Genetics of male infertility

50% of infertility is attributable to males

Infertility is usually defined as the inability of a couple to conceive after one year of unprotected sexual intercourse. It affects at least 180 million people. About one sixth of all couples worldwide have an issue with infertility. About 50% of all cases of infertility may be attributed to males. However, in several infertile couples, male and female factors co-exist.

Some studies suggest that there is an increased risk for testicular and prostate cancer in infertile men, especially if they are azoospermic. Out of curiosity, sperm count decrease has been recorded the in the general male population. More in detail, the average sperm count showed a reduction of 47 millions/ml between 1940s and the 1990s. The causes are still unknown, however long term exposure to environmental toxins has been hypothesized. In parallel, improved access to medical care may have helped unveiling cases of oligo/azoospermia which would be previously underdiagnosed.

Semen analysis

Semen analysis is the keystone for evaluating male infertility. Semen should be collected twice, once at day 1 and the second time at day 1+7. Abstinence is indicated 3 days before the first specimen collection. The following parameters must be evaluated: volume, pH, leukocytes, immature germ cells and liquefaction. Spermatozoa must be assessed for count, concentration, vitality, motility, progression, debris, and morphology.

Azoospermia indicates the lack of sperm in the ejaculate. This condition can be divided in obstructive azoospermia (OA) or non-obstructive azoospermia (NOA), depending on the presence or absence of obstruction within the reproductive trait. NOA accounts for 60% of azoospermic patients, whereas OA accounts for around 40%.

Oligozoospermia (also know as oligospermia) is defined by a lower amount of sperm in the ejaculate compared with the general population (< 15 millions/ml). Sperm decrease can be mild (5-15 millions/ml, mild oligozoospermia), moderate (1-5 millions/ml, moderate oligozoospermia) or severe (<1 million/ml, severe oligozoospermia). In oligozoospermia, motility and/or morphology of spermatozoa may be altered as well (defining conditions known as asthenozoospermia, teratozoospermia, or asthenoteratozoospermia).

Spectrum of genetic causes of male infertility

Male infertility has genetic causes in about 15% of cases. Chromosomal rearrangements (such as Robertsonian translocations and reciprocal translocations) are the most frequent ones among the genetic causes of male infertility.  Single-gene point mutations (i.e. monogenic causes) are also possible, although they are rarer. Surprisingly, over 200 genetic disorders related to male infertility are reported in the OMIM database.

Pathogenic mutations may occur in genes coding for proteins involved in spermatogenesis and the development of the male reproductive system. Spermatogenesis is a complex process, which takes place in the seminiferous tubules. More than 2,000 testis-specific genes are involved in spermatogenesis.

Chromosomal abnormalities

Robertsonian and reciprocal translocations

Robertsonian translocations are the most common form of unbalanced chromosomal translocation. A Robertsonian translocation occurs when two acrocentric chromosomes (13-15, 21 and 22) fuse together at their centric ends. Individuals with Robertsonian translocation have 45 chromosomes instead of 46. The loss of the short arms of the two acrocentric chromosomes is not deleterious for the carrier, but can affect fertility and/or pregnancy outcome due to the production of genetically unbalanced gametes. Robertsonians translocations are found in 0.9%-3.4% of infertile men with severe spermatogenic dysfunction. Similarly, balanced reciprocal translocations may also cause infertility or recurrent pregnancy loss. Notably, these chromosomal rearrangements may also lead to fetal malformations and the birth of a syndromic baby.

Klinefelter syndrome

The most common genetic condition (and also the most frequent chromosomal aneuploidy in human males) associated to male infertility is Klinefelter syndrome (KS). KS is characterized by the presence of one or more extra X chromosome in the cells of a male individual. So, a male with KS shows a karyotype with two or more X chromosomes (47,XXY is the most common karyotype).

Y chromosome microdeletions

After chromosomal rearrangements and Klinefelter syndrome, chromosome Y microdeletions encompassing the male-specific region (male-specific region of the Y chromosome – MSY) are the most common cause of male infertility. Y chromosome microdeletions are not detectable by karyotype analysis because they are too small. Notably, the MSY region spans 95% of the DNA sequence of the entire Y chromosome (the remaining 5% of the Y chromosome sequence is consistent with the small pseudoautosomal regions, which are located at the edge of the short and long arm of the chromosome). Three important sub-regions of the MSY were identified: AZFa, AZFb and AZFc.

Patients with complete AZFa deletions tend to develop a phenotype consistent with azoospermia and SCO syndrome (or Sertoli Cell Only syndrome, a condition in which the germ cells are absent in testis). Patients with partial deletions of this region may have a variable phenotype, ranging from azoospermia to less severe phenotypes.
The AZFb region is involved throughout spermatogenesis. Deletions of this region cause maturation arrest of the spermatozoa. Men with complete deletions of AZFa or complete AZFb deletions are not able to conceive naturally. No viable sperm can be detected in testis.
Complete AZFc deletions are the most common. Men with AZFc deletions have the least severe spermatogenic phenotype, ranging from azoospermia to mild oligozoospermia.

Currently, only complete AZF region deletions have shown prognostic value. By contrast, partial deletions should be carefully evaluated, taking into account which genes have been lost. For instance, mutations in the SRY gene are reported in males with 46,XY complete gonadal dysgenesis and a female phenotype. Two intragenic mutations in the USP9Y gene have been associated to NOA, whereas conflicting literature data have been published for USP9Y deletion. Complete and partial deletions of the RBMY gene are associated to male infertility. The DAZ gene, which is represented in the DNA sequence by four, almost identical copies, is also frequently deleted in infertile men.

