1
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Colaco S, Modi D. Azoospermia factor c microdeletions and outcomes of assisted reproductive technology: a systematic review and meta-analysis. Fertil Steril 2024; 121:63-71. [PMID: 37923163 DOI: 10.1016/j.fertnstert.2023.10.029] [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: 07/21/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/07/2023]
Abstract
OBJECTIVE To investigate whether Azoospermia Factor c (AZFc) microdeletions affect Assisted Reproductive Technology (ART) outcomes. DESIGN Systematic review and meta-analysis. SETTING Not applicable. PATIENTS Infertile men with and without AZFc microdeletions. INTERVENTION(S) Electronic databases were searched for case-control studies reporting sperm retrieval rates and outcomes of ART in infertile men with and without AZFc microdeletions from inception to April 2023. Study quality was assessed using the Newcastle-Ottawa Scale. Summary effect sizes (odds ratio [OR] with 95% confidence interval [CI]) were calculated for both categories of infertile men. MAIN OUTCOME MEASURES The primary outcome was successful sperm retrieval and the secondary outcomes were outcomes of ART. RESULTS Case-control studies reporting sperm retrieval rates and ART outcomes in men with AZFa and AZFb deletions were unavailable. On the basis of the data from 3,807 men, sperm retrieval rates were found to be higher in men with AZFc microdeletions compared to their non-deleted counterparts [OR = 1.82, 95% CI 0.97, 3.41], but the difference was not statistically significant. A significantly lower fertilization rate (OR = 0.61, 95% CI [0.50, 0.74]), clinical pregnancy rate (OR = 0.61, 95% CI [0.42, 0.89]), and live birth rate (OR = 0.54, 95% CI [0.40, 0.72]) were observed in men with AZFc deletions compared with men without deletions. There was no statistically significant difference in rates of embryo cleavage, blastocyst formation, good-quality embryos, implantation, and miscarriage between the two groups. On correcting for female factors, the fertilization rate (OR = 0.76, 95% CI [0.71, 0.82]), cleavage rate (OR = 0.54, 95% CI [0.41, 0.72]), clinical pregnancy rate (OR = 0.39, 95% CI [0.30, 0.52]), and live birth rate (OR = 0.48, 95% CI [0.35, 0.65]) were significantly lower in men with AZFc deletions compared with controls. CONCLUSIONS Presence of AZFc microdeletions adversely affects outcomes of ART in infertile men. Further in-depth studies delineating the role of the AZF genes in embryonic development are necessary to understand the full-impact of this finding. CLINICAL TRIAL REGISTRATION NUMBER CRD42022311738.
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Affiliation(s)
- Stacy Colaco
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, India.
| | - Deepak Modi
- Molecular and Cellular Biology Laboratory, ICMR-National Institute for Research in Reproductive and Child Health, Mumbai, Maharashtra, India
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2
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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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Sharifi Tabar M, Parsania C, Chen H, Su XD, Bailey CG, Rasko JE. Illuminating the dark protein-protein interactome. CELL REPORTS METHODS 2022; 2:100275. [PMID: 36046620 PMCID: PMC9421580 DOI: 10.1016/j.crmeth.2022.100275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In living systems, a complex network of protein-protein interactions (PPIs) underlies most biochemical events. The human protein-protein interactome has been surveyed using yeast two-hybrid (Y2H)- and mass spectrometry (MS)-based approaches such as affinity purification coupled to MS (AP-MS). Despite decades of systematic investigations and collaborative multi-disciplinary efforts, there is no "gold standard" for documenting PPIs. A surprisingly large fraction of the human interactome remains uncharted, which we refer to as the "dark interactome." In this review, we highlight the complexity of the human interactome and discuss the current status of the human reference interactome maps. We discuss why a large proportion of the human interactome has remained refractory to traditional approaches. We propose an experimental model that can enable the identification of the dark interactome in a cell-type-specific manner. We also propose a framework to implement when embarking on studies designed to rigorously identify and characterize protein interactions.
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Affiliation(s)
- Mehdi Sharifi Tabar
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Chirag Parsania
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Hong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Charles G. Bailey
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cancer & Gene Regulation Laboratory Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
| | - John E.J. Rasko
- Gene & Stem Cell Therapy Program Centenary Institute, The University of Sydney, Camperdown, NSW 2050, Australia
- Faculty of Medicine & Health, The University of Sydney, Sydney, NSW 2006, Australia
- Cell & Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia
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4
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Zhang K, Yang J, Qin Z, Lu T, Lou D, Ran Q, Huang H, Cheng S, Zellmer L, Ma H, Liao DJ. Establishment of New Genetic Markers and Methods for Sex Determination of Mouse and Human Cells using Polymerase Chain Reactions and Crude DNA Samples. Curr Genomics 2022; 23:275-288. [PMID: 36777874 PMCID: PMC9875541 DOI: 10.2174/1389202923666220610121344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/20/2022] [Accepted: 04/04/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The currently available methods for sexing human or mouse cells have weaknesses. Therefore, it is necessary to establish new methods. Methods: We used bioinformatics approach to identify genes that have alleles on both the X and Y chromosomes of mouse and human genomes and have a region showing a significant difference between the X and Y alleles. We then used polymerase chain reactions (PCR) followed by visualization of the PCR amplicons in agarose gels to establish these genomic regions as genetic sex markers. Results: Our bioinformatics analyses identified eight mouse sex markers and 56 human sex markers that are new, i.e. are previously unreported. Six of the eight mouse markers and 14 of the 56 human markers were verified using PCR and ensuing visualization of the PCR amplicons in agarose gels. Most of the tested and untested sex markers possess significant differences in the molecular weight between the X- and Y-derived PCR amplicons and are thus much better than most, if not all, previously-reported genetic sex markers. We also established several simple and essentially cost-free methods for extraction of crude genomic DNA from cultured cells, blood samples, and tissues that could be used as template for PCR amplification. Conclusion: We have established new sex genetic markers and methods for extracting genomic DNA and for sexing human and mouse cells. Our work may also lend some methodological strategies to the identification of new genetic sex markers for other organismal species.
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Affiliation(s)
- Keyin Zhang
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China
| | - Jianglin Yang
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P. R. China;,Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Zhenwei Qin
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Tianzu Lu
- Department of Stomatology, School of Stomatology, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China
| | - Didong Lou
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Qianchuan Ran
- Forensic Science Section, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang 550025, Guizhou Province, P.R. China
| | - Hai Huang
- Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Shuqiang Cheng
- Center for Clinical Laboratories, Guizhou Medical University Hospital, 4 Beijing Rd, Guiyang 550004, Guizhou Province, P.R. China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center, 730 South 8th St., Minneapolis, MN 5415
| | - Hong Ma
- Department of Stomatology, School of Stomatology, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Address correspondence to these authors at the Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-85186752814; E-mail: and Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University 9 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-851-88512238; E-mail:
| | - Dezhong J. Liao
- Department of Pathology, School of Clinical Medicine, Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China;,Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P. R. China;,Address correspondence to these authors at the Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-85186752814; E-mail: and Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University 9 Beijing Road, Guiyang 550004, Guizhou Province, P.R. China; Tel/Fax: 86-851-88512238; E-mail:
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5
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Xu Y, Pang Q. Repetitive DNA Sequences in the Human Y Chromosome and Male Infertility. Front Cell Dev Biol 2022; 10:831338. [PMID: 35912115 PMCID: PMC9326358 DOI: 10.3389/fcell.2022.831338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
The male-specific Y chromosome, which is well known for its diverse and complex repetitive sequences, has different sizes, genome structures, contents and evolutionary trajectories from other chromosomes and is of great significance for testis development and function. The large number of repetitive sequences and palindrome structure of the Y chromosome play an important role in maintaining the stability of male sex determining genes, although they can also cause non-allelic homologous recombination within the chromosome. Deletion of certain Y chromosome sequences will lead to spermatogenesis disorders and male infertility. And Y chromosome genes are also involved in the occurrence of reproductive system cancers and can increase the susceptibility of other tumors. In addition, the Y chromosome has very special value in the personal identification and parentage testing of male-related cases in forensic medicine because of its unique paternal genetic characteristics. In view of the extremely high frequency and complexity of gene rearrangements and the limitations of sequencing technology, the analysis of Y chromosome sequences and the study of Y-gene function still have many unsolved problems. This article will introduce the structure and repetitive sequence of the Y chromosome, summarize the correlation between Y chromosome various sequence deletions and male infertility for understanding the repetitive sequence of Y chromosome more systematically, in order to provide research motivation for further explore of the molecules mechanism of Y-deletion and male infertility and theoretical foundations for the transformation of basic research into applications in clinical medicine and forensic medicine.
