A Large Panel of Isogenic APP and PSEN1 Mutant Human iPSC Neurons Reveals Shared Endosomal Abnormalities Mediated by APP β-CTFs, Not Aβ

Familial Alzheimer’s disease (fAD) results from mutations in the amyloid precursor protein (APP) and presenilin (PSEN1 and PSEN2) genes. Here we leveraged recent advances in induced pluripotent stem cell (iPSC) and CRISPR/Cas9 genome editing technologies to generate a panel of isogenic knockin human iPSC lines carrying APP and/or PSEN1 mutations. Global transcriptomic and translatomic profiling revealed that fAD mutations have overlapping effects on the expression of AD-related and endocytosis-associated genes. Mutant neurons also increased Rab5+ early endosome size. APP and PSEN1 mutations had discordant effects on Aβ production but similar effects on APP β C-terminal fragments (β-CTFs), which accumulate in all mutant neurons. Importantly, endosomal dysfunction correlated with accumulation of β-CTFs, not Aβ, and could be rescued by pharmacological modulation of β-secretase (BACE). These data display the utility of our mutant iPSCs in studying AD-related phenotypes in a non-overexpression human-based system and support mounting evidence that β-CTF may be critical in AD pathogenesis. •Large panel of isogenic APP and PSEN1 mutant iPSCs generated by CRISPR/Cas9 knockin•Transcriptomic and translatomic analyses identify changes in AD and endosomal genes•Rab5 early endosome enlargement is common in APP and PSEN1 mutant neurons•β-CTF mediates endosomal dysfunction, not Aβ Kwart and Gregg et al. generated a comprehensive panel of isogenic autosomal dominant familial Alzheimer’s disease (fAD) mutant human iPSCs. Differentiated neurons demonstrated common alterations in early endosomes mediated by accumulation of β-CTF, not Aβ.