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Marić T, Castillo-Madeen H, Klarić ML, Barišić A, Trgovec-Greif L, Murphy MW, Juchnewitsch AG, Lillepea K, Dutta A, Žunić L, Stendahl AM, Punab M, Pomm K, Mendoza DM, Lopes AM, Šorgić AM, Vugrek O, Gonçalves J, Almstrup K, Aston KI, Belužić R, Ježek D, Bertoša B, Laan M, Bojanac AK, Conrad DF, Barbalić M. Diminished DNA binding affinity of DMRT1 caused by heterozygous DM domain mutations is a cause of male infertility. Hum Mol Genet 2025; 34:481-491. [PMID: 39777458 PMCID: PMC11891871 DOI: 10.1093/hmg/ddae197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 12/11/2024] [Accepted: 12/19/2024] [Indexed: 01/11/2025] Open
Abstract
The most severe form of male infertility is idiopathic non-obstructive azoospermia (NOA), a complete sperm absence in the ejaculate. We performed exome sequencing in the Croatian infertile brothers with NOA and found a variant in DMRT1 (Doublesex and mab-3 related transcription factor 1) gene that was further assessed by the EMSA assay and molecular dynamic simulations. We additionally screened for DMRT1 mutations in 1940 infertile men diagnosed with spermatogenic failure, 644 normozoospermic controls, and 105 females with primary ovarian insufficiency (POI) recruited to the GEnetics of Male INfertility Initiative (GEMINI) or Estonian Andrology (ESTAND) cohorts. DMRT1 p.Pro74Leu (chr9:g.842059C > T) variant was detected in infertile brothers in the highly conserved position within the DNA binding DM domain of the protein. EMSA assay showed reduced DNA binding of DMRT1P74L and molecular dynamic simulations showed differences in structural and dynamical properties between the wild type protein and DMRT1P74L. Plausible disease-causing DMRT1 variants were only identified in infertile men (13/1940; 0.67%), and none in 639 fertile controls. Burden testing showed an excess of rare deleterious DM domain mutations in the infertility cohort compared to gnomAD v.4.0 population-based controls (Fisher's exact test, p = 1.44 x 10-5). Three rare deleterious variants in DMRT1 were found in 104 cases of POI. The findings of this study strengthen the evidence of DMRT1 variants being a causal factor for male infertility and provide the distribution of likely pathogenic variants across the gene. This is also the first study to suggest that DMRT1 variants may also be linked to POI.
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Affiliation(s)
- Tihana Marić
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 2, Zagreb 10000, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 2, Zagreb 10000, Croatia
| | - Helen Castillo-Madeen
- Division of Genetics, ONPRC & Oregon Health & Science University, 505 N.W. 185th Avenue, Beaverton, OR, USA
| | | | - Antun Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, Zagreb 10000, Croatia
| | | | - Mark W Murphy
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN, USA
| | - Anna-Grete Juchnewitsch
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila tn 19, Tartu, Estonia
| | - Kristiina Lillepea
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila tn 19, Tartu, Estonia
| | - Avirup Dutta
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila tn 19, Tartu, Estonia
| | | | - Alexandra M Stendahl
- Division of Genetics, ONPRC & Oregon Health & Science University, 505 N.W. 185th Avenue, Beaverton, OR, USA
| | - Margus Punab
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila tn 19, Tartu, Estonia
- Andrology Clinic, Tartu University Hospital, Ludvig Puusepa 8, Tartu, Estonia
| | - Kristjan Pomm
- Andrology Clinic, Tartu University Hospital, Ludvig Puusepa 8, Tartu, Estonia
| | - Daniel M Mendoza
- Andrology Department, Universitat Autònoma de Barcelona, Plaça Cívica, 08193 Bellaterra, Barcelona, Spain
| | - Alexandra M Lopes
- University of Porto, Praça de Gomes Teixeira, 4099-002 Porto, Portugal
| | - Ana Merkler Šorgić
- University Hospital Zagreb, Ulica Mije Kišpatića 12, Zagreb 10000, Croatia
