A homozygous SPDYA variant associated with meiotic arrest and failed microdissection testicular sperm extraction in non-obstructive azoospermia

Background Non-obstructive azoospermia (NOA) with meiotic maturation arrest is a severe form of male infertility for which genetic diagnosis may inform counseling and sperm-retrieval expectations. Methods Whole-exome sequencing was performed in a consanguineous family with NOA, followed by SPDYA variant screening in 31 unrelated NOA patients and 469 men with documented reproductive outcomes. The proband underwent clinical evaluation and microdissection testicular sperm extraction (micro-TESE). Testicular histology, immunofluorescence staining, and meiotic chromosome-spread analysis were used to assess spermatogenic progression. Structural modeling, immunoblotting, co-immunoprecipitation, and exploratory bulk RNA sequencing were performed using testicular material from the proband and a pooled obstructive azoospermia control reference. The three libraries per condition were technical library replicates, not independent biological replicates. Results A homozygous SPDYA missense variant (NM_182756.4:c.596G>A; p.R199H) was identified in the proband, and both parents were heterozygous carriers. No additional biallelic deleterious SPDYA variants were detected in the screening cohort. The patient showed NOA, reduced testicular volume, spermatocyte-stage maturation arrest, and failed micro-TESE. Cytological analyses showed absence of post-meiotic germ cells, persistent nuclear γH2AX, failed XY body formation, and no pachytene or diplotene spermatocytes. Structural modeling and co-immunoprecipitation were compatible with weakened SPDYA-CDK2 association, and immunoblotting showed lower apparent abundance of SPDYA, CDK2, and SUN1 in the patient sample. Exploratory transcriptomic profiling showed fold-change-based tissue-level trends consistent with early meiotic arrest and loss of post-meiotic germ-cell programs, rather than direct transcriptional effects of the variant. Conclusion This single case suggests that biallelic SPDYA variants may be associated with poor sperm retrieval outcomes in severe meiotic arrest, but larger multicenter cohorts are strictly required before SPDYA can be used for clinical prediction or surgical decision-making.