Y-chromosomal DNA haplotypes in infertile European males carrying Y-microdeletions

COVID-19 and human reproduction: A pandemic that packs a serious punch

The COVID-19 pandemic has led to a worldwide health emergency that has impacted 188 countries at last count. The rapid community transmission and relatively high mortality rates with COVID-19 in modern times are relatively unique features of this flu pandemic and have resulted in an unparalleled global health crisis. SARS-CoV-2, being a respiratory virus, mainly affects the lungs, but is capable of infecting other vital organs, such as brain, heart and kidney. Emerging evidence suggests that the virus also targets male and female reproductive organs that express its main receptor ACE2, although it is as yet unclear if this has any implications for human fertility. Furthermore, professional bodies have recommended discontinuing fertility services during the pandemic such that reproductive services have also been affected. Although increased safety measures have helped to mitigate the propagation of COVID-19 in a number of countries, it seems that there is no predictable timeline to containment of the virus, a goal likely to remain elusive until an effective vaccine becomes available  and widely distributed across the globe. In parallel, research on reproduction has been postponed for obvious reasons, while diagnostic tests that detect the virus or antibodies against it are of vital importance to support public health policies, such as social distancing and our obligation to wear masks in public spaces. This review aims to provide an overview of critical research and ethics issues that have been continuously emerging in the field of reproductive medicine as the COVID-19 pandemic tragically unfolds.Abbreviations: ACE2: angiotensin- converting enzyme 2; ART: Assisted reproductive technology; ASRM: American Society for Reproductive Medicine; CCR9: C-C Motif Chemokine Receptor 9; CDC: Centers for Disease Control and Prevention; COVID-19: Coronavirus disease 2019; Ct: Cycle threshold; CXCR6: C-X-C Motif Chemokine Receptor 6; ELISA: enzyme-linked immunosorbent assay; ESHRE: European Society of Human Reproduction and Embryology; ET: Embryo transfer; FSH: Follicle Stimulating Hormone; FFPE: formalin fixed paraffin embedded; FYCO1: FYVE And Coiled-Coil Domain Autophagy Adaptor 1; IFFS: International Federation of Fertility Societies; IUI: Intrauterine insemination; IVF: In vitro fertilization; LH: Luteinizing Hormone; LZTFL1: Leucine Zipper Transcription Factor Like 1; MAR: medically assisted reproduction services; MERS: Middle East Respiratory syndrome; NGS: Next Generation Sequencing; ORF: Open Reading Frame; PPE: personal protective equipment; RE: RNA Element; REDa: RNA Element Discovery algorithm; RT-PCR: Reverse=trascriptase transcriptase-polymerase chain reaction; SARS: Severe acute respiratory syndrome; SARS-CoV-2: Severe Acute Respiratory Syndrome Coronavirus 2; SLC6A20: Solute Carrier Family 6 Member 20; SMS: Single Molecule Sequencing; T: Testosterone; TMPRSS2: transmembrane serine protease 2; WHO: World Health Organization; XCR1: X-C Motif Chemokine Receptor.

Spermatogenic failure and the Y chromosome

The Y chromosome harbors a number of genes essential for testis development and function. Its highly repetitive structure predisposes this chromosome to deletion/duplication events and is responsible for Y-linked copy-number variations (CNVs) with clinical relevance. The AZF deletions remove genes with predicted spermatogenic function en block and are the most frequent known molecular causes of impaired spermatogenesis (5-10% of azoospermic and 2-5% of severe oligozoospermic men). Testing for this deletion has both diagnostic and prognostic value for testicular sperm retrieval in azoospermic men. The most dynamic region on the Yq is the AZFc region, presenting numerous NAHR hotspots leading to partial losses or gains of the AZFc genes. The gr/gr deletion (a partial AZFc deletion) negatively affects spermatogenic efficiency and it is a validated, population-dependent risk factor for oligozoospermia. In certain populations, the Y background may play a role in the phenotypic expression of partial AZFc rearrangements and similarly it may affect the predisposition to specific deletions/duplication events. Also, the Yp contains a gene array, TSPY1, with potential effect on germ cell proliferation. Despite intensive investigations during the last 20 years on the role of this sex chromosome in spermatogenesis, a number of clinical and basic questions remain to be answered. This review is aimed at providing an overview of the role of Y chromosome-linked genes, CNVs, and Y background in spermatogenesis.

