Copper metabolism-related genes SCO2 and PARK7 in pulmonary tuberculosis: diagnostic value, immune infiltration and single-cell virtual knockout analysis with clinical validation

Abstract Background Pulmonary tuberculosis (PTB) remains a leading cause of death from a single infectious agent. Copper is central to the host–pathogen interaction, with macrophages accumulating the metal for bactericidal activity while M. tuberculosis deploys dedicated detoxification systems. Copper metabolism-related genes in PTB blood and their link to immunity remain poorly defined. We therefore aimed to identify key copper metabolism-related genes in PTB, assess their diagnostic value and characterise their link to immune infiltration. Methods GSE28623 (training) and GSE83456 (validation) were retrieved from GEO with copper metabolism-related genes from GeneCards. Differentially expressed genes (DEGs) were defined by limma (adjusted P  0.5), and weighted gene co-expression network analysis (WGCNA) identified the disease module. The DEG, module and copper gene sets were intersected. Candidates underwent enrichment, protein–protein interaction (PPI) and MCODE analysis, and least absolute shrinkage and selection operator (LASSO) regression with cross-validation, followed by external validation and receiver operating characteristic (ROC) analysis. Peripheral blood from 20 treatment-naïve PTB patients and 20 healthy controls was analysed by real-time PCR; immune infiltration was quantified by ssGSEA, drug prediction used NetworkAnalyst 3.0, and knockout simulation used scTenifoldKnk on GSE281148. Results In total 2240 DEGs were identified (1039 upregulated, 1201 downregulated) and the WGCNA blue module correlated most strongly with PTB (r = 0.85; 670 genes). The three-way intersection yielded 15 candidates enriched in copper ion binding; PPI/MCODE defined an eight-gene core module and LASSO nominated SCO2 and PARK7. Both were upregulated in the validation set and in clinical samples: PARK7 1.45 ± 0.42 versus 1.05 ± 0.42 and SCO2 1.12 ± 0.56 versus 0.62 ± 0.39 (P < 0.001 and P = 0.002, respectively; AUC 0.808, 95% CI 0.639–0.953 and AUC 0.759, 95% CI 0.593–0.892). Both correlated positively with macrophage and neutrophil and negatively with protective adaptive immune cells. Knockout simulation concentrated PARK7 perturbation in oxidative stress/apoptosis modules and SCO2 perturbation in interferon and Th1/Th17 pathways. Conclusions SCO2 and PARK7 are aberrantly expressed in active PTB peripheral blood and associate with copper imbalance and immune dysregulation; both show moderate diagnostic value and are candidate host-directed therapy targets.