| | - Oliver Vugrek
- Ruđer Bošković Institute, Bijenička Cesta 54, Zagreb 10000, Croatia
| | - Joao Gonçalves
- Departamento de Genética Humana, INSA, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Kristian Almstrup
- Copenhagen University Hospital - Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Kenneth I Aston
- Andrology and IVF Laboratory, University of Utah School of Medicine, 675 Arapeen Dr 201 Suite 201, Salt Lake City, UT, USA
| | - Robert Belužić
- Ruđer Bošković Institute, Bijenička Cesta 54, Zagreb 10000, Croatia
| | - Davor Ježek
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 2, Zagreb 10000, Croatia
- University Hospital Zagreb, Ulica Mije Kišpatića 12, Zagreb 10000, Croatia
| | - Branimir Bertoša
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102A, Zagreb 10000, Croatia
| | - Maris Laan
- Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila tn 19, Tartu, Estonia
| | - Ana Katušić Bojanac
- Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Šalata 2, Zagreb 10000, Croatia
- Department of Medical Biology, University of Zagreb School of Medicine, Šalata 2, Zagreb 10000, Croatia
| | - Donald F Conrad
- Division of Genetics, ONPRC & Oregon Health & Science University, 505 N.W. 185th Avenue, Beaverton, OR, USA
| | - Maja Barbalić
- Genom Ltd., Ilica 190, Zagreb 10000, Croatia
- Faculty of Science, University of Split, Ruđera Bošković 33, Split 21000, Croatia
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Guzmán-Jiménez A, González-Muñoz S, Cerván-Martín M, Garrido N, Castilla JA, Gonzalvo MC, Clavero A, Molina M, Luján S, Santos-Ribeiro S, Vilches MÁ, Espuch A, Maldonado V, Galiano-Gutiérrez N, Santamaría-López E, González-Ravina C, Quintana-Ferraz F, Gómez S, Amorós D, Martínez-Granados L, Ortega-González Y, Burgos M, Pereira-Caetano I, Bulbul O, Castellano S, Romano M, Albani E, Bassas L, Seixas S, Gonçalves J, Lopes AM, Larriba S, Palomino-Morales RJ, Carmona FD, Bossini-Castillo L. A comprehensive study of common and rare genetic variants in spermatogenesis-related loci identifies new risk factors for idiopathic severe spermatogenic failure. Hum Reprod Open 2024; 2024:hoae069. [PMID: 39678461 PMCID: PMC11645127 DOI: 10.1093/hropen/hoae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 10/11/2024] [Indexed: 12/17/2024] Open
Abstract
STUDY QUESTION Can genome-wide genotyping data be analysed using a hypothesis-driven approach to enhance the understanding of the genetic basis of severe spermatogenic failure (SPGF) in male infertility? SUMMARY ANSWER Our findings revealed a significant association between SPGF and the SHOC1 gene and identified three novel genes (PCSK4, AP3B1, and DLK1) along with 32 potentially pathogenic rare variants in 30 genes that contribute to this condition. WHAT IS KNOWN ALREADY SPGF is a major cause of male infertility, often with an unknown aetiology. SPGF can be due to either multifactorial causes, including both common genetic variants in multiple genes and environmental factors, or highly damaging rare variants. Next-generation sequencing methods are useful for identifying rare mutations that explain monogenic forms of SPGF. Genome-wide association studies (GWASs) have become essential approaches for deciphering the intricate genetic landscape of complex diseases, offering a cost-effective and rapid means to genotype millions of genetic variants. Novel methods have demonstrated that GWAS datasets can be used to infer rare coding variants that are causal for male infertility phenotypes. However, this approach has not been previously applied to characterize the genetic component of a whole case-control cohort. STUDY DESIGN SIZE DURATION We employed a hypothesis-driven approach focusing on all genetic variation identified, using a GWAS platform and subsequent genotype imputation, encompassing over 20 million polymorphisms and a total of 1571 SPGF patients and 2431 controls. Both common (minor allele frequency, MAF > 0.01) and rare (MAF < 0.01) variants were investigated within a total of 1797 loci with a reported role in spermatogenesis. This gene panel was meticulously assembled through comprehensive searches in the literature and various databases focused on male infertility genetics. PARTICIPANTS/MATERIALS SETTING METHODS This study involved a European cohort using previously and newly generated data. Our analysis consisted of three independent methods: (i) variant-wise association analyses using logistic regression models, (ii) gene-wise association analyses using combined multivariate and collapsing burden tests, and (iii) identification and characterisation of highly damaging rare coding variants showing homozygosity only in SPGF patients. MAIN RESULTS AND THE ROLE OF CHANCE The variant-wise analyses revealed an association between SPGF and SHOC1-rs12347237 (P = 4.15E-06, odds ratio = 2.66), which was likely explained by an altered binding affinity of key transcription factors in regulatory regions and the disruptive effect of coding variants within the gene. Three additional genes (PCSK4, AP3B1, and DLK1) were identified as novel relevant players in human male infertility using the gene-wise burden test approach (P < 5.56E-04). Furthermore, we linked a total of 32 potentially pathogenic and recessive coding variants of the selected genes to 35 different cases. LARGE SCALE DATA Publicly available via GWAS catalog (accession number: GCST90239721). LIMITATIONS REASONS FOR CAUTION The analysis of low-frequency variants presents challenges in achieving sufficient statistical power to detect genetic associations. Consequently, independent studies with larger sample sizes are essential to replicate our results. Additionally, the specific roles of the identified variants in the pathogenic mechanisms of SPGF should be assessed through functional experiments. WIDER IMPLICATIONS OF THE FINDINGS Our findings highlight the benefit of using GWAS genotyping to screen for both common and rare variants potentially implicated in idiopathic cases of SPGF, whether due to complex or monogenic causes. The discovery of novel genetic risk factors for SPGF and the elucidation of the underlying genetic causes provide new perspectives for personalized medicine and reproductive counselling. STUDY FUNDING/COMPETING INTERESTS This work was supported by the Spanish Ministry of Science and Innovation through the Spanish National Plan for Scientific and Technical Research and Innovation (PID2020-120157RB-I00) and the Andalusian Government through the research projects of 'Plan Andaluz de Investigación, Desarrollo e Innovación (PAIDI 2020)' (ref. PY20_00212) and 'Proyectos de Investigación aplicada FEDER-UGR 2023' (ref. C-CTS-273-UGR23). S.G.-M. was funded by the previously mentioned projects (ref. PY20_00212 and PID2020-120157RB-I00). A.G.-J. was funded by MCIN/AEI/10.13039/501100011033 and FSE 'El FSE invierte en tu futuro' (grant ref. FPU20/02926). IPATIMUP integrates the i3S Research Unit, which is partially supported by the Portuguese Foundation for Science and Technology (FCT), financed by the European Social Funds (COMPETE-FEDER) and National Funds (projects PEstC/SAU/LA0003/2013 and POCI-01-0145-FEDER-007274). S.S. is supported by FCT funds (10.54499/DL57/2016/CP1363/CT0019), ToxOmics-Centre for Toxicogenomics and Human Health, Genetics, Oncology and Human Toxicology, and is also partially supported by the Portuguese Foundation for Science and Technology (UIDP/00009/2020 and UIDB/00009/2020). S. Larriba received support from Instituto de Salud Carlos III (grant: DTS18/00101), co-funded by FEDER funds/European Regional Development Fund (ERDF)-a way to build Europe) and from 'Generalitat de Catalunya' (grant 2021SGR052). S. Larriba is also sponsored by the 'Researchers Consolidation Program' from the SNS-Dpt. Salut Generalitat de Catalunya (Exp. CES09/020). All authors declare no conflict of interest related to this study.
