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Gupta V, Ben-Mahmoud A, Ku B, Velayutham D, Jan Z, Yousef Aden A, Kubbar A, Alshaban F, Stanton LW, Jithesh PV, Layman LC, Kim HG. Identification of two novel autism genes, TRPC4 and SCFD2, in Qatar simplex families through exome sequencing. Front Psychiatry 2023; 14:1251884. [PMID: 38025430 PMCID: PMC10644705 DOI: 10.3389/fpsyt.2023.1251884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
This study investigated the genetic underpinnings of autism spectrum disorder (ASD) in a Middle Eastern cohort in Qatar using exome sequencing. The study identified six candidate autism genes in independent simplex families, including both four known and two novel autosomal dominant and autosomal recessive genes associated with ASD. The variants consisted primarily of de novo and homozygous missense and splice variants. Multiple individuals displayed more than one candidate variant, suggesting the potential involvement of digenic or oligogenic models. These variants were absent in the Genome Aggregation Database (gnomAD) and exhibited extremely low frequencies in the local control population dataset. Two novel autism genes, TRPC4 and SCFD2, were discovered in two Qatari autism individuals. Furthermore, the D651A substitution in CLCN3 and the splice acceptor variant in DHX30 were identified as likely deleterious mutations. Protein modeling was utilized to evaluate the potential impact of three missense variants in DEAF1, CLCN3, and SCFD2 on their respective structures and functions, which strongly supported the pathogenic natures of these variants. The presence of multiple de novo mutations across trios underscored the significant contribution of de novo mutations to the genetic etiology of ASD. Functional assays and further investigations are necessary to confirm the pathogenicity of the identified genes and determine their significance in ASD. Overall, this study sheds light on the genetic factors underlying ASD in Qatar and highlights the importance of considering diverse populations in ASD research.
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Affiliation(s)
- Vijay Gupta
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Afif Ben-Mahmoud
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Dinesh Velayutham
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Abdi Yousef Aden
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Ahmad Kubbar
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Fouad Alshaban
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence W. Stanton
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Puthen Veettil Jithesh
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Hyung-Goo Kim
- Neurological Disorder Research Center, Qatar Biomedical Research Institute (QBRI), Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
- College of Health & Life Sciences, Qatar Foundation, Hamad Bin Khalifa University (HBKU), Doha, Qatar
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Ran M, Huang H, Hu B, Hu S, Hu J, Li L, He H, Liu H, Wang J. Comparative Analysis of Testicular Histology and lncRNA-mRNA Expression Patterns Between Landes Geese ( Anser anser) and Sichuan White Geese ( Anser cygnoides). Front Genet 2021; 12:627384. [PMID: 33737948 PMCID: PMC7963104 DOI: 10.3389/fgene.2021.627384] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 11/13/2022] Open
Abstract
Landes geese and Sichuan White geese are two important genetic materials for commercial goose breeding. However, the differences in the male reproductive capacity between these two breeds and the potential molecular mechanisms and associated key genes have not been reported to date. The present study compared the testicular histology and mRNA-long non-coding RNA (lncRNA) expression patterns to reveal the differences in male reproductive performance between Sichuan White geese and Landes geese, as well as to explore the underlying molecular mechanisms. Histological results showed that the testicular organ index, semen volume, and long diameter of seminiferous tubules of Landes geese were significantly larger than those of Sichuan White geese. Analyses of mRNA-lncRNA expression profile showed that compared with Sichuan White geese, a total of 462 differentially expressed mRNAs (DEGs) (173 up-regulated and 289 down-regulated) and 329 differentially expressed lncRNAs (DE lncRNAs) (280 up-regulated, 49 down-regulated) were identified in Landes geese. Among these DEGs, there were 10 spermatogenesis-related and highly expressed (FPKM > 10) DEGs. Except for SEPP1, all of these DEGs were significantly up-regulated in the testes of Landes geese. Functional enrichment analysis indicated that the pathway related to metabolism progress and phosphoinositol signal is vitally responsible for differences in male reproductive performance between Landes geese and Sichuan White geese. These results show that compared with Sichuan White geese, the spermatogenesis in the testis of Landes geese was more active, which may be mainly related to the inositol phosphate signal. These data contribute to a better understanding of the mechanisms underlying different male reproductive performances between Landes geese and Sichuan White geese. This knowledge might eventually provide a theoretical basis for improving male reproductive performance in geese.
