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Traditional bulk RNA sequencing techniques provide valuable information for deciphering disease pathogenesis but lack the resolution to capture variation among specific cell clusters during disease progression. In contrast, single-cell transcriptomics, including single-cell RNA sequencing (scRNA-seq), enables detailed examination of distinct retinal clusters in both healthy and diseased states, uncovering unique gene expression signatures and early molecular changes preceding photoreceptor cell death in IRDs. These insights not only deepen our understanding of the complex pathogenesis of IRDs but also highlight potential targets for novel therapeutic interventions. In this review, we examine the recent literature on the application of single-cell transcriptomics in IRDs to explore how these techniques enhance our understanding of disease mechanisms and contribute to the identification of new therapeutic targets.<\/jats:p>","DOI":"10.3390\/genes16091088","type":"journal-article","created":{"date-parts":[[2025,9,16]],"date-time":"2025-09-16T10:06:25Z","timestamp":1758017185000},"page":"1088","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Single-Cell Transcriptomics in Inherited Retinal Dystrophies: Current Findings and Emerging Perspectives"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-2165-7132","authenticated-orcid":false,"given":"Linda","family":"Nguyen","sequence":"first","affiliation":[{"name":"MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3638-1960","authenticated-orcid":false,"given":"Catalina A.","family":"Vallejos","sequence":"additional","affiliation":[{"name":"MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5218-134X","authenticated-orcid":false,"given":"Pleasantine","family":"Mill","sequence":"additional","affiliation":[{"name":"MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5605-4540","authenticated-orcid":false,"given":"Roly","family":"Megaw","sequence":"additional","affiliation":[{"name":"MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK"},{"name":"Princess Alexandra Eye Pavilion, NHS Lothian, Chalmers Street, Edinburgh EH3 9HA, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,16]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"a017111","DOI":"10.1101\/cshperspect.a017111","article-title":"Clinical characteristics and current therapies for inherited retinal degenerations","volume":"5","author":"Sahel","year":"2014","journal-title":"Cold Spring Harb. 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