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Affiliation(s)
- Yong Xu
- Department of Emergency Surgery, Jining NO 1 People’s Hospital, Jining, China
| | - Qianqian Pang
- Institute of Forensic Medicine and Laboratory Medicine, Jining Medical University, Jining, China
- *Correspondence: Qianqian Pang,
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6
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Burgos CF, Cikutovic R, Alarcón M. MicroRNA expression in male infertility. Reprod Fertil Dev 2022; 34:805-818. [PMID: 35760398 DOI: 10.1071/rd21131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 05/25/2022] [Indexed: 11/23/2022] Open
Abstract
Male infertility is a multifactorial disorder that involves different physiopathological mechanisms and multiple genes. In this sense, we analyse the role of miRNAs in this pathology. Gene expression analysis can provide relevant information to detect biomarkers, signalling pathways, pathologic mechanisms, and potential therapeutic targets for the disease. In this review, we describe four miRNA microarrays related to patients who present infertility diseases, including azoospermia, asthenozoospermia, and oligoasthenozoospermic. We selected 13 miRNAs with altered expressions in testis tissue (hsa-miR-122-5p, hsa-miR-145-5p, hsa-miR-16-5p, hsa-miR-193a-3p, hsa-miR-19a-3p, hsa-miR-23a-3p, hsa-miR-30b-5p, hsa-miR-34b-5p, hsa-miR-34c-5p, hsa-miR-374b-5p, hsa-miR-449a, hsa-miR-574-3p and hsa-miR-92a-3p), and systematically examine the mechanisms of four relevant miRNAs (hsa-miR-16-5p, hsa-miR-19a-3p, hsa-miR-92a-3p and hsa-miR-30b-5p) which we found that regulated a large number of proteins. An interaction network was generated, and its connections allowed us to identify signalling pathways and interactions between proteins associated with male infertility. In this way, we confirm that the most affected and relevant pathway is the PI3K-Akt signalling.
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Affiliation(s)
- C F Burgos
- Department of Physiology, Faculty of Biological Sciences, Universidad de Concepción, Concepcion, Chile
| | - R Cikutovic
- Universidad de Talca, Talca, 360000 Maule, Chile
| | - M Alarcón
- Department of Clinical Biochemistry and Immunohaematology, Faculty of Health Sciences, Universidad de Talca, Talca, Chile
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7
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Khani F, Nafian S, Mollamohammadi S, Nemati S, Shokoohian B, Hassani SN, Baharvand H, Soleimanpour-Lichaei HR, Salekdeh GH. Y Chromosome Genes May Play Roles in the Development of Neural Rosettes from Human Embryonic Stem Cells. Stem Cell Rev Rep 2022; 18:3008-3020. [PMID: 35661078 DOI: 10.1007/s12015-022-10392-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2022] [Indexed: 01/24/2024]
Abstract
BACKGROUND The human Y chromosome harbors genes that are mainly involved in the growth, development, sexual dimorphism, and spermatogenesis process. Despite many studies, the function of the male-specific region of the Y chromosome (MSY) awaits further clarification, and a cell-based approach can help in this regard. RESULTS In this study, we have developed four stable transgenic male embryonic stem cell (ESCs) lines that can overexpress male-specific genes HSFY1, RBMY1A1, RPS4Y1, and SRY. As a proof of principle, we differentiated one of these cell lines (RPS4Y1 over-expressing ESCs) to the neural stem cell (rosette structure) and characterized them based on the expression level of lineage markers. RPS4Y1 expression in the Doxycycline-treated group was significantly higher than control groups at transcript and protein levels. Furthermore, we found Doxycycline-treated group had a higher differentiation efficiency than the untreated control groups. CONCLUSIONS Our results suggest that the RPS4Y1 gene may play a critical role in neurogenesis. Also, the generated transgenic ESC lines can be widely employed in basic and preclinical studies, such as sexual dimorphism of neural and cardiac functions, the development of cancerous and non-cancerous disease models, and drug screening.
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Affiliation(s)
- Farzaneh Khani
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Simin Nafian
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Sepideh Mollamohammadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Shiva Nemati
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Bahare Shokoohian
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Seyedeh Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, 13145-871, Tehran, Iran
| | - Hamid Reza Soleimanpour-Lichaei
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering & Biotechnology (NIGEB), P.O.Box: 14965-161, Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, 16656-59911, Tehran, Iran. .,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.
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8
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Heydari R, Jangravi Z, Maleknia S, Seresht-Ahmadi M, Bahari Z, Salekdeh GH, Meyfour A. Y chromosome is moving out of sex determination shadow. Cell Biosci 2022; 12:4. [PMID: 34983649 PMCID: PMC8724748 DOI: 10.1186/s13578-021-00741-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/21/2021] [Indexed: 01/05/2023] Open
Abstract
Although sex hormones play a key role in sex differences in susceptibility, severity, outcomes, and response to therapy of different diseases, sex chromosomes are also increasingly recognized as an important factor. Studies demonstrated that the Y chromosome is not a ‘genetic wasteland’ and can be a useful genetic marker for interpreting various male-specific physiological and pathophysiological characteristics. Y chromosome harbors male‑specific genes, which either solely or in cooperation with their X-counterpart, and independent or in conjunction with sex hormones have a considerable impact on basic physiology and disease mechanisms in most or all tissues development. Furthermore, loss of Y chromosome and/or aberrant expression of Y chromosome genes cause sex differences in disease mechanisms. With the launch of the human proteome project (HPP), the association of Y chromosome proteins with pathological conditions has been increasingly explored. In this review, the involvement of Y chromosome genes in male-specific diseases such as prostate cancer and the cases that are more prevalent in men, such as cardiovascular disease, neurological disease, and cancers, has been highlighted. Understanding the molecular mechanisms underlying Y chromosome-related diseases can have a significant impact on the prevention, diagnosis, and treatment of diseases.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Jangravi
- Department of Biochemistry, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Samaneh Maleknia
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrshad Seresht-Ahmadi
- Department of Basic Science and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Zahra Bahari
- Department of Physiology and Medical Physics, Faculty of Medicine, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | | | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran. .,Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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9
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Chowen JA, Garcia-Segura LM. Role of glial cells in the generation of sex differences in neurodegenerative diseases and brain aging. Mech Ageing Dev 2021; 196:111473. [PMID: 33766745 DOI: 10.1016/j.mad.2021.111473] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/14/2021] [Accepted: 03/16/2021] [Indexed: 12/11/2022]
Abstract
Diseases and aging-associated alterations of the nervous system often show sex-specific characteristics. Glial cells play a major role in the endogenous homeostatic response of neural tissue, and sex differences in the glial transcriptome and function have been described. Therefore, the possible role of these cells in the generation of sex differences in pathological alterations of the nervous system is reviewed here. Studies have shown that glia react to pathological insults with sex-specific neuroprotective and regenerative effects. At least three factors determine this sex-specific response of glia: sex chromosome genes, gonadal hormones and neuroactive steroid hormone metabolites. The sex chromosome complement determines differences in the transcriptional responses in glia after brain injury, while gonadal hormones and their metabolites activate sex-specific neuroprotective mechanisms in these cells. Since the sex-specific neuroprotective and regenerative activity of glial cells causes sex differences in the pathological alterations of the nervous system, glia may represent a relevant target for sex-specific therapeutic interventions.
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Affiliation(s)
- Julie A Chowen
- Department of Endocrinology, Hospital Infantil Universitario Niño Jesús, Instituto de Investigación la Princesa, Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutriciόn (CIBEROBN), Instituto de Salud Carlos III, and IMDEA Food Institute, CEIUAM+CSIC, Madrid, Spain.
| | - Luis M Garcia-Segura
- Instituto Cajal, Consejo Superior de Investigaciones Científicas (CSIC) and Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain.
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10
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Witherspoon L, Dergham A, Flannigan R. Y-microdeletions: a review of the genetic basis for this common cause of male infertility. Transl Androl Urol 2021; 10:1383-1390. [PMID: 33850774 PMCID: PMC8039600 DOI: 10.21037/tau-19-599] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The human Y-chromosome contains genetic material responsible for normal testis development and spermatogenesis. The long arm (Yq) of the Y-chromosome has been found to be susceptible to self-recombination during spermatogenesis predisposing this area to deletions. The incidence of these deletions is estimated to be 1/4,000 in the general population but has been found to be much higher in infertile men. Currently, Y-microdeletions are the second most commonly identified genetic cause of male infertility after Klinefelter syndrome. This has led to testing for these deletions becoming standard practice in men with azoospermia and severe oligospermia. There are three commonly identified Y-microdeletions in infertile males, termed azoospermia factor (AZF) microdeletions AZFa, AZFb and AZFc. With increased understanding and investigation of this genetic basis for infertility a more comprehensive understanding of these deletions has evolved, with several other deletion subtypes being identified. Understanding the genetic basis and pathology behind these Y-microdeletions is essential for any clinician involved in reproductive medicine. In this review we discuss the genetic basis of Y-microdeletions, the various subtypes of deletions, and current technologies available for testing. Our understanding of this issue is evolving in many areas, and in this review we highlight future testing opportunities that may allow us to stratify men with Y-microdeletion associated infertility more accurately
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Affiliation(s)
- Luke Witherspoon
- Division of Urology, Department of Surgery, The Ottawa Hospital and University of Ottawa, Ottawa, ON, Canada
| | - Ali Dergham
- School of Medicine, Faculty of Health Sciences, Queen's University, Kingston, ON, Canada
| | - Ryan Flannigan
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Urology, Weill Cornell Medicine, New York, NY, USA
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11
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Nafian Dehkordi S, Khani F, Hassani SN, Baharvand H, Soleimanpour-Lichaei HR, Salekdeh GH. The Contribution of Y Chromosome Genes to Spontaneous Differentiation of Human Embryonic Stem Cells into Embryoid Bodies In Vitro. CELL JOURNAL 2021; 23:40-50. [PMID: 33650819 PMCID: PMC7944136 DOI: 10.22074/cellj.2021.7145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/30/2019] [Indexed: 11/04/2022]
Abstract
Objective Sexual dimorphism in mammals can be described as subsequent transcriptional differences from their distinct sex chromosome complements. Following X inactivation in females, the Y chromosome is the major genetic difference between sexes. In this study, we used a male embryonic stem cell line (Royan H6) to identify the potential role of the male-specific region of the Y chromosome (MSY) during spontaneous differentiation into embryoid bodies (EBs) as a model of early embryonic development. Materials and Methods In this experimental study, RH6 cells were cultured on inactivated feeder layers and Matrigel. In a dynamic suspension system, aggregates were generated in the same size and were spontaneously differentiated into EBs. During differentiation, expression patterns of specific markers for three germ layers were compared with MSY genes. Results Spontaneous differentiation was determined by downregulation of pluripotent markers and upregulation of fourteen differentiation markers. Upregulation of the ectoderm markers was observed on days 4 and 16, whereas mesoderm markers were upregulated on the 8th day and endodermic markers on days 12-16. Mesoderm markers correlated with 8 MSY genes namely DDX3Y, RPS4Y1, KDM5D, TBL1Y, BCORP1, PRY, DAZ, and AMELY, which were classified as a mesoderm cluster. Endoderm markers were co-expressed with 7 MSY genes, i.e. ZFY, TSPY, PRORY, VCY, EIF1AY, USP9Y, and RPKY, which were grouped as an endoderm cluster. Finally, the ectoderm markers correlated with TXLNGY, NLGN4Y, PCDH11Y, TMSB4Y, UTY, RBMY1, and HSFY genes of the MSY, which were categorized as an ectoderm cluster. In contrast, 2 MSY genes, SRY and TGIF2LY, were more highly expressed in RH6 cells compared to EBs. Conclusion We found a significant correlation between spontaneous differentiation and upregulation of specific MSY genes. The expression alterations of MSY genes implied the potential responsibility of their gene co-expression clusters for EB differentiation. We suggest that these genes may play important roles in early embryonic development.
