Rare double sex and mab-3-related transcription factor 1 regulatory variants in severe spermatogenic failure

Trans-ethnic GWAS meta-analysis of idiopathic spermatogenic failure highlights the immune-mediated nature of Sertoli cell-only syndrome

Non-obstructive azoospermia, a severe form of male infertility caused by spermatogenic failure (SPGF), has a largely unknown genetic basis across ancestries. To our knowledge, this is the first trans-ethnic meta-analysis of genome-wide association studies on SPGF, involving 2255 men with idiopathic SPGF and 3608 controls from European and Asian populations. Using logistic regression and inverse variance methods, we identify two significant genetic associations with Sertoli cell-only (SCO) syndrome, the most extreme SPGF phenotype. The G allele of rs34915133, in the major histocompatibility complex class II region, significantly increases SCO risk (P = 5.25E-10, OR = 1.57), supporting a potential immune-related cause. Additionally, the rs10842262 variant in the SOX5 gene region is also a genetic marker of SCO (P = 5.29E-09, OR = 0.72), highlighting the key role of this gene in the male reproductive function. Our findings reveal shared genetic factors in male infertility across ancestries and provide insights into the molecular mechanisms underlying SCO.

Familial DMRT1-related non-obstructive azoospermia: a case report

PURPOSE

To report an exceptional case of male-to-male transmission of genetically based non-obstructive azoospermia (NOA) and varicocele through a naturally obtained pregnancy.

SUBJECTS AND METHODS

A father and his son were both diagnosed with NOA after centrifugation and varicocele. The father has no other clinical concerns apart from infertility, detected after many attempts of having another child, but given his urological situation (bilateral varicocele and NOA) assisted reproductive techniques were discouraged. After genetic counseling, several genetic-chromosomal analyses were carried out in the son (karyotype, chromosome Y microdeletions, CFTR screening, NGS infertility panels, and finally array-CGH).

RESULTS

After a series of inconclusive tests, array-CGH detected a deletion of 224-283 kb (del9p24.3) involving part of the KANK1 and DMRT1 genes, inherited from the father. Haploinsufficiency of DMRT1 was therefore considered the determining factor in the development of azoospermia in the family by a loss of function mechanism.

CONCLUSION

The confirmation of father-to-son transmission of a deletion including DMRT1 represents an important point for clinicians dealing with male infertility, even when complete azoospermia is repetitively detected, and must be of hope for a relevant portion of men. Inclusion criteria for the access to assisted reproductive techniques may also be reconsidered and worthy of a greater number of clinical insights. Finally, since DMRT1 alterations have been associated with NOA and abnormal testicular development, but not specifically with varicocele, further studies are required to validate this issue, as varicocele may have played a crucial role in this case.

Genetic variants underlying spermatogenic arrests in men with non-obstructive azoospermia

Spermatogenic arrest is a severe form of non-obstructive azoospermia (NOA), which occurs in 10-15% of infertile men. Interruption in spermatogenic progression at premeiotic, meiotic, or postmeiotic stage can lead to arrest in men with NOA. Recent studies have intensively focused on defining genetic variants underlying these spermatogenic arrests by making genome/exome sequencing. A number of variants were discovered in the genes involving in mitosis, meiosis, germline differentiation and other basic cellular events. Herein, defined variants in NOA cases with spermatogenic arrests and created knockout mouse models for the related genes are comprehensively reviewed. Also, importance of gene panel-based screening for NOA cases was discussed. Screening common variants in these infertile men with spermatogenic arrests may contribute to elucidating the molecular background and designing novel treatment strategies.

TAD Evolutionary and functional characterization reveals diversity in mammalian TAD boundary properties and function

Topological associating domains (TADs) are self-interacting genomic units crucial for shaping gene regulation patterns. Despite their importance, the extent of their evolutionary conservation and its functional implications remain largely unknown. In this study, we generate Hi-C and ChIP-seq data and compare TAD organization across four primate and four rodent species, and characterize the genetic and epigenetic properties of TAD boundaries in correspondence to their evolutionary conservation. We find that only 14% of all human TAD boundaries are shared among all eight species (ultraconserved), while 15% are human-specific. Ultraconserved TAD boundaries have stronger insulation strength, CTCF binding, and enrichment of older retrotransposons, compared to species-specific boundaries. CRISPR-Cas9 knockouts of two ultraconserved boundaries in mouse models leads to tissue-specific gene expression changes and morphological phenotypes. Deletion of a human-specific boundary near the autism-related AUTS2 gene results in upregulation of this gene in neurons. Overall, our study provides pertinent TAD boundary evolutionary conservation annotations, and showcase the functional importance of TAD evolution.

