The diagnosis of male factor infertility due to abnormal semen parameters concerns ~10% of men (Jungwirth et al., 2012; Datta et al., 2016). In today’s andrology workup, ~60% of patients with spermatogenic failure remain idiopathic (Punab et al., 2017). Among the known causes, the most widely considered genetic factors are karyotype abnormalities (up to 17% of patients) and recurrent de novo microdeletions of the Y-chromosomal Azoospermia Factor a (AZFa) (~0.8 Mb), AZFb (~6.2 Mb), and AZFc (~3.5 Mb) regions (2–10%) (Punab et al., 2017; Olesen et al., 2017; Tüttelmann et al., 2011). For more than 15 years, testing for AZF deletions has been strongly recommended in the diagnostic workup for infertility patients with sperm concentration of <5 × 10⁶/ml (ASRM, 2015; Krausz et al., 2014). Most deletion carriers represent patients with either azoospermia (no sperm) or cryptozoospermia (>0–1 million sperm/ejaculate) (Punab et al., 2017; Kohn et al., 2019; Stahl et al., 2010). The most prevalent deletion type is AZFc (~80%), followed by the loss of AZFa (0.5–4%), AZFb (1–5%), and AZFbc (1–3%) regions (Figure 1A). Excess of recurrent AZFc deletions is promoted by the region’s complex genomic structure comprised of long direct and inverted amplicons of nearly identical DNA segments that lead to aberrant meiotic rearrangements in gametogenesis (Kuroda-Kawaguchi et al., 2001; Skaletsky et al., 2003; Figure 1B). The AZFc full deletions remove all the multicopy DAZ (deleted in azoospermia 1), BPY2 (basic charge Y-linked 2), and CDY1 (chromodomain Y-linked 1) genes that are expressed in a testis-enriched manner and considered important in spermatogenesis (Figure 1C).

Figure 1 with 1 supplement see all

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The palindromic structure of the AZFc region also facilitates partial deletions that are rather frequently detected in the general population (Repping et al., 2003; Repping et al., 2004; Rozen et al., 2012; Fernandes et al., 2004). The most prevalent partial deletion types, named after the involved amplicons as g(reen)-r(ed)/g(reen)-r(ed) (lost segment ~1.6 Mb) and b(lue)2/b(lue)3 (~1.8 Mb) reduce the copy number of DAZ, BPY2, and CDY1 genes by roughly 50% (Figure 1B,C, Figure 1—figure supplement 1). The published data on the contribution of gr/gr and b2/b3 deletions to spermatogenic failure are inconsistent. In European populations, the carrier status of the gr/gr deletion increases a risk to low sperm counts ~1.8-fold (Rozen et al., 2012; Bansal et al., 2016a; Krausz et al., 2009). Its more variable effect on spermatogenesis has been shown in Middle Eastern and Asian populations, where the gr/gr deletion is completely fixed in some Y lineages, for example haplogroups D2 and Q1a that are common in Japan and some parts of China (de Carvalho et al., 2006; Teitz et al., 2018). In contrast, the b2/b3 deletion appears to be a risk factor for spermatogenic impairment in several East Asian and African, but not in European or South Asian populations (Bansal et al., 2016b; Colaco and Modi, 2018). Notably, the b2/b3 deletion is completely fixed in Y haplogroup N3 that has a high frequency (up to 90% in some populations) in Finno-Ugric-, Baltic-, and some Turkic-speaking people living in Northern Eurasia (Rozen et al., 2012; Fernandes et al., 2004; Ilumäe et al., 2016). Thus, it is unlikely that the carriership of a gr/gr or b2/b3 deletion per se has an effect on male fertility potential. It has been proposed that this broad phenotypic variability may be explained by the diversity of gr/gr and b2/b3 deletion subtypes (Machev, 2004). Y chromosomes carrying partial AZFc deletions may differ for the content, dosage, or genetic variability of the retained genes, the overall genetic composition reflected by phylogenetic haplogroups or the presence of additional structural variants. Only limited studies have analyzed the subtypes of gr/gr or b2/b3 deletions, and no straightforward conclusions have been reached for their link to spermatogenic failure (Krausz et al., 2009; Ghorbel et al., 2016; Krausz and Casamonti, 2017).

