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Adriano MRG, Bortolai A, Madia FAR, da Silva Carvalho GF, Nascimento AM, Zanardo EA, Wolff BM, Waisberg J, Bos-Mikich A, Kulikowski LD, Dias AT. Cytogenetics investigation in 151 Brazilian infertile male patients and genomic analysis in selected cases: experience of 14 years in a public genetic service. BMC Res Notes 2024; 17:67. [PMID: 38444014 PMCID: PMC10916190 DOI: 10.1186/s13104-024-06710-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
OBJECTIVES Male infertility accounts for approximately 30% of cases of reproductive failure. The characterization of genetic variants using cytogenomic techniques is essential for the adequate clinical management of these patients. We aimed to conduct a cytogenetic investigation of numerical and structural rearrangements and a genomic study of Y chromosome microdeletions/microduplications in infertile men derived from a single centre with over 14 years of experience. RESULTS We evaluated 151 infertile men in a transversal study using peripheral blood karyotypes and 15 patients with normal karyotypes through genomic investigation by multiplex ligation-dependent probe amplification (MLPA) or polymerase chain reaction of sequence-tagged sites (PCR-STS) techniques. Out of the 151 patients evaluated by karyotype, 13 presented chromosomal abnormalities: two had numerical alterations, and 11 had structural chromosomal rearrangements. PCR-STS detected a BPY2 gene region and RBMY2DP pseudogene region microdeletion in one patient. MLPA analysis allowed the identification of one patient with CDY2B_1 and CDY2B_2 probe duplications (CDY2B and NLGN4Y genes) and one patient with BPY2_1, BPY2_2, and BPY2_4 probe duplications (PRY and RBMY1J genes).
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Affiliation(s)
- Márcia Regina Gimenes Adriano
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil.
| | - Adriana Bortolai
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
| | - Fabricia Andreia Rosa Madia
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Gleyson Francisco da Silva Carvalho
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Amom Mendes Nascimento
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Evelin Aline Zanardo
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Beatriz Martins Wolff
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Jaques Waisberg
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
| | - Adriana Bos-Mikich
- Departamento de Ciências Morfológicas, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, 90050-170, Brasil
| | - Leslie Domenici Kulikowski
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
| | - Alexandre Torchio Dias
- Laboratório de Citogenética, Serviço de Laboratório de Análises Clínicas, Instituto de Assistência Médica do Servidor Público do Estado de São Paulo (IAMSPE), São Paulo, SP, 04039-901, Brasil
- Laboratório de Citogenômica, Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, 05403-000, Brasil
- Universidade Paulista - UNIP - Instituto de Ciências da Saúde - Curso de Biomedicina, São Paulo, Brasil
- CITOGEM Biotecnologia, São Paulo, Brasil
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Hajiesmaeil M, Ravasini F, Risi F, Magnarini G, Olivieri A, D'Atanasio E, Galehdari H, Trombetta B, Cruciani F. High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis. Sci Rep 2023; 13:11857. [PMID: 37481605 PMCID: PMC10363161 DOI: 10.1038/s41598-023-39069-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
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Affiliation(s)
- Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Magnarini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', Pavia University, Pavia, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy.