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Affiliation(s)
- Simin Nafian Dehkordi
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Farzaneh Khani
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyedeh Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran, Iran
| | - Hamid Reza Soleimanpour-Lichaei
- Department of Stem Cells and Regenerative Medicine, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran. .,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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12
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Zhou Q, Xu M, Wang X, Yu M, Chen X, Lu J, Zhou R, Zhang J, Ling X, Ji J. Deficiency of TBL1XR1 causes asthenozoospermia. Andrologia 2021; 53:e13980. [PMID: 33528066 DOI: 10.1111/and.13980] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/20/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
Transducin (β)-like 1 X-linked receptor 1 (TBL1XR1) is an evolutionarily conserved protein related to spermatozoa. To clarify its role and mechanism of action in spermatozoa, qRT-PCR was used to analyse the expression of TBL1XR1 in human spermatozoa and mouse testes. The mice were established as an animal model by injecting the mice testes with small interfering RNA against TBL1XR1 or control siRNA. Our results indicated that deficiency of TBL1XR1 in mice reduced the motility of spermatozoa and disrupted the histone-to-protamine transition. We also found the decreased expression of TBL1XR1 in the spermatozoa of human patients with asthenozoospermia (AZ) compared with that in the spermatozoa of healthy males. Moreover, we carried out chromatin immunoprecipitation analyses and found that genes downstream of TBL1XR1 were related to sperm motility. Thus, TBL1XR1 might be related to sperm motility and might function through its downstream genes. Our data highlight the role of TBL1XR1 involved in spermatozoa and provide new molecular insights into the intricate systems required for male fertility.
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Affiliation(s)
- Qiao Zhou
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Miaofei Xu
- Cellular and Molecular Pathology Branch, National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Xin Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Department of Histology and Embryology, Nanjing Medical University, Nanjing, China
| | - Mingming Yu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xiaojiao Chen
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jing Lu
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ran Zhou
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Junqiang Zhang
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiufeng Ling
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Juan Ji
- The Affiliated Obstetrics and Gynecology Hospital with Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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13
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Alikhani M, Karamzadeh R, Rahimi P, Adib S, Baharvand H, Salekdeh GH. Human Proteome Project and Human Pluripotent Stem Cells: Odd Bedfellows or a Perfect Match? J Proteome Res 2020; 19:4747-4753. [PMID: 33124832 DOI: 10.1021/acs.jproteome.0c00689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims at the identification of missing proteins (MPs) and the functional characterization of functionally unannotated PE1 (uPE1) proteins. A major challenge in addressing this goal is that many human proteins and MPs are silent in adult cells. A promising approach to overcome such challenge is to exploit the advantage of novel tools such as pluripotent stem cells (PSCs), which are capable of differentiation into three embryonic germ layers, namely, the endoderm, mesoderm, and ectoderm. Here we present several examples of how the Human Y Chromosome Proteome Project (Y-HPP) benefited from this approach to meet C-HPP goals. Furthermore, we discuss how integrating CRISPR engineering, human-induced pluripotent stem cell (hiPSC)-derived disease modeling systems, and organoid technologies provides a unique platform for Y-HPP and C-HPP for MP identification and the functional characterization of human proteins, especially uPE1s.
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Affiliation(s)
- Mehdi Alikhani
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
| | - Razieh Karamzadeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
| | - Pardis Rahimi
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
| | - Samane Adib
- Department of Anatomy, Faculty of Medical Sciences, Tarbiat Modares University, Tehran 14115-111, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran.,Department of Developmental Biology, University of Science and Culture, Tehran 146196815, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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14
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The Role of Number of Copies, Structure, Behavior and Copy Number Variations (CNV) of the Y Chromosome in Male Infertility. Genes (Basel) 2019; 11:genes11010040. [PMID: 31905733 PMCID: PMC7016774 DOI: 10.3390/genes11010040] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/17/2019] [Accepted: 12/23/2019] [Indexed: 12/11/2022] Open
Abstract
The World Health Organization (WHO) defines infertility as the inability of a sexually active, non-contracepting couple to achieve spontaneous pregnancy within one year. Statistics show that the two sexes are equally at risk. Several causes may be responsible for male infertility; however, in 30–40% of cases a diagnosis of idiopathic male infertility is made in men with normal urogenital anatomy, no history of familial fertility-related diseases and a normal panel of values as for endocrine, genetic and biochemical markers. Idiopathic male infertility may be the result of gene/environment interactions, genetic and epigenetic abnormalities. Numerical and structural anomalies of the Y chromosome represent a minor yet significant proportion and are the topic discussed in this review. We searched the PubMed database and major search engines for reports about Y-linked male infertility. We present cases of Y-linked male infertility in terms of (i) anomalies of the Y chromosome structure/number; (ii) Y chromosome misbehavior in a normal genetic background; (iii) Y chromosome copy number variations (CNVs). We discuss possible explanations of male infertility caused by mutations, lower or higher number of copies of otherwise wild type, Y-linked sequences. Despite Y chromosome structural anomalies are not a major cause of male infertility, in case of negative results and of normal DNA sequencing of the ascertained genes causing infertility and mapping on this chromosome, we recommend an analysis of the karyotype integrity in all cases of idiopathic fertility impairment, with an emphasis on the structure and number of this chromosome.
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15
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Taleahmad S, Alikhani M, Mollamohammadi S, Yousefi M, Taei A, Hassani SN, Baharvand H, Salekdeh GH. Inhibition of Human Y Chromosome Gene, SRY, Promotes Naïve State of Human Pluripotent Stem Cells. J Proteome Res 2019; 18:4254-4261. [PMID: 31580082 DOI: 10.1021/acs.jproteome.9b00396] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Although males and females have a variety of sexually dimorphic features related to hormonal effects, the genetic basis of dimorphism relies on early embryo development. Two pluripotent states, naïve and primed, emerge during early mammalian development. Identification of signaling pathways that induce differences between these two states can help to modulate conversion of primed cells to naïve cells. Naïve cells have a shorter doubling time and longer survival than their primed counterparts when passaged as single cells. In this study, we sought to explore the role of Y chromosome genes on human pluripotent stem cells (hPSCs) by investigating differential expressions of the male-specific region of the Y chromosome (MSY) genes in primed and naïve cells. Interestingly, we found that several MSY genes, including SRY, showed higher expression levels in primed compared to naïve human embryonic stem cells (hESCs). We hypothesize that SRY prevents WNT/β-catenin signaling by its interaction and inhibition of β-catenin activation in the nucleus. Results of the loss-of-function approach conducted by depletion of SRY indicated increased expressions of pluripotency marker genes and alkaline phosphatase (ALP) activity in the primed cells. SRY reduction was associated with overexpression of WNT signaling target genes AXIN2, Brachury, TCF1, TBX2, and TBX3. We suggest that inhibition of SRY may result in activation of β-catenin and up-regulation of the WNT signaling pathway, both of which are important to naïve conversion.
