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Zhang Q, Bao X, Cui M, Wang C, Ji J, Jing J, Zhou X, Chen K, Tang L. Identification and validation of key biomarkers based on RNA methylation genes in sepsis. Front Immunol 2023; 14:1231898. [PMID: 37701433 PMCID: PMC10493392 DOI: 10.3389/fimmu.2023.1231898] [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: 05/31/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Background RNA methylation is closely involved in immune regulation, but its role in sepsis remains unknown. Here, we aim to investigate the role of RNA methylation-associated genes (RMGs) in classifying and diagnosing of sepsis. Methods Five types of RMGs (m1A, m5C, m6Am, m7G and Ψ) were used to identify sepsis subgroups based on gene expression profile data obtained from the GEO database (GSE57065, GSE65682, and GSE95233). Unsupervised clustering analysis was used to identify distinct RNA modification subtypes. The CIBERSORT, WGCNA, GO and KEGG analysis were performed to explore immune infiltration pattern and biological function of each cluster. RF, SVM, XGB, and GLM algorithm were applied to identify the diagnostic RMGs in sepsis. Finally, the expression levels of the five key RMGs were verified by collecting PBMCs from septic patients using qRT-PCR, and their diagnostic efficacy for sepsis was verified in combination with clinical data using ROC analysis. Results Sepsis was divided into three subtypes (cluster 1 to 3). Cluster 1 highly expressed NSUN7 and TRMT6, with the characteristic of neutrophil activation and upregulation of MAPK signaling pathways. Cluster 2 highly expressed NSUN3, and was featured by the regulation of mRNA stability and amino acid metabolism. NSUN5 and NSUN6 were upregulated in cluster 3 which was involved in ribonucleoprotein complex biogenesis and carbohydrate metabolism pathways. In addition, we identified that five RMGs (NSUN7, NOP2, PUS1, PUS3 and FTO) could function as biomarkers for clinic diagnose of sepsis. For validation, we determined that the relative expressions of NSUN7, NOP2, PUS1 and PUS3 were upregulated, while FTO was downregulated in septic patients. The area under the ROC curve (AUC) of NSUN7, NOP2, PUS1, PUS3 and FTO was 0.828, 0.707, 0.846, 0.834 and 0.976, respectively. Conclusions Our study uncovered that dysregulation of RNA methylation genes (m1A, m5C, m6Am, m7G and Ψ) was closely involved in the pathogenesis of sepsis, providing new insights into the classification of sepsis endotypes. We also revealed that five hub RMGs could function as novel diagnostic biomarkers and potential targets for treatment.
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Affiliation(s)
- Qianqian Zhang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaowei Bao
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Mintian Cui
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chunxue Wang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Jinlu Ji
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Jiongjie Jing
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaohui Zhou
- Research Center for Translational Medicine, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Kun Chen
- Translational Medical Center for Stem Cell Therapy, Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
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2
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Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
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Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
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3
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Liao W, Xiao H, He J, Huang L, Liao Y, Qin J, Yang Q, Qu L, Ma F, Li S. Identification and verification of feature biomarkers associated with immune cells in neonatal sepsis. Eur J Med Res 2023; 28:105. [PMID: 36855207 PMCID: PMC9972688 DOI: 10.1186/s40001-023-01061-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/12/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Neonatal sepsis (NS), a life-threatening condition, is characterized by organ dysfunction and is the most common cause of neonatal death. However, the pathogenesis of NS is unclear and the clinical inflammatory markers currently used are not ideal for diagnosis of NS. Thus, exploring the link between immune responses in NS pathogenesis, elucidating the molecular mechanisms involved, and identifying potential therapeutic targets is of great significance in clinical practice. Herein, our study aimed to explore immune-related genes in NS and identify potential diagnostic biomarkers. Datasets for patients with NS and healthy controls were downloaded from the GEO database; GSE69686 and GSE25504 were used as the analysis and validation datasets, respectively. Differentially expressed genes (DEGs) were identified and Gene Set Enrichment Analysis (GSEA) was performed to determine their biological functions. Composition of immune cells was determined and immune-related genes (IRGs) between the two clusters were identified and their metabolic pathways were determined. Key genes with correlation coefficient > 0.5 and p < 0.05 were selected as screening biomarkers. Logistic regression models were constructed based on the selected biomarkers, and the diagnostic models were validated. RESULTS Fifty-two DEGs were identified, and GSEA indicated involvement in acute inflammatory response, bacterial detection, and regulation of macrophage activation. Most infiltrating immune cells, including activated CD8 + T cells, were significantly different in patients with NS compared to the healthy controls. Fifty-four IRGs were identified, and GSEA indicated involvement in immune response and macrophage activation and regulation of T cell activation. Diagnostic models of DEGs containing five genes (PROS1, TDRD9, RETN, LOC728401, and METTL7B) and IRG with one gene (NSUN7) constructed using LASSO algorithm were validated using the GPL6947 and GPL13667 subset datasets, respectively. The IRG model outperformed the DEG model. Additionally, statistical analysis suggested that risk scores may be related to gestational age and birth weight, regardless of sex. CONCLUSIONS We identified six IRGs as potential diagnostic biomarkers for NS and developed diagnostic models for NS. Our findings provide a new perspective for future research on NS pathogenesis.