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Affiliation(s)
- Mingxia Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Huaxuan Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Bo Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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Loebenstein M, Thorup J, Cortes D, Clasen-Linde E, Hutson JM, Li R. Cryptorchidism, gonocyte development, and the risks of germ cell malignancy and infertility: A systematic review. J Pediatr Surg 2020; 55:1201-1210. [PMID: 31327540 DOI: 10.1016/j.jpedsurg.2019.06.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/18/2019] [Accepted: 06/28/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND/AIM Cryptorchidism, or undescended testis (UDT) occurs in 1%-4% of newborn males and leads to a risk of infertility and testicular malignancy. Recent research suggests that infertility and malignancy in UDT may be caused by abnormal development of the neonatal germ cells, or gonocytes, which normally transform into spermatogonial stem cells (SSC) or undergo apoptosis during minipuberty at 2-6 months in humans (2-6 days in mice). We aimed to identify the current knowledge on how UDT is linked to infertility and malignancy. METHODS Here we review the literature from 1995 to the present to assess the possible causes of infertility and malignancy in UDT, from both human studies and animal models. RESULTS Both the morphological steps and many of the genes involved in germ cell development are now characterized, but the factors involved in gonocyte transformation and apoptosis in both normal and cryptorchid testes are not fully identified. During minipuberty there is evidence for the hypothalamic-pituitary axis stimulating gonocyte transformation, but without known direct control by LH and androgen, although FSH may have a role. An arrested gonocyte maybe the origin of later malignancy at least in syndromic cryptorchid testes in humans, which is consistent with the recent finding that gonocytes are normally absent in a rodent model of congenital cryptorchidism, where malignancy has not been reported. CONCLUSION The results of this review strengthen the view that malignancy and infertility in men with previous UDT may be caused by abnormalities in germ cell development during minipuberty. TYPE OF STUDY Systematic review (secondary, filtered) LEVEL OF EVIDENCE: Level I.
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Affiliation(s)
- Moshe Loebenstein
- Douglas Stephens Surgical Research Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Australia
| | - Jorgen Thorup
- Department of Paediatric Surgery, Rigshospitalet, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dina Cortes
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Section of Endocrinology, Department of Pediatrics, Copenhagen University Hospital Hvidovre, Denmark
| | - Erik Clasen-Linde
- Department of Pathology, Copenhagen University Hospital Rigshospitalet, Denmark
| | - John M Hutson
- Douglas Stephens Surgical Research Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Australia; Department of Urology, The Royal Children's Hospital, Melbourne, Australia
| | - Ruili Li
- Douglas Stephens Surgical Research Group, Murdoch Children's Research Institute, Melbourne, Australia; Department of Paediatrics, University of Melbourne, Australia.
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Transcriptional regulatory network analysis of the over-expressed genes in adipose tissue. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0145-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Tang A, Yan Q, Sun L, Diao R, Yu Z, Zhang Z, Gui Y, Cai Z. Developmental expression of ACRV1 in humans and mice. Andrologia 2011; 44:16-22. [PMID: 21488928 DOI: 10.1111/j.1439-0272.2010.01095.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
To identify the developmental expression of the ACRV1 gene in humans and mice, testes cDNA samples were collected at different post-natal days (days 4, 9, 18, 35, 54, and 6 months) from Balb/c mice and were hybridised to the mouse whole genome 430 2.0 Array (Affymetrix Inc.) chip. The characteristics of ACRV1 were analysed using various cellular and molecular biotechnologies. The results showed that the expression of mouse ACRV1 was not detected in mouse testes on days 4, 9, and 18 but was present on days 35, 54, and 6 months. Using RT-PCR analysis of mouse ACRV1, we determined that mouse ACRV1 was expressed specifically in the mouse testis, and its expression began at days 35. Western blot analysis demonstrated that human ACRV1 was primarily expressed in human testes, and immunofluorescent and immunohistochemistry staining showed that human ACRV1 protein was predominantly located in round and elongated spermatids in human testes, indicating that ACRV1 may play an important role in mammalian spermatogenesis and may be a target of a contraceptive vaccine.