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3
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Nakagawa Y, Tada A, Kojo K, Tsuchiya H, Kurobe M, Uchida M, Yamasaki K, Iwamoto T, Sato Y. Analysis of the correlation between gene copy deletion in the AZFc region and male infertility in Japanese men. Reprod Biol 2023; 23:100728. [PMID: 36640629 DOI: 10.1016/j.repbio.2022.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 12/26/2022] [Accepted: 12/29/2022] [Indexed: 01/15/2023]
Abstract
Deletion of the azoospermia factor c (AZFc), located on the long arm of the Y chromosome, is a cause of male infertility. The structure of the Y chromosome is diversified by the copy number of various genes, such as deleted in azoospermia (DAZ), basic protein Y2, chromodomain Y1, testis-specific transcript Y-linked 4, and Golgi autoantigen golgin subfamily a2 like Y, located in the AZF region. In this study, we investigated the deletion of each gene copy and analyzed its relationship with Japanese male infertility. Deletions of single nucleotide variants of each gene copy in 721 proven fertile men as controls, 139 patients with non-obstructive azoospermia (NOA), and 56 patients with oligozoospermia (OS) were analyzed via polymerase chain reaction-restriction fragment length polymorphism analysis. Their association with infertility was analyzed using logistic regression analysis adjusted for the Y-chromosome haplogroup, D1a2a. Deletions of DAZ/II in the r1 region and DAZ/V in the r1 and r2 regions showed significant associations with NOA (odds ratio [OR] = 4.15, 95 % confidence interval [CI] = 1.18-14.6, P = 0.026; OR = 4.19, 95 % CI = 1.19-14.7, P = 0.025, respectively). They did not show any association with OS. Partial deletion of the AZFc region affects spermatogenesis in Japanese male.
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Affiliation(s)
- Yusuke Nakagawa
- Department of Pharmaceutical Information Science, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8505, Japan
| | - Atsushi Tada
- Department of Pharmaceutical Information Science, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8505, Japan
| | - Kosuke Kojo
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan; Department of Urology, University of Tsukuba Hospital, Ibaraki 305-8576, Japan
| | - Haruki Tsuchiya
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan
| | - Masahiro Kurobe
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan
| | - Masahiro Uchida
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan; Urology department, Tsukuba Gakuen Hospital, Ibaraki 305-0854, Japan
| | - Kazumitsu Yamasaki
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan; Urology department, Tsukuba Gakuen Hospital, Ibaraki 305-0854, Japan
| | - Teruaki Iwamoto
- Center for Infertility and IVF, International University of Health and Welfare Hospital, Tochigi 329-2763, Japan; Department of Male Infertility, Reproduction Center, Sanno Hospital, Tokyo 107-0052, Japan
| | - Youichi Sato
- Department of Pharmaceutical Information Science, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima 770-8505, Japan.
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Hallast P, Kibena L, Punab M, Arciero E, Rootsi S, Grigorova M, Flores R, Jobling MA, Poolamets O, Pomm K, Korrovits P, Rull K, Xue Y, Tyler-Smith C, Laan M. A common 1.6 mb Y-chromosomal inversion predisposes to subsequent deletions and severe spermatogenic failure in humans. eLife 2021; 10:65420. [PMID: 33781384 PMCID: PMC8009663 DOI: 10.7554/elife.65420] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 12/19/2022] Open
Abstract
Male infertility is a prevalent condition, affecting 5–10% of men. So far, few genetic factors have been described as contributors to spermatogenic failure. Here, we report the first re-sequencing study of the Y-chromosomal Azoospermia Factor c (AZFc) region, combined with gene dosage analysis of the multicopy DAZ, BPY2, and CDYgenes and Y-haplogroup determination. In analysing 2324 Estonian men, we uncovered a novel structural variant as a high-penetrance risk factor for male infertility. The Y lineage R1a1-M458, reported at >20% frequency in several European populations, carries a fixed ~1.6 Mb r2/r3 inversion, destabilizing the AZFc region and predisposing to large recurrent microdeletions. Such complex rearrangements were significantly enriched among severe oligozoospermia cases. The carrier vs non-carrier risk for spermatogenic failure was increased 8.6-fold (p=6.0×10−4). This finding contributes to improved molecular diagnostics and clinical management of infertility. Carrier identification at young age will facilitate timely counselling and reproductive decision-making.
