Abstract
Human tissue transcriptomics are crucial for understanding neurodegeneration but limited by cross-sectional post-mortem sampling, which represents end-stage disease. Subtype and Stage Inference (SuStaIn) modeling addresses these limitations by inferring temporal gene expression dynamics while also identifying potential transcriptomic subtypes. Applied to bulk RNA-seq data from post-mortem lumbar spinal cord in amyotrophic lateral sclerosis (ALS), SuStaIn unraveled that more advanced transcriptomic stages were associated with higher microglia and reduced neuron proportions, which mapped onto two ALS subtypes: Immune/Apoptosis/Proteostasis subtype with early immune/apoptotic/proteostatic dysregulation, worse prognosis and higher microglia proportions; Synapse/RNA-Metabolism subtype with early synaptic/RNA-processing deficits, lower male prevalence and neuron loss. Lumbar patterns demonstrated high concordance with cervical patterns and a strong correlation in staging across regional tissues. These findings revealed subtype-specific mechanisms underlying ALS heterogeneities, prioritized key genes driving subtyping/staging as potential therapeutic targets. More broadly, we established a framework to decode temporal dynamics from traditionally constrained post-mortem transcriptomic studies.