The current study represents the largest in-depth investigation of AZFc partial deletions in men recruited by a single European clinical center. We analysed 1190 Estonian idiopathic patients with male factor infertility in comparison to 1134 reference men from the same population, including 2000 subjects with sperm parameter data available. Y chromosomes carrying gr/gr or b2/b3 deletions were investigated for additional genomic rearrangements, Y-chromosomal haplogroups, and dosage and sequence variation of the retained DAZ, BPY2, and CDY genes. The study aimed to determine the role and contribution of gr/gr and b2/b3 deletion subtypes in spermatogenic failure and to explore their potential in the clinical perspective.

We conducted a comprehensive investigation of partial deletion subtypes of the Y-chromosomal AZFc region in 2324 Estonian men, approximately half with idiopathic spermatogenic impairment (n = 1190) in comparison to the reference group (n = 1134). Importantly, 2000 men had undergone full and uniformly conducted andrological workup at a single clinical center, facilitating fine-scale genotype–phenotype analysis. Previously, no study had undertaken re-sequencing of the retained DAZ, BPY2, and CDY genes along with the assessment of the Y haplogroup, dosage, and retained/deleted genes in the gr/gr or b2/b3-deleted chromosomes in both infertile men and controls. Concordant with the reports from other European populations, the gr/gr, but not the b2/b3 deletion, is a risk factor for spermatogenic impairment in Estonian men with >2-fold increased susceptibility to infertility (Figure 1D). However, the gathered data on the large group of reference men in the current study demonstrated the existence of Y chromosomes carrying a gr/gr deletion without any documented effect on andrological parameters (Supplementary file 3). As a novel finding, the study uncovered complex AZFc rearrangements within a specific Y haplogroup, R1a1-M458 and its sub-lineages, causing severe spermatogenic failure in the majority of carriers (Figure 3, Table 3). This Y lineage has undergone a ~1.6 Mb r2/r3 inversion in the AZFc region that has disrupted the structure of the palindromes P1 and P2, promoting subsequent recurrent deletions and consequently, severely impaired the process of spermatogenesis.

Consistent with key early observations (Rozen et al., 2012; Krausz et al., 2009; Machev, 2004), this study supports the recurrent nature and high subtype diversity of the AZFc partial losses that are currently considered jointly under the umbrella term ‘gr/gr deletions’. The 44 detected gr/gr deletions in our study sample were estimated to have originated independently at least 26 times across the Y phylogenetic tree and include seven different combinations of DAZ and CDY1 gene losses. Apparently, there is a substantial undescribed heterogeneity in the spread and structure of gr/gr deletions that in turn contributes to the phenotypic variability of the genetic effects. Unexpectedly, one in four Estonian gr/gr deletion carriers belonged to the Y-chromosomal haplogroup R1a1-M458 (and its sub-lineages) (Figure 2A,B; 22.7% vs 5.1% reported as the Estonian population frequency; Underhill et al., 2015). Notably, a previous study has reported a significant enrichment of the haplogroup R1a (ancestral lineage to the R1a1-M458) among gr/gr-deleted chromosomes in the Polish population (Rozen et al., 2012), which has a high prevalence, 25%, of R1a1-M458 (Underhill et al., 2015; Figure 4A, Supplementary file 15). All the Estonian gr/gr cases and also additional b2/b3 deletion chromosomes representing this Y lineage carried unusual retained DAZ gene pairs (DAZ1-DAZ3 or DAZ2-DAZ4) in combination with either CDY1a or CDY1b gene copy (Figure 2). These complex AZFc rearrangements were best explained by a preceding (and apparently fixed in R1a1-M458) ~1.6 Mb inversion between the homologous r2 and r3 amplicons, followed by recurrent secondary partial AZFc deletions (Figure 3A). The latter are facilitated by large ampliconic segments positioned in the same orientation. Inversions in the AZFc region are not uncommon, but none of the previously described inversions is expected to substantially disrupt the core palindromic structure of the AZFc region (Figure 1—figure supplement 1; Repping et al., 2004; Machev, 2004). In contrast, the r2/r3 inversion disrupts the structure of palindrome P1 and expands the size of the P2 palindrome more than twofold (Figure 3A). The critical role of intact P1–P2 palindromes in the AZFc structure is supported by the observation that no Y chromosomes have been described with a single DAZ gene copy, whereas the inverted DAZ gene pairs form the ‘heart’ of both P1 and P2. In future studies, long-read sequencing technologies should be applied to determine the detailed genomic structure of the AZFc region in the R1a1-M458 chromosomes and the exact chromosomal breakpoints of the identified r2/r3 inversion and secondary deletion events in oligozoospermia patients.

