Prominin-1 Regulates Retinal Pigment Epithelium Homeostasis: Transcriptomic Insights into Degenerative Mechanisms

Inherited retinal degenerations (IRDs), driven by pathogenic mutations, often involve primary dysfunction of the retinal pigment epithelium (RPE)-a pathogenic feature shared with atrophic age-related macular degeneration (aAMD), despite aAMD's multifactorial etiology. <i>Prominin-1</i> (<i>Prom1</i>), traditionally linked to photoreceptor pathology, has an unclear role in RPE homeostasis. We assessed Prom1 expression in C57BL/6J mouse retina sections and RPE flat mounts using immunohistochemistry and generated <i>Prom1</i>-knockout (KO) mouse RPE cells via CRISPR/Cas9. Bulk RNA sequencing with DESeq2 and gene set enrichment analysis (GSEA) revealed <i>Prom1</i>-regulated pathways. <i>Prom1</i>-KO cells exhibited upregulation of <i>Grem1</i>, <i>Slc7a11</i>, <i>Serpine2</i>, <i>Il1r1</i>, and <i>IL33</i> and downregulation of <i>Ablim1</i>, <i>Cldn2</i>, <i>IGFBP-2</i>, <i>BMP3</i>, and <i>OGN</i>. Hallmark pathway interrogation identified reduced expression of <i>PINK1</i> (mitophagy) and <i>MerTK</i> (phagocytosis), implicating defects in mitochondrial quality control and outer segment clearance. Enrichment analysis revealed activation of E2F/MYC targets, mTORC1 signaling, oxidative phosphorylation, and TNFα/NF-κB signaling, alongside suppression of apical junctions, bile acid metabolism, and Epithelial-Mesenchymal Transition (EMT) pathways. These findings suggest <i>Prom1</i> safeguards RPE integrity by modulating stress responses, mitochondrial turnover, phagocytosis, metabolism, and junctional stability. Our study uncovers <i>Prom1</i>-dependent signaling networks, providing mechanistic insights into RPE degeneration relevant to both IRD and aAMD, and highlights potential therapeutic targets for preserving retinal health.