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Zong W, Zhao R, Wang X, Zhou C, Wang J, Chen C, Niu N, Zheng Y, Chen L, Liu X, Hou X, Zhao F, Wang L, Wang L, Song C, Zhang L. Population genetic analysis based on the polymorphisms mediated by transposons in the genomes of pig. DNA Res 2024; 31:dsae008. [PMID: 38447059 PMCID: PMC11090087 DOI: 10.1093/dnares/dsae008] [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: 12/23/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/08/2024] Open
Abstract
Transposable elements (TEs) mobility is capable of generating a large number of structural variants (SVs), which can have considerable potential as molecular markers for genetic analysis and molecular breeding in livestock. Our results showed that the pig genome contains mainly TE-SVs generated by short interspersed nuclear elements (51,873/76.49%), followed by long interspersed nuclear elements (11,131/16.41%), and more than 84% of the common TE-SVs (Minor allele frequency, MAF > 0.10) were validated to be polymorphic. Subsequently, we utilized the identified TE-SVs to gain insights into the population structure, resulting in clear differentiation among the three pig groups and facilitating the identification of relationships within Chinese local pig breeds. In addition, we investigated the frequencies of TEs in the gene coding regions of different pig groups and annotated the respective TE types, related genes, and functional pathways. Through genome-wide comparisons of Large White pigs and Chinese local pigs utilizing the Beijing Black pigs, we identified TE-mediated SVs associated with quantitative trait loci and observed that they were mainly involved in carcass traits and meat quality traits. Lastly, we present the first documented evidence of TE transduction in the pig genome.
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Affiliation(s)
- Wencheng Zong
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Runze Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- College of Animal Science, Shanxi Agricultural University, Jinzhong, China
| | - Xiaoyan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Chenyu Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinbu Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Cai Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Naiqi Niu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yao Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Li Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xin Liu
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xinhua Hou
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Fuping Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ligang Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lixian Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengyi Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Longchao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Qu R, Zhang Z, Wu L, Li Q, Mu J, Zhao L, Yan Z, Wang W, Zeng Y, Liu R, Dong J, Li Q, Sun X, Wang L, Sang Q, Chen B, Kuang Y. ADGB variants cause asthenozoospermia and male infertility. Hum Genet 2023; 142:735-748. [PMID: 36995441 DOI: 10.1007/s00439-023-02546-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
Asthenozoospermia is one of the main factors leading to male infertility, but the genetic mechanisms have not been fully elucidated. Variants in the androglobin (ADGB) gene were identified in an infertile male characterized by asthenozoospermia. The variants disrupted the binding of ADGB to calmodulin. Adgb-/- male mice were infertile due to reduced sperm concentration (< 1 × 106 /mL) and motility. Spermatogenesis was also abnormal, with malformation of both elongating and elongated spermatids, and there was an approximately twofold increase in apoptotic cells in the cauda epididymis. These exacerbated the decline in sperm motility. It is surprising that ICSI with testicular spermatids allows fertilization and eventually develops into blastocyst. Through mass spectrometry, we identified 42 candidate proteins that are involved in sperm assembly, flagella formation, and sperm motility interacting with ADGB. In particular, CFAP69 and SPEF2 were confirmed to bind to ADGB. Collectively, our study suggests the potential important role of ADGB in human fertility, revealing its relevance to spermatogenesis and infertility. This expands our knowledge of the genetic causes of asthenozoospermia and provides a theoretical basis for using ADGB as an underlying genetic marker for infertile males.
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Affiliation(s)
- Ronggui Qu
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhang
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Ling Wu
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Qun Li
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Jian Mu
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Lin Zhao
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Zheng Yan
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Wenjing Wang
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Yang Zeng
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Ruyi Liu
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Jie Dong
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Qiaoli Li
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Lei Wang
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China
| | - Qing Sang
- The Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering and the Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, 200032, China.
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China.
| | - Yanping Kuang
- Department of Assisted Reproduction, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
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Wang J, Wang W, Shen L, Zheng A, Meng Q, Li H, Yang S. Clinical detection, diagnosis and treatment of morphological abnormalities of sperm flagella: A review of literature. Front Genet 2022; 13:1034951. [PMID: 36425067 PMCID: PMC9679630 DOI: 10.3389/fgene.2022.1034951] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2023] Open
Abstract
Sperm carries male genetic information, and flagella help move the sperm to reach oocytes. When the ultrastructure of the flagella is abnormal, the sperm is unable to reach the oocyte and achieve insemination. Multiple morphological abnormalities of sperm flagella (MMAF) is a relatively rare idiopathic condition that is mainly characterized by multiple defects in sperm flagella. In the last decade, with the development of high-throughput DNA sequencing approaches, many genes have been revealed to be related to MMAF. However, the differences in sperm phenotypes and reproductive outcomes in many cases are attributed to different pathogenic genes or different pathogenic mutations in the same gene. Here, we will review information about the various phenotypes resulting from different pathogenic genes, including sperm ultrastructure and encoding proteins with their location and functions as well as assisted reproductive technology (ART) outcomes. We will share our clinical detection and diagnosis experience to provide additional clinical views and broaden the understanding of this disease.