Figure 4

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As a likely scenario, the r2/r3 inversion plus deletion may predispose to spermatogenic impairment through substantial destabilization of the intra-chromosomal structure affecting meiotic recombination and chromosomal segregation. The removal of some specific genetic factor(s) being responsible for the phenotypic outcome seems a less likely explanation as the gr/gr deletion locations are variable, and so far, no reproducible associations with the exact deleted regions or specific gene copies have been identified. However, recent reports have uncovered an abundance of Y-chromosomal non-coding RNAs and their potential functional involvement in spermatogenesis (Johansson et al., 2019). The AZFc region contains at least one multicopy family of non-coding RNA genes, TTTY4 (Testis-Specific Transcript, Y-Linked 4) with testis-enriched expression. These genes are located in the three g1–g3 duplicons flanking the P1 and P2 palindromic ‘hearts’. The phenotypic consequences of TTTY4 copy number changes are still to be studied. Among 12 Estonian subjects carrying the AZFc r2/r3 inversion plus deletions and with available data for sperm counts, nine cases exhibited severe spermatogenic failure, two cases had moderate oligozoospermia, and only one case (aged 18 years) was normozoospermic (Figure 3B,C). This represented ~8- to 9-fold enrichment of this complex rearrangement among men with severely reduced sperm counts (0–10 × 10⁶; Table 3). This genetic effect was observed specifically on the effectiveness of spermatogenesis, whereas the measurements of bitesticular volume and reproductive hormone levels did not stand out among the rest of analyzed infertile men. Unfortunately, none of the patients carrying the r2/r3 inversion plus deletion had undergone a testicular biopsy during their infertility workup. The histopathological pattern of germ cell abnormalities among these cases remains to be investigated in follow-up studies. This knowledge would facilitate understanding of the consequences this Y-chromosomal rearrangement on spermatogenesis and so maximize the benefit of molecular diagnostics in evidence-based clinical management decisions.

To our knowledge, no other Y-lineage-specific risk variants for spermatogenic impairment have been reported so far. Previously, the DAZ2–DAZ4 deletion had been shown as a high-risk factor for male infertility in the Tunisian population, but the Y haplogroups of those subjects were not investigated (Ghorbel et al., 2016). The survival of such a high-risk lineage in the population seems at first sight surprising, but may be accounted for by its possible age-specific effects on spermatogenesis, which may be exacerbated by the recent general decline in sperm count (Andersson et al., 2008). In the past, this lineage may not have been disadvantageous. The possible age-related progressive worsening of the reproductive phenotype among r2/r3 inversion plus deletion carriers should be investigated in follow-up, ideally longitudinal, studies of sufficiently large numbers of patients to make robust conclusions.

This study outcome has notable clinical implications for the improvement of molecular diagnostics and reducing the proportion of idiopathic male factor infertility cases. In Northern and Central Europe, the prevalence of R1a1-M458 haplogroup carrying the r2/r3 inversion ranges from ~1% in the Netherlands and Denmark to ~2–5% in Austria, Hungary, Germany, Baltics, and most Balkan countries, whereas it is widespread in Slavic populations and carried by 12–26% of men (Figure 4A, Supplementary file 15; Underhill et al., 2015). In non-European populations, the R1a1-M458 Y chromosomes are virtually non-existent (for details, see Underhill et al., 2015). However, in some European populations, recurrent secondary AZFc partial deletions on Y chromosomes representing the R1a1-M458 haplogroup (and its sub-lineages) may potentially explain from 0.3% up to ~9% of cases presenting severe spermatogenic impairment (sperm counts < 10 million per ejaculate) (Figure 4B). Further studies in other populations and large samples of patients and normozoospermic controls are required to fully establish the value of extending the current recommended testing of Y-chromosomal deletions by including the analysis of this novel Y-lineage-specific pathogenic AZFc rearrangement.