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Affiliation(s)
- Weiqiang Liao
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Huimin Xiao
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Jinning He
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Lili Huang
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Yanxia Liao
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Jiaohong Qin
- Department of Pediatrics, Dongguan Houjie Hospital, Dongguan, 523945 China
| | - Qiuping Yang
- grid.488525.6Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655 China
| | - Liuhong Qu
- Department of Neonatology, The Maternal and Child Health Care Hospital of Huadu, Guangzhou, 510800, China.
| | - Fei Ma
- Department of Neonatology, Maternal and Child Health Research Institute, Zhuhai Women and Children's Hospital, Zhuhai, 519001, China.
| | - Sitao Li
- Department of Pediatrics, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, China.
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4
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Li M, Tao Z, Zhao Y, Li L, Zheng J, Li Z, Chen X. 5-methylcytosine RNA methyltransferases and their potential roles in cancer. J Transl Med 2022; 20:214. [PMID: 35562754 PMCID: PMC9102922 DOI: 10.1186/s12967-022-03427-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/05/2022] [Indexed: 12/28/2022] Open
Abstract
In recent years, 5-methylcytosine (m5C) RNA modification has emerged as a key player in regulating RNA metabolism and function through coding as well as non-coding RNAs. Accumulating evidence has shown that m5C modulates the stability, translation, transcription, nuclear export, and cleavage of RNAs to mediate cell proliferation, differentiation, apoptosis, stress responses, and other biological functions. In humans, m5C RNA modification is catalyzed by the NOL1/NOP2/sun (NSUN) family and DNA methyltransferase 2 (DNMT2). These RNA modifiers regulate the expression of multiple oncogenes such as fizzy-related-1, forkhead box protein C2, Grb associated-binding protein 2, and TEA domain transcription factor 1, facilitating the pathogenesis and progression of cancers. Furthermore, the aberrant expression of methyltransferases have been identified in various cancers and used to predict the prognosis of patients. In this review, we present a comprehensive overview of m5C RNA methyltransferases. We specifically highlight the potential mechanism of action of m5C in cancer. Finally, we discuss the prospect of m5C-relative studies.
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Affiliation(s)
- Mingyang Li
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Zijia Tao
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Yiqiao Zhao
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Lei Li
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Jianyi Zheng
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Zeyu Li
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China
| | - Xiaonan Chen
- Department of Urology, Shengjing Hospital of China Medical University, No. 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning, People's Republic of China.
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5
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Yang W, Zhao P, Cao P, Miao C, Ji X, Gao Y, Li P, Cheng J. Global interpretation of novel alternative splicing events in human congenital pulmonary airway malformations: A pilot study. J Cell Biochem 2022; 123:736-745. [PMID: 35064685 DOI: 10.1002/jcb.30216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Weili Yang
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Pu Zhao
- Department of Neonatology Shaanxi Provincial People's Hospital Xi'an Shaanxi China
| | - Ping Cao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Chunlin Miao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Xiang Ji
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Ya Gao
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Peng Li
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
| | - Jiwen Cheng
- Department of Pediatric Surgery The Second Affiliated Hospital of Xi'an Jiaotong University Xi'an Shaanxi China
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6
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Wu W, Chen Y, Cheng Y, Tang Q, Pan F, Tang N, Sun Z, Wang X, London SJ, Xia Y. Association between ambient particulate matter exposure and semen quality in fertile men. Environ Health 2022; 21:16. [PMID: 35034648 PMCID: PMC8762955 DOI: 10.1186/s12940-022-00831-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/07/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Several studies have suggested adverse effects of particulate matter (PM) exposure on male reproductive health; few have investigated the association between PM exposure and semen quality in a large population of fertile men. METHODS We evaluated 14 parameters of semen quality in 1554 fertile men in Nanjing from 2014 to 2016. Individual exposure to particular matter ≤10 μm in diameter (PM10) and ≤ 2.5 μm in diameter (PM2.5) during key periods of sperm development (0-90, 0-9, 10-14, 15-69, and 70-90 days before semen collection) were estimated by inverse distance weighting interpolation. Associations between PM exposure and semen quality were estimated using multivariable linear regression. RESULTS Higher 90-days average PM2.5 was in association with decreased sperm motility (2.21% for total motility, 1.93% for progressive motility per 10 μg/m3 increase, P < 0.001) and four quantitative aspects of sperm motion (curvilinear velocity (VCL), straight line velocity (VSL), average path velocity (VAP), and amplitude of lateral head displacement (ALH), P < 0.01). The association between PM2.5 exposure and semen quality were generally stronger for the earlier exposure window (70-90 days prior to ejaculation) than for recent exposure (0-9, 10-14, or 15-69 days). In the subgroup of men who had normal sperm parameters (n = 1019), similar results were obtained. Ninety-days PM10 exposure was associated only with decreased VCL and VAP and was not related to sperm concentration. CONCLUSIONS Exposure to PM2.5 adversely affects semen quality, specifically lower sperm motility, in fertile men.
