Gene regulatory behaviors of mutant CRX proteins demonstrated with late-stage human retinal organoids.

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 day) 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.