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Affiliation(s)
- Sara Taleahmad
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Mehdi Alikhani
- Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Sepideh Mollamohammadi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Meisam Yousefi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Adeleh Taei
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Seyedeh Nafiseh Hassani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran.,Department of Developmental Biology , University of Science and Culture , Tehran 113145-871 , Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology, ACECR , Tehran 16635-148 , Iran.,Department of Molecular Sciences , Macquarie University , Sydney , NSW 2109 , Australia.,Department of Systems and Synthetic Biology , Agricultural Biotechnology Research Institute of Iran , Karaj 313593315 , Iran
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16
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Meyfour A, Pahlavan S, Ansari H, Baharvand H, Salekdeh GH. Down-Regulation of a Male-Specific H3K4 Demethylase, KDM5D, Impairs Cardiomyocyte Differentiation. J Proteome Res 2019; 18:4277-4282. [PMID: 31560558 DOI: 10.1021/acs.jproteome.9b00395] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Despite the small number of Y chromosome genes, their adequate expression is required for regulation of transcription, translation, and protein stability in males, not just for sex determination. In addition to the role in male fertility, the Y chromosome has a significant role in the development and sexual dimorphism of healthy and disease phenotypes. We observed that KDM5D along with its X-counterpart, KDM5C, are up-regulated during the cardiac mesoderm stage of development. Down-regulation of KDM5D using siRNA resulted in accumulation of differentiating cells in the S-phase of the cell cycle and impaired progression to cardiomyocytes as reflected by an altered expression pattern of cardiac progenitor specific markers. Furthermore, while control cells started spontaneous beating at a normal physiological range on day 7 of differentiation induction, no spontaneous beating was observed in KDM5D down-regulated cells. Interestingly, the knockdown of KDM5D had no significant effect on the expression level of its X-counterpart, KDM5C. Thus, we suggest that KDM5D, in cooperation with its X homologue as a dose-sensitive gene, may have an important role in cardiomyocyte differentiation. Our study presents further evidence on the contribution of Y chromosome genes to sex-dependent development outside of sex determination.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases , Shahid Beheshti University of Medical Sciences , Tehran 19839-63113 , Iran.,Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Hassan Ansari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran.,Department of Developmental Biology , University of Science and Culture , Tehran 13145-871 , Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center , Royan Institute for Stem Cell Biology and Technology , ACECR, Tehran 16635-148 , Iran.,Department of Systems and Synthetic Biology , Agricultural Biotechnology Research Institute of Iran , Karaj 313593315 , Iran.,Department of Molecular Science , Macquarie University , Sydney , NSW 2109 , Australia
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17
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Cao NTT, Nguyen KT, Vu NT, Nguyen VC, Trinh TM, Nguyen NTB, Trinh LTB, Lam TTT, Cao BL, Dang TN. Analysis of the length polymorphisms in sequence-tagged-site sY1291 on Y chromosome in Vietnamese men of infertile couples. Sci Rep 2019; 9:9654. [PMID: 31427585 PMCID: PMC6700317 DOI: 10.1038/s41598-019-45649-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
This study aims to analyze the length polymorphisms in sequence-tagged-site (STS) sY1291 of the Y chromosome in Vietnamese men of infertile couples. All 322 DNA samples were amplified with the sY1291 primer by the quantitative fluorescent polymerase chain reaction (QF-PCR) assay. DNA sequencing technique was employed to evaluate the accuracy of QF-PCR results. The study showed 273 out of 322 DNA samples had the presence of STS sY1291, accounted for 84.78%. The QF-PCR results showed that there were various lengths in STS sY1291: 507 bp, 512 bp, 523 bp and 527 bp. The most prevalent length in STS sY1291 was 507 bp (87.5%), the others were 512 bp (4.8%), 523 bp (4.8%) and 527 bp (2.9%). We found that the observed length polymorphisms derived from differences in the number of mononucleotide Thymine (T) repeats in its structure. It stretched from 22 T to 39 T. DNA sequencing results identified that the number of mononucleotide T repeats causes these polymorphisms. However, the pair-wise alignment between the obtained and reference sequence was 77%. It can be seen that the length polymorphisms in STS sY1291 observed in QF-PCR results was accurate but it is still difficult to sequence fragments with mononucleotide repeats.
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Affiliation(s)
- Nguyen Thi Tai Cao
- Department of Biology - Genetics, Faculty of Basic Science, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam.
| | - Kien Trung Nguyen
- Department of Physiology, Faculty of Medicine, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam
| | - Nhuan Thi Vu
- Department of Biology - Genetics, Faculty of Basic Science, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam
| | - Vieng Chung Nguyen
- Faculty of Endocrinology, Can Tho Obstetrics and Gynecology Hospital, Can Tho city, Vietnam
| | - Thiet Minh Trinh
- Department of Biology - Genetics, Faculty of Basic Science, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam
| | - Ngoc Thi Bich Nguyen
- Faculty of Endocrinology, Can Tho Obstetrics and Gynecology Hospital, Can Tho city, Vietnam
| | - Lien Thi Bich Trinh
- Faculty of Endocrinology, Can Tho Obstetrics and Gynecology Hospital, Can Tho city, Vietnam
| | - Tien Thi Thuy Lam
- Department of Foreign language, Faculty of Basic Science, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam
| | - Binh Luong Cao
- Department of Foreign language, Faculty of Basic Science, Can Tho University of Medicine and Pharmacy, Can Tho city, Vietnam
| | - Tra Ngoc Dang
- Department of Biology - Technology, Quoc Hoc Quy Nhon Highschool, Quy Nhon City, Vietnam
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18
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Colaco S, Modi D. Consequences of Y chromosome microdeletions beyond male infertility. J Assist Reprod Genet 2019; 36:1329-1337. [PMID: 31214882 DOI: 10.1007/s10815-019-01492-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/16/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE The human Y chromosome plays a central role in sex determination and spermatogenesis. The azoospermia factor (AZF) loci on the Y chromosome contain genes that were thought to be testis specific with their deletions leading to spermatogenic failure. However, beyond the testis, the AZF genes (mainly those in AZFa and AZFb loci) are widely expressed in multiple tissues. Further, these genes are predicted to play roles in processes such as gene regulation and protein synthesis. These observations suggest that the AZF genes may have functions beyond regulation of fertility. RESULTS Three major areas have emerged where alternations in AZF genes have effects beyond infertility. (1) Poor-quality embryos are generated in assisted reproduction when sperm from men harboring Y chromosome microdeletions are used, (2) a higher preponderance of neuropsychiatry disorders is observed in men with deletions in AZF genes, and (3) copy number variations and altered expression of AZF genes are found in several cancers. CONCLUSION While our data is preliminary and observational in nature, systematic studies are required to address how genetic alterations in the Y chromosome can affect the health of men beyond infertility. This information will provide a different perspective in the area of androgenetics and have implications in devising strategies for maintaining the overall well-being of infertile males.
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Affiliation(s)
- Stacy Colaco
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India.
| | - Deepak Modi
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India.
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19
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Meyfour A, Hosseini M, Sobhanian H, Pahlavan S. Iran's Contribution to Human Proteomic Research. CELL JOURNAL 2019; 21:229-235. [PMID: 31210427 PMCID: PMC6582420 DOI: 10.22074/cellj.2019.6303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/17/2018] [Indexed: 11/04/2022]
Abstract
Proteomics is a powerful approach to study the whole set of proteins expressed in an organism, organ, tissue or cell resulting in valuable information on physiological or pathological state of a biological system. High throughput proteomic data facilitated the understanding of various biological systems with respect to normal and pathological conditions particularly in the instances of human clinical manifestations. The important role of proteins as the functional gene products encouraged scientists to apply this technology to gain a better understanding of extremely complex biological systems. In last two decades, several proteomics teams have been gradually formed in Iran. In this review, we highlight the most important findings of proteomic research groups in Iran at various areas of stem cells, Y chromosome, infertility, infectious disease and biomarker discovery.
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Affiliation(s)
- Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mahya Hosseini
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.Electronic Address:
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20
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Patel R, Khalifa AO, Isali I, Shukla S. Prostate cancer susceptibility and growth linked to Y chromosome genes. Front Biosci (Elite Ed) 2018; 10:423-436. [PMID: 29293466 PMCID: PMC6152832 DOI: 10.2741/e830] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The role of Y chromosome in prostate cancer progression and incidence is not well known. Among the 46 chromosomes, Y chromosome determines the male gender. The Y chromosome is smaller than the X chromosome and contains only 458 genes compared to over 2000 genes found in the X chromosome. The Y chromosome is prone to high mutation rates, created exclusively in sperm cells due to the highly oxidative environment of the testis. Y chromosome harbors epigenetic information, which affects the expression of genes associated with the incidence and progression of prostate cancer. In this review, we focus on Y chromosome related genetic abnormalities, likely to be involved in the development and progression of prostate cancer.
