Context-dependent remodeling of aging-related and neurodevelopmental pathways in human cerebral organoids across APOE genotypes
Year: 2026
Type: conference-paper
Abstract: Apolipoprotein E (APOE) genotype is a major determinant of late-onset Alzheimer’s disease risk and a modulator of neural aging, yet the effects of APOE isoforms on developmental trajectories in human neural tissue remain incompletely understood. Here, we combined single-cell RNA sequencing with quantitative proteomics in induced pluripotent stem cell-derived isogenic human cerebral organoids carrying APOE ε2/ε2, ε3/ε3, or ε4/ε4 alleles to characterize genotype- and stress-dependent remodeling across cellular, transcriptional, and secretory axes. We profiled ~46,000 cells across control and irradiation-induced senescence conditions using single-cell RNAseq. Raw counts were denoised with CellBender to remove ambient-RNA contamination, and scVI was applied to learn a latent embedding while adjusting for stress-related and technical covariates before clustering and pseudotime trajectory analysis. Cells were annotated using snapseed with marker panels adapted from the Human Neural Organoid Cell Atlas (HNOCA), and cell-type composition differences were tested with scCODA. Cell-type composition differed significantly across APOE genotypes at baseline, with APOE4 organoids showing a higher relative abundance of glial and excitatory neuronal populations. After adjusting for these compositional differences, residual genotype-dependent differences in differentiation trajectories persisted, indicating that APOE4 affects both the cell types and their progression through development. Following irradiation, organoids exhibited genotype-dependent transcriptional responses and changes in inferred regulatory activity beyond the baseline compositional differences. In parallel, data-independent acquisition mass spectrometry quantified >6,500 proteins across organoid lysates and secretomes under basal and senescence conditions. Single-sample gene-set enrichment analysis (ssGSEA) showed APOE isoforms differentially regulated aging-associated pathways, with APOE4 exhibiting increased senescence signatures and an inflammatory senescence-associated secretory phenotype (SASP), while APOE2 showed reduced senescence and a SASP enriched in antioxidant enzymes and chaperones. Together, these results suggest that APOE4-associated risk biology already emerges in developmental tissue composition and stress-response programs prior to aging-related insults.
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7204015032