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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>The paired box transcription factor PAX6 is a master regulator of eye development. Pathogenic PAX6 variants predominantly cause aniridia, resulting in a wide range of ocular anomalies affecting both the anterior and posterior segments of the eye. However, a detailed examination of the transcriptomic alterations that occur with these variants during early eye development has not yet been undertaken. To investigate this, human-induced pluripotent stem cells (hiPSC)-derived 3D optic vesicle-like organoids were generated up to day 35 from an aniridia patient with a heterozygous nonsense PAX6R261X variant. Bulk RNA sequencing analysis revealed dysregulation of genes in the cadherin and semaphorin receptor binding pathways in PAX6R261X optic vesicles compared with healthy controls, including upregulation of SEMA3A and CDH1 and downregulation of CDH4. These genes are known to be involved in iris and foveal development but have not previously been found to be dysregulated at the optic vesicle stage, suggesting they have a spatiotemporal impact on eye development. This study reveals a novel link between the cadherins, semaphorins and aniridia and suggests a novel pathway that may contribute to iris and foveal hypoplasia in patients with pathogenic PAX6 variants. Expanding our knowledge of the complex interactions governing early eye development provides novel candidates for the development of potential targeted therapies and can help to guide translational research.<\/jats:p>","DOI":"10.3390\/ijms27198449","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T13:32:12Z","timestamp":1790083932000},"page":"8449","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Early Eye Organoids Demonstrate Cadherin and Semaphorin Disruption in PAX6-Related Aniridia"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8492-2608","authenticated-orcid":false,"given":"Nicola","family":"Cronbach","sequence":"first","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Justynska","sequence":"additional","affiliation":[{"name":"Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C\u00e9cile","family":"M\u00e9j\u00e9case","sequence":"additional","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"},{"name":"The Francis Crick Institute, London NW1 1AT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0763-3516","authenticated-orcid":false,"given":"Philippa","family":"Harding","sequence":"additional","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7565-4071","authenticated-orcid":false,"given":"Jonathan","family":"Eintracht","sequence":"additional","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5629-5026","authenticated-orcid":false,"given":"James","family":"Boot","sequence":"additional","affiliation":[{"name":"The Francis Crick Institute, London NW1 1AT, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elsa","family":"Berg","sequence":"additional","affiliation":[{"name":"Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6525 GA Nijmegen, The Netherlands"},{"name":"Department of Human Genetics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6814-8365","authenticated-orcid":false,"given":"Dulce","family":"Lima Cunha","sequence":"additional","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"},{"name":"Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences (RIMLS), 6525 GA Nijmegen, The Netherlands"},{"name":"Department of Human Genetics, Radboud University Medical Centre, 6525 GA Nijmegen, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1688-5360","authenticated-orcid":false,"given":"Mariya","family":"Moosajee","sequence":"additional","affiliation":[{"name":"Institute of Ophthalmology, University College London, London EC1V 9EL, UK"},{"name":"The Francis Crick Institute, London NW1 1AT, UK"},{"name":"Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1038\/ejhg.2012.100","article-title":"Aniridia","volume":"20","author":"Hingorani","year":"2012","journal-title":"Eur. 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