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Affiliation(s)
- A Tang
- Guangdong Key Lab of Male Reproductive Medicine and Genetics, Peking University Shenzhen Hospital, Shenzhen, Guangdong, China
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Yu Z, Wu B, Tang A, Chen J, Guo X, Qin J, Gui Y, Cai Z. Expression profile of a novel germ cell-specific gene, TSCPA, in mice and human. ACTA ACUST UNITED AC 2009; 29:535-9. [DOI: 10.1007/s11596-009-0502-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Indexed: 11/25/2022]
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Xiao L, Wang Y, Zhou Y, Sun Y, Sun W, Wang L, Zhou C, Zhou J, Zhang J. Identification of a novel human cancer/testis gene MAEL that is regulated by DNA methylation. Mol Biol Rep 2009; 37:2355-60. [DOI: 10.1007/s11033-009-9741-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 08/05/2009] [Indexed: 01/10/2023]
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Xiang Y, Nie DS, Zhang QJ, Zhu WB, Du J, Li W, Lu GX. Cloning, characterization and identification ofRcet1-v1andRcet1-v2, two novel splice variants of mouseRcet1related toCressubgroup of family 2 cystatins. ACTA ACUST UNITED AC 2009; 19:13-9. [DOI: 10.1080/10425170601101501] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Zhou Y, Qin D, Tang A, Zhou D, Qin J, Yan B, Diao R, Jiang Z, Cai Z, Gui Y. Developmental expression pattern of a novel gene, TSG23/Tsg23, suggests a role in spermatogenesis. Mol Hum Reprod 2009; 15:223-30. [PMID: 19240080 DOI: 10.1093/molehr/gap015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A novel gene, TSG23/Tsg23, was identified by comparing the expression profiles of human adult and fetal testis using Affymetrix Genechips. RT-PCR analysis from multiple human and mouse tissues indicated TSG23/Tsg23 mRNA was mainly expressed in the testis. In situ hybridization revealed that TSG23/Tsg23 mRNA was located in spermatocytes and round spermatids of the seminiferous tubules in human and mouse testis. To further confirm the result from RT-PCR, the antibody for human TSG23 was generated against the protein encoded by the gene. Western blot analysis demonstrated that TSG23 was mainly expressed in human testis, with a molecular weight of about 23 kDa. Immunohistochemistry showed that TSG23 was predominantly located in spermatocytes and round spermatids, consistent with the results from in situ hybridization. In order to explore the function of TSG23 in spermatogenesis, the study compared the expression of TSG23 in the testis from fertile persons and from patients with azoospermia. The results showed that there was less expression in patients with obstructive azoospermia compared with fertile persons, and no detectable TSG23 at mRNA and protein levels in patients with non-obstructive azoospermia. The expression of Tsg23 mRNA was considerably decreased in a time-dependent manner in the testis of an azoospermic mouse model induced by Busulfan. These data suggest that TSG23/Tsg23 is involved in human and mouse spermatogenesis.
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Affiliation(s)
- Yongcui Zhou
- Department of Physiology, Medical College of Shantou University, Shantou 515041, People's Republic of China
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Tang A, Yu Z, Gui Y, Zhu H, Zhang L, Zhang J, Cai Z. Characteristics of 292 Testis-Specific Genes in Human. Biol Pharm Bull 2007; 30:865-72. [PMID: 17473427 DOI: 10.1248/bpb.30.865] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
To explore their genomic and functional characteristics, 292 human testis-specific genes were obtained from a UniGene library and a full-scale analysis was made. Various bioinformatics tools were applied to analyze the gene ontology and chromosome location, and the expression profiles of eight selected candidates from the 292 genes were analyzed using RT-PCR for 12 adult human tissues. The results showed that of the total 292 genes, 153 were known (114 assigned genes and 39 named genes), and 139 were unknown. Of the 114 assigned genes, 63 were labeled to molecular function, 28 to cellular component, 23 to biological process. All 292 genes are distributed on human chromosomes at different gene density, lower gene density appears on chromosomes 21 (R=0.22), X (R=0.33), 14 (R=0.39), 10 (R=0.61), 8 (R=0.63), and 18 (R=0.67) and higher density on chromosomes 19 (R=3.65), 20 (R=1.83), 16 (R=1.74), and 17 (R=1.64). The expression profile of the eight selected genes in the 12 human tissues showed that five candidate genes: Hs.443729, Hs.115366, Hs.558087, Hs.534501, and Hs.132104 were expressed exclusively in human testis; Hs.132310, Hs.443299 were expressed highly in testis and also expressed weakly in human heart; Hs.160370 was expressed in human testis, ovary, uterus, and not expressed in other tissues. Our study can be a basis for characterization of the function of human testis-specific genes during male mammalian spermatogenesis.