The evidence from the literature has shown that the increased prevalence of either gr/gr or b2/b3 deletions in infertility cases appears to be population-dependent (Bansal et al., 2016a; Bansal et al., 2016b). It can be speculated that also in other populations some specific Y lineages may carry AZFc structural variants that in combination with partial deletions (or other rearrangements) predispose to chromosomal instability in the complex process of spermatogenesis involving multiple well-coordinated cell divisions. So far, the largest study of the Y-chromosomal phylogeny of gr/gr deletion carriers included 152 infertile subjects representing seven countries with different population genetic structures (Krausz et al., 2009). However, the number of cases per population was low and the study included only 17 fertile men. Also, the study did not include fine-scale analysis of Y sub-lineages and the retained gene content. Long-range re-sequencing of the whole AZFc region in large numbers of men would be the preferred approach to uncover its structural complexity. Additional pathogenic AZFc rearrangements may also exist among Estonian infertile men. Even after omitting the cases carrying a gr/gr deletion at the r2/r3 inversion background, a non-significant enrichment of the remaining gr/gr deletion chromosomes can be observed in patients compared to reference men (1.9 vs 1.1%, p<0.1; Table 2).

In addition to the main finding, our deep re-sequencing dataset revealed that neither the dosage, sequence variation, nor exact copy of the retained DAZ, BPY2, and CDY1 gene showed any detectable effect on spermatogenic parameters. All chromosomes with AZFc partial deletions exhibit extremely low overall sequence variation of the retained DAZ, BPY2, and CDY genes. This observation is consistent with previous reports showing low levels of genetic diversity of the human Y chromosome (Jobling and Tyler-Smith, 2017) and suggesting that novel variants may be rapidly removed by active gene conversion among Y-chromosomal duplicate genes or selective constraint (Hallast et al., 2013; Rozen et al., 2003; Trombetta and Cruciani, 2017). Among the re-sequenced 382 chromosomes with b2/b3 deletions, no pathogenic mutations were detected in the single retained BPY2 and CDY1 gene copies. At the same time, the high rates of large structural rearrangements and copy number variation in the Y chromosome are well established, contrasting with low levels of sequence variation (Teitz et al., 2018; Shi et al., 2019). One in five or six Estonian Y chromosomes with gr/gr and b2/b3 deletions had undergone secondary rearrangements with no apparent effect on tested andrological parameters and fertility potential (Table 2). In the literature, the data about the effects of secondary duplications after an initial AZFc partial deletion on sperm parameters are inconclusive. Some studies have suggested increased pathogenicity (Lu et al., 2011; Yang et al., 2010; Lin et al., 2007; Ye et al., 2013; Yang et al., 2015), whereas others have reported neutral or even positive effects on spermatogenesis (Krausz et al., 2009; Giachini et al., 2008; Lo Giacco et al., 2014; Noordam et al., 2011). However, further copy number reductions in this genomic region appear to be very rare – none of the 44 gr/gr or 631 b2/b3 deletion carriers were identified with further reductions beyond what is expected from the initial deletion.

The current study is the largest and most detailed to date in terms of both the number of patients with spermatogenic impairment and reference samples with available andrological data from a single population, and detailed characterization of the genetic diversity of the AZFc region and phylogenetic background of the Y chromosomes. Yet, the total number of identified cases with the r2/r3 inversion followed by a deletion was relatively small and also inadequate to reach the statistical power in association testing with andrological parameters. Follow-up replication studies utilizing sample cohorts from populations with high(er) R1a1-M458 frequency (e.g. Polish, Czech) should be undertaken to confirm the prevalence and significance of the identified risk variant. The biggest challenge of such studies is the availability of sufficiently large sample collections of both patients and reference cases with andrological data. The identification of men with R1a1-M458 Y chromosomes and characterization of subsequent deletion subtypes only require standard inexpensive laboratory techniques such as PCR, restriction fragment length polymorphism (RFLP) analysis, and Sanger sequencing.