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Affiliation(s)
- Pille Hallast
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Laura Kibena
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Margus Punab
- Andrology Unit, Tartu University Hospital, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Elena Arciero
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Siiri Rootsi
- Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Marina Grigorova
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Rodrigo Flores
- Institute of Genomics, Estonian Biocentre, University of Tartu, Tartu, Estonia
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Olev Poolamets
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Paul Korrovits
- Andrology Unit, Tartu University Hospital, Tartu, Estonia
| | - Kristiina Rull
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Women's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Yali Xue
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Chris Tyler-Smith
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Liu X, Zhang H, Yu Y, Fei J, Jiang Y, Liu R, Wang R, Zhang G. Deletion of b1/b3 shows risk for expanse of Yq microdeletion in male offspring: Case report of novel Y chromosome variations. Medicine (Baltimore) 2020; 99:e22124. [PMID: 32925763 PMCID: PMC7489624 DOI: 10.1097/md.0000000000022124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
RATIONALE This study aimed to report 1 family case with novel Y chromosome structural variations by an established next-generation sequencing (NGS) method using unique STSs. PATIENT CONCERNS The case studied was from a family with a father and son (the proband). G-band staining was used for karyotype analysis. Y chromosome microdeletions were detected by sequence-tagged site (STS)-PCR analysis and a new NGS screening strategy. DIAGNOSES Semen analysis showed that the proband was azoospermic. The patient had an abnormal karyotype (45,X[48%]/46,XY[52%]). His father exhibited a normal karyotype. STS-PCR analysis showed that the proband had a deletion of the AZFb+c region, and his father had no deletion of STS markers examined. The sequencing method revealed that the patient had DNA sequence deletions from nt 20099846 to nt 28365090 (8.3 Mb), including the region from yel4 to the Yq terminal, and his father exhibited a deletion of b1/b3 and duplication of gr/gr. INTERVENTIONS The proband was advised to undergo genetic counseling, and consider the use of sperm from a sperm bank or adoption to become a father. OUTCOMES The proband was azoospermic. AZFc partial deletions may produce a potential risk for large AZFb+c deletions or abnormal karyotypes causing spermatogenic failure in men. LESSONS The NGS method can be considered a clinical diagnostic tool to detect Y chromosome microdeletions. The partial AZFc deletions and/or duplications can be a risk of extensive deletions in offspring.
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Affiliation(s)
- Xiangyin Liu
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Hongguo Zhang
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Yang Yu
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Jia Fei
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
| | - Yuting Jiang
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Ruizhi Liu
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Ruixue Wang
- Center for Reproductive Medicine, Center of Prenatal Diagnosis, First Hospital, Jilin University, Changchun
| | - Guirong Zhang
- Peking Medriv Academy of Genetics and Reproduction, Peking, China
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Xie S, Zhang Y, Yang Y. Is the primary AZFc duplication a potential risk for male infertility?: A systematic review and meta-analysis. Andrology 2020; 8:996-1004. [PMID: 32298532 DOI: 10.1111/andr.12800] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 03/14/2020] [Accepted: 04/08/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Numerous studies have been performed to investigate the association between the primary AZFc duplication and male infertility risk; however, the sample sizes have been small and the results have been controversial. A meta-analysis was performed to assess these associations. METHODS A systematic search was conducted to identify all relevant studies from the PubMed, Web of Science, Medline, CNKI, and Wanfang databases up to October 22, 2019. The odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to assess the strength of associations. All of the statistical analyses were conducted by using RevMan 5.3. RESULTS Eleven studies were identified that involved 3140 infertile men and 2280 fertile men. Overall, there was a statistically significant association between the primary AZFc duplication and male infertility (OR = 1.66, 95% CI = 1.29-2.14, P < .0001). In the subgroup analysis by ethnic group, a statistically significant association between the primary AZFc duplication and male infertility was observed in Asian men (OR = 2.26, 95% CI = 1.64-3.12, P < .00001), but not in European men (OR = 0.90, 95% CI = 0.59-1.38, P = .64). For subtypes of the primary AZFc duplication, a statistically significant association was observed between the gr/gr duplication-only (OR = 2.71, 95% CI = 1.38-5.32, P = .004) and infertility in Asian men. Asian men with the primary AZFc duplication resulting in more than four DAZ genes were found to be at an increased risk for infertility (OR = 2.70, 95% CI = 1.49-4.89, P = .001). CONCLUSION Our meta-analysis provides an unprecedented illustration of how the association between the primary AZFc duplication and male infertility may be dependent on ethnicity or geographic location. Furthermore, gr/gr duplication or increased DAZ copy number can be detrimental to spermatogenesis in Asian men.
