Integrated Bulk and Single-Cell Transcriptomic Analysis Reveals Mitochondrial Transporter Gene Programs in Human...

Mitochondrial protein import and transporter systems play essential roles in maintaining metabolic competence and proteostasis in stem cells. However, the transcriptional architecture of mitochondrial translocase (TOM/TIM) complexes and transporter genes in human spermatogonial stem cells (SSCs) remains poorly defined. We performed an integrative analysis combining bulk microarray profiling of human SSC-enriched populations (n=3 biological replicates per group) with complementary single-cell RNA-sequencing (scRNA-seq) datasets. Differential expression (limma; |log₂FC| ≥ 2, adj. P < 0.05), co-expression network construction (WGCNA), protein-protein interaction mapping (STRING/cytoHubba), and miRNA-mRNA regulatory inference were used to identify key mitochondrial transporter nodes. Validation of hub-gene expression patterns was performed using an independent scRNA-seq dataset. Cell-type identity of SSC-enriched cultures was confirmed by immunocytochemistry for established SSC markers. Integrated multi-omics analyses revealed a coordinated enrichment of mitochondrial transporter genes in SSCs, including upregulation of TOMM and TIMM family members and selected ATPase and SLC transporters relative to fibroblasts. Hub genes (TOMM22, TIMM17A, ATP6V1A, SLC25A3) showed high network centrality and were consistently enriched in undifferentiated SSC clusters across multiple scRNA-seq datasets. miRNA-mRNA interaction modeling identified several SSC-expressed miRNAs (e.g., hsa-miR-4732-3p, hsa-miR-6503-3p) as potential post-transcriptional regulators of mitochondrial transporter networks. Human SSCs exhibit a distinctive mitochondrial transporter gene program characterized by enhanced expression of protein-import machinery and metabolic transport components. These findings provide a comprehensive molecular framework for understanding mitochondrial regulation in SSCs and establish new candidate targets for probing germline metabolism and stem-cell maintenance.