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Affiliation(s)
- Andrea Guzmán-Jiménez
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
| | - Sara González-Muñoz
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
| | - Miriam Cerván-Martín
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), CSIC, Granada, Spain
| | - Nicolás Garrido
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - José A Castilla
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
- Departamento de Anatomía y Embriología Humana, Facultad de Medicina, Universidad de Granada, Granada, Spain
| | - M Carmen Gonzalvo
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
- Unidad de Reproducción, UGC Obstetricia y Ginecología, HU Virgen de las Nieves, Granada, Spain
| | - Ana Clavero
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
- Unidad de Reproducción, UGC Obstetricia y Ginecología, HU Virgen de las Nieves, Granada, Spain
| | - Marta Molina
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
- Unidad de Reproducción, UGC Obstetricia y Ginecología, HU Virgen de las Nieves, Granada, Spain
| | - Saturnino Luján
- Servicio de Urología, Hospital Universitari i Politecnic La Fe e Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Samuel Santos-Ribeiro
- IVI-RMA Lisbon, Lisbon, Portugal
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Lisbon, Lisbon, Portugal
| | - Miguel Ángel Vilches
- Ovoclinic & Ovobank, Clínicas de Reproducción Asistida y Banco de óvulos, Marbella, Málaga, Spain
| | - Andrea Espuch
- Hospital Universitario Torrecárdenas, Unidad de Reproducción Humana Asistida, Almería, Spain
| | - Vicente Maldonado
- UGC de Obstetricia y Ginecología, Complejo Hospitalario de Jaén, Jaén, Spain
| | | | | | - Cristina González-Ravina
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Fernando Quintana-Ferraz
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Susana Gómez
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - David Amorós
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | | | | | - Miguel Burgos
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
| | - Iris Pereira-Caetano
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisbon, Portugal
| | - Ozgur Bulbul
- Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital, IRCCS, Milan, Italy
| | - Stefano Castellano
- Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital, IRCCS, Milan, Italy
| | - Massimo Romano
- Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital, IRCCS, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Elena Albani
- Division of Gynecology and Reproductive Medicine, Department of Gynecology, Fertility Center, Humanitas Research Hospital, IRCCS, Milan, Italy
| | - Lluís Bassas
- Laboratory of Seminology and Embryology, Andrology Service-Fundació Puigvert, Barcelona, Spain
| | - Susana Seixas
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
| | - João Gonçalves
- Departamento de Genética Humana, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisbon, Portugal
- ToxOmics—Centro de Toxicogenómica e Saúde Humana, Nova Medical School, Lisbon, Portugal
| | - Alexandra M Lopes
- Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal
- CGPP-IBMC—Centro de Genética Preditiva e Preventiva, Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
| | - Sara Larriba
- Human Molecular Genetics Group, Bellvitge Biomedical Research Institute (IDIBELL), L’Hospitalet de Llobregat, Barcelona, Spain
| | - Rogelio J Palomino-Morales
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
- Departamento de Bioquímica y Biología Molecular I, Universidad de Granada, Granada, Spain
| | - F David Carmona
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
| | - Lara Bossini-Castillo
- Departamento de Genética e Instituto de Biotecnología, Centro de Investigación Biomédica (CIBM), Universidad de Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, Granada, Spain
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Severi G, Ambrosini E, Caramanna L, Monti L, Magini P, Innella G. Familial DMRT1-related non-obstructive azoospermia: a case report. J Assist Reprod Genet 2024; 41:3173-3177. [PMID: 39259317 PMCID: PMC11621264 DOI: 10.1007/s10815-024-03250-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2024] [Accepted: 09/01/2024] [Indexed: 09/13/2024] Open
Abstract
PURPOSE To report an exceptional case of male-to-male transmission of genetically based non-obstructive azoospermia (NOA) and varicocele through a naturally obtained pregnancy. SUBJECTS AND METHODS A father and his son were both diagnosed with NOA after centrifugation and varicocele. The father has no other clinical concerns apart from infertility, detected after many attempts of having another child, but given his urological situation (bilateral varicocele and NOA) assisted reproductive techniques were discouraged. After genetic counseling, several genetic-chromosomal analyses were carried out in the son (karyotype, chromosome Y microdeletions, CFTR screening, NGS infertility panels, and finally array-CGH). RESULTS After a series of inconclusive tests, array-CGH detected a deletion of 224-283 kb (del9p24.3) involving part of the KANK1 and DMRT1 genes, inherited from the father. Haploinsufficiency of DMRT1 was therefore considered the determining factor in the development of azoospermia in the family by a loss of function mechanism. CONCLUSION The confirmation of father-to-son transmission of a deletion including DMRT1 represents an important point for clinicians dealing with male infertility, even when complete azoospermia is repetitively detected, and must be of hope for a relevant portion of men. Inclusion criteria for the access to assisted reproductive techniques may also be reconsidered and worthy of a greater number of clinical insights. Finally, since DMRT1 alterations have been associated with NOA and abnormal testicular development, but not specifically with varicocele, further studies are required to validate this issue, as varicocele may have played a crucial role in this case.
