Interpreting the molecular and cellular landscape of PCOS through bulk transcriptomics, single-cell transcriptomics and machine learning

BACKGROUND: Polycystic ovary syndrome (PCOS) is a prevalent endocrine-metabolic disorder in women, hallmarked by hyperandrogenism, anovulation, and polycystic ovarian morphology. This study integrates multi-omics and machine-learning analyses to elucidate the molecular mechanisms and cellular constituents underlying PCOS, aiming to uncover potential therapeutic targets and enhance diagnostic precision. METHODS: Bulk and single-cell RNA sequencing identified key granulosa cell subpopulations and gene expression patterns in PCOS; subsequently, machine-learning algorithms were applied to construct a diagnostic model and to screen for key gene signatures. Consequently, the identified signatures were validated at both mRNA and protein levels in independent clinical samples using qPCR and western blotting. RESULTS: Compared with controls, PCOS patients exhibited a markedly increased proportion of the GC9 granulosa cell subset, which displayed an active proliferative phenotype. Up-regulated genes in PCOS were closely associated with immune function, responsiveness to stimuli, and diverse cellular biological processes. Machine-learning analysis further pinpointed a three-gene signature-comprising HLA-DRA, SRM, and CTSL-and yielded a diagnostic model with superior accuracy and specificity. Moreover, validation in clinical samples confirmed significant up-regulation of HLA-DRA, SRM, and CTSL at both mRNA and protein levels in follicular cells of PCOS patients. CONCLUSIONS: Our findings delineate a previously unrecognized cellular landscape and gene signature associated with PCOS, thereby proposing novel diagnostic and therapeutic targets.