Integrative single-cell transcriptomics and Mendelian randomization prioritize FN1 and DCN in intervertebral disc degeneration.

Intervertebral disc degeneration (IDD) is a major contributor to low back pain, yet its cellular heterogeneity and the relevance of circulating extracellular-matrix proteins to disease susceptibility remain incompletely understood. We integrated public single-cell RNA sequencing datasets from healthy and degenerative human intervertebral discs with protein quantitative trait locus-based Mendelian randomization (MR) and exploratory functional assays in primary human nucleus pulposus cells. After quality control, normalization, Harmony integration, clustering, and reference-guided annotation, single-cell analysis revealed disease-associated shifts in cell-state composition and transcriptional programs related to extracellular-matrix organization, focal adhesion, inflammatory signaling, IL-6-JAK-STAT3 signaling, transforming growth factor-beta signaling, and oxidative phosphorylation. Network analyses repeatedly prioritized fibronectin 1 (FN1), decorin (DCN), CCN2, EGFR, and COL1A1 as extracellular-matrix-associated candidates. A numerical consistency audit indicated that the reported FN1 MR estimate was not statistically significant after recalculation from beta and standard error, whereas DCN showed a nominally positive inverse-variance-weighted association, with less consistent support from alternative estimators. In primary nucleus pulposus cells, siRNA-mediated reduction of FN1 or DCN was accompanied by lower expression of selected matrix and inflammatory markers in a TNF-alpha model. Overall, this study prioritizes extracellular-matrix candidates and disease-associated cell states for further mechanistic validation rather than establishing definitive causal drivers.