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Affiliation(s)
- Riddhi Patel
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Ahmad O Khalifa
- Urology Dept. Case Western Reserve University, Cleveland, Ohio and Menofia University, Shebin Al kom, Egpt
| | - Ilaha Isali
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA
| | - Sanjeev Shukla
- Department of Urology, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, USA,
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21
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Colaco S, Modi D. Genetics of the human Y chromosome and its association with male infertility. Reprod Biol Endocrinol 2018; 16:14. [PMID: 29454353 PMCID: PMC5816366 DOI: 10.1186/s12958-018-0330-5] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that recur in infertile males are termed as AZF (Azoospermia Factor) microdeletions viz. AZFa, AZFb and AZFc. As estimated from data of nearly 40,000 Y chromosomes, the global prevalence of Yq microdeletions is 7.5% in infertile males; however the European infertile men are less susceptible to Yq microdeletions, the highest prevalence is in Americans and East Asian infertile men. In addition, partial deletions of the AZFc locus have been associated with infertility but the effect seems to be ethnicity dependent. Analysis of > 17,000 Y chromosomes from fertile and infertile men has revealed an association of gr/gr deletion with male infertility in Caucasians and Mongolian men, while the b2/b3 deletion is associated with male infertility in African and Dravidian men. Clinically, the screening for Yq microdeletions would aid the clinician in determining the cause of male infertility and decide a rational management strategy for the patient. As these deletions are transmitted to 100% of male offspring born through assisted reproduction, testing of Yq deletions will allow the couples to make an informed choice regarding the perpetuation of male infertility in future generations. With the emerging data on association of Yq deletions with testicular cancers and neuropsychiatric conditions long term follow-up data is urgently needed for infertile men harboring Yq deletions. If found so, the information will change the current the perspective of androgenetics from infertility and might have broad implication in men health.
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Affiliation(s)
- Stacy Colaco
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India
| | - Deepak Modi
- Department of Molecular and Cellular Biology, ICMR-National Institute for Research in Reproductive Health, JM Street, Parel, Mumbai, Maharashtra, 400012, India.
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22
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Meyfour A, Pooyan P, Pahlavan S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Chromosome-Centric Human Proteome Project Allies with Developmental Biology: A Case Study of the Role of Y Chromosome Genes in Organ Development. J Proteome Res 2017; 16:4259-4272. [PMID: 28914051 DOI: 10.1021/acs.jproteome.7b00446] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the main goals of Chromosome-Centric Human Proteome Project is to identify protein evidence for missing proteins (MPs). Here, we present a case study of the role of Y chromosome genes in organ development and how to overcome the challenges facing MPs identification by employing human pluripotent stem cell differentiation into cells of different organs yielding unprecedented biological insight into adult silenced proteins. Y chromosome is a male-specific sex chromosome which escapes meiotic recombination. From an evolutionary perspective, Y chromosome has preserved 3% of ancestral genes compared to 98% preservation of the X chromosome based on Ohno's law. Male specific region of Y chromosome (MSY) contains genes that contribute to central dogma and govern the expression of various targets throughout the genome. One of the most well-known functions of MSY genes is to decide the male-specific characteristics including sex, testis formation, and spermatogenesis, which are majorly formed by ampliconic gene families. Beyond its role in sex-specific gonad development, MSY genes in coexpression with their X counterparts, as single copy and broadly expressed genes, inhibit haplolethality and play a key role in embryogenesis. The role of X-Y related gene mutations in the development of hereditary syndromes suggests an essential contribution of sex chromosome genes to development. MSY genes, solely and independent of their X counterparts and/or in association with sex hormones, have a considerable impact on organ development. In this Review, we present major recent findings on the contribution of MSY genes to gonad formation, spermatogenesis, and the brain, heart, and kidney development and discuss how Y chromosome proteome project may exploit developmental biology to find missing proteins.
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Affiliation(s)
- Anna Meyfour
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Paria Pooyan
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Sara Pahlavan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | - Hamid Gourabi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute , 19395-4644 Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , 19395-4644 Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Academic Center for Education, Culture and Research , 81589-68433 Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , 31535-1897 Karaj, Iran
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23
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Meyfour A, Ansari H, Pahlavan S, Mirshahvaladi S, Rezaei-Tavirani M, Gourabi H, Baharvand H, Salekdeh GH. Y Chromosome Missing Protein, TBL1Y, May Play an Important Role in Cardiac Differentiation. J Proteome Res 2017; 16:4391-4402. [PMID: 28853286 DOI: 10.1021/acs.jproteome.7b00391] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Despite evidence for sex-specific cardiovascular physiology and pathophysiology, the biological basis for this dimorphism remains to be explored. Apart from hormonal factors, gender-related characteristics may reside in the function of sex chromosomes during cardiac development. In this study, we investigated the differential expression of the male-specific region of the Y chromosome (MSY) genes and their X counterparts during cardiac differentiation of human embryonic stem cells (hESC). We observed alterations in mRNA and protein levels of TBL1Y, PCDH11Y, ZFY, KDM5D, USP9Y, RPS4Y1, DDX3Y, PRY, XKRY, BCORP1, RBMY, HSFY, and UTY, which accompanied changes in intracellular localization. Of them, the abundance of a Y chromosome missing protein, TBL1Y, showed a significant increase during differentiation while the expression level of its X counterpart decreased. Consistently, reducing TBL1Y cellular level using siRNA approach influenced cardiac differentiation by reducing its efficacy as well as increasing the probability of impaired contractions. TBL1Y knockdown may have negatively impacted cardiogenesis by CtBP stabilization. Furthermore, we presented compelling experimental evidence to distinguish TBL1Y from TBL1X, its highly similar X chromosome homologue, and proposed reclassification of TBL1Y as "found missing protein" (PE1). Our results demonstrated that MSY proteins may play an important role in cardiac development.
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Affiliation(s)
- Anna Meyfour
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | | | | | | | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , 19839-63113 Tehran, Iran
| | | | - Hossein Baharvand
- Department of Developmental Biology, University of Science and Culture , 13145-871 Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , Karaj, Iran
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24
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Zhou JH, Zhou QZ, Yang JK, Lyu XM, Bian J, Guo WB, Chen ZJ, Xia M, Xia H, Qi T, Li X, Liu CD. MicroRNA-27a-mediated repression of cysteine-rich secretory protein 2 translation in asthenoteratozoospermic patients. Asian J Androl 2017; 19:591-595. [PMID: 27517483 PMCID: PMC5566855 DOI: 10.4103/1008-682x.185001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/05/2016] [Accepted: 06/08/2016] [Indexed: 12/28/2022] Open
Abstract
Cysteine-rich secretory protein 2 (CRISP2) is an important protein in spermatozoa that plays roles in modulating sperm flagellar motility, the acrosome reaction, and gamete fusion. Spermatozoa lacking CRISP2 exhibit low sperm motility and abnormal morphology. However, the molecular mechanisms underlying the reduction of CRISP2 in asthenoteratozoospermia (ATZ) remain unknown. In this study, low expression of CRISP2 protein rather than its mRNA was observed in the ejaculated spermatozoa from ATZ patients as compared with normozoospermic males. Subsequently, bioinformatic prediction, luciferase reporter assays, and microRNA-27a (miR-27a) transfection experiments revealed that miR-27a specifically targets CRISP2 by binding to its 3' untranslated region (3'-UTR), suppressing CRISP2 expression posttranscriptionally. Further evidence was provided by the clinical observation of high miR-27a expression in ejaculated spermatozoa from ATZ patients and a negative correlation between miR-27a expression and CRISP2 protein expression. Finally, a retrospective follow-up study supported that both high miR-27a expression and low CRISP2 protein expression were associated with low progressive sperm motility, abnormal morphology, and infertility. This study demonstrates a novel mechanism responsible for reduced CRISP2 expression in ATZ, which may offer a potential therapeutic target for treating male infertility, or for male contraception.
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Affiliation(s)
- Jun-Hao Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Qi-Zhao Zhou
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Jian-Kun Yang
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Xiao-Ming Lyu
- Laboratory Medical Center, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Jun Bian
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Wen-Bin Guo
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Zi-Jian Chen
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Ming Xia
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hui Xia
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Tao Qi
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xin Li
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- Cancer Research Institute, Southern Medical University, Guangzhou, China
| | - Cun-Dong Liu
- Department of Urology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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25
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Alikhani M, Mirzaei M, Sabbaghian M, Parsamatin P, Karamzadeh R, Adib S, Sodeifi N, Gilani MAS, Zabet-Moghaddam M, Parker L, Wu Y, Gupta V, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia. J Proteomics 2017; 162:141-154. [DOI: 10.1016/j.jprot.2017.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/17/2022]
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26
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Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome. Genetica 2017; 145:295-305. [PMID: 28421323 DOI: 10.1007/s10709-017-9965-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 04/08/2017] [Indexed: 10/19/2022]
Abstract
Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome.
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27
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Kothandaraman N, Agarwal A, Abu-Elmagd M, Al-Qahtani MH. Pathogenic landscape of idiopathic male infertility: new insight towards its regulatory networks. NPJ Genom Med 2016; 1:16023. [PMID: 29263816 PMCID: PMC5685305 DOI: 10.1038/npjgenmed.2016.23] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 12/11/2022] Open
Abstract
Idiopathic male infertility (IMI) affects nearly 10-15% of men in their prime reproductive age. More than 500 target genes were postulated to be associated with this disease condition through various genomic studies. The challenge is to determine the functional role of these genes and proteins that form part of a larger network leading to pathogenesis of the IMI phenotype in humans. In the current study, we have catalogued all of the genes associated with IMI from published studies, as well as looked at reactive oxygen species and antioxidant genes, the two key physiological determinants essential for normal spermatogenesis. Any imbalance in these genes through mutation, single-nucleotide polymorphisms (SNPs) or other forms could result in abnormal regulation of genes leading to infertility. SNPs catalogued in the current study, representing a third of the IMI genes, could possibly explain the various hidden factors associated with this condition. The enriched biological functions in SNPs, as well as functional analysis of IMI genes, resulted in the identification of novel gene pairs, from which we proposed new models to describe the underlying pathogenesis of this disease condition. The outcome of this study will give a new set of genes and proteins that could help explain the disease from a global perspective previously not addressed using standard approaches. Genes corresponding to proteins identified from the current study for spermatozoa and seminal plasma showed functional correlation based on their localization, which gave further confirmation of their roles in defective spermatogenesis as seen in IMI.
