Genetic and epigenetic insights into non-obstructive azoospermia: mechanisms, biomarkers, and clinical perspectives

Non-obstructive azoospermia (NOA) is one of the most severe manifestations of male infertility, accounting for up to 70% of azoospermic cases and affecting approximately 1% of the male population. Advances in genomics and epigenetics have transformed our understanding of NOA from a primarily idiopathic condition into a biologically heterogeneous disorder driven by diverse molecular mechanisms. This review synthesizes the current knowledge of the genetic and epigenetic landscape of NOA, integrating chromosomal abnormalities, single-gene mutations, and non-coding RNA (ncRNA) dysregulation. First, we systematically examine classical and emerging chromosomal defects-including karyotype anomalies, Y-chromosome microdeletions, and structural rearrangements-that disrupt meiotic pairing and chromatin organization. Next, we explore syndromic and non-syndromic monogenic mutations affecting meiotic regulators, DNA repair factors, transcription regulators, and chromatin remodelers. Particular emphasis is placed on recently identified genes such as SYCP1, SYCE1 and HORMAD1, whose pathogenic variants are frequently linked to spermatogenic arrest. We then discuss the expanding role of ncRNAs-including microRNAs, PIWI-interacting RNAs, long non-coding RNAs, and circular RNAs-in regulating germ cell apoptosis, transposon silencing, and epigenetic reprogramming. Furthermore, we highlight the translational potential of these molecular insights (including gene variants, ncRNAs and protein) in clinical applications. Genotype-guided sperm retrieval, non-invasive biomarkers, and multi-omic approaches are discussed as promising tools to improve diagnosis and treatment. Moreover, we summarize current and emerging strategies for the treatment and fertility preservation of NOA. Finally, we identify persisting challenges, such as genotypic heterogeneity and incomplete functional validation, and emphasize the need to elucidate interactions between ncRNA and classical genetic pathways to uncover regulatory hierarchies underlying NOA. By integrating molecular genetics with testicular histopathology and clinical phenotypes, this review highlights emerging genetic and ncRNA biomarkers and underscores their potential applications in the clinical management of NOA. Ultimately, a comprehensive understanding of the genetic and epigenetic underpinnings of NOA will be essential for advancing precision diagnostics and improving reproductive outcomes in affected men.