Epigenetics and male reproduction: the consequences of paternal lifestyle on fertility, embryo development, and children lifetime health

The correlation between epigenetics and human reproduction represents a very interesting field of study, mainly due to the possible transgenerational effects related to epigenetic modifications of male and female gametes. In the present review, we focused our attention to the role played by epigenetics on male reproduction, evidencing at least four different levels at which sperm epigenetic modifications could affect reproduction: (1) spermatogenesis failure; (2) embryo development; (3) outcome of assisted reproduction technique (ART) protocols, mainly as concerning genomic imprinting; and (4) long-term effects during the offspring lifetime. The environmental agents responsible for epigenetic modifications are also examined, suggesting that the control of paternal lifestyle prior to conception could represent in the next future a novel hot topic in the management of human reproduction.

Human Chromosome Y and Haplogroups; introducing YDHS Database

BACKGROUND

As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants.

METHODS

The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis.

RESULTS

YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs

CONCLUSIONS

Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.

Partial microdeletions in the Y-chromosome AZFc region are not a significant risk factor for spermatogenic impairment in Tunisian infertile men

Azoospermia factor (AZF) subdeletions were reported to be significant risk factors for spermatogenesis. In this study, we screened classical and partial microdeletions of the Y-chromosome AZF region in a group of 261 infertile men. Partial deletions were also screened in a control group of fertile men (n=124). In addition, Y haplogroups were analyzed in 24 gr/gr deleted patients. Among the 261 studied infertile men, seven subjects were found to have classical microdeletions. The most common partial deletion of AZFc (gr/gr) was observed in 13.02% of infertile men and in 12.90% of fertile men. The b1/b3 deletion was identified in 4.98% of infertile men and in 2.41% of fertile men. In addition, the b2/b3 deletion was identified in 1.53% of infertile patients but not in the control group. Our results suggest that partial AZFc deletions are not associated with spermatogenic failure in the Tunisian population.

Azoospermia factor and male infertility

Recently, work has shown that azoospermia factor (AZF) microdeletions result from homologous recombination between almost identical blocks in this gene region. These microdeletions in the Y chromosome are a common molecular genetic cause of spermatogenetic failure leading to male infertility. After completion of the sequencing of the Y chromosome, the classical definition of AZFa, AZFb, and AZFc was modified to five regions, namely AZFa, P5/proximal-P1, P5/distal-P1, P4/distal-P1, and AZFc, as a result of the determination of Y chromosomal structure. Moreover, partial AZFc deletions have also been reported, resulting from recombination in their sub-ampliconic identical pair sequences. These deletions are also implicated in a possible association with Y chromosome haplogroups. In this review, we address Y chromosomal complexity and the modified categories of the AZF deletions. Recognition of the association of Y deletions with male infertility has implications for the diagnosis, treatment, and genetic counseling of infertile men, in particular candidates for intracytoplasmic sperm injection.

Y chromosome variation in Europe: Continental and local processes in the formation of the extant gene pool

The polymorphism of the male-specific portion of the Y chromosome has been increasingly used to describe the composition of the European gene pool and to reconstruct its formation. Here the theoretical grounds and the limitations of this approach are presented, together with the different views on debated issues. The emerging picture for the composition of the male gene pool of the continent is illustrated, but local peculiarities that represent departures from the main trends are also highlighted, in order to illustrate the main unifying feature, i.e. the overlay of recent patterns onto more ancient ones. A synopsis of the main findings and conclusions obtained in regional studies has also been compiled.

An evolutionary perspective on Y-chromosomal variation and male infertility

Genetic variation on the Y chromosome is one of the best-documented causes of male infertility, but the genes responsible have still not been identified. This review discusses how an evolutionary perspective may help with interpretation of the data available and suggest novel approaches to identify key genes. Comparison with the chimpanzee Y chromosome indicates that USP9Y is dispensable in apes, but that multiple copies of TSPY1 may have an important role. Comparisons between infertile and control groups in search of genetic susceptibility factors are more complex for the Y chromosome than for the rest of the genome because of population stratification and require unusual levels of confirmation. But the extreme population stratification exhibited by the Y also allows populations particularly suitable for some studies to be identified, such as the partial AZFc deletions common in Northern European populations where further dissection of this complex structural region would be facilitated.

