Integrative transcriptomic and experimental analyses prioritize TPT1 as a PANoptosis-associated candidate molecular marker in sarcopenia
TL;DR
This study prioritizes TPT1 as a candidate molecular marker associated with the bulk-transcriptomic sarcopenia phenotype and network and gene set variation analyses associated lower TPT1 expression with inflammatory, oxidative-stress, cell-death, and stress-adaptive pathways.
Abstract
Background Sarcopenia lacks sensitive molecular markers for early detection, and its relationship with integrated inflammatory cell-death programs remains unclear. PANoptosis integrates apoptotic, pyroptotic, and necroptotic signaling and therefore provides a plausible framework for investigating inflammatory-stress remodeling in aging skeletal muscle. Methods We integrated four bulk-transcriptomic datasets from the Gene Expression Omnibus into a training cohort (66 controls; 37 sarcopenia) and used GSE111016 as an external validation cohort (20 controls; 20 sarcopenia). We intersected differentially expressed genes with a curated PANoptosis-associated gene set and then performed enrichment analysis; least absolute shrinkage and selection operator (LASSO), random forest and extreme gradient boosting (XGBoost) feature selection; nomogram and receiver operating characteristic (ROC) analyses; CIBERSORT immune-cell deconvolution; and single-nucleus RNA sequencing (snRNA-seq) reanalysis. We assessed tumor protein, translationally controlled 1 (TPT1) expression in D-galactose-treated mouse and C2C12 models. Results Among 608 differentially expressed genes, 47 overlapped with the curated PANoptosis-associated gene set. These genes were enriched in apoptotic signaling; cytokine, nuclear factor kappa B (NF-κB), tumor necrosis factor (TNF), and nucleotide-binding oligomerization domain (NOD)-like receptor pathways; regulated necrosis; extracellular-matrix remodeling; and impaired oxidative phosphorylation. Three machine-learning algorithms converged on neurotrophic receptor tyrosine kinase 1 (NTRK1), TPT1, and TNF receptor-associated protein 1 (TRAP1). TPT1 showed the strongest single-gene discrimination, with areas under the ROC curve of 0.819 (95% confidence interval [CI], 0.737–0.900) in the training cohort and 0.753 (95% CI, 0.598–0.907) in the external cohort. Immune-cell deconvolution linked the candidate genes to estimated mast-cell, plasma-cell, cluster of differentiation 8-positive (CD8+) T-cell, and macrophage proportions. Single-nucleus analysis of 97,154 nuclei from 17 donors showed broad TPT1 expression across myonuclear, satellite-cell, stromal, endothelial, and immune compartments, with lower expression in older muscle. Network and gene set variation analyses associated lower TPT1 expression with inflammatory, oxidative-stress, cell-death, and stress-adaptive pathways. In D-galactose-treated mice and C2C12 myotubes, muscle-wasting or senescence-like changes coincided with lower TPT1 protein abundance. Conclusion This study prioritizes TPT1 as a candidate molecular marker associated with the bulk-transcriptomic sarcopenia phenotype. The aging-muscle and D-galactose analyses provide biological context but do not establish sarcopenia specificity or causality. Prospective clinical validation and functional perturbation studies are required.