Monogenic causes

Cystic Fibrosis

Ductal dysfunction refers to any defect that alter the sperm transport system in the urogenital tract. They can cause azoospermia or oligozoospermia, even if the testis are normal. There is a congenital form of absence of the vas deferens (CAVD), caused by one pathogenic mutation plus one reduced penetrance allele (5T) in the CFTR gene.

Androgen insensitivity syndrome

The AR gene codes for the androgen receptor, which is essential for male phenotype development and spermatogenesis. Mutations in the AR gene show a phenotypic spectrum that ranges from phenotypic female with complete androgen insensitivity to undervirilized male phenotype with partial androgen insensitivity, up to normal male genital phenotype with impaired sperm production. An expansion of a trinucleotide CAG repeat in the AR gene can also cause Kennedy disease, a form of spinal muscular atrophy. In Kennedy disease, decreased fertility and testicular atrophy can be observed, although not in all patients.

Other monogenic causes of male infertility

We mentioned that the hypothalamic-pituitary axis has an important role in normal development of the testis. Congenital hypogonadotropic hypogonadism (CHH) is a rare complex genetic disease with variable expressivity and penetrance caused by a pathogenic mutation in one of several different genes. CHH has an incidence of 1:8,000 and is commonly characterized by absent or delayed puberty, sparse hair, gynecomastia, cryptorchidism, micropenis and very low testicular volume. However, in some cases, reduced spermatogenesis and mild hypoandrogenism may be the only symptoms. Sometimes CHH is associated with loss or reduced sense of smell (anosmia or hyposmia), a condition which is also referred to as Kallmann syndrome.

Spermatogenic failure caused by mutations in the AURKC gene is characterized by macrocephaly and large-headed and multiflagellated spermatozoa. It is a rare condition, which may be detected in as low as <1% of subfertile men.

Globozoospermia is a very rare condition, affecting 0.1% of infertile men, characterized by round-headed spermatozoa, Such spermatozoa are unable to fertilize the oocyte. This condition is caused by pathogenic mutations in a bunch of genes (DPY19L2, ZPBP, PICK1, and SPATA16).

Asthenoteratozoospermia with multiple morphological abnormalities can be caused, in up to 25% of cases, by bi-allelic mutations in the DNAH1 gene.

Bi-allelic mutations in the DNAI1 or DNAH5 genes are detected in up to 30% of primary ciliary dyskinesia (PCD) patients. PCD is a multisystemic disease with a prevalence of around 1:20,000. PCD is characterized by chronic respiratory tract infections, abnormally positioned internal organs (situs inversus) and asthenozoospermia. I addition to DNAI1 and DNAH5, more than 20 other genes are know to be related to PCD.

The CATSPER gene cluster codes for a sperm-specific ion channels, which are essential for sperm motility. The CATSPER complex contains 4 subunits encoded by the CATSPER1, CATSPER2, CATSPER3 and CATSPER4 genes. Bi-allelic mutation in the CATSPER1 gene cause nonsyndromic asthenoteratospermia. Homozygous deletions of the CATSPER2 gene and the neighbouring STRC gene cause asthenoteratospermia with nonsyndromic deafness.

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Leslie et al. Male Infertility. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2021 Jan. 2021 Feb 12. PMID: 32965929.

Kuroda et al. Genetic disorders and male infertility. Reprod Med Biol. 2020 Jun 27;19(4):314-322. PMID: 33071633

Krausz et Riera-Escamilla. Genetics of male infertility. Nat Rev Urol. 2018 Jun;15(6):369-384. PMID: 29622783.

Ferlin et al. Genetic causes of male infertility. Reprod Toxicol. 2006 Aug;22(2):133-41. PMID: 16806807.

Shamsi et Dada. Genetic and epigenetic factors: Role in male infertility. Indian J Urol. 2011 Jan;27(1):110-20. PMID: 21716934.

Precone et al. Male Infertility Diagnosis: Improvement of Genetic Analysis Performance by the Introduction of Pre-Diagnostic Genes in a Next-Generation Sequencing Custom-Made Panel. Front Endocrinol (Lausanne)
. 2021 Jan 26;11:605237. PMID: 33574797.

Brilli et Forti. Managing infertility in patients with Klinefelter syndrome. Expert Rev Endocrinol Metab. 2014 May;9(3):239-250. PMID: 30736163.

Punjani et al. Clinical implications of Y chromosome microdeletions among infertile men. Best Pract Res Clin Endocrinol Metab. 2020 Nov 5;101471. PMID: 33214080.

Fan et Silber. Y Chromosome Infertility. In: GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2021. 2002 Oct 31 [updated 2019 Aug 1]. PMID: 20301513.

Dickinson et Collaco. Cystic Fibrosis. Pediatr Rev. 2021 Feb;42(2):55-67. PMID: 33526571

Ong et al. Cystic Fibrosis and Congenital Absence of the Vas Deferens. In: GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2020. 2001 Mar 26 [updated 2017 Feb 2]. PMID: 20301428.ù

Wong et al. Congenital absence of the vas deferens: Cystic fibrosis transmembrane regulatory gene mutations. Best Pract Res Clin Endocrinol Metab. 2020 Dec 1;101476. PMID: 33353780.

Hildebrand et al. CATSPER-Related Male Infertility. In: GeneReviews® [Internet]. Seattle (WA): University of Washington, Seattle; 1993–2021. 2009 Dec 3 [updated 2017 Mar 23]. PMID: 20301780.


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