Study of azoospermia factor-a deletion caused by homologous recombination between the human endogenous retroviral elements and population-specific alleles in Japanese infertile males

OBJECTIVE

To evaluate the relationship between the status of homologous recombination and population-specific alleles in infertile Japanese males with azoospermia factor (AZF)-a deletions and to characterize the clinical features of these patients.

DESIGN

Retrospective deletion study in infertile Japanese men.

SETTING

University hospital and reproductive clinic.

PATIENT(S)

A total of 931 consecutive patients visiting a male-infertility clinic were genetically evaluated.

INTERVENTION(S)

Patients were analyzed for Y-chromosomal microdeletions and the breakpoints of intrachromosomal homologous recombination of human endogenous retrovirus (HERV) 15qy; in addition, Y-haplogroup typing on the basis of polymerase chain reaction also was performed. Endogenous retroviruses contribute to the evolution of the host genome and can be associated with disease.

MAIN OUTCOME MEASURE(S)

Presence or absence of appropriately sized polymerase chain reaction products.

RESULT(S)

Four cases of AZFa deletions were found. All patients with AZFa deletions had an azoospermia and breakpoints in the ID2 region of HERV15qy. Three of the four cases were derived from Y-haplogroup D2b. Testicular sperm extraction procedures were performed in three of these four patients, and elongated spermatids were recovered in two. However, no pregnancies were successfully achieved.

CONCLUSION(S)

Y-haplotype D2b, specific for some Japanese clade, may be associated with HERV breakpoints that lead to intrachromosomal homologous recombination. From the clinical point of view, the testicular sperm extraction procedure is not applicable to males with complete AZFa deletions.

Male infertility: role of genetic background

Male infertility represents one of the clearest examples of a complex disease with a substantial genetic basis. Numerous male mouse models, mutation screening and association studies reported over the last few years reveal the high prevalence of genetic causes of spermatogenic impairment, accounting for 10-15% of severe male infertility, including chromosomal aberrations and single gene mutations. Natural selection prevents the transmission of mutations causing infertility, but this protective mechanism may be overcome by assisted reproduction techniques. Consequently, the identification of genetic factors is important for appropriate management of the infertile couple. However, a large proportion of infertile males are diagnosed as idiopathic, reflecting poor understanding of the basic mechanisms regulating spermatogenesis and sperm function. Furthermore, the molecular mechanisms underlying spermatogenic damage in cases of genetic infertility (for example Yq microdeletions) are not known. These problems can be addressed only by large scale association studies and testicular or spermatozoal expression studies in well-defined alterations of spermatogenesis. It is conceivable that these studies will have important diagnostic and therapeutic implications in the future. This review discusses the genetic causes of male infertility known to date, the genetic polymorphisms possibly associated with male infertility, and reports novel results of global gene expression profiling of normal human testis by microarray technology.

Y-chromosome haplogroups and susceptibility to azoospermia factor c microdeletion in an Italian population

BACKGROUND

A limited number of studies aimed at investigating the possible association of Y-chromosome haplogroups with microdeletions of the azoospermia factors (AZFs) or with particular infertile phenotypes, but definitive conclusions have not been attained. The main confounding elements in these association studies are the small sample sizes and the lack of homogeneity in the geographical origin of studied populations, affecting, respectively, the statistical power and the haplogroup distribution.

MATERIALS AND METHODS

To assess whether some Y-chromosome haplogroups are predisposing to, or protecting against, azoospermia factor c (AZFc; b2/b4) deletions, 31 north Italian patients carrying the AZFc b2/b4 microdeletion were characterised for 8 Y-chromosome haplogroups, and compared with the haplogroup frequency shown by a north Italian population without the microdeletion (n = 93).

