Aging & Longevity

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

TL;DR

Two lysosome-related molecular subtypes were identified in intervertebral disc degeneration, with lysosomal gene-signature scores positively associated with senescence scores, and PLD3 functionally supporting lysosomal homeostasis, suggesting that lysosome-modulating interventions may have therapeutic potential.

Key Findings

Two distinct lysosome-related molecular subtypes of intervertebral disc degeneration were identified: a senescence/inflammation-enriched subtype and a metabolism-enriched subtype.

  • Subtypes were identified using consensus clustering of integrated bulk transcriptomic datasets GSE56081 and GSE70362.
  • Single-cell RNA-sequencing data from GSE153066 was also incorporated into the multiomics integration.
  • One subtype was characterized by enrichment in senescence and inflammation pathways, while the other was enriched in metabolic pathways.
  • Weighted gene coexpression network analysis and machine-learning algorithms were among the methods used to define these subtypes.

The lysosomal gene-signature score was positively associated with the senescence score after adjustment for total cellular transcript counts.

  • Partial r = 0.422 after covariate adjustment for total cellular transcript counts.
  • Empirical permutation p = 0.0005.
  • The authors interpret this as supporting 'coordinated transcriptional activation rather than enhanced degradative function.'
  • Covariate-adjusted correlation testing was used to control for potential confounding by total transcript counts.

HYAL1, MMD, PLD3, and ANK3 were prioritized as candidate hub genes associated with lysosomal dysfunction in IVDD.

  • Hub genes were identified using a combination of weighted gene coexpression network analysis, machine-learning algorithms, and immune-signature analysis.
  • Candidate genes were evaluated in both human and rat disc tissues.
  • Multiple machine-learning algorithms were applied in the prioritization process.

PLD3 knockdown aggravated H2O2-induced lysosomal impairment, matrix degeneration, and senescence in nucleus pulposus cells.

  • Experiments were conducted in H2O2-treated nucleus pulposus cells (NPCs) as an oxidative stress model.
  • Lysosomal function was assessed using LysoTracker staining, cathepsin activity, and autophagy-related markers.
  • PLD3 knockdown produced worsened lysosomal impairment, matrix degeneration, and cellular senescence compared to controls.

PLD3 overexpression produced opposing protective effects on lysosomal function, matrix integrity, and senescence in H2O2-treated nucleus pulposus cells.

  • PLD3 overexpression was tested in the same H2O2-treated NPC model used for knockdown experiments.
  • Protective effects were observed across lysosomal impairment, matrix degeneration, and senescence-associated outcomes.
  • Results functionally support PLD3 as a contributor to lysosomal homeostasis in disc cells.

Lithocholic acid (LA) partially improved lysosomal and autophagic function and attenuated senescence-associated changes in vitro.

  • LA treatment partially improved acidic lysosomal compartments and cathepsin activity.
  • LA also improved autophagic degradation and senescence-associated changes in cultured NPCs.
  • Experiments were conducted in cultured nucleus pulposus cells.

Lithocholic acid attenuated degeneration-associated histological and molecular alterations in a rat needle-puncture model of IVDD in vivo.

  • A rat needle-puncture model was used as the preclinical in vivo system.
  • LA treatment attenuated degeneration-associated histological alterations.
  • LA treatment also attenuated degeneration-associated molecular alterations.
  • These in vivo findings complement the in vitro results, providing preclinical support for lysosome-modulating therapeutic approaches.

What This Means

This research suggests that the small cellular compartments called lysosomes — which act as the cell's waste disposal and recycling system — play an important role in the deterioration of spinal discs, a condition called intervertebral disc degeneration (IVDD). By analyzing gene activity data from human disc tissue samples and combining several computational methods, the researchers found that patients with disc degeneration could be grouped into two distinct biological subtypes: one characterized by cellular aging and inflammation, and another by altered metabolism. Both subtypes showed signs of lysosomal dysfunction, and the degree of lysosomal gene activity was closely linked to markers of cellular aging, suggesting these processes are coordinated rather than independent. The study also identified four specific genes — HYAL1, MMD, PLD3, and ANK3 — as likely key players in this lysosomal dysfunction. Experiments in disc cells grown in the laboratory showed that reducing the activity of one of these genes, PLD3, made cells more vulnerable to damage, speeding up lysosomal breakdown, tissue matrix deterioration, and cellular aging. Conversely, increasing PLD3 activity had protective effects, supporting its role in maintaining lysosomal health. Finally, the researchers tested a naturally occurring compound called lithocholic acid (LA) as a potential treatment. In laboratory cell experiments and in a rat model of disc degeneration, LA partially restored lysosomal function, improved the cells' ability to clear waste through autophagy, and reduced signs of tissue degeneration. This research suggests that targeting lysosomal function — particularly through agents like lithocholic acid or by modulating genes like PLD3 — could represent a new avenue for treating intervertebral disc degeneration, though further studies would be needed to translate these findings to clinical use.

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Citation

Yang Y, Li H, Ou Y, Yu Y, Sun K, Chen S, et al.. (2026). Lysosomal Dysfunction Is Associated With Intervertebral Disc Degeneration: Multiomics and Machine Learning Identify Molecular Subtypes and Hub Genes.. The journal of gene medicine. https://doi.org/10.1002/jgm.70109