Novel homozygous variants in piRNA pathway factors lead to male infertility in humans

Abstract

Research question: Given the association between abnormal PIWI-interacting RNA (piRNA) biogenesis and human male infertility, are there novel variants of genes involved in the piRNA pathway responsible for human azoospermia or oligozoospermia?

Design: Whole-exome sequencing and Sanger sequencing were performed to identify and validate potential deleterious variants associated with spermatogenesis in a cohort of 592 idiopathic infertile men. The impact of variants on protein expression was validated using in-vitro experiments. The functional effects of the candidate gene variants were evaluated by haematoxylin and eosin staining, immunofluorescence and small RNA sequencing. Intracytoplasmic sperm injection (ICSI) was performed in the EXD1-affected individual.

Results: Homozygous variants in three genes crucial for piRNA biogenesis were identified in infertile men from four unrelated families. Notably, a homozygous missense variant (c.3587T>C, p.L1196P) and a homozygous frameshift variant (c.179_186del, p.Q61Gfs*22) in TDRD9 were identified in two patients. The patient carrying the frameshift variant in TDRD9 exhibited incomplete arrest of spermatogenesis and partial meiotic defects. In addition, a homozygous HENMT1 frameshift variant (c.47_75del, p.F16Sfs*3) was identified in one patient whose testicular tissue showed reduced abundance of piRNA. These three patients were diagnosed with non-obstructive azoospermia. Finally, the fourth patient harboured the first reported loss-of-function variant of EXD1 (c.550C>T, p.R184*), and exhibited oligoasthenoteratozoospermia characterized by acrosomal hypoplasia; ICSI treatment in this case resulted in a live birth, suggesting its potential utility for further investigation in larger cohorts.

Conclusions: Novel homozygous variants were identified in TDRD9, HENMT1 and EXD1, broadening the piRNA-related genetic spectrum in male infertility. EXD1 stop-gain variant was linked to male infertility for the first time, with ICSI showing potential efficacy. This provides a theoretical basis for genetic counselling and potential clinical treatment of these patients.

Keywords: Gene variants; Non-obstructive azoospermia; Oligoasthenoteratozoospermia; Whole-exome sequencing; piRNA pathway.