Functional assessment of DMRT1 variants and their pathogenicity for isolated male infertility

OBJECTIVE

To study the impact of Doublesex and mab-3-related transcription factor 1 (DMRT1) gene variants on the encoded protein's function and the variants' pathogenic relevance for isolated male infertility caused by azoospermia.

DESIGN

This study established a novel luciferase assay for DMRT1 missense variants using 2 different target promotors and validated the assay by analyzing previously published variants associated with differences in sex development.

SETTING

University genetics research institute and tertiary referral center for couples' infertility.

PATIENT(S)

Eleven infertile men with severely impaired spermatogenesis resulting in crypto- or azoospermia and carrying rare heterozygous missense variants in DMRT1 were identified within the Male Reproductive Genomics study.

MAIN OUTCOME MEASURE(S)

Luciferase assays with human DMRT1 variants to test functional effects on the CYP19A1 and Stra8 target promoters.

RESULT(S)

We first developed and refined luciferase assays to reliably test the functional impact of DMRT1 missense variants. Next, the assay was validated by analyzing 2 DMRT1 variants associated with differences in sex development, of which c.240G>C p.(Arg80Ser) displayed highly significant effects on both target promoters compared with the wild-type protein (-40% and +100%, respectively) and c.331A>G p.(Arg111Gly) had a significant effect on the Stra8 promoter (-76%). We then systematically characterized 11 DMRT1 variants identified in infertile men. The de novo variant c.344T>A p.(Met115Lys) showed a pronounced loss of function in both DMRT1 target promoters (-100% and -86%, respectively). Variants c.308A>G p.(Lys103Arg) and c.991G>C p.(Asp331His) showed a significant gain of function exclusively for the CYP19A1 promoter (+15% and +19%, respectively). Based on these results, 3 variants were reclassified according to clinical guidelines.

CONCLUSION(S)

The present study highlights the importance of functionally characterizing DMRT1 variants of uncertain clinical significance. Using luciferase assays for diagnostic purposes enables an improved causal diagnosis for isolated male infertility.

The role of mab-3 in spermatogenesis and ontogenesis of pinewood nematode, Bursaphelenchus xylophilus

BACKGROUND

Bursaphelenchus xylophilus is one of the most destructive invasive species, causing extensive economic losses worldwide. The sex ratio of female to male of B. xylophilus plays an important role in the nematode infestation. However, little is known about the processes of its sex determination. The double sex/mab-3-related family of transcription factors are highly conserved in animals, playing crucial roles in sex determination, spermatogenesis and ontogenesis. We therefore investigated its orthologue, Bxy-mab-3, in B. xylophilus.

RESULTS

Bxy-mab-3 has two typical conserved DNA-binding domains. It was observed in J2 (the second-stage of juveniles), J3, J4 and male adults (specifically on the spicules), but not in eggs or female adults via mRNA in situ hybridization. RNA-Seq indicated significantly higher expression in males. RNAi showed that the body size and sperm size of male adults were markedly smaller than those of the controls. Meanwhile, almost all the RNAi-treated males failed to mate with the normal females, even 26.34% of interfered males did not produce sperm. However, RNAi of Bxy-mab-3 had no effect on the sex ratio of B. xylophilus.

CONCLUSION

Bxy-mab-3 is indispensable for spermatogenesis, ontogenesis and mating behavior. It is a typical sex-determination gene with differential expression in males and females. However, knocking down Bxy-mab-3 expression could not alter the sex ratio as seen in other species. Our findings contribute towards a better understanding of the molecular events of Bxy-mab-3 in B. xylophilus, which provides promising hints for control of pine wilt disease by blocking ontogenesis and decreasing nematode fecundity.