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Affiliation(s)
| | | | | | | | | | | | - Shenmin Yang
- Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou, China
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A novel refined pyroptosis and inflammasome-related genes signature for predicting prognosis and immune microenvironment in pancreatic ductal adenocarcinoma. Sci Rep 2022; 12:18384. [PMID: 36319832 PMCID: PMC9626462 DOI: 10.1038/s41598-022-22864-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/20/2022] [Indexed: 01/01/2023] Open
Abstract
Pyroptosis is an inflammatory form of cell death, which plays a key role in the development of auto-inflammation and cancer. This study aimed to construct a pyroptosis and inflammasome-related genes for predicting prognosis of the pancreatic ductal adenocarcinoma (PDAC). This study was based primarily on the one-way analysis of variance, univariate Cox regression analysis, Least absolute shrinkage and selection operator (LASSO) Cox regression, a risk-prognostic signature, gene set variation analysis (GSVA), and immune microenvironment analysis, using PDAC data from The Cancer Genome Atlas and International Cancer Genome Consortium databases for the analysis of the role of 676 pyroptosis and inflammasome-related genes in PDAC retrieved from the Reactome and GeneCards databases. Lastly, we collected six paired PDAC and matched normal adjacent tissue samples to verify the expression of signature genes by quantitative real-time PCR (qRT-PCR). We identified 18 candidate pyroptosis and inflammasome-related genes that differed significantly between pathologic grades (stages) of PDAC patients. The univariate Cox and LASSO analyses pointed to six genes as the best variables for constructing a prognostic signature, including ACTA2, C1QTNF9, DNAH8, GATM, LBP, and NGF. The results of the risk prognostic model indicated that the AUCs at 1, 3, and 5 years were greater than 0.62. GSVA revealed that 'GLYCOLYSIS', 'P53 PATHWAY', 'KRAS SIGNALING UP', and 'INFLAMMATORY RESPONSE' hallmark gene sets were associated with the risk score. The high-risk group was associated with poor prognosis and was characterized by a lower infiltration of cells involved in anti-tumor immunity; whereas the low-risk group with higher T cells, NK cells, and macrophages showed relatively better survival and significantly higher upregulation of cytolytic scores and inflammation scores. Additionally, crucial pyroptosis and inflammasome-related genes were further validated by qRT-PCR. Our study revealed the prognostic role of the pyroptosis and inflammasome-related genes in PDAC for the first time. Simultaneously, the biological and prognostic heterogeneity of PDAC had been demonstrated, deepening our molecular understanding of this tumor.
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Levkova M, Radanova M, Angelova L. Potential role of dynein-related genes in the etiology of male infertility: A systematic review and a meta-analysis. Andrology 2022; 10:1484-1499. [PMID: 36057791 DOI: 10.1111/andr.13287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/21/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND The dynein-related genes may have a role in the etiology of male infertility, particularly in cases of impaired sperm motility. OBJECTIVES The goal of this review is to compile a list of the most important dynein-related candidate genes that may contribute to male factor infertility. MATERIALS AND METHODS Databases were searched using the keywords "dynein", "male", "infertility" and by applying strict inclusion criteria. A meta-analysis was also performed by using the eligible case-control studies. The odd ratios (OR), the Z-test score, and the level of significance were determined using a fixed model with a p value of 0.05. Funnel plots were used to check for publication bias. RESULTS There were 35 studies that met the inclusion criteria. There were a total of fifteen genes responsible for the production of dynein structural proteins, the production of dynein assembling factors, and potentially associated with male infertility. A total of five case-control studies were eligible for inclusion in the meta-analysis. Variants in the dynein-related genes were linked to an increased the risk of male infertility (OR = 21.52, 95% Confidence Interval (CI) 8.34 - 55.50, Z test = 6.35, p < 0.05). The percentage of heterogeneity, I2 , was 47.00%. The lack of variants in the dynein genes was an advantage and this was statistically significant. DISCUSSION The results from the present review illustrate that pathogenic variants in genes both for dynein synthesis and for dynein assembly factors could be associated with isolated cases of male infertility without any other symptoms. CONCLUSIONS The genes addressed in this study, which are involved in both the production and assembly of dynein, could be used as molecular targets for future research into the etiology of sperm motility problems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Mariya Levkova
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria.,Laboratory of Medical Genetics, St. Marina Hospital, Hristo Smirnenski Blv 1, Varna, 9000, Bulgaria
| | - Maria Radanova
- Department of Biochemistry, Molecular Medicine and Nutrigenomics, Medical University Varna, Tzar Osvoboditel Str 84b, Varna, 9000, Bulgaria
| | - Lyudmila Angelova
- Department of Medical Genetics, Medical University Varna, Marin Drinov Str 55, Varna, 9000, Bulgaria
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Wu X, Zhou L, Shi J, Cheng CY, Sun F. Multiomics analysis of male infertility. Biol Reprod 2022; 107:118-134. [PMID: 35639635 DOI: 10.1093/biolre/ioac109] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/12/2022] [Accepted: 05/17/2022] [Indexed: 11/14/2022] Open
Abstract
Infertility affects 8-12% of couples globally, and the male factor is a primary cause in approximately 50% of couples. Male infertility is a multifactorial reproductive disorder, which can be caused by paracrine and autocrine factors, hormones, genes, and epigenetic changes. Recent studies in rodents and most notably in humans using multiomics approach have yielded important insights into understanding the biology of spermatogenesis. Nonetheless, the etiology and pathogenesis of male infertility are still largely unknown. In this review, we summarized and critically evaluated findings based on the use of advanced technologies to compare normal and obstructive azoospermia (OA) versus non-obstructive azoospermia (NOA) men, including whole-genome bisulfite sequencing (WGBS), single cell RNA-seq (scRNA-seq), whole exome sequencing (WES), and ATAC-seq. It is obvious that the multiomics approach is the method of choice for basic research and clinical studies including clinical diagnosis of male infertility.