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Affiliation(s)
- Narasimhan Kothandaraman
- American Centre for Reproductive Medicine, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ashok Agarwal
- American Centre for Reproductive Medicine, Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Muhammad Abu-Elmagd
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Centre of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammed H Al-Qahtani
- Centre of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
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28
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Singh N, Johnstone DB, Martin KA, Tempera I, Kaplan MJ, Denny MF. Alterations in nuclear structure promote lupus autoimmunity in a mouse model. Dis Model Mech 2016; 9:885-97. [PMID: 27483354 PMCID: PMC5007980 DOI: 10.1242/dmm.024851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/01/2016] [Indexed: 02/06/2023] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disorder characterized by the development of autoantibodies that recognize components of the cell nucleus. The vast majority of lupus research has focused on either the contributions of immune cell dysfunction or the genetics of the disease. Because granulocytes isolated from human SLE patients had alterations in neutrophil nuclear morphology that resembled the Pelger-Huet anomaly, and had prominent mis-splicing of mRNA encoding the nuclear membrane protein lamin B receptor (LBR), consistent with their Pelger-Huet-like nuclear morphology, we used a novel mouse model system to test the hypothesis that a disruption in the structure of the nucleus itself also contributes to the development of lupus autoimmunity. The lupus-prone mouse strain New Zealand White (NZW) was crossed with c57Bl/6 mice harboring a heterozygous autosomal dominant mutation in Lbr (B6.Lbr(ic/+)), and the (NZW×B6.Lbr(ic))F1 offspring were evaluated for induction of lupus autoimmunity. Only female (NZW×B6.Lbr(ic))F1 mice developed lupus autoimmunity, which included splenomegaly, kidney damage and autoantibodies. Kidney damage was accompanied by immune complex deposition, and perivascular and tubule infiltration of mononuclear cells. The titers of anti-chromatin antibodies exceeded those of aged female MRL-Fas(lpr) mice, and were predominantly of the IgG2 subclasses. The anti-nuclear antibody staining profile of female (NZW×B6.Lbr(ic))F1 sera was complex, and consisted of an anti-nuclear membrane reactivity that colocalized with the A-type lamina, in combination with a homogeneous pattern that was related to the recognition of histones with covalent modifications that are associated with gene activation. An anti-neutrophil IgM recognizing calreticulin, but not myeloperoxidase (MPO) or proteinase 3 (PR3), was also identified. Thus, alterations in nuclear structure contribute to lupus autoimmunity when expressed in the context of a lupus-prone genetic background, suggesting a mechanism for the development of lupus autoimmunity in genetically predisposed individuals that is induced by the disruption of nuclear architecture.
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MESH Headings
- Animals
- Autoantibodies/blood
- Autoantibodies/immunology
- Autoantigens/blood
- Autoantigens/immunology
- Autoimmunity
- Calreticulin/metabolism
- Cell Nucleus/pathology
- Cell Separation
- Crosses, Genetic
- Disease Models, Animal
- Female
- Granulocytes/metabolism
- Granulocytes/pathology
- Histones/metabolism
- Humans
- Immunoglobulin M/immunology
- Kidney/pathology
- Lamin Type A/metabolism
- Lupus Erythematosus, Systemic/blood
- Lupus Erythematosus, Systemic/immunology
- Lupus Erythematosus, Systemic/pathology
- Male
- Mice, Inbred C57BL
- Myeloblastin/metabolism
- Peroxidase/metabolism
- RNA Splicing/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Splenomegaly/pathology
- Transcriptional Activation
- Lamin B Receptor
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Affiliation(s)
- Namrata Singh
- Internal Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Duncan B Johnstone
- Section of Nephrology, Internal Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA
| | - Kayla A Martin
- Department of Microbiology/Immunology, Fels Institute for Cancer Research, Temple University, Philadelphia, PA 19140, USA
| | - Italo Tempera
- Department of Microbiology/Immunology, Fels Institute for Cancer Research, Temple University, Philadelphia, PA 19140, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael F Denny
- Section of Rheumatology, Temple University School of Medicine, Philadelphia, PA 19140, USA
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29
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Abstract
Male and female differ genetically by their respective sex chromosome composition, that is, XY as male and XX as female. Although both X and Y chromosomes evolved from the same ancestor pair of autosomes, the Y chromosome harbors male-specific genes, which play pivotal roles in male sex determination, germ cell differentiation, and masculinization of various tissues. Deletions or translocation of the sex-determining gene, SRY, from the Y chromosome causes disorders of sex development (previously termed as an intersex condition) with dysgenic gonads. Failure of gonadal development results not only in infertility, but also in increased risks of germ cell tumor (GCT), such as gonadoblastoma and various types of testicular GCT. Recent studies demonstrate that either loss of Y chromosome or ectopic expression of Y chromosome genes is closely associated with various male-biased diseases, including selected somatic cancers. These observations suggest that the Y-linked genes are involved in male health and diseases in more frequently than expected. Although only a small number of protein-coding genes are present in the male-specific region of Y chromosome, the impacts of Y chromosome genes on human diseases are still largely unknown, due to lack of in vivo models and differences between the Y chromosomes of human and rodents. In this review, we highlight the involvement of selected Y chromosome genes in cancer development in men.
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Affiliation(s)
| | - Yun-Fai Chris Lau
- Division of Cell and Developmental Genetics, Department of Medicine, Veterans Affairs Medical Center, Institute for Human Genetics, University of California, San Francisco, California 94121, USA
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30
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Ansari-Pour N, Razaghi-Moghadam Z, Barneh F, Jafari M. Testis-Specific Y-Centric Protein-Protein Interaction Network Provides Clues to the Etiology of Severe Spermatogenic Failure. J Proteome Res 2016; 15:1011-22. [PMID: 26794825 DOI: 10.1021/acs.jproteome.5b01080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Pinpointing causal genes for spermatogenic failure (SpF) on the Y chromosome has been an ever daunting challenge with setbacks during the past decade. Since complex diseases result from the interaction of multiple genes and also display considerable missing heritability, network analysis is more likely to explicate an etiological molecular basis. We therefore took a network medicine approach by integrating interactome (protein-protein interaction (PPI)) and transcriptome data to reconstruct a Y-centric SpF network. Two sets of seed genes (Y genes and SpF-implicated genes (SIGs)) were used for network reconstruction. Since no PPI was observed among Y genes, we identified their common immediate interactors. Interestingly, 81% (N = 175) of these interactors not only interacted directly with SIGs, but also they were enriched for differentially expressed genes (89.6%; N = 43). The SpF network, formed mainly by the dys-regulated interactors and the two seed gene sets, comprised three modules enriched for ribosomal proteins and nuclear receptors for sex hormones. Ribosomal proteins generally showed significant dys-regulation with RPL39L, thought to be expressed at the onset of spermatogenesis, strongly down-regulated. This network is the first global PPI network pertaining to severe SpF and if experimentally validated on independent data sets can lead to more accurate diagnosis and potential fertility recovery of patients.
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Affiliation(s)
- Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Zahra Razaghi-Moghadam
- Faculty of New Sciences and Technology, University of Tehran , North Kargar Street, Tehran 143995-7131, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
| | - Farnaz Barneh
- Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences , Tehran 198396-3113, Iran
| | - Mohieddin Jafari
- Drug Design and Bioinformatics Unit, Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran , Tehran 131694-3551, Iran.,School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM) , Tehran 19395-5531, Iran
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31
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Johansson MM, Van Geystelen A, Larmuseau MHD, Djurovic S, Andreassen OA, Agartz I, Jazin E. Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups. PLoS One 2015; 10:e0137223. [PMID: 26322892 PMCID: PMC4554990 DOI: 10.1371/journal.pone.0137223] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/13/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The human Y chromosome is almost always excluded from genome-wide investigations of copy number variants (CNVs) due to its highly repetitive structure. This chromosome should not be forgotten, not only for its well-known relevance in male fertility, but also for its involvement in clinical phenotypes such as cancers, heart failure and sex specific effects on brain and behaviour. RESULTS We analysed Y chromosome data from Affymetrix 6.0 SNP arrays and found that the signal intensities for most of 8179 SNP/CN probes in the male specific region (MSY) discriminated between a male, background signals in a female and an isodicentric male containing a large deletion of the q-arm and a duplication of the p-arm of the Y chromosome. Therefore, this SNP/CN platform is suitable for identification of gain and loss of Y chromosome sequences. In a set of 1718 males, we found 25 different CNV patterns, many of which are novel. We confirmed some of these variants by PCR or qPCR. The total frequency of individuals with CNVs was 14.7%, including 9.5% with duplications, 4.5% with deletions and 0.7% exhibiting both. Hence, a novel observation is that the frequency of duplications was more than twice the frequency of deletions. Another striking result was that 10 of the 25 detected variants were significantly overrepresented in one or more haplogroups, demonstrating the importance to control for haplogroups in genome-wide investigations to avoid stratification. NO-M214(xM175) individuals presented the highest percentage (95%) of CNVs. If they were not counted, 12.4% of the rest included CNVs, and the difference between duplications (8.9%) and deletions (2.8%) was even larger. CONCLUSIONS Our results demonstrate that currently available genome-wide SNP platforms can be used to identify duplications and deletions in the human Y chromosome. Future association studies of the full spectrum of Y chromosome variants will demonstrate the potential involvement of gain or loss of Y chromosome sequence in different human phenotypes.
