Spatial Transcriptomic Evidence Consistent with Reactivation of Embryonic Neural Pathways in Amyotrophic Lateral Sclerosis

Background: Neurodegenerative diseases may involve the aberrant reactivation of developmental programs that are normally silenced after embryogenesis. We hypothesized that amyotrophic lateral sclerosis (ALS) is associated with reactivation of an embryonic cytoskeletal program centered on the Arp2/3 actin nucleation complex, actomyosin contractility, intracellular transport, and developmental glial pathways. Methods: We analyzed a publicly available spatial transcriptomic dataset comprising 1,034,910 Visium spots from 64 human donors (25 ALS, 18 ALS with cognitive impairment [ALSci], and 21 neurologically normal controls) across Brodmann areas 44 and 46. Donor-level and library-level analyses evaluated expression of 14 prespecified genes (ACTR2, ACTR3, ARPC1A, ARPC1B, ARPC2, ARPC3, ARPC4, ARPC5, ARPC5L, RAC1, MYH10, KIF5C, SOX9, and MEGF10). Mixed-effects linear models adjusted for brain region, age, sex, and postmortem interval, with donor included as a random effect. False discovery rate (FDR) correction was applied to gene-level analyses. Results: An aggregate Arp2/3 pathway score was significantly higher in ALS than in controls after multivariable adjustment. At the individual gene level, all 14 prespecified genes demonstrated higher expression in ALS than in controls, indicating coordinated activation of the pathway. ARPC5 remained significant after FDR correction (β for control versus ALS = −0.110, 95% CI −0.172 to −0.048; FDR = 0.014). ACTR3, RAC1, ARPC4, MEGF10, KIF5C, SOX9, ARPC1A, and ARPC1B showed nominally significant increases with consistent directionality. Increasing age was independently associated with lower pathway activity, whereas ALS was associated with higher pathway activity, suggesting disease-related reactivation of a developmental program that normally declines with aging. Conclusions: Spatial transcriptomic analysis of more than one million cortical locations from 64 human donors is consistent with coordinated upregulation of an embryonic Arp2/3–actomyosin gene program in ALS. These findings provide spatial transcriptomic evidence consistent with aberrant reactivation of developmental pathways in ALS. Independent validation in additional cohorts, including spinal cord tissue, will be important to determine whether this transcriptional program represents a fundamental mechanism underlying ALS pathogenesis.