Human iPSC-RPE with the PSEN1H163R pathogenic variant recapitulates Alzheimer’s disease features and reveals melanosome defects

Background Alzheimer’s disease (AD) is characterised by progressive cognitive decline and accumulation of pathological markers such as β-amyloid (Aβ) plaques and Tau tangles. Emerging evidence suggests these markers can also be detected in the retina, positioning it as a potential surrogate for investigating AD pathophysiology. The retinal pigment epithelium (RPE) shares features with the brain and is critical for retinal health, yet its role in AD pathology remains underexplored. Methods We generated RPE cells from human induced pluripotent stem cells carrying the PSEN1 ^H163R pathogenic variant for AD, alongside its CRISPR-corrected isogenic control. AD-associated phenotypes were assessed. Results RPE cell cultures from the two cohorts displayed expression of Aβ and Tau, with notable differences in levels and organisation. Total Aβ ₁₋₄₂ and Aβ _{1−42:1−40} ratio in PSEN1 ^H163R RPE cell lysates were significantly elevated compared to the CRISPR isogenic controls and volume of Aβ ⁺ deposits was significantly larger in PSEN1 ^H163R RPE cells. Total and phosphorylated Tau proteins were also detected in both cohorts, with altered spatial organisation and localisation of pTau in PSEN1 ^H163R . Proteomic profiling identified more than 1,800 significantly dysregulated proteins in PSEN1 ^H163R RPE cells, including key AD-related proteins such as MAPT, APP, APBB1 and NRBF2. Upregulated pathways involved autophagy, intracellular trafficking and neurodegeneration, while downregulated pathways implicated mitochondrial respiration, RNA metabolism, and protein folding. Proteomics analysis of conditioned media further revealed altered secretion of matrix-associated proteins as well as increased APOE and APP in PSEN1 ^H163R RPE samples. PSEN1 ^H163R RPE cells demonstrated dysregulation in melanosome biogenesis, marked by decreased expression of core melanogenic proteins (PMEL, TYR, DCT) by proteomics analysis; and altered melanosome morphology and pigmentation by electron microscopy. Conclusion In conclusion, these findings support the RPE as a relevant and accessible in vitro model for AD research, offering insights into the role of PSEN1 in Aβ and Tau dysregulation, disease mechanisms and melanosome biogenesis, providing a promising approach to understand PSEN1 biology in the context of disease and potential biomarker discovery. It is also the first to describe a relationship between PSEN1 ^H163R and melanosomes in a human cellular model.