Disease gene discovery in male infertility: past, present and future

Identifying the genes causing male infertility is important to increase our biological understanding as well as the diagnostic yield and clinical relevance of genetic testing in this disorder. While significant progress has been made in some areas, mainly in our knowledge of the genes underlying rare qualitative sperm defects, the same cannot be said for the genetics of quantitative sperm defects. Technological advances and approaches in genomics are critical for the process of disease gene identification. In this review we highlight the impact of various technological developments on male infertility gene discovery as well as functional validation, going from the past to the present and the future. In particular, we draw attention to the use of unbiased genomics approaches, the development of increasingly relevant functional assays and the importance of large-scale international collaboration to advance disease gene identification in male infertility.

Evaluation of Male Fertility-Associated Loci in a European Population of Patients with Severe Spermatogenic Impairment

Infertility is a growing concern in developed societies. Two extreme phenotypes of male infertility are non-obstructive azoospermia (NOA) and severe oligospermia (SO), which are characterized by severe spermatogenic failure (SpF). We designed a genetic association study comprising 725 Iberian infertile men as a consequence of SpF and 1058 unaffected controls to evaluate whether five single-nucleotide polymorphisms (SNPs), previously associated with reduced fertility in Hutterites, are also involved in the genetic susceptibility to idiopathic SpF and specific clinical entities. A significant difference in the allele frequencies of USP8-rs7174015 was observed under the recessive model between the NOA group and both the control group (p = 0.0226, OR = 1.33) and the SO group (p = 0.0048, OR = 1.78). Other genetic associations for EPSTI1-rs12870438 and PSAT1-rs7867029 with SO and between TUSC1-rs10966811 and testicular sperm extraction (TESE) success in the context of NOA were observed. In silico analysis of functional annotations demonstrated cis-eQTL effects of such SNPs likely due to the modification of binding motif sites for relevant transcription factors of the spermatogenic process. The findings reported here shed light on the molecular mechanisms leading to severe phenotypes of idiopathic male infertility, and may help to better understand the contribution of the common genetic variation to the development of these conditions.

Genetic Landscape of Nonobstructive Azoospermia and New Perspectives for the Clinic

Nonobstructive azoospermia (NOA) represents the most severe expression of male infertility, involving around 1% of the male population and 10% of infertile men. This condition is characterised by the inability of the testis to produce sperm cells, and it is considered to have an important genetic component. During the last two decades, different genetic anomalies, including microdeletions of the Y chromosome, karyotype defects, and missense mutations in genes involved in the reproductive function, have been described as the primary cause of NOA in many infertile men. However, these alterations only explain around 25% of azoospermic cases, with the remaining patients showing an idiopathic origin. Recent studies clearly suggest that the so-called idiopathic NOA has a complex aetiology with a polygenic inheritance, which may alter the spermatogenic process. Although we are far from a complete understanding of the molecular mechanisms underlying NOA, the use of the new technologies for genetic analysis has enabled a considerable increase in knowledge during the last years. In this review, we will provide a comprehensive and updated overview of the genetic basis of NOA, with a special focus on the possible application of the recent insights in clinical practice.

Sequence analysis of 37 candidate genes for male infertility: challenges in variant assessment and validating genes

BACKGROUND

The routine genetic analysis for diagnosing male infertility has not changed over the last twenty years, and currently available tests can only determine the etiology of 4% of unselected infertile patients. Thus, to create new diagnostic assays, we must better understand the molecular and genetic mechanisms of male infertility. Although next-generation sequencing allows for simultaneous analysis of hundreds of genes and the discovery of novel candidates related to male infertility, so far only a few gene candidates have enough sound evidence to support the gene-disease relationship.

OBJECTIVE

Since complementary studies are required to validate genes, we aimed to analyze the presence of potentially pathogenic rare variants in a set of candidate genes related to azoospermia in a hitherto understudied South American population.

SUBJECTS AND METHODS

We performed whole exome sequencing in a group of 16 patients with non-obstructive azoospermia from Ribeirão Preto, Brazil. Based on a recent systematic review of monogenic causes of male infertility, we selected a set of 37 genes related to azoospermia, Sertoli-Cell-Only histology, and spermatogenic arrest to analyze. The identified variants were confirmed by Sanger sequencing, and their functional consequence was predicted by in silico programs.

