Cell type specific analysis of ALS associated proteins reveals immune-regulated targets

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder characterized by the degeneration of upper and lower motor neurons. While four core familial ALS genes (SOD1, C9orf72, FUS, and TARDBP) have been extensively studied, more than 30 additional genes have recently been implicated in the disease, many of which remain poorly explored in ALS pathobiology. Using knock-out cells as controls, we characterized antibodies against 33 ALS-associated proteins, including ACSL5, ALS2, ANG, ANXA11, ATXN2, C9orf72, CAV1, CCNF, CHCHD10, CHMP2B, FIG4, FUS, HNRNPA1, HNRNPA2B1, KIF5A, LGALS1, MATR3, NEK1, OPTN, PFN1, SETX, SIGMAR1, SOD1, SPG11, SQSTM1, TAF15, TARDBP, TBK1, TIA1, TUBA4A, UBQLN2, VAPB, VCP, and profiled protein expression for these ALS proteins across human induced pluripotent stem cell (iPSC)-derived and primary neurological cell types (neurons and glia). We uncovered diverse and cell-type-specific expression signatures that were often not concordant with mRNA expression datasets. Notably, 22 proteins were expressed in glial populations, with ten dynamically regulated by inflammatory cues in microglia cells, underscoring immune-responsive pathways as important contributors to ALS pathogenesis.