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Affiliation(s)
- Xiaolong Wu
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Liwei Zhou
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Jie Shi
- Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - C Yan Cheng
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
| | - Fei Sun
- Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.,Institute of Reproductive Medicine, Nantong University School of Medicine, Nantong, Jiangsu 226001, China
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Wei X, Sha Y, Wei Z, Zhu X, He F, Zhang X, Liu W, Wang Y, Lu Z. Bi-allelic mutations in DNAH7 cause asthenozoospermia by impairing the integrality of axoneme structure. Acta Biochim Biophys Sin (Shanghai) 2021; 53:1300-1309. [PMID: 34476482 DOI: 10.1093/abbs/gmab113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Indexed: 11/13/2022] Open
Abstract
Asthenozoospermia is the most common cause of male infertility. Dynein protein arms play a crucial role in the motility of both the cilia and flagella, and defects in these proteins generally impair the axoneme structure and cause primary ciliary dyskinesia. But relatively little is known about the influence of dynein protein arm defects on sperm flagella function. Here, we recruited 85 infertile patients with idiopathic asthenozoospermia and identified bi-allelic mutations in DNAH7 (NM_018897.3) from three patients using whole-exome sequencing. These variants are rare, highly pathogenic, and very conserved. The spermatozoa from the patients with DNAH7 bi-allelic mutations showed specific losses in the inner dynein arms. The expression of DNAH7 in the spermatozoa from the DNAH7-defective patients was significantly decreased, but these patients were able to have their children via intra-cytoplasmic sperm injection treatment. Our study is the first to demonstrate that bi-allelic mutations in DNAH7 may impair the integrality of axoneme structure, affect sperm motility, and cause asthenozoospermia in humans. These findings may extend the spectrum of etiological genes and provide new clues for the diagnosis and treatment of patients with asthenozoospermia.
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Affiliation(s)
- Xiaoli Wei
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Yanwei Sha
- Department of Andrology, United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital and School of Medicine, Xiamen University, Xiamen 361005, China
| | - Zijie Wei
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Xingshen Zhu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Fengming He
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Xiaoya Zhang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
| | - Wensheng Liu
- Obstetrics and Gynecology Center, Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yifeng Wang
- Obstetrics and Gynecology Center, Department of Obstetrics and Gynecology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Zhongxian Lu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen 361102, China
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Diagnostics and Management of Male Infertility in Primary Ciliary Dyskinesia. Diagnostics (Basel) 2021; 11:diagnostics11091550. [PMID: 34573892 PMCID: PMC8467018 DOI: 10.3390/diagnostics11091550] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022] Open
Abstract
Primary ciliary dyskinesia (PCD), a disease caused by the malfunction of motile cilia, manifests mainly with chronic recurrent respiratory infections. In men, PCD is also often associated with infertility due to immotile sperm. Since causative mutations for PCD were identified in over 50 genes, the role of these genes in sperm development should be investigated in order to understand the effect of PCD mutations on male fertility. Previous studies showed that different dynein arm heavy chains are present in respiratory cilia and sperm flagellum, which may partially explain the variable effects of mutations on airways and fertility. Furthermore, recent studies showed that male reproductive tract motile cilia may play an important part in sperm maturation and transport. In some PCD patients, extremely low sperm counts were reported, which may be due to motile cilia dysfunction in the reproductive tract rather than problems with sperm development. However, the exact roles of PCD genes in male fertility require additional studies, as do the treatment options. In this review, we discuss the diagnostic and treatment options for men with PCD based on the current knowledge.
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