Lysosomal Dysfunction Is Associated With Intervertebral Disc Degeneration: Multiomics and Machine Learning Identify Molecular Subtypes and Hub Genes

Abstract

Intervertebral disc degeneration (IVDD) is closely associated with cellular senescence and defective autophagic degradation, but the molecular heterogeneity and functional significance of lysosome‐related alterations remain incompletely understood. We integrated bulk transcriptomic datasets (GSE56081 and GSE70362) and single‐cell RNA‐sequencing data (GSE153066) using consensus clustering, weighted gene coexpression network analysis, machine‐learning algorithms, immune‐signature analysis, and covariate‐adjusted correlation testing. Candidate genes were evaluated in human and rat disc tissues, and PLD3 was further examined by knockdown and overexpression in H2O2‐treated nucleus pulposus cells (NPCs). Lysosomal function was assessed using LysoTracker staining, cathepsin activity, and autophagy‐related markers, and the preclinical effects of lithocholic acid (LA) were evaluated in cultured NPCs and a rat needle‐puncture model. Two lysosome‐related molecular subtypes were identified: a senescence/inflammation‐enriched subtype and a metabolism‐enriched subtype. The lysosomal gene‐signature score was positively associated with the senescence score after adjustment for total cellular transcript counts (partial r = 0.422; empirical permutation p = 0.0005), supporting coordinated transcriptional activation rather than enhanced degradative function. HYAL1, MMD, PLD3, and ANK3 were prioritized as candidate hub genes. PLD3 knockdown aggravated H2O2‐induced lysosomal impairment, matrix degeneration, and senescence, whereas PLD3 overexpression produced opposing protective effects. LA partially improved acidic lysosomal compartments, cathepsin activity, autophagic degradation, and senescence‐associated changes in vitro and attenuated degeneration‐associated histological and molecular alterations in vivo. These findings reveal distinct lysosome‐related phenotypes in IVDD, functionally support PLD3 as a contributor to lysosomal homeostasis, and suggest that lysosome‐modulating interventions may have therapeutic potential.