Transcriptomic profiling uncovers mis-splicing and gene fusions in amyotrophic lateral sclerosis

Advances in transcriptomics have transformed our understanding of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, revealing disrupted gene expression profiles and highlighting the multi-system biology of ALS. Despite major advances, transcriptomic studies have only begun to capture the complexity and the molecular hierarchy of transcriptomic alterations in ALS. To resolve and characterize the transcriptome in ALS, we performed a comprehensive reanalysis of bulk RNA sequencing from the New York Genome Center ALS Consortium cohort across five post-mortem tissues including motor and frontal cortex, cervical and lumbar spinal cord, and cerebellum. By deploying dual analytical pipelines - one reference-based to model canonical events and one de novo to detect transcript structural novelties - we disentangled the quantitative and qualitative architectures of ALS. Our reference-based analysis revealed that ALS transcriptome is defined primarily by splicing failure rather than changes in gene expression. Aberrant splicing events, particularly intron retention, outnumbered differentially expressed genes by an order of magnitude. This widespread loss of fidelity disproportionately affected RNA-binding proteins, suggesting a collapse in their autoregulatory feedback loops. Deconvolution of these signals identified distinct cellular vulnerabilities: transcriptional disruptions were enriched in glial cells in sporadic cases but in neuronal cells in C9ORF72-positive cases. Furthermore, we observed sex-specific dysregulation, with male patients exhibiting greater disruption in guanosine triphosphatase signaling and ciliary organization pathways. In parallel, our de novo analysis uncovered a significant burden of disease-specific gene fusions that were absent in controls. Whole-genome sequencing of the same individuals, together with a larger reference population confirmed that disease-specific fusions do not arise from genomic structural variants, indicating a transcriptional rather than genomic origin. Investigation into the mechanism of these RNA-based fusions revealed a critical deviation in splice site definition: while canonical splice junctions exhibit a high density of binding motifs for polyA-binding or 3-cleaveage proteins approximately 50 base pairs upstream of the splice donor site (left junction), ALS-specific fusion junctions displayed a dramatic depletion of these motifs in the same region. Functionally, the presence of these sparse disease-specific fusions was strongly correlated with severe splicing outliers in genes governing guanosine triphosphatase activity, converging with the tissue- and male-specific defects identified in our reference-based analysis. Altogether, our results delineated a transcriptome characterized by aberrant splicing with tissue-and sex-specific changes and identified structural-variant-independent RNA fusions as candidate disease modifiers that may amplify pathology. This integrated view provides a mechanistic scaffold for splicing-centered and RNA-structural therapeutic strategies for ALS.