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Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yangwei Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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Kuzmanovska M, Noveski P, Terzic M, Plaseski T, Kubelka-Sabit K, Filipovski V, Lazarevski S, Sukarova Stefanovska E, Plaseska-Karanfilska D. Y-chromosome haplogroup architecture confers susceptibility to azoospermia factor c microrearrangements: a retrospective study. Croat Med J 2019. [PMID: 31187956 PMCID: PMC6563173 DOI: 10.3325/cmj.2019.60.273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim To assess the association between azoospermia factor c microrearrangements and semen quality, and between Y-chromosome background with distinct azoospermia factor c microrearrangements and semen quality impairment. Methods This retrospective study, carried out in the Research Center for Genetic Engineering and Biotechnology “Georgi D. Efremov,” involved 486 men from different ethnic backgrounds referred for couple infertility from 2002-2017: 338 were azoospermic/oligozoospermic and 148 were normozoospermic. The azoospermia factor c microrearrangements were analyzed with sequence tagged site and sequence family variant markers, quantitative fluorescent polymerase chain reaction, and multiplex ligation probe amplification analysis. The Y-haplogroups of all participants were determined with direct single nucleotide polymorphism typing and indirect prediction with short tandem repeat markers. Results Our participants had two types of microdeletions: gr/gr and b2/b3; three microduplications: b2/b4, gr/gr, and b2/b3; and one complex rearrangement gr/gr deletion + b2/b4 duplication. Impaired semen quality was not associated with microrearrangements, but b2/b4 and gr/gr duplications were significantly associated with haplogroup R1a (P < 0.001 and P = 0.003, respectively) and b2/b3 deletions with haplogroup E (P = 0.005). There were significantly more b2/b4 duplication carriers in Albanians than in Macedonians with haplogroup R1a (P = 0.031). Conclusion Even though azoospermia factor c partial deletions/duplications and Y-haplogroups were not associated with impaired semen quality, specific deletions/duplications were significantly associated with distinct haplogroups, implying that the Y chromosome background may confer susceptibility to azoospermia factor c microrearrangements.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Dijana Plaseska-Karanfilska
- Dijana Plaseska-Karanfilska, Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Krste Misirkov 2, 1000 Skopje, North Macedonia,
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Cioppi F, Casamonti E, Krausz C. Age-Dependent De Novo Mutations During Spermatogenesis and Their Consequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:29-46. [DOI: 10.1007/978-3-030-21664-1_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Teitz LS, Pyntikova T, Skaletsky H, Page DC. Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages. Am J Hum Genet 2018; 103:261-275. [PMID: 30075113 DOI: 10.1016/j.ajhg.2018.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Amplicons-large, highly identical segmental duplications-are a prominent feature of mammalian Y chromosomes. Although they encode genes essential for fertility, these amplicons differ vastly between species, and little is known about the selective constraints acting on them. Here, we develop computational tools to detect amplicon copy number with unprecedented accuracy from high-throughput sequencing data. We find that one-sixth (16.9%) of 1,216 males from the 1000 Genomes Project have at least one deleted or duplicated amplicon. However, each amplicon's reference copy number is scrupulously maintained among divergent branches of the Y chromosome phylogeny, including the ancient branch A00, indicating that the reference copy number is ancestral to all modern human Y chromosomes. Using phylogenetic analyses and simulations, we demonstrate that this pattern of variation is incompatible with neutral evolution and instead displays hallmarks of mutation-selection balance. We also observe cases of amplicon rescue, in which deleted amplicons are restored through subsequent duplications. These results indicate that, contrary to the lack of constraint suggested by the differences between species, natural selection has suppressed amplicon copy number variation in diverse human lineages.
