide sepofarsen in Leber congenital amaurosis type 10: a phase 1b\/2 trial","volume":"28","author":"Russell","year":"2022","journal-title":"Nat Med"},{"key":"2026101506243165200_ref8","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1016\/S0140-6736(17)31868-8","article-title":"Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial","volume":"390","author":"Russell","year":"2017","journal-title":"Lancet"},{"key":"2026101506243165200_ref9","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1001\/archophthalmol.2011.298","article-title":"Gene therapy for leber congenital amaurosis caused by RPE65 mutations: safety and efficacy in 15 children and adults followed up to 3 years","volume":"130","author":"Jacobson","year":"2012","journal-title":"Arch Ophthalmol"},{"key":"2026101506243165200_ref10","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22094534","article-title":"An update on gene therapy for inherited retinal dystrophy: experience in Leber congenital amaurosis clinical trials","volume":"22","author":"Chiu","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2026101506243165200_ref11","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1016\/S0092-8674(00)80440-7","article-title":"Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor","volume":"91","author":"Freund","year":"1997","journal-title":"Cell"},{"key":"2026101506243165200_ref12","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1080\/13816810.2017.1373831","article-title":"A novel dominant CRX mutation causes adult-onset macular dystrophy","volume":"39","author":"Griffith","year":"2018","journal-title":"Ophthalmic Genet"},{"key":"2026101506243165200_ref13","doi-asserted-by":"publisher","first-page":"6934","DOI":"10.1167\/iovs.14-14715","article-title":"The phenotypic variability of retinal dystrophies associated with mutations in CRX, with report of a novel macular dystrophy phenotype","volume":"55","author":"Hull","year":"2014","journal-title":"Invest Ophthalmol Vis Sci"},{"key":"2026101506243165200_ref14","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1093\/hmg\/8.2.299","article-title":"Leber congenital amaurosis caused by a homozygous mutation (R90W) in the homeodomain of the retinal transcription factor CRX: direct evidence for the involvement of CRX in the development of photoreceptor function","volume":"8","author":"Swaroop","year":"1999","journal-title":"Hum Mol Genet"},{"key":"2026101506243165200_ref15","doi-asserted-by":"publisher","first-page":"D980","DOI":"10.1093\/nar\/gkt1113","article-title":"ClinVar: public archive of relationships among sequence variation and human phenotype","volume":"42","author":"Landrum","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2026101506243165200_ref16","doi-asserted-by":"publisher","first-page":"e002030","DOI":"10.1136\/bmjophth-2024-002030","article-title":"Systematic review of genotype-phenotype associations in CRX-associated retinal dystrophies","volume":"10","author":"Banjak","year":"2025","journal-title":"BMJ Open Ophthalmol"},{"key":"2026101506243165200_ref17","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13619-021-00097-1","article-title":"Retinal organoids as models for development and diseases","volume":"10","author":"Zhang","year":"2021","journal-title":"Cell Regeneration"},{"key":"2026101506243165200_ref18","doi-asserted-by":"publisher","first-page":"525","DOI":"10.1016\/j.stemcr.2016.03.001","article-title":"Retinal organoids from pluripotent stem cells efficiently recapitulate Retinogenesis","volume":"6","author":"Volkner","year":"2016","journal-title":"Stem Cell Reports"},{"key":"2026101506243165200_ref19","doi-asserted-by":"publisher","first-page":"1496","DOI":"10.1002\/stem.3089","article-title":"Deciphering retinal diseases through the generation of three dimensional stem cell-derived organoids: concise review","volume":"37","author":"Artero Castro","year":"2019","journal-title":"Stem Cells"},{"key":"2026101506243165200_ref20","doi-asserted-by":"publisher","first-page":"100918","DOI":"10.1016\/j.preteyeres.2020.100918","article-title":"Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease","volume":"83","author":"Mullin","year":"2021","journal-title":"Prog Retin Eye Res"},{"key":"2026101506243165200_ref21","doi-asserted-by":"publisher","first-page":"1644","DOI":"10.1016\/j.celrep.2020.01.007","article-title":"Single-cell transcriptomic comparison of human Fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures","volume":"30","author":"Sridhar","year":"2020","journal-title":"Cell Rep"},{"key":"2026101506243165200_ref22","doi-asserted-by":"publisher","DOI":"10.3390\/genes16091088","article-title":"Single-cell transcriptomics in inherited retinal dystrophies: current findings and emerging perspectives","volume":"16","author":"Nguyen","year":"2025","journal-title":"Genes (Basel)"},{"key":"2026101506243165200_ref23","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1016\/j.stemcr.2020.12.018","article-title":"Gene therapy of dominant CRX-Leber congenital amaurosis using patient stem cell-derived retinal organoids","volume":"16","author":"Kruczek","year":"2021","journal-title":"Stem Cell Reports"},{"key":"2026101506243165200_ref24","doi-asserted-by":"publisher","first-page":"2690","DOI":"10.1016\/j.stemcr.2021.09.007","article-title":"Allele-specific gene editing to rescue dominant CRX-associated LCA7 phenotypes in a retinal organoid model","volume":"16","author":"Chirco","year":"2021","journal-title":"Stem Cell Reports"},{"key":"2026101506243165200_ref25","doi-asserted-by":"publisher","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2026101506243165200_ref26","doi-asserted-by":"publisher","first-page":"110294","DOI":"10.1016\/j.celrep.2021.110294","article-title":"Single-cell