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Affiliation(s)
- Giulia Severi
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Enrico Ambrosini
- Medical Genetics Unit, University Hospital of Parma, Parma, Italy
| | - Luca Caramanna
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Luigi Monti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Pamela Magini
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giovanni Innella
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
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Deng J, Huang Y, Liang J, Jiang Y, Chen T. Medaka ( Oryzias latipes) Dmrt3a Is Involved in Male Fertility. Animals (Basel) 2024; 14:2406. [PMID: 39199940 PMCID: PMC11350882 DOI: 10.3390/ani14162406] [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: 07/22/2024] [Revised: 08/11/2024] [Accepted: 08/14/2024] [Indexed: 09/01/2024] Open
Abstract
Research across various species has demonstrated that the doublesex and mab-3-related transcription factor 3 (dmrt3) plays pivotal roles in testis development. However, the precise molecular mechanisms of dmrt3 remain unclear. In this study, we investigated the role of dmrt3 (dmrt3a) in testis development using the model organism medaka (Oryzias latipes). SqRT-PCR and ISH analyses revealed that dmrt3a is predominantly expressed in the testis, especially in the spermatid and spermatozoon. Using CRISPR/Cas9, we generated two dmrt3a homozygous mutants (-8 bp and -11 bp), which exhibited significantly reduced fertilization rates and embryo production. Additionally, the number of germ cells and sperm motility were markedly decreased in the dmrt3a mutants, manifesting as the symptoms of asthenozoospermia and oligozoospermia. Interestingly, RNA-Seq analysis showed that the deficiency of dmrt3a could lead to a significant downregulation of numerous genes related to gonadal development and severe disruptions in mitochondrial function. These results suggested that dmrt3a is essential for spermatogenesis and spermatozoa energy production. This paper provides new insights and perspectives for further exploring the molecular mechanisms underlying spermatogenesis and addressing male reproductive issues.
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Affiliation(s)
- Ju Deng
- State Key Laboratory of Mariculture Breeding, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Jimei University, Xiamen 361021, China; (J.D.); (Y.H.); (J.L.); (Y.J.)
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
| | - Yan Huang
- State Key Laboratory of Mariculture Breeding, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Jimei University, Xiamen 361021, China; (J.D.); (Y.H.); (J.L.); (Y.J.)
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
| | - Jingjie Liang
- State Key Laboratory of Mariculture Breeding, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Jimei University, Xiamen 361021, China; (J.D.); (Y.H.); (J.L.); (Y.J.)
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
| | - Yuewen Jiang
- State Key Laboratory of Mariculture Breeding, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Jimei University, Xiamen 361021, China; (J.D.); (Y.H.); (J.L.); (Y.J.)
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
| | - Tiansheng Chen
- State Key Laboratory of Mariculture Breeding, Engineering Research Center of the Modern Technology for Eel Industry, Ministry of Education, Jimei University, Xiamen 361021, China; (J.D.); (Y.H.); (J.L.); (Y.J.)
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Fisheries College, Jimei University, Xiamen 361021, China
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Stallmeyer B, Dicke AK, Tüttelmann F. How exome sequencing improves the diagnostics and management of men with non-syndromic infertility. Andrology 2024. [PMID: 39120565 DOI: 10.1111/andr.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Revised: 07/07/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Male infertility affects approximately 17% of all men and represents a complex disorder in which not only semen parameters such as sperm motility, morphology, and number of sperm are highly variable, but also testicular phenotypes range from normal spermatogenesis to complete absence of germ cells. Genetic factors significantly contribute to the disease but chromosomal aberrations, mostly Klinefelter syndrome, and microdeletions of the Y-chromosome have remained the only diagnostically and clinically considered genetic causes. Monogenic causes remain understudied and, thus, often unidentified, leaving the majority of the male factor couple infertility pathomechanistically unexplained. This has been changing mostly because of the introduction of exome sequencing that allows the analysis of multiple genes in large patient cohorts. As a result, pathogenic variants in single genes have been associated with non-syndromic forms of all aetiologic sub-categories in the last decade. This review highlights the contribution of exome sequencing to the identification of novel disease genes for isolated (non-syndromic) male infertility by presenting the results of a comprehensive literature search. Both, reduced sperm count in azoospermic and oligozoospermic patients, and impaired sperm motility and/or morphology, in asthenozoospermic and/or teratozoospermic patients are highly heterogeneous diseases with well over 100 different candidate genes described for each entity. Applying the standardized evaluation criteria of the ClinGen gene curation working group, 70 genes with at least moderate evidence to contribute to the disease are highlighted. The implementation of these valid disease genes in clinical exome sequencing is important to increase the diagnostic yield in male infertility and, thus, improve clinical decision-making and appropriate genetic counseling. Future advances in androgenetics will continue to depend on large-scale exome and genome sequencing studies of comprehensive international patient cohorts, which are the most promising approaches to identify additional disease genes and provide reliable data on the gene-disease relationship.