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10
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Yan Y, Yang X, Liu Y, Shen Y, Tu W, Dong Q, Yang D, Ma Y, Yang Y. Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia. Hum Reprod 2018; 32:1521-1531. [PMID: 28498920 DOI: 10.1093/humrep/dex100] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/28/2017] [Indexed: 02/05/2023] Open
Abstract
STUDY QUESTION What is the influence of copy number variation (CNV) in functional RNA binding motif protein Y-linked family 1 (RBMY1) on spermatogenic phenotypes? SUMMARY ANSWER The RBMY1 functional copy dosage is positively correlated with sperm motility, and dosage insufficiency is an independent risk factor for asthenozoospermia. WHAT IS KNOWN ALREADY RBMY1, a multi-copy gene expressed exclusively in the adult testis, is one of the most important candidates for male infertility in the azoospermia factor (AZF) region of the Y-chromosome. RBMY1 encodes an RNA-binding protein that serves as a pre-mRNA splicing regulator during spermatogenesis, and male mice deficient in Rbmy are sterile. STUDY DESIGN, SIZE, DURATION A total of 3127 adult males were recruited from 2009 to 2016; of this group, the dosage of RBMY1 functional copy were investigated in 486 fertile males. In the remaining 2641 males with known spermatogenesis status, 1070 Y-chromosome haplogroup (Y-hg) O3* or O3e carriers without chromosomal aberration or known AZF structure mutations responsible for spermatogenic impairment, including 506 men with normozoospermia and 564 men with oligozoospermia or/and asthenozoospermia, were screened, and the RBMY1 functional copy dosage and copy conversion were determined to explore their associations with sperm phenotypes. The correlation between RBMY1 dosage and its mRNA level or RBMY1 protein level and the correlation between sperm RBMY1 level and motility were analysed in 15 testis tissue samples and eight semen samples. Ten additional semen samples were used to confirm the subcellular localization of RBMY1 in individual sperm. PARTICIPANTS/MATERIALS, SETTING, METHODS All the Han volunteers donating whole blood, semen and testis tissue were from southwest China. RBMY1 copy number, copy conversion, mRNA/protein amount and protein location in sperm were detected using the AccuCopy® assay method, paralog ratio test, quantitative PCR, western blotting and immunofluorescence staining methods, respectively. MAIN RESULTS AND THE ROLE OF CHANCE This study identified Y-hg-independent CNV of functional RBMY1 in the enrolled population. A difference in the distribution of RBMY1 copy number was observed between the group with normal sperm motility and the group with asthenozoospermia. A positive correlation between the RBMY1 copy dosage and sperm motility was identified, and the males with fewer than six copies of RBMY1 showed an elevated risk for asthenozoospermia relative to those with six RBMY1 copies, the most common dosage in the population. The RBMY1 copy dosage was positively correlated with its mRNA and protein level in the testis. Sperm with high motility were found to carry more RBMY1 protein than those with relatively low motility. The RBMY1 protein was confirmed to predominantly localize in the neck and mid-piece region of sperm as well as the principal piece of the sperm tail. Our population study completes a chain of evidence suggesting that RBMY1 influences the susceptibility of males to asthenozoospermia by modulating sperm motility. LIMITATIONS REASONS FOR CAUTION High sequence similarity between the RBMY1 functional copies and a large number of pseudogenes potentially reduces the accuracy of the copy number detection. The mechanism underlying the CNV in RBMY1 is still unclear, and the effect of the structural variations in the RBMY1 copy cluster on the copy dosage of other protein-coding genes located in the region cannot be excluded, which may potentially bias our observations. WIDER IMPLICATIONS OF THE FINDINGS Asthenozoospermia is a multi-factor complex disease with a limited number of proven susceptibility genes. This study identified a novel genomic candidate independently contributing to the condition, enriching our understanding of the role of AZF-linked genes in male reproduction. Our finding provides insight into the physiological and pathological characteristics of RBMY1 in terms of sperm motility, supplies persuasive evidence of the significance of RBMY1 copy number analysis in the clinical counselling of male infertility resulting from asthenozoospermia. STUDY FUNDING/COMPETING INTEREST(S) This work was funded by the National Natural Science Foundation of China (Nos. 81370748 and 30971598). The authors have no conflicts of interest.
