Whole‐genome sequencing identifies new candidate genes for nonobstructive azoospermia

Abstract

Background Genetic causes that lead to spermatogenetic failure in patients with nonobstructive azoospermia (NOA) have not been yet completely established. Objective To identify low‐frequency NOA‐associated single nucleotide variants (SNVs) using whole‐genome sequencing (WGS). Materials and methods Men with various types of NOA (n = 39), including samples that had been previously tested with whole‐exome sequencing (WES; n = 6) and did not result in diagnostic conclusions. Variants were annotated using the Ensembl Variant Effect Predictor, utilizing frequencies from GnomAD and other databases to provide clinically relevant information (ClinVar), conservation scores (phyloP), and effect predictions (i.e., MutationTaster). Structural protein modeling was also performed. Results Using WGS, we revealed potential NOA‐associated SNVs, such as: TKTL1, IGSF1, ZFPM2, VCX3A (novel disease causing variants), ESX1, TEX13A, TEX14, DNAH1, FANCM, QRICH2, FSIP2, USP9Y, PMFBP1, MEI1, PIWIL1, WDR66, ZFX, KCND1, KIAA1210, DHRSX, ZMYM3, FAM47C, FANCB, FAM50B (genes previously known to be associated with infertility) and ALG13, BEND2, BRWD3, DDX53, TAF4, FAM47B, FAM9B, FAM9C, MAGEB6, MAP3K15, RBMXL3, SSX3 and FMR1NB genes, which may be involved in spermatogenesis. Discussion and conclusion In this study, we identified novel potential candidate NOA‐associated genes in 29 individuals out of 39 azoospermic males. Note that in 5 out of 6 patients subjected previously to WES analysis, which did not disclose potentially causative variants, the WGS analysis was successful with NOA‐associated gene findings.

Scrutinizing the human TEX genes in the context of human male infertility

“…These findings clearly demonstrate that LoF vari-ants in TEX13B are not a monogenic cause of human azoospermia, which stands in stark contrast to previously published data attributing azoospermia to impaired TEX13B function and to genetic variants in TEX13B. 7,9,10 Similarly, based on our findings, we consider it unlikely that variants in TEX13C are a monogenic cause of azoospermia, again contradicting a previous report. 7 Our results are underlined by the fact that spermatogenesis and fertility is normal in two different TEX13 ortholog KD fly lines.…”

“…Again, this stands in contrast to recent studies describing FAM9A (TEX39A) as a novel candidate gene for male infertility. 8,9 Recent data suggest that FAM9B (TEX39B) is involved in the formation of the synaptonemal complex. 36 Fittingly, FAM9B (TEX39B) colocalizes to SYCP3 and to foci of DNA double-strand breaks, marked by γH2AX.…”

“…Moreover, a recent publication attributes post-meiotic arrest in one man to a hemizygous missense variant in FAM9B (TEX39B). 9 It is questionable, though, if the inframe insertion found in M442 and the splice site variant found in M1915 are the cause of azoospermia in both men. As no splicing alteration was detected for this variant by the minigene assay in vitro, it seems unlikely that this variant causes splicing effects in vivo.…”

“…This applies to, for example, TEX13A, TEX13B, TEX13C, FAM9A (TEX39A), and FAM9B (TEX39B), which can, therefore, only be described as azoospermia candidate genes. [7][8][9][10] The TEX genes and their potential impact on fertility have recently been reviewed. 11 However, so far the complete list of human proteincoding TEX genes has not been analyzed systematically in the context of male infertility.…”

Novel FSIP2 Variants Induce Super-Length Mitochondrial Sheath and Asthenoteratozoospermia in Humans

“…Deficiencies of FSIP2 were associated with DFS, MMAF and globozoospermia 31 - 33 , 42 . Recurrent FSIP2 amplification had been linked to testicular germ cell tumor 63 , and FSIP2 was also reported as a novel potential candidate gene for nonobstructive azoospermia 64 . Here, we found that biallelic variants of FSIP2 were not only associated with DFS, MMAF described previously, but also related to the multiple axoneme, the lengthened MS and lower mitochondrial ATP utilization.…”