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Affiliation(s)
- Wei Wu
- State Key Laboratory of Reproductive Medicine, Institute of Applied Toxicology, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, USA.
| | - Yiqiu Chen
- State Key Laboratory of Reproductive Medicine, Institute of Applied Toxicology, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yuting Cheng
- State Key Laboratory of Reproductive Medicine, Institute of Applied Toxicology, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Qiuqin Tang
- Department of Obstetrics, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Feng Pan
- Department of Urology, The Affiliated Obstetrics and Gynecology Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Naijun Tang
- Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin, China
| | - Zhiwei Sun
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Applied Toxicology, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, USA
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Applied Toxicology, School of Public Health, Nanjing Medical University, 101 Longmian Avenue, Nanjing, 211166, China.
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China.
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7
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Harris M, Schuh MP, McKinney D, Kaufman K, Erkan E. Whole Exome Sequencing in a Population With Severe Congenital Anomalies of Kidney and Urinary Tract. Front Pediatr 2022; 10:898773. [PMID: 35990004 PMCID: PMC9386178 DOI: 10.3389/fped.2022.898773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/01/2022] [Indexed: 11/25/2022] Open
Abstract
Fetal and neonatal interventions (e.g., amnioinfusions, amniotic shunting, and infant dialysis) have increased survival of infants with severe Congenital Anomalies of the Kidney and Urinary Tract (CAKUT), however, outcomes vary dramatically. Our aim was to perform Whole Exome Sequencing (WES) in a unique severe CAKUT population with the goal to identify new variants that will enhance prediction of postnatal outcomes. We performed trio WES on five infants with severe CAKUT (undergoing fetal interventions and/or those who initiated renal replacement therapy (RRT) within 1 month of life) and their parents as well as three singletons. We identified three potential candidate gene variants (NSUN7, MTMR3, CEP162) and validated two variants in known CAKUT genes (GATA3 and FRAS1) showing strong enrichment in this severe phenotype population. Based on our small pilot study of a unique severe CAKUT population, WES appears to be a potential tool to help predict the course of infants with severe CAKUT prenatally.
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Affiliation(s)
- Meredith Harris
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Nephrology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, United States
| | - Meredith P Schuh
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - David McKinney
- University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Kenneth Kaufman
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Elif Erkan
- Division of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,University of Cincinnati College of Medicine, Cincinnati, OH, United States
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8
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Gao Y, Wu H, Xu Y, Shen Q, Xu C, Geng H, Lv M, Tan Q, Li K, Tang D, Song B, Zhou P, Wei Z, He X, Cao Y. Novel biallelic mutations in SLC26A8 cause severe asthenozoospermia in humans owing to midpiece defects: Insights into a putative dominant genetic disease. Hum Mutat 2021; 43:434-443. [PMID: 34923715 DOI: 10.1002/humu.24322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 12/23/2022]
Abstract
To investigate the genetic cause of male infertility characterized by severe asthenozoospermia, two unrelated infertile men with severe asthenozoospermia from nonconsanguineous Chinese families were enrolled, and whole exome sequencing were performed to identify the potential pathogenic mutations. Novel compound heterozygous mutations (NK062 III-1: c.290T>C, p.Leu97Pro; c.1664delT, p.Ile555Thrfs*11/NK038 III-1: c.212G>T, p.Arg71Leu; c.290T>C, p.Leu97Pro) in SLC26A8 were identified. All mutations were inherited from their heterozygous parents and are predicted to be disease-causing by sorts intolerant from tolerant, PolyPhen-2, Mutation Taster, and Combined Annotation Dependent Depletion. In silico mutant SLC26A8 models predict that mutations p.Leu97Pro and p.Arg71Leu cause changes in the α-helix, which may result in functional defects in the protein. Notably, heterozygous male carriers of each mutation in both families were