nf-sarcopipe enables integrative discovery of exercise-responsive miRNAs and miRNA–mRNA regulatory networks associated with skeletal muscle adaptation

Skeletal muscle dynamically adapts to physiological stimuli such as exercise through coordinated molecular and structural remodeling processes. Circulating microRNAs (miRNAs) represent promising non-invasive biomarkers of exercise responsiveness and skeletal muscle physiological states; however, most analytical frameworks rely solely on annotated miRNAs and overlook novel candidates. Here, we present nf-sarcopipe, a modular Nextflow pipeline that integrates de novo and reference-guided miRNA discovery with transcriptomic analysis and regulatory network reconstruction. The pipeline is organized into three complementary modules: 1) Preprocessing, 2) miRNA Discovery, and 3) Target Prediction & mRNA Integration. Using publicly available datasets from active and sedentary young women, the pipeline identified reproducible miRNA signatures and prioritized a small set of structurally supported, high-confidence de novo candidates. Previously reported exercise-associated miRNAs compiled from the literature were additionally incorporated for comparative candidate evaluation. Although the available datasets were derived from different tissues, confounding-aware analyses enabled the identification of coherent transcriptional signatures associated with exercise responsiveness. Integrative miRNA–mRNA analysis uncovered consistent regulatory interactions linking circulating miRNAs—both novel and known—to pathways involved in immune response, extracellular matrix remodeling, autophagy, and skeletal muscle adaptation. Together, these results establish nf-sarcopipe as a robust and scalable framework for complementary miRNA discovery and for investigating regulatory mechanisms associated with exercise-induced skeletal muscle adaptation.