Machine learning and single-cell analysis identify the mitophagy-associated gene TOMM22 as a potential diagnostic biomarker for intervertebral disc degeneration

Abstract

Background: Mitophagy selectively eliminates potentially cytotoxic and damaged mitochondria and effectively prevents excessive cytotoxicity from damaged mitochondria, thereby attenuating inflammatory and oxidative responses. However, the potential role of mitophagy in intervertebral disc degeneration remains to be elucidated. Methods: The GSVA method, two machine learning methods (SVM-RFE algorithm and random forest), the CIBERSORT and MCPcounter methods, as well as the consensus clustering method and the WGCNA algorithm were used to analyze the involvement of mitophagy in intervertebral disc degeneration, the diagnostic value of mitophagy-associated genes in intervertebral disc degeneration, and the infiltration of immune cells, and identify the gene modules that were closely related to mitophagy. Single-cell analysis was used to detect mitophagy scores and TOMM22 expression, and pseudo-temporal analysis was used to explore the function of TOMM22 in nucleus pulposus cells. In addition, TOMM22 expression was compared between human normal and degenerated intervertebral disc tissue samples by immunohistochemistry and PCR. Results: This study identified that the mitophagy pathway score was elevated in intervertebral disc degeneration compared with the normal condition. A strong link was present between mitophagy genes and immune cells, which may be used to typify intervertebral disc degeneration. The single-cell level showed that mitophagy-associated gene TOMM22 was highly expressed in medullary cells of the disease group. Further investigations indicated the upregulation of TOMM22 expression in late-stage nucleus pulposus cells and its role in cellular communication. In addition, human intervertebral disc tissue samples established that TOMM22 levels were higher in disc degeneration samples than in normal samples. Conclusions: Our findings revealed that mitophagy may be used in the diagnosis of intervertebral disc degeneration and its typing, and TOMM22 is a molecule in this regard and may act as a potential diagnostic marker in intervertebral disc degeneration.

Keywords

• Mitophagy
• Single-cell analysis
• Machine learning
• IDD (intervertebral disc degeneration)
• Human tissue sample validation