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.
