Genomic study of TEX15 variants: prevalence and allelic heterogeneity in men with spermatogenic failure

Abstract

Introduction: Human spermatogenesis is a highly intricate process that requires the input of thousands of testis-specific genes. Defects in any of them at any stage of the process can have detrimental effects on sperm production and/or viability. In particular, the function of many meiotic proteins encoded by germ cell specific genes is critical for maturation of haploid spermatids and viable spermatozoa, necessary for fertilization, and is also extremely sensitive to even the slightest change in coding DNA. Methods: Here, using whole exome and genome approaches, we identified and reported novel, clinically significant variants in testis-expressed gene 15 (TEX15), in unrelated men with spermatogenic failure (SPGF). Results: TEX15 mediates double strand break repair during meiosis. Recessive loss-of-function (LOF) TEX15 mutations are associated with SPGF in humans and knockout male mice are infertile. We expand earlier reports documenting heterogeneous allelic pathogenic TEX15 variants that cause a range of SPGF phenotypes from oligozoospermia (low sperm) to nonobstructive azoospermia (no sperm) with meiotic arrest and report the prevalence of 0.6% of TEX15 variants in our patient cohort. Among identified possible LOF variants, one homozygous missense substitution c.6835G>A (p.Ala2279Thr) co-segregated with cryptozoospermia in a family with SPGF. Additionally, we observed numerous cases of inferred in trans compound heterozygous variants in TEX15 among unrelated individuals with varying degrees of SPGF. Variants included splice site, insertions/deletions (indels), and missense substitutions, many of which resulted in LOF effects (i.e., frameshift, premature stop, alternative splicing, or potentially altered posttranslational modification sites). Conclusion: In conclusion, we performed an extensive genomic study of familial and sporadic SPGF and identified potentially damaging TEX15 variants in 7 of 1097 individuals of our combined cohorts. We hypothesize that SPGF phenotype severity is dictated by individual TEX15 variant's impact on structure and function. Resultant LOFs likely have deleterious effects on crossover/recombination in meiosis. Our findings support the notion of increased gene variant frequency in SPGF and its genetic and allelic heterogeneity as it relates to complex disease such as male infertility.

Keywords: TEX15; male infertility; next-generation sequencing; non-obstructive azoospermia (NOA); oligozoospermia.

FIGURE 1

Single-cell transcriptome profiling of TEX15 in the adult human testis. (A) UMAP visualization of annotated testicular cell types in the adult human testis from global clustering of 13,597 cells. Each dot represents a single testicular cell and is colored based on cell type. (B) UMAP plot demonstrating RNA expression pattern of TEX15 is predominant in the human testicular germ cells. Red represents a high expression level, as shown on the color key at the bottom right.

FIGURE 2

Pedigree of Pakistani family with proband presenting with cryptozoospermia and male infertility. Normal male and female members are represented with an open square or circle, respectively. The affected proband is shown with a filled symbol. A vertical line with double horizontal lines indicates an infertile couple (noted with “Cryptozoospermia” diagnosis). The arrow symbol accompanied by the letter “P” represents the proband for this family. Text in parentheses indicates TEX15 nucleotide at genomic position 8:30843344T (hg38).

FIGURE 3

TEX15 schematic. Bolded variants listed above the sequence are variants identified within our cohorts; the variants below the sequence are variants from previously identified literature. The orange square represents the domain of unknown function 3715 (DUF3715); the overlapping light blue square represents the predicted ADP-Ribosylation domain. The two areas in yellow and dark blue represent the two TEX15 domains.

FIGURE 4

Structural modeling of TEX15 reveals some globular regions and the first partial TEX15 structural model of intrinsically disordered regions. (A) Structural model of the C-terminal region of TEX15 from residue 1901–2,500 generated by AlphaFold (Jumper et al., 2021). The individual TEX15 domains are colored N- to C-terminally in orange, purple, and cyan, respectively. Positions of individual mutations indicated with arrows. (B) Left, a zoomed view of the predicted structural environment around A2279. Right, two alternative rotamers for the A2279T mutation. Red arrows indicate steric clashes that could be introduced upon mutation of this amino acid to threonine.