ATAC-seq of fetal human retina and stem-cell-derived retinal organoids shows changing chromatin landscapes during cell fate acquisition","volume":"38","author":"Finkbeiner","year":"2022","journal-title":"Cell Rep"},{"key":"2026101506243165200_ref27","doi-asserted-by":"publisher","DOI":"10.1172\/JCI173892","article-title":"NR2E3 loss disrupts photoreceptor cell maturation and fate in human organoid models of retinal development","volume":"134","author":"Mullin","year":"2024","journal-title":"J Clin Invest"},{"key":"2026101506243165200_ref28","doi-asserted-by":"publisher","first-page":"2421","DOI":"10.1016\/j.stemcr.2022.09.006","article-title":"Molecular pathology of usher 1B patient-derived retinal organoids at single cell resolution","volume":"17","author":"Leong","year":"2022","journal-title":"Stem Cell Reports"},{"key":"2026101506243165200_ref29","doi-asserted-by":"publisher","first-page":"109856","DOI":"10.1016\/j.exer.2024.109856","article-title":"Modeling autosomal dominant retinitis pigmentosa by using patient-specific retinal organoids with a class-3 RHO mutation","volume":"241","author":"Lin","year":"2024","journal-title":"Exp Eye Res"},{"key":"2026101506243165200_ref30","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1038\/s41597-025-05079-5","article-title":"Longitudinal scRNA-seq of retinal organoids derived from Stargardt disease patient with ABCA4 mutation","volume":"12","author":"Zhao","year":"2025","journal-title":"Sci Data"},{"key":"2026101506243165200_ref31","doi-asserted-by":"publisher","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol"},{"key":"2026101506243165200_ref32","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.87147","article-title":"Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms","volume":"12","author":"Zheng","year":"2023","journal-title":"Elife"},{"key":"2026101506243165200_ref33","doi-asserted-by":"publisher","DOI":"10.1101\/gr.279340.124","article-title":"Aberrant homeodomain-DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models","volume":"35","author":"Zheng","year":"2025","journal-title":"Genome Res"},{"key":"2026101506243165200_ref34","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.48216","article-title":"Cis-regulatory basis of sister cell type divergence in the vertebrate retina","volume":"8","author":"Murphy","year":"2019","journal-title":"Elife"},{"key":"2026101506243165200_ref35","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1038\/nmeth.4401","article-title":"chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data","volume":"14","author":"Schep","year":"2017","journal-title":"Nat Methods"},{"key":"2026101506243165200_ref36","doi-asserted-by":"publisher","DOI":"10.1101\/gr.278133.123","article-title":"Pathogenic variants in CRX have distinct cis -regulatory effects on enhancers and silencers in photoreceptors","volume":"34","author":"Shepherdson"},{"key":"2026101506243165200_ref37","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1101\/gr.231886.117","article-title":"A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo","volume":"28","author":"Hughes","year":"2018","journal-title":"Genome Res"},{"key":"2026101506243165200_ref38","doi-asserted-by":"publisher","first-page":"E1472","DOI":"10.1002\/humu.21268","article-title":"Two novel CRX mutant proteins causing autosomal dominant Leber congenital amaurosis interact differently with NRL","volume":"31","author":"Nichols","year":"2010","journal-title":"Hum Mutat"},{"key":"2026101506243165200_ref39","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.ydbio.2021.09.005","article-title":"Development and diversification of bipolar interneurons in the mammalian retina","volume":"481","author":"West","year":"2022","journal-title":"Dev Biol"},{"key":"2026101506243165200_ref40","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/stcltm\/szad028","article-title":"Propensity of patient-derived iPSCs for retinal differentiation: implications for autologous cell replacement","volume":"12","author":"Cooke","year":"2023","journal-title":"Stem Cells Transl Med"},{"key":"2026101506243165200_ref41","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","journal-title":"Nat Biotechnol"},{"key":"2026101506243165200_ref42","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat Methods"},{"key":"2026101506243165200_ref43","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest Neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst"},{"key":"2026101506243165200_ref44","doi-asserted-by":"publisher","first-page":"1728","DOI":"10.1038\/nprot.2012.101","article-title":"Identifying ChIP-seq enrichment using MACS","volume":"7","author":"Feng","year":"2012","journal-title":"Nat Protoc"},{"key":"2026101506243165200_ref45","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1186\/s12864-018-4772-0","article-title":"Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics","volume":"19","author":"Street","year":"2018","journal-title":"BMC Genomics"}],"container-title":["Human Molecular Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/35\/21\/ddag107\/71962617\/ddag107.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hmg\/article-pdf\/35\/21\/ddag107\/71962617\/ddag107.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T10:24:39Z","timestamp":1792059879000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hmg\/article\/doi\/10.1093\/hmg\/ddag107\/8917270"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":45,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2026,10,13]]}},"URL":"https:\/\/doi.org\/10.1093\/hmg\/ddag107","relation":{},"ISSN":["0964-6906","1460-2083"],"issn-type":[{"value":"0964-6906","type":"print"},{"value":"1460-2083","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"ddag107"}}