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Affiliation(s)
- Martin M. Johansson
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
- * E-mail: (MMJ); (EJ)
| | - Anneleen Van Geystelen
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - Maarten H. D. Larmuseau
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
- Forensic Biomedical Sciences, Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ole A. Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Agartz
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Elena Jazin
- Department of Organismal Biology, EBC, Uppsala University, Uppsala, Sweden
- * E-mail: (MMJ); (EJ)
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32
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Rengaraj D, Kwon WS, Pang MG. Bioinformatics Annotation of Human Y Chromosome-Encoded Protein Pathways and Interactions. J Proteome Res 2015; 14:3503-18. [PMID: 26279084 DOI: 10.1021/acs.jproteome.5b00491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We performed a comprehensive analysis of human Y chromosome-encoded proteins, their pathways, and their interactions using bioinformatics tools. From the NCBI annotation release 107 of human genome, we retrieved a total of 66 proteins encoded on Y chromosome. Most of the retrieved proteins were also matched with the proteins listed in the core databases of the Human Proteome Project including neXtProt, PeptideAtlas, and the Human Protein Atlas. When we examined the pathways of human Y-encoded proteins through KEGG database and Pathway Studio software, many of proteins fall into the categories related to cell signaling pathways. Using the STRING program, we found a total of 49 human Y-encoded proteins showing strong/medium interaction with each other. While using the Pathway studio software, we found that a total of 16 proteins interact with other chromosome-encoded proteins. In particular, the SRY protein interacted with 17 proteins encoded on other chromosomes. Additionally, we aligned the sequences of human Y-encoded proteins with the sequences of chimpanzee and mouse Y-encoded proteins using the NCBI BLAST program. This analysis resulted in a significant number of orthologous proteins between human, chimpanzee, and mouse. Collectively, our findings provide the scientific community with additional information on the human Y chromosome-encoded proteins.
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Affiliation(s)
- Deivendran Rengaraj
- Department of Animal Science and Technology, Chung-Ang University , Anseong, Gyeonggi-Do 456-756, Republic of Korea
| | - Woo-Sung Kwon
- Department of Animal Science and Technology, Chung-Ang University , Anseong, Gyeonggi-Do 456-756, Republic of Korea
| | - Myung-Geol Pang
- Department of Animal Science and Technology, Chung-Ang University , Anseong, Gyeonggi-Do 456-756, Republic of Korea
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33
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Ahmadi Rastegar D, Sharifi Tabar M, Alikhani M, Parsamatin P, Sahraneshin Samani F, Sabbaghian M, Sadighi Gilani MA, Mohammad Ahadi A, Mohseni Meybodi A, Piryaei A, Ansari-Pour N, Gourabi H, Baharvand H, Salekdeh GH. Isoform-Level Gene Expression Profiles of Human Y Chromosome Azoospermia Factor Genes and Their X Chromosome Paralogs in the Testicular Tissue of Non-Obstructive Azoospermia Patients. J Proteome Res 2015; 14:3595-605. [PMID: 26162009 DOI: 10.1021/acs.jproteome.5b00520] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The human Y chromosome has an inevitable role in male fertility because it contains many genes critical for spermatogenesis and the development of the male gonads. Any genetic variation or epigenetic modification affecting the expression pattern of Y chromosome genes may thus lead to male infertility. In this study, we performed isoform-level gene expression profiling of Y chromosome genes within the azoospermia factor (AZF) regions, their X chromosome counterparts, and few autosomal paralogues in testicular biopsies of 12 men with preserved spermatogenesis and 68 men with nonobstructive azoospermia (NOA) (40 Sertoli-cell-only syndrome (SCOS) and 28 premiotic maturation arrest (MA)). This was undertaken using quantitative real-time PCR (qPCR) at the transcript level and Western blotting (WB) and immunohistochemistry (IHC) at the protein level. We profiled the expression of 41 alternative transcripts encoded by 14 AZFa, AZFb, and AZFc region genes (USP9Y, DDX3Y, XKRY, HSFY1, CYORF15A, CYORF15B, KDM5D, EIF1AY, RPS4Y2, RBMY1A1, PRY, BPY2, DAZ1, and CDY1) as well as their X chromosome homologue transcripts and a few autosomal homologues. Of the 41 transcripts, 18 were significantly down-regulated in men with NOA when compared with those of men with complete spermatogenesis. In contrast, the expression of five transcripts increased significantly in NOA patients. Furthermore, to confirm the qPCR results at the protein level, we performed immunoblotting and IHC experiments (based on 24 commercial and homemade antibodies) that detected 10 AZF-encoded proteins. In addition, their localization in testis cell types and organelles was determined. Interestingly, the two missing proteins, XKRY and CYORF15A, were detected for the first time. Finally, we focused on the expression patterns of the significantly altered genes in 12 MA patients with successful sperm retrieval compared to those of 12 MA patients with failed sperm retrieval to predict the success of sperm retrieval in azoospermic men. We showed that HSFY1-1, HSFY1-3, BPY2-1, KDM5C2, RBMX2, and DAZL1 transcripts could be used as potential molecular markers to predict the presence of spermatozoa in MA patients. In this study, we have identified isoform level signature that can be used to discriminate effectively between MA, SCOS, and normal testicular tissues and suggests the possibility of diagnosing the presence of mature sperm cell in azoospermic men to prevent additional testicular sperm extraction (TESE) surgery.
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Affiliation(s)
- Diba Ahmadi Rastegar
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Mehdi Sharifi Tabar
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Mehdi Alikhani
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | - Pouria Parsamatin
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran
| | | | | | | | - Ali Mohammad Ahadi
- Department of Genetics, Faculty of Science, Shahrekord University , Shahrekord, Iran
| | | | - Abbas Piryaei
- Anatomy and Cell Biology Department, School of Medicine, Shahid Beheshti University of Medical Sciences , Tehran, Iran
| | - Naser Ansari-Pour
- Faculty of New Sciences and Technology, University of Tehran , Tehran, Iran
| | | | | | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology, ‡Stem Cells and Developmental Biology Group, and ∇Department of Stem Cells and Developmental Biology at Cell Science Research Center, §Department of Andrology and ⊥Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute for Stem Cell Biology and Technology, and ○Department of Developmental Biology, University of Science and Culture, ACECR , Tehran, Iran.,Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran , Karaj, Iran
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Vakilian H, Mirzaei M, Sharifi Tabar M, Pooyan P, Habibi Rezaee L, Parker L, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. DDX3Y, a Male-Specific Region of Y Chromosome Gene, May Modulate Neuronal Differentiation. J Proteome Res 2015; 14:3474-83. [PMID: 26144214 DOI: 10.1021/acs.jproteome.5b00512] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Although it is apparent that chromosome complement mediates sexually dimorphic expression patterns of some proteins that lead to functional differences, there has been insufficient evidence following the manipulation of the male-specific region of the Y chromosome (MSY) gene expression during neural development. In this study, we profiled the expression of 23 MSY genes and 15 of their X-linked homologues during neural cell differentiation of NTERA-2 human embryonal carcinoma cell line (NT2) cells in three different developmental stages using qRT-PCR, Western blotting, and immunofluorescence. The expression level of 12 Y-linked genes significantly increased over neural differentiation, including RBMY1, EIF1AY, DDX3Y, HSFY1, BPY2, PCDH11Y, UTY, RPS4Y1, USP9Y, SRY, PRY, and ZFY. We showed that siRNA-mediated knockdown of DDX3Y, a DEAD box RNA helicase enzyme, in neural progenitor cells impaired cell cycle progression and increased apoptosis, consequently interrupting differentiation. Label-free quantitative shotgun proteomics based on a spectral counting approach was then used to characterize the proteomic profile of the cells after DDX3Y knockdown. Among 917 reproducibly identified proteins detected, 71 proteins were differentially expressed following DDX3Y siRNA treatment compared with mock treated cells. Functional grouping indicated that these proteins were involved in cell cycle, RNA splicing, and apoptosis, among other biological functions. Our results suggest that MSY genes may play an important role in neural differentiation and demonstrate that DDX3Y could play a multifunctional role in neural cell development, probably in a sexually dimorphic manner.
