X Chromosome-Linked CNVs in Male Infertility: Discovery of Overall Duplication Load and Recurrent, Patient-Specific Gains with Potential Clinical Relevance

Abstract

IntroductionSpermatogenesis is a highly complex process involving several thousand genes, only a minority of which have been studied in infertile men. In a previous study, we identified a number of Copy Number Variants (CNVs) by high-resolution array-Comparative Genomic Hybridization (a-CGH) analysis of the X chromosome, including 16 patient-specific X chromosome-linked gains. Of these, five gains (DUP1A, DUP5, DUP20, DUP26 and DUP40) were selected for further analysis to evaluate their clinical significance.Materials and MethodsThe copy number state of the five selected loci was analyzed by quantitative-PCR on a total of 276 idiopathic infertile patients and 327 controls in a conventional case-control setting (199 subjects belonged to the previous a-CGH study). For one interesting locus (intersecting DUP1A) additional 338 subjects were analyzed.Results and DiscussionAll gains were confirmed as patient-specific and the difference in duplication load between patients and controls is significant (p = 1.65×10−4). Two of the CNVs are private variants, whereas 3 are found recurrently in patients and none of the controls. These CNVs include, or are in close proximity to, genes with testis-specific expression. DUP1A, mapping to the PAR1, is found at the highest frequency (1.4%) that was significantly different from controls (0%) (p = 0.047 after Bonferroni correction). Two mechanisms are proposed by which DUP1A may cause spermatogenic failure: i) by affecting the correct regulation of a gene with potential role in spermatogenesis; ii) by disturbing recombination between PAR1 regions during meiosis. This study allowed the identification of novel spermatogenesis candidate genes linked to the 5 CNVs and the discovery of the first recurrent, X-linked gain with potential clinical relevance.

Genetics of male infertility: from research to clinic

“…DUP1A, instead, was found exclusively and at a significantly higher frequency in patients. This gain fully duplicates a long non-coding RNA (LINC00685) that potentially acts as a negative regulator of a gene with potential role in spermatogenesis, PPP2R3B; according to our hypothesis, the mechanism by which DUP1A could lead to spermatogenic failure is a misbalanced ratio of the PPP2R3B and its antisense, causing a decrease in PPP2R3B transcription in the developing germ cells (Chianese et al 2014). Our data together with the identification of two SCOS patients with a duplication disrupting the PPP2R3B gene (Tü ttelmann et al 2011) indicate that CNVs mapping into this region and affecting either PPP2R3B or the long non-coding RNA (LINC00685) are good mutational targets for future case-control studies.…”

“…In fact, the two variants DUP1a and CNV69 were objects of large follow-up studies, together with other recurrent deletions, CNV67 and CNV64 (Chianese et al 2014, Lo Giacco et al 2014b. The first study analyzed three recurrent deletions (frequency O1%) in a large case-control setting (nZ1255) for their exclusive (CNV67) and prevalent (CNV64 and CNV69) presence in patients.…”

“…For instance, deletion carriers displayed a higher probability of having impaired spermatogenesis (ORZ1.9 and 2.2 for CNV64 and CNV69 respectively) as well as sperm concentration and total motile sperm number was lower in carriers compared to non-carriers The most interesting deletion was CNV67 because it was exclusively found in patients with a frequency of 1.1% (P!0.01) and is likely to involve the MAGE9A genea CTA family member -and/or its regulatory elements (Lo Giacco et al 2014b). Similarly, a follow-up study was performed on five selected gains (DUP1A, DUP5, DUP20, DUP26 and DUP40), which include, or are in close proximity to, genes with testis-specific expression and potential implication in spermatogenesis (Chianese et al 2014). While four of the five CNVs (DUP5, DUP20, DUP26 and DUP40) did not individually reach statistical significance, they remained patient-specific.…”

MECHANISMS IN ENDOCRINOLOGY: Aberrations of the X chromosome as cause of male infertility

“…In contrast, genome-wide CNV analyses in infertile men are thus far only performed in research settings (10,85,86,87), of which some have focused specifically on the X chromosome (88,89,90). When comparing infertile (oligo-or azoospermic) with fertile (or normozoospermic) men, the consistent finding of the available studies is a significantly higher overall 'burden' of microdeletions, especially on the sex chromosomes (10,85,88,89). In addition, one study has reported an increase of single nucleotide variations (SNVs) in infertile men compared with controls (10), and it has been speculated that infertility may be associated with an increased overall genome instability.…”

New Molecular Technologies in Genetic Diagnosis of Male Infertility

“…Исследование вариаций числа копий при нарушении репродуктивной функции В последние годы начато активное исследование микроструктурных перестроек хромосом, CNV, в том числе при различных формах нарушения развития и функции органов мужской и женской репродуктивной системы, при бесплодии и невынашивании беременно-сти, а также для детекции (скрининга) хромосомных му-таций у эмбриона до его имплантации и у плодов при потере беременности [16][17][18][19][20][21][22][23][24][25][26][27][28].…”