In summary, we have undertaken a comprehensive study of the carriers of AZFc partial gr/gr and b2/b3 deletions and uncovered high levels of structural variation in the AZFc locus, but low sequence diversity of the coding genes within the region. As a major finding, we discovered a large inversion specific to the Y lineage R1a1-M458 that represents a hotspot for subsequent AZFc partial deletions. Men carrying Y chromosomes with this complex rearrangement have >10 fold increased risk of severe spermatogenic failure, but the consequences of this risk could potentially be alleviated by early identification of the variant carriers and facilitating the storage of their sperm samples. Our study results thus have the potential to improve clinical diagnostics and management of idiopathic impaired spermatogenesis in a significant fraction of men originating from Northern and Central European populations.

Illumina MiSeq re-sequencing data are available through the European Genome-phenome Archive (EGA, https://www.ebi.ac.uk/) under the accession number: EGAS00001002157.

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Author details

1. Pille Hallast

   1. Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
   2. Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom

   Contribution

   Conceptualization, Resources, Data curation, Formal analysis, Supervision, Funding acquisition, Validation, Investigation, Visualization, Methodology, Writing - original draft, Project administration, Writing - review and editing

   For correspondence

   pille.hallast@ut.ee

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-0588-3987

2. Laura Kibena

   Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia

   Contribution

   Data curation, Formal analysis, Validation, Investigation, Methodology, Writing - review and editing

   Competing interests

   No competing interests declared

3. Margus Punab

   1. Andrology Unit, Tartu University Hospital, Tartu, Estonia
   2. Institute of Clinical Medicine, University of Tartu, Tartu, Estonia

   Contribution

   Resources, Data curation, Supervision, Writing - review and editing

   Competing interests

   No competing interests declared

4. Elena Arciero

   Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom

   Contribution

   Investigation, Writing - review and editing

   Competing interests

   No competing interests declared

5. Siiri Rootsi

   Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia

   Contribution

   Resources, Data curation, Writing - review and editing

   Competing interests

   No competing interests declared

6. Marina Grigorova

   Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia

   Contribution

   Resources, Data curation, Writing - review and editing

   Competing interests

   No competing interests declared

7. Rodrigo Flores

   Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia

   Contribution

   Resources, Data curation, Writing - review and editing

   Competing interests

   No competing interests declared

8. Mark A Jobling

   Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom

   Contribution

   Resources, Writing - review and editing

   Competing interests

   No competing interests declared

9. Olev Poolamets

   Andrology Unit, Tartu University Hospital, Tartu, Estonia

   Contribution

   Resources, Data curation, Writing - review and editing

   Competing interests

   No competing interests declared

10. Kristjan Pomm

    Andrology Unit, Tartu University Hospital, Tartu, Estonia

    Contribution

    Resources, Data curation, Writing - review and editing

    Competing interests

    No competing interests declared

11. Paul Korrovits

    Andrology Unit, Tartu University Hospital, Tartu, Estonia

    Contribution

    Resources, Data curation, Writing - review and editing

    Competing interests

    No competing interests declared

12. Kristiina Rull

    1. Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
    2. Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
    3. Women’s Clinic, Tartu University Hospital, Tartu, Estonia

    Contribution

    Resources, Data curation, Writing - review and editing

    Competing interests

    No competing interests declared

13. Yali Xue

    Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom

    Contribution

    Resources, Supervision, Writing - review and editing

    Competing interests

    No competing interests declared

14. Chris Tyler-Smith

    Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom

    Contribution

    Resources, Supervision, Funding acquisition, Writing - review and editing

    Contributed equally with

    Maris Laan

    Competing interests

    No competing interests declared

15. Maris Laan

    Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia

    Contribution

    Resources, Formal analysis, Supervision, Funding acquisition, Investigation, Writing - original draft, Writing - review and editing

    Contributed equally with

    Chris Tyler-Smith

    For correspondence

    maris.laan@ut.ee

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-8519-243X

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