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Affiliation(s)
- Birgit Stallmeyer
- Centre of Medical Genetics, Institute of Reproductive Genetics, University of Münster, Munster, Germany
| | - Ann-Kristin Dicke
- Centre of Medical Genetics, Institute of Reproductive Genetics, University of Münster, Munster, Germany
| | - Frank Tüttelmann
- Centre of Medical Genetics, Institute of Reproductive Genetics, University of Münster, Munster, Germany
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Muranishi Y, Kobori Y, Katoh-Fukui Y, Tamaoka S, Hattori A, Osaka A, Okada H, Nakabayashi K, Hata K, Kawai T, Ogata-Kawata H, Iwahata T, Saito K, Kon M, Shinohara N, Fukami M. Systematic molecular analyses for 115 karyotypically normal men with isolated non-obstructive azoospermia. Hum Reprod 2024; 39:1131-1140. [PMID: 38511217 DOI: 10.1093/humrep/deae057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
STUDY QUESTION Do copy-number variations (CNVs) in the azoospermia factor (AZF) regions and monogenic mutations play a major role in the development of isolated (non-syndromic) non-obstructive azoospermia (NOA) in Japanese men with a normal 46, XY karyotype? SUMMARY ANSWER Deleterious CNVs in the AZF regions and damaging sequence variants in eight genes likely constitute at least 8% and approximately 8% of the genetic causes, respectively, while variants in other genes play only a minor role. WHAT IS KNOWN ALREADY Sex chromosomal abnormalities, AZF-linked microdeletions, and monogenic mutations have been implicated in isolated NOA. More than 160 genes have been reported as causative/susceptibility/candidate genes for NOA. STUDY DESIGN, SIZE, DURATION Systematic molecular analyses were conducted for 115 patients with isolated NOA and a normal 46, XY karyotype, who visited our hospital between 2017 and 2021. PARTICIPANTS/MATERIALS, SETTING, METHODS We studied 115 unrelated Japanese patients. AZF-linked CNVs were examined using sequence-tagged PCR and multiplex ligation-dependent probe amplification, and nucleotide variants were screened using whole exome sequencing (WES). An optimized sequence kernel association test (SKAT-O), a gene-based association study using WES data, was performed to identify novel disease-associated genes in the genome. The results were compared to those of previous studies and our in-house control data. MAIN RESULTS AND THE ROLE OF CHANCE Thirteen types of AZF-linked CNVs, including the hitherto unreported gr/gr triplication and partial AZFb deletion, were identified in 63 (54.8%) cases. When the gr/gr deletion, a common polymorphism in Japan, was excluded from data analyses, the total frequency of CNVs was 23/75 (30.7%). This frequency is higher than that of the reference data in Japan and China (11.1% and 14.7%, respectively). Known NOA-causative AZF-linked CNVs were found in nine (7.8%) cases. Rare damaging variants in known causative genes (DMRT1, PLK4, SYCP2, TEX11, and USP26) and hemizygous/multiple-heterozygous damaging variants in known spermatogenesis-associated genes (TAF7L, DNAH2, and DNAH17) were identified in nine cases (7.8% in total). Some patients carried rare damaging variants in multiple genes. SKAT-O detected no genes whose rare damaging variants were significantly accumulated in the patient group. LIMITATIONS, REASONS FOR CAUTION The number of participants was relatively small, and the clinical information of each patient was fragmentary. Moreover, the pathogenicity of identified variants was assessed only by in silico analyses. WIDER IMPLICATIONS OF THE FINDINGS This study showed that various AZF-linked CNVs are present in more than half of Japanese NOA patients. These results broadened the structural variations of AZF-linked CNVs, which should be considered for the molecular diagnosis of spermatogenic failure. Furthermore, the results of this study highlight the etiological heterogeneity and possible oligogenicity of isolated NOA. STUDY FUNDING/COMPETING INTEREST(S) This study was supported by Grants from the Japan Society for the Promotion of Science (21K19283 and 21H0246), the Japan Agency for Medical Research and Development (22ek0109464h0003), the National Center for Child Health and Development, the Canon Foundation, the Japan Endocrine Society, and the Takeda Science Foundation. The results of this study were based on samples and patient data obtained from the International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan. The authors have no conflicts of interest to disclose. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Yuki Muranishi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yoshitomo Kobori
