Retinal Organoid Single-Cell Transcriptomics Reveals Effects of PRPF31 Mutation on Early Müller Glial Activation and Progressive Photoreceptor Degeneration

Retinitis pigmentosa (RP) encompasses a group of inherited retinal disorders characterized by progressive degeneration of rod and cone photoreceptors, leading to vision loss. Among RP subtypes, RP11 is linked to mutations in PRPF31, a key spliceosome component, resulting in retinal cell dysfunction. Although PRPF31 is ubiquitously expressed, its mutations predominantly impact retinal cells, leading to the progressive loss of photoreceptors. Despite significant progress, studies focused on photoreceptor and retinal pigment epithelium dysfunction in late disease stages, leaving early molecular events and the involvement of other retinal cell types unresolved. Moreover, comprehensive single-cell analyses capturing dynamic transcriptional changes across all retinal populations at early and late differentiation stages are still lacking. Using patient-derived Retinal Organoids (ROs), this study investigates the developmental trajectory of PRPF31-RP11 mutation through a series of morphological, functional, molecular and transcriptomics analysis. Our results show that ROs recapitulate in vitro key features of RP, including photoreceptor loss and functional impairment. Single-cell RNA sequencing revealed early Müller glial expansion, retinal ganglion cell stress, and progressive photoreceptor degeneration. Findings identify dysregulated molecular pathways associated with phototransduction, oxidative stress, and inflammation, providing insights into RP11 pathogenesis and potential therapeutic targets.