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Affiliation(s)
- Aifa Tang
- Shenzhen Key Laboratory of Male Reproduction and Genetics, Peking University Shenzhen Hospital, Medical Center for PKU-HKUST, Shenzhen, PR China
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Yu Z, Tang A, Gui Y, Guo X, Zhu H, Long Y, Li Z, Cai Z. Identification and characteristics of a novel testis-specific gene, Tsc21, in mice and human. Mol Biol Rep 2006; 34:127-34. [PMID: 17091336 DOI: 10.1007/s11033-006-9026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Accepted: 09/11/2006] [Indexed: 11/25/2022]
Abstract
Testis-specific genes are essential for spermatogenesis in mammalian male reproduction. We have identified a novel gene, Tsc21, exclusively expressed in mice and human testes from the results of the Affymetrix Genechip analysis in the six developmental stages of testis of postnatal Balb/C mice. The full cDNA length of Tsc21 was 810 bp, with a 543 bp open reading frame encoding a 180 amino acids protein with a predicted molecular weight of 21.040 kDa. A Blast search in the mouse genome database localized the Tsc21 gene to mice chromosome 6C3. Multiple amino acid sequence alignment of human, mouse, and rat homologous genes showed that mice Tsc21 protein was highly homologous with the human Tsc21 gene (70%) and rat Tsc21 gene (86%). The results of reverse transcriptase-polymerase chain reaction analysis showed that the mice Tsc21 is exclusively expressed in the testis and epididymis of mice, and its expression is only detected after the mice is 35 days old. Human Tsc21 is also exclusively expressed in testis of human. Considering the expression profile Tsc21 in mice and human, we propose that Tsc21 may play a role during mammalian male spermatogenesis. Our study should be a basis for function characterization of the Tsc21 gene, leading to the elucidation of the molecular events underlying mammalian male reproduction.
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Affiliation(s)
- Zhendong Yu
- Laboratory of Male Reproductive Medicine, Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, Peking University, Shenzhen 518036, People's Republic of China
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Lin YH, Lin YM, Teng YN, Hsieh TYT, Lin YS, Kuo PL. Identification of ten novel genes involved in human spermatogenesis by microarray analysis of testicular tissue. Fertil Steril 2006; 86:1650-8. [PMID: 17074343 DOI: 10.1016/j.fertnstert.2006.04.039] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2005] [Revised: 04/18/2006] [Accepted: 08/08/2006] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To identify novel genes that are down-regulated in the testicular tissue of infertile men. DESIGN Prospective study. SETTING University-based reproductive clinics and genetics laboratory. PATIENTS Nine patients with normal spermatogenesis, and 15 patients with maturation arrest (MA) or Sertoli cell-only syndrome (SCOS). INTERVENTION Testicular samples of patients with the same histology were pooled for complementary DNA (cDNA) microarray analysis. MAIN OUTCOME MEASURE Novel, down-regulated genes. RESULTS In total, 300 genes were significantly down-regulated in SCOS or MA samples, and 10 novel sterility-related genes were identified. Of the 10 novel genes, 6 genes (Hs.126780, Hs.553658, Hs.274135, Hs.268122, Hs.531701, and Hs.171130) encode proteins with predictable functional domains, and all these functional domains are believed to correlate with spermatogenesis and/or spermiogenesis. Conversely, the other 4 genes (Hs.351582, Hs.407480, Hs.552781, and Hs.355570) do not encompass known functional domains. Two genes (Hs.407480 and Hs.552781) lack mouse orthologues. Most novel genes showed a testis-specific expression pattern in both mice and humans. Reverse transcription-polymerase chain reaction (RT-PCR) showed three distinct types of developmental stage-dependent expressions of message ribonucleic acid (mRNA) for these novel genes in murine testes. CONCLUSION These 10 novel genes provide targets to elucidate novel pathways involved in human spermatogenesis.
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Affiliation(s)
- Ying-Hung Lin
- Graduate Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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