Data Sheet 2_Machine learning-driven discovery of NETs-associated diagnostic biomarkers and molecular subtypes in tuberculosis.pdf

ObjectNETs constitute a pivotal mechanism in the pathogenesis and progression of TB. Despite their recognized importance, the genetic underpinnings of NETs in TB remain inadequately elucidated. Accordingly, the present study endeavors to delineate the molecular characteristics of NRGs in TB, with the objective of reliably identifying associated molecular clusters and biomarkers.
MethodsGene expression profiles were analyzed from integrated datasets retrieved from the GEO database. Differential analysis, WGCNA, and an ensemble of 113 machine learning algorithms were employed to identify the core NETs genes. Subsequently, TB patients were stratified into distinct subtypes based on the expression profiles of these core genes, and the differences in immune infiltration characteristics among the subtypes were systematically compared. Finally, RT-qPCR was utilized to validate the differential expression of the key NETs core genes.
ResultsAnalysis of the integrated GSE83456 and GSE54992 datasets yielded 630 DEGs. WGCNA subsequently identified a module comprising 1,252 genes, from which 26 key NETs genes were extracted via intersection with known NRGs. Among the ensemble of 113 machine learning methods, the “StepgIm[both]+RF” algorithm demonstrated superior performance, ultimately identifying six core NETs genes. Consensus clustering based on the expression profiles of these core genes stratified patients into two distinct subtypes. Functional enrichment analysis further underscored the predominance of immune-related pathways in subtype B. Moreover, immune infiltration analysis revealed marked differences in immune cell composition between the subtypes, thereby confirming a close association between the core NETs genes and these immunological disparities.
ConclusionCore NETs genes are pivotal in the pathogenesis and progression of tuberculosis, and they hold significant promise as novel biomarkers for the early diagnosis and targeted treatment of TB.