RESULTS

We identified potential pathogenic variants in seven genes in six patients. Two variants, c.671A>G (p.(Asn224Ser)) in DMRT1 and c.91C>T (p.(Arg31Cys)) in REC8, have already been described in association with azoospermia. We also found new variants in genes that already have moderate evidence of being linked to spermatogenic failure (TEX15, KLHL10), in genes with limited evidence (DNMT3B, TEX14) and in one novel promising candidate gene that has no evidence so far (SYCE1L).

DISCUSSION

Although this study included a small number of patients, the process of rationally selecting genes allowed us to detect rare potentially pathogenic variants, providing supporting evidence for validating candidate genes associated with azoospermia.

Disorders of spermatogenesis: Perspectives for novel genetic diagnostics after 20 years of unchanged routine

Infertility is a common condition estimated to affect 10-15% of couples. The clinical causes are attributed in equal parts to the male and female partners. Diagnosing male infertility mostly relies on semen (and hormone) analysis, which results in classification into the two major phenotypes of oligo- and azoospermia. The clinical routine analyses have not changed over the last 20 years and comprise screening for chromosomal aberrations and Y‑chromosomal azoospermia factor deletions. These tests establish a causal genetic diagnosis in about 4% of unselected men in infertile couples and 20% of azoospermic men. Gene sequencing is currently only performed in very rare cases of hypogonadotropic hypogonadism and the CFTR gene is routinely analysed in men with obstructive azoospermia. Still, a large number of genes have been proposed to be associated with male infertility by, for example, knock-out mouse models. In particular, those that are exclusively expressed in the testes are potential candidates for further analyses. However, the genome-wide analyses (a few array-CGH, six GWAS, and some small exome sequencing studies) performed so far have not lead to improved clinical diagnostic testing. In 2017, we started to routinely analyse the three validated male infertility genes: NR5A1, DMRT1, and TEX11. Preliminary analyses demonstrated highly likely pathogenic mutations in these genes as a cause of azoospermia in 4 men, equalling 5% of the 80 patients analysed so far, and increasing the diagnostic yield in this group to 25%. Over the past few years, we have observed a steep increase in publications on novel candidate genes for male infertility, especially in men with azoospermia. In addition, concerted efforts to achieve progress in elucidating genetic causes of male infertility and to introduce novel testing strategies into clinical routine have been made recently. Thus, we are confident that major breakthroughs concerning the genetics of male infertility will be achieved in the near future and will translate into clinical routine to improve patient/couple care.

CRISPR/Cas9-mediated simultaneous knockout of Dmrt1 and Dmrt3 does not recapitulate the 46,XY gonadal dysgenesis observed in 9p24.3 deletion patients

DM domain transcription factors play important roles in sexual development in a wide variety of species from invertebrate to humans. Among seven mammalian family members of DM domain transcription factors, DMRT1 has been studied in mouse and human for its conserved role in male gonadal identity. Chromosomal deletion of 9p24.3, the region in which DMRT1 is located, is associated with 46,XY gonadal dysgenesis. Dmrt1 knockout (KO) mice also showed male-to-female gonadal reprogramming. However, the phenotype of Dmrt1 KO mouse appears only after birth while 46,XY gonadal dysgenesis occurs during the developmental phase, and the cause behind this difference remained unknown. We hypothesized that in human the function of other DMRT genes clustered with DMRT1, namely DMRT3, might also be impaired by the chromosomal deletion, which leads to the gonadal dysgenesis phenotype. Thus, simultaneous loss of multiple DM domain genes in mice could have a more severe impact on gonadal development. To address this issue, we generated double KO mice for Dmrt1 and Dmrt3 via the CRISPR/Cas9 system. Comparing adult and neonatal testes of single and double KO mice, we found that loss of Dmrt1 or Dmrt3, or both, does not have apparent effect on male gonadal formation during embryonic development. Our study demonstrated that the discrepancy between human with 9p24.3 deletion and Dmrt1 KO mouse could not be explained by the simultaneous loss of Dmrt3 gene. CRISPR/Cas9 is a versatile and straightforward approach to elucidate the questions that were otherwise difficult to address with conventional methods.

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We have generated Dmrt1 KO, Dmrt3 KO and Dmrt1/3 DKO mice via the CRISPR/Cas9 system.

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.CRISPR/Cas9-mediated gene KO could generate 3 KO lines via single microinjection.

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Double KO of Dmrt1 and Dmrt3 could not recapitulate human 9p24.3 deletion symptom.