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Affiliation(s)
- Haghighat Vakilian
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Mehdi Sharifi Tabar
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Paria Pooyan
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lida Habibi Rezaee
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Lindsay Parker
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Paul A Haynes
- Department of Chemistry and Biomolecular Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
| | - Hamid Gourabi
- Department of Genetics at Reproductive Biomedicine Research Center, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran
| | - Hossein Baharvand
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Department of Developmental Biology, University of Science and Culture , Sharif Esfahani Blvd, Park Street, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Stem Cells Biology & Technology, Royan Institute , Banihashem Sq., Banihashem St., Ressalat highway, Tehran, Iran.,Seed and Plant Improvement Institute's Campus, Agricultural Biotechnology Research Institute of Iran , Mahdasht Road, Karaj, Iran
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Tiirikka T, Moilanen JS. Human Chromosome Y and Haplogroups; introducing YDHS Database. Clin Transl Med 2015; 4:60. [PMID: 26061870 PMCID: PMC4477006 DOI: 10.1186/s40169-015-0060-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As the high throughput sequencing efforts generate more biological information, scientists from different disciplines are interpreting the polymorphisms that make us unique. In addition, there is an increasing trend in general public to research their own genealogy, find distant relatives and to know more about their biological background. Commercial vendors are providing analyses of mitochondrial and Y-chromosomal markers for such purposes. Clearly, an easy-to-use free interface to the existing data on the identified variants would be in the interest of general public and professionals less familiar with the field. Here we introduce a novel metadatabase YDHS that aims to provide such an interface for Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants. METHODS The database uses ISOGG Y-DNA tree as the source of mutations and haplogroups and by using genomic positions of the mutations the database links them to genes and other biological entities. YDHS contains analysis tools for deeper Y-SNP analysis. RESULTS YDHS addresses the shortage of Y-DNA related databases. We have tested our database using a set of different cases from literature ranging from infertility to autism. The database is at http://www.semanticgen.net/ydhs CONCLUSIONS Y-chromosomal DNA (Y-DNA) haplogroups and sequence variants have not been in the scientific limelight, excluding certain specialized fields like forensics, mainly because there is not much freely available information or it is scattered in different sources. However, as we have demonstrated Y-SNPs do play a role in various cases on the haplogroup level and it is possible to create a free Y-DNA dedicated bioinformatics resource.
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Affiliation(s)
- Timo Tiirikka
- Department of Clinical Genetics, Oulu University Hospital, PEDEGO Research Unit, University of Oulu, and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, PO Box 23, FI-90029, Oulu, Finland,
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Khosravi P, Gazestani VH, Asgari Y, Law B, Sadeghi M, Goliaei B. Network-based approach reveals Y chromosome influences prostate cancer susceptibility. Comput Biol Med 2014; 54:24-31. [DOI: 10.1016/j.compbiomed.2014.08.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/14/2014] [Accepted: 08/17/2014] [Indexed: 11/26/2022]
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Xu RH, Zheng LY, He DL, Meng J, Xia LP, Hao XB, Zhang ZZ. Profiling of differentially expressed microRNAs (miRNAs) during differentiation of rat hepatic oval cells (HOCs) into hepatocellular carcinoma (HCC) cells. Clin Transl Oncol 2014; 17:230-7. [PMID: 25257837 DOI: 10.1007/s12094-014-1218-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/16/2014] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To explore the expression profile of miRNAs during differentiation of rat hepatic oval cells (HOCs) into hepatocellular carcinoma cells (HCC). METHODS Proliferation of rat HOCs was induced by chemical carcinogen, 3'-methyl-4-dimethylaminoazobenzene (3'-Me-DAB) in male rats. By using Percoll density gradient centrifugation method, HOCs were isolated, followed by continuous cultivation in vitro. The isolated HOCs were identified via Thy-1 and C-kit detection under laser scanning confocal microscope. Total miRNA was then extracted from HOCs during cell differentiation for microarray hybridization. Differentially expressed miRNAs among the indicated time points were identified. The target genes of identified miRNAs were predicted using PicTar, Target-Scan, and miRanda; then the functions and pathways of the genes were enriched. Y chromosome-specific polymerase chain reaction (PCR) technique was utilized to trace the differentiation of the male HOCs in carcinogen-induced HCC of female rats. RESULTS It was shown that isolated HOCs expressed stem cells markers of Thy-1 and C-kit in cytoplasm and membrane. Among 1,210 miRNAs identified, 22 were differentially expressed (P < 0.05, fold change ≥2), including 19 up-regulated and 3 down-regulated ones. The predicted target genes of these miRNAs were enriched in several functions, including axon guidance, angiogenesis, post-transcriptional protein modification, and small molecular metabolism. For PCR-based SRY detection, HCC genomic DNA of female rats from the experimental group displayed the same PCR product as that from normal male rat. CONCLUSION Differentially expressed miRNAs exerted important roles during the differentiation process of HOCs to HCC.
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Affiliation(s)
- R H Xu
- Department of Oncology Surgery, The Affiliated Hospital of Hainan Medical College, Haikou, 570102, China
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Steegenga WT, Mischke M, Lute C, Boekschoten MV, Pruis MG, Lendvai A, Verkade HJ, Boekhorst J, Timmerman HM, Plösch T, Müller M. Sexually dimorphic characteristics of the small intestine and colon of prepubescent C57BL/6 mice. Biol Sex Differ 2014; 5:11. [PMID: 25243059 PMCID: PMC4169057 DOI: 10.1186/s13293-014-0011-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/20/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND There is increasing appreciation for sexually dimorphic effects, but the molecular mechanisms underlying these effects are only partially understood. In the present study, we explored transcriptomics and epigenetic differences in the small intestine and colon of prepubescent male and female mice. In addition, the microbiota composition of the colonic luminal content has been examined. METHODS At postnatal day 14, male and female C57BL/6 mice were sacrificed and the small intestine, colon and content of luminal colon were isolated. Gene expression of both segments of the intestine was analysed by microarray analysis. DNA methylation of the promoter regions of selected sexually dimorphic genes was examined by pyrosequencing. Composition of the microbiota was explored by deep sequencing. RESULTS Sexually dimorphic genes were observed in both segments of the intestine of 2-week-old mouse pups, with a stronger effect in the small intestine. Amongst the total of 349 genes displaying a sexually dimorphic effect in the small intestine and/or colon, several candidates exhibited a previously established function in the intestine (i.e. Nts, Nucb2, Alox5ap and Retnlγ). In addition, differential expression of genes linked to intestinal bowel disease (i.e. Ccr3, Ccl11 and Tnfr) and colorectal cancer development (i.e. Wt1 and Mmp25) was observed between males and females. Amongst the genes displaying significant sexually dimorphic expression, nine genes were histone-modifying enzymes, suggesting that epigenetic mechanisms might be a potential underlying regulatory mechanism. However, our results reveal no significant changes in DNA methylation of analysed CpGs within the selected differentially expressed genes. With respect to the bacterial community composition in the colon, a dominant effect of litter origin was found but no significant sex effect was detected. However, a sex effect on the dominance of specific taxa was observed. CONCLUSIONS This study reveals molecular dissimilarities between males and females in the small intestine and colon of prepubescent mice, which might underlie differences in physiological functioning and in disease predisposition in the two sexes.
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Affiliation(s)
- Wilma T Steegenga
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Mona Mischke
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Carolien Lute
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Mark V Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands
| | - Maurien Gm Pruis
- Center for Liver, Digestive and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Agnes Lendvai
- Center for Liver, Digestive and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Henkjan J Verkade
- Center for Liver, Digestive and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | - Torsten Plösch
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Michael Müller
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, Wageningen, The Netherlands ; Norwich Medical School, University of East Anglia, Norwich, UK
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Islam MT, Garg G, Hancock WS, Risk BA, Baker MS, Ranganathan S. Protannotator: A Semiautomated Pipeline for Chromosome-Wise Functional Annotation of the “Missing” Human Proteome. J Proteome Res 2013; 13:76-83. [DOI: 10.1021/pr400794x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | | | - William S. Hancock
- Barnett
Institute, Northeastern University, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Brian A. Risk
- College
of Arts and Sciences, Boise State University, 1910 University Drive, Boise, Idaho 83725, United States
| | | | - Shoba Ranganathan
- Department
of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, 117599 Singapore
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Chen H, Yi M, Sheng Y, Cheng H, Zhou R. A novel testis-enriched gene Spata33 is expressed during spermatogenesis. PLoS One 2013; 8:e67882. [PMID: 23844118 PMCID: PMC3699523 DOI: 10.1371/journal.pone.0067882] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/23/2013] [Indexed: 12/03/2022] Open
Abstract
With an increasing incidence of male idiopathic infertility, identification of novel genes involved in spermatogenesis is an important aspect for the understanding of human testicular failure. In the present study, we have identified a novel gene Spata33, also called as 4732415M23Rik or C16orf55, which is conserved in mammalian species. Spata33 was predominantly expressed in the postpartum and adult mouse testes at mRNA and protein levels. Its expression was increased during the first wave of the spermatogenesis, indicating that Spata33 may be associated with the meiotic process. Further immunohistochemistry analysis revealed that Spata33 was mainly expressed in the spermatocytes, spermatogonia and round spermatids. Its expression was uniformly distributed in the nucleus and cytosol in these germ cells, which was further confirmed by Spata33-tagged with GFP staining in the GC-1 and TM4 cells. These results indicated that Spata33 was predominantly expressed in the mouse testis and associated with spermatogenesis. Identification and characterization of the novel testis-enriched gene Spata33 may provide a new route for understanding of spermatogenesis failure.
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Affiliation(s)
- Hengling Chen
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Minhan Yi
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Yue Sheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
| | - Hanhua Cheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
- * E-mail: (HC); (RZ)
| | - Rongjia Zhou
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan, People’s Republic of China
- * E-mail: (HC); (RZ)
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