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Affiliation(s)
- Yuanlong Yan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Wenling Tu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Dong Yang
- Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan 610031, China
| | - Yongyi Ma
- Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan 610016, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, No. 1, Keyuan Road 4, Gaopeng Street, Chengdu, Sichuan 610041, China
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Shen Y, Xu J, Yang X, Liu Y, Ma Y, Yang D, Dong Q, Yang Y. Evidence for the involvement of the proximal copy of the MAGEA9 gene in Xq28-linked CNV67 specific to spermatogenic failure. Biol Reprod 2017; 96:610-616. [PMID: 28339631 DOI: 10.1093/biolre/iox006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/03/2017] [Indexed: 02/05/2023] Open
Abstract
Spermatogenic failure characterized by impaired sperm production is a common multifactorial disease with molecular and cytogenetic causes for its extreme phenotype that include azoospermia and severe oliogzoospermia. Recently, a high-resolution array-comparative genomic hybridization analysis of the X chromosome and a subsequent cohort study revealed three X-linked microdeletions (CNV64, CNV67, and CNV69) that were associated with decreased sperm production in a mixed group that included Spanish and Italian males. To confirm their spermatogenic effect, we examined the hemizygous deletions and copy dosage of the MAGE family member A9 (MAGEA9) gene, which is a potential X-linked candidate for the CNV67-related spermatogenic phenotype, to investigate their association with spermatogenic failure in 1722 Han males from southwest China. The individuals in this group consisted of 884 patients with idiopathic azoospermia/oliogzoospermia and 838 controls with normozoospermia. Our results showed that both CNV64 and CNV69 were more common in patients than in controls. Similar to that reported previously, the CNV67 was also identified as being specific to spermatogenic failure in our population, although it was rare. More importantly, the paralog ratio tests and sequence family variant analyses provided evidence that the CNV67 might cause a partial deletion of the proximal copy of the MAGEA9 and suggests that CNV67-related spermatogenic failure may be attributed to the functional defect of the Cancer/Testis gene. Our findings highlight the potential of the Xq-linked CNV67 to serve as a novel detection target in the etiological diagnosis of spermatogenic failure and male infertility, although its pathogenic mechanism remains to be elucidated.
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Affiliation(s)
- Ying Shen
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jinyan Xu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiling Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yongyi Ma
- Department of Jinxin Genetic Research, Jinjiang Maternal and Child Health Hospital, Chengdu, Sichuan, China
| | - Dong Yang
- Chengdu Reproductive Medicine Institute, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan, China
| | - Qiang Dong
- Department of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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Spermatogenic failure and the Y chromosome. Hum Genet 2017; 136:637-655. [PMID: 28456834 DOI: 10.1007/s00439-017-1793-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/30/2017] [Indexed: 12/29/2022]
Abstract
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.
