Integrative Transcriptomics Identifies Ubiquitination-Related Genes BIRC2, COPS5, and TBK1 as Novel Biomarkers of T-Cell Dysregulation in Amyotrophic Lateral Sclerosis

Ailing Jiang, Yanzhen Huang, Xianting Que, Chonglin Li, Ziqun Lin, Wen Huang Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of ChinaCorrespondence: Wen Huang, Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, No. 6 Shuangyong Road, Nanning, Guangxi, 530021, People’s Republic of China, Tel +86-771-5356504, Email [email protected]: Amyotrophic lateral sclerosis (ALS) is marked by immune dysregulation; however, the role of T cell-ubiquitination-related genes (TURGs) in its pathogenesis remains unclear. This study aimed to investigate the contribution of TURGs to T-cell dysfunction and ubiquitination imbalance in ALS.Patients and Methods: Differentially expressed genes were identified through analysis of bulk transcriptomes (GSE112680). CIBERSORT deconvolution and weighted gene co-expression network analysis were employed to define T-cell-associated modules. Integration with ubiquitination-related gene sets yielded T cell–ubiquitination-related differentially expressed genes (TURDEGs). Functional enrichment analysis and protein-protein interaction network construction, combined with multi-algorithm selection, facilitated the development of a risk-prediction model. Mechanistic insights were derived from Gene Set Enrichment Analysis, immune profiling, co-expression and regulatory network analyses, and drug-target prediction. Single-cell transcriptomic analysis provided insights into cellular-level pathogenic mechanisms in ALS. qPCR was used to validate core TURDEGs expression in peripheral blood samples from patients with ALS.Results: Thirty-nine TURDEGs were identified and exhibited significant enrichment in pathways related to ubiquitination, immune activation, autophagy, and NOD-like receptor signaling. BIRC2, COPS5, and TBK1 were identified as core genes. The resulting risk-prediction model demonstrated significant potential for clinical application. Immune infiltration analysis revealed positive correlations between core genes and CD4⁺ resting memory T cells, as well as negative correlations between COPS5, TBK1, and regulatory T cells. Adavosertib and MRS2211 were identified as potent modulators of TBK1 and BIRC2, respectively. Single-cell transcriptomics highlighted enhanced T cell–neutrophil interactions, suggesting a remodeling of the immune communication network in ALS. qPCR validation confirmed significantly increased expression of these genes in patients with ALS (p< 0.05).Conclusion: TURDEGs-mediated T cell dysfunction and ubiquitination imbalance play critical roles in ALS pathogenesis, unveiling novel biomarkers and potential personalized therapeutic targets.Keywords: amyotrophic lateral sclerosis, t cell ubiquitination-related genes, immune dysregulation, risk-prediction model, biomarkers