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Satoshi Tamaoka
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Akiyoshi Osaka
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Hiroshi Okada
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Tomoko Kawai
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Toshiyuki Iwahata
- International Center for Reproductive Medicine, Dokkyo Medical University Saitama Medical Center, Koshigaya, Japan
| | - Kazuki Saito
- Department of Comprehensive Reproductive Medicine, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masafumi Kon
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Nobuo Shinohara
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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Yi S, Wang W, Su L, Meng L, Li Y, Tan C, Liu Q, Zhang H, Fan L, Lu G, Hu L, Du J, Lin G, Tan YQ, Tu C, Zhang Q. Deleterious variants in X-linked RHOXF1 cause male infertility with oligo- and azoospermia. Mol Hum Reprod 2024; 30:gaae002. [PMID: 38258527 DOI: 10.1093/molehr/gaae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/24/2023] [Indexed: 01/24/2024] Open
Abstract
Oligozoospermia and azoospermia are two common phenotypes of male infertility characterized by massive sperm defects owing to failure of spermatogenesis. The deleterious impact of candidate variants with male infertility is to be explored. In our study, we identified three hemizygous missense variants (c.388G>A: p.V130M, c.272C>T: p.A91V, and c.467C>T: p.A156V) and one hemizygous nonsense variant (c.478C>T: p.R160X) in the Rhox homeobox family member 1 gene (RHOXF1) in four unrelated cases from a cohort of 1201 infertile Chinese men with oligo- and azoospermia using whole-exome sequencing and Sanger sequencing. RHOXF1 was absent in the testicular biopsy of one patient (c.388G>A: p.V130M) whose histological analysis showed a phenotype of Sertoli cell-only syndrome. In vitro experiments indicated that RHOXF1 mutations significantly reduced the content of RHOXF1 protein in HEK293T cells. Specifically, the p.V130M, p.A156V, and p.R160X mutants of RHOXF1 also led to increased RHOXF1 accumulation in cytoplasmic particles. Luciferase assays revealed that p.V130M and p.R160X mutants may disrupt downstream spermatogenesis by perturbing the regulation of doublesex and mab-3 related transcription factor 1 (DMRT1) promoter activity. Furthermore, ICSI treatment could be beneficial in the context of oligozoospermia caused by RHOXF1 mutations. In conclusion, our findings collectively identified mutated RHOXF1 to be a disease-causing X-linked gene in human oligo- and azoospermia.
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Affiliation(s)
- Sibing Yi
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Weili Wang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Center for Biology Post-Doctoral studies, College of Life Science, Hunan Normal University, Changsha, China
| | - Lilan Su
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Lanlan Meng
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Yong Li
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Chen Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Qiang Liu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Department of Hepatobiliary Surgery, Hunan Cancer Hospital and the Affiliated Cancer of Xiangya School of Medicine, Central South University, Changsha, China
| | - Huan Zhang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Liqing Fan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Guangxiu Lu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Liang Hu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Center for Biology Post-Doctoral studies, College of Life Science, Hunan Normal University, Changsha, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Juan Du
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Ge Lin
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Center for Biology Post-Doctoral studies, College of Life Science, Hunan Normal University, Changsha, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Center for Biology Post-Doctoral studies, College of Life Science, Hunan Normal University, Changsha, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
| | - Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
| | - Qianjun Zhang
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, Hunan, China
- Center for Biology Post-Doctoral studies, College of Life Science, Hunan Normal University, Changsha, China
- Key Laboratory of Stem Cell and Reproduction Engineering, Ministry of Health, Changsha, China
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