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Human Y chromosome copy number variation in the next generation sequencing era and beyond. Hum Genet 2017; 136:591-603. [PMID: 28378101 PMCID: PMC5418319 DOI: 10.1007/s00439-017-1788-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 03/25/2017] [Indexed: 11/16/2022]
Abstract
The human Y chromosome provides a fertile ground for structural rearrangements owing to its haploidy and high content of repeated sequences. The methodologies used for copy number variation (CNV) studies have developed over the years. Low-throughput techniques based on direct observation of rearrangements were developed early on, and are still used, often to complement array-based or sequencing approaches which have limited power in regions with high repeat content and specifically in the presence of long, identical repeats, such as those found in human sex chromosomes. Some specific rearrangements have been investigated for decades; because of their effects on fertility, or their outstanding evolutionary features, the interest in these has not diminished. However, following the flourishing of large-scale genomics, several studies have investigated CNVs across the whole chromosome. These studies sometimes employ data generated within large genomic projects such as the DDD study or the 1000 Genomes Project, and often survey large samples of healthy individuals without any prior selection. Novel technologies based on sequencing long molecules and combinations of technologies, promise to stimulate the study of Y-CNVs in the immediate future.
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Abstract
The azoospermia factor (AZF) region on the Y chromosome consists of genes required for spermatogenesis. Among the three subregions, the AZFc subregion located at the distal portion of AZF is the driver for genetic variation in Y chromosome. The candidate gene of AZFc is known as deleted in azoospermia gene, which is studied with interest because it is involved in germ cell development and most frequently deleted genes leading to oligozoospermia and azoospermia. Recently, two partial deletions in AZFc gr/gr and b2/b3 are characterized at the molecular level which showed homologous recombination between amplicons, affecting spermatogenesis process. There are novel methods and commercially available kits for accurate screening and characterization of microdeletions. It is important to detect the AZFc microdeletions through genetic screening and counseling those infertile men who planned to avail assisted reproduction techniques such as undergoing intracytoplasmic sperm injection or in vitro fertilization.
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Affiliation(s)
- Mili Nailwal
- Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, Anand, Gujarat, India
| | - Jenabhai B Chauhan
- Department of Genetics, Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences, Anand, Gujarat, India
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Bansal SK, Gupta G, Rajender S. Y chromosome b2/b3 deletions and male infertility: A comprehensive meta-analysis, trial sequential analysis and systematic review. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2016; 768:78-90. [PMID: 27234565 DOI: 10.1016/j.mrrev.2016.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 04/16/2016] [Accepted: 04/18/2016] [Indexed: 11/30/2022]
Abstract
The correlation of Y-chromosome b2/b3 partial deletions with spermatogenic failure remains dubious. We undertook a systematic review of the literature followed by meta-analyses and trial sequential analyses in order to compare the frequency of b2/b3 deletions between oligo/azoospermic infertile and normozoospermicmen. Out of twenty-four studies reviewed for meta-analysis, twenty reported no correlation between this deletion and male infertility and two studies each reported a direct and inverse correlation. In the collective analysis, 241 out of 8892 (2.71%) oligo/azoospermic individuals and 118 out of 5842 (2.02%) normozoospermic controls had a b2/b3 deletion, suggesting a relatively higher frequency of deletions in the cases. Eventually, meta-analysis showed a significant correlation between b2/b3 deletions and the risk of spermatogenic loss/infertility (Fixed model: OR=1.313, 95% CI=1.04-1.65, p=0.02; Random model: OR=1.315, 95% CI=1.02-1.70, p=0.037). Further meta-analysis on studies grouped by ethnicity and geographic regions showed that the b2/b3 deletions are significantly associated with spermatogenic loss/infertility in Mongolians, Nigro-Caucasians, East Asians and Africans, but not in Caucasians, Europeans, South Asians and Dravidians. In summary, the Y-chromosome b2/b3 deletions increase infertility risk; however, it may be significant only in the Mongolian populations and the East Asian region.
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Affiliation(s)
- Sandeep Kumar Bansal
- Central Drug Research Institute, Council of Scientific and Industrial Research (CSIR), Lucknow, India
| | - Gopal Gupta
- Central Drug Research Institute, Council of Scientific and Industrial Research (CSIR), Lucknow, India
| | - Singh Rajender
- Central Drug Research Institute, Council of Scientific and Industrial Research (CSIR), Lucknow, India.
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