RESULTS AND DISCUSSION

A significant difference was observed between the two populations, patients with microdeletions showing a higher frequency of the E haplogroup (29.3% vs 9.7%, p<0.01). The geographical homogeneity of the microdeleted samples and of the control population, controlled at microgeographical level, allows the possibility that the geographical structure of the Y genetic variability has affected our results to be excluded.

CONCLUSION

Thus, it is concluded that in the north Italian population Y-chromosome background affects the occurrence of AZFc b2/b4 deletions.

Genetic causes of male infertility

Genetic causes account for 10-15% of severe male infertility, including chromosomal aberrations and single gene mutations. Natural selection prevents the transmission of mutations causing infertility, while this protective mechanism may be overcome by assisted reproduction techniques. Consequently the identification of genetic factors has become good practice for appropriate management of the infertile couple. Furthermore, patients affected by some forms of genetic alterations produce a higher frequency of sperm with aneuploidies. Sperm aneuploidies are the direct result of the constitutional genetic abnormality or are caused by meiotic errors induced by the altered testicular environment that these men present. In this review we will report and discuss the genetic causes of male infertility known up to date and we will analyse genetic polymorphisms possibly associated with male infertility.

Y chromosome variants and male reproductive function

The detailed analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions of the long arm of the human Y chromosome, termed AZFa, AZFb and AZFc, (AZF: AZoospermia Factor) that are currently deleted in men with otherwise unexplained spermatogenic failure. Screening for these deletions is now common in many infertility centres and in some instances they have a prognostic relevance. Recently, attention has turned to partial deletions of the AZFc region. At first sight some of these deletions appear to have little effect on fertility, whilst others appear to be associated with significant risk for developing spermatogenic failure. However, the relationship between these partial AZFc deletions, reduced sperm counts and infertility is the subject of a continuing intense debate. There is a pressing need to clarify the impact of partial AZFc deletions on human spermatogenesis. This requires large-scale studies on well-characterized normospermic and oligo/azoospermic individuals of different ethnic origins with multiple informative AZFc markers if the correlation between these deletions and the phenotype is finally to be resolved. The definition of Y chromosome variants (haplotypes) in cases of partial AZFc deletions is likely to play an essential role in understanding the contribution of the deletion to reduced sperm counts.

AZF deletions and Y chromosomal haplogroups: history and update based on sequence

AZF deletions are genomic deletions in the euchromatic part of the long arm of the human Y chromosome (Yq11) associated with azoospermia or severe oligozoospermia. Consequently, it can be assumed that these deletions remove Y chromosomal genes required for spermatogenesis. However, these 'classical' or 'complete' AZF deletions, AZFa, AZFb and AZFc, represent only a subset of rearrangements in Yq11. With the benefit of the Y chromosome sequence, more rearrangements (deletions, duplications, inversions) inside and outside the classical AZF deletion intervals have been elucidated and intra-chromosomal non-allelic homologous recombinations (NAHRs) of repetitive sequence blocks have been identified as their major cause. These include duplications in AZFa, AZFb and AZFc and the partial AZFb and AZFc deletions of which some were summarized under the pseudonym 'gr/gr' deletions. At least some of these rearrangements are associated with distinct Y chromosomal haplogroups and are present with similar frequencies in fertile and infertile men. This suggests a functional redundancy of the AZFb/AZFc multi-copy genes. Alternatively, the functional contribution(s) of these genes to human spermatogenesis might be different in men of different Y haplogroups. That raises the question whether, the frequency of Y haplogroups with different AZF gene contents in distinct human populations leads to a male fertility status that varies between populations or whether, the presence of the multiple Y haplogroups implies a balancing selection via genomic deletion/amplification mechanisms.

