Integrating neuroimaging, transcriptomics and single-cell sequencing identifies candidate molecular features of cortical vulnerability in amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a rapidly progressive neurodegenerative disease that leads to reductions in cortical surface area (SA) and thickness (TH). However, the genetic and molecular mechanisms underlying these cortical structural alterations remain unclear. This study integrates neuroimaging, transcriptomic, genetic, and single-cell data to explore region-specific vulnerabilities related to SA and TH alterations in ALS. High-resolution T1-weighted MRI from 73 sporadic ALS patients and 70 healthy controls were used to quantify SA and TH. Two-sample Mendelian randomization (MR) assessed associations of these structural phenotypes on ALS risk. Imaging signatures were coupled to Allen Human Brain Atlas expression data with partial least squares regression and region-wise differential expression genes to derive SA- and TH-intersect gene sets. Summary-data-based Mendelian randomization (SMR) integrating expression quantitative trait loci, methylation quantitative trait loci, and ALS genome-wide association studies was used to identify candidate molecular QTL signals, followed by exploratory analysis in public single-cell RNA sequencing datasets. Sporadic ALS patients exhibited reduced SA in the left precentral gyrus (t = -3.588, p FDR = 0.025) and decreased cortical TH in the left frontal pole (t = -3.460, p FDR = 0.025). MR analysis identified nominal associations between ALS risk and several cortical structural phenotypes, including paracentral SA and frontal pole TH. Integrated imaging-transcriptomic analysis identified 215 SA-intersect and 979 TH-intersect genes, which were enriched in synaptic processes and neuroactive ligand-receptor interactions. SA-intersect genes showed enrichment in oligodendrocyte-related cell types, while TH-intersect genes showed astrocyte-related enrichment. SMR-based prioritization nominated MOBP and ZNHIT3 as candidate genes associated with SA- and TH-related structural alteration patterns, respectively. In public C9orf72-associated ALS single-cell data, MOBP expression differed in oligodendrocytes ( p < 0.001), whereas ZNHIT3 expression was lower in astrocytes ( p < 0.001). This multimodal analysis suggests that regional cortical vulnerability in ALS may involve convergent structural, genetic, transcriptomic, and glial cell-type-related features. MOBP and ZNHIT3 were prioritized as candidate genes associated with ALS-related cortical structural alteration patterns. Future longitudinal and experimental studies are needed to validate their biological relevance and potential translational implications.