Y chromosome polymorphisms in medicine

Ninety-five percent of the length of the human Y chromosome is inherited as a single block in linkage from father to male offspring as a haploid entity. Thus, the Y chromosome represents an invaluable record of all mutations that have occurred along male lineages throughout evolution. For this reason, Y chromosomal DNA variation has been mainly used for investigations on human evolution and for forensic purposes or paternity analysis. Recently, Y chromosomal polymorphisms have been applied in molecular medicine from the perspective of male-specific (spermatogenic failure, testis and prostate cancer) and prevalently male-associated (hypertension, autism) diseases. The absence of recombination on the MSY (male-specific Y) region means that polymorphisms, located in this region, are in tight association with potential functional variations associated with Y-linked phenotypes. Thus, an indirect way to explore if Y chromosome genes are involved in the etiology of a specific disease is the definition of Y chromosome haplogroups in patients versus disease-free and/or the general population. Data on patients with reduced sperm count and prostate cancer indicate that the 'at risk Y haplogroup' may be different in different populations. The situation is rather contradictory for other male-specific or male-associated diseases and further multicenter--possibly multiethnic--studies are needed.

The human Y chromosome: an evolutionary marker comes of age

Until recently, the Y chromosome seemed to fulfil the role of juvenile delinquent among human chromosomes--rich in junk, poor in useful attributes, reluctant to socialize with its neighbours and with an inescapable tendency to degenerate. The availability of the near-complete chromosome sequence, plus many new polymorphisms, a highly resolved phylogeny and insights into its mutation processes, now provide new avenues for investigating human evolution. Y-chromosome research is growing up.

Male reproductive function and the human Y chromosome: is selection acting on the Y?

The human Y chromosome encodes genes that are essential for male sex determination, spermatogenesis and protection against Turner stigmata. In recent years mutations have been identified in Y-chromosome genes associated with these phenotypes and a series of microdeletions of the long arm of the Y have been defined that are specifically associated with male infertility. In parallel, the discovery of polymorphic markers on the Y, comprising of both slow-mutating binary markers and rapidly-mutating microsatellites, has enabled the high resolution definition of a large number of paternal lineages (haplogroups). These Y-chromosome haplogroups have been extensively used to trace population movements and understand human origins and histories, but recently a growing number of association studies have been performed aimed at assessing the relationship between the Y-chromosome background and Y-linked phenotypes such as infertility and male-specific cancers. These preliminary studies, comparing haplogroup distributions between case and control populations, are promising and suggest an association between different Y-chromosome lineages, sperm counts and prostate cancer. However, we highlight the need to extend these studies to other world populations. Increased sample numbers and a better haplogroup resolution using additional binary markers in association studies are necessary. By these approaches novel associations between Y-chromosome haplotypes and disease may be revealed and the degree to which selection is acting on the human Y chromosome may be determined.

Screening for microdeletions in human Y chromosome--AZF candidate genes and male infertility

About 30% of couple infertilities are of male origin, some of them caused by genetic abnormalities of the Y chromosome. Deletions in AZF region can cause severe spermatogenic defects ranging from non-obstructive azoospermia to oligospermia. The intracytoplasmatic sperm injection technique (ICSI) is rapidly becoming a versatile procedure for human assisted reproduction in case of male infertility. The use of ICSI allows Y chromosome defects to be passed from father. The goal of our study is to evaluate the frequency of microdeletions in the long arm of Y chromosome, within the AZF regions, in these cases of infertilities, using molecular genetics techniques. Thirty infertile men with azoospermia or oligozoospermia, determined by spermogram, were studied after exclusion of patients with endocrine or obstructive causes of infertility. Peripheral blood DNA was extracted from each patient, then amplified by multiplex PCR with STS genomic markers from the Y chromosome AZF zones. Each case was checked by multiplex PCR through coamplification with the SRY marker. Three men with microdeletions of the long arm of the Y chromosome were diagnosed among the 30 patients, corresponding to a proportion of 10%. The relatively high proportion of microdeletions found in our population suggest the need for strict patient selection to avoid unnecessary screening for long arm Y chromosome microdeletions. The molecular diagnostics was performed according to the current European Academy of Andrology laboratory guidelines for molecular diagnosis of Y chromosomal microdeletions.

Relationship between Y-chromosomal DNA haplotype and sperm count in Italy

Forty Italian individuals with sperm counts in the range 20-130x10(6)/ml were typed with eleven Y-specific binary markers. Five Y haplogroups (1, 2, 3, 9 and 21) were present in the sample. In Italy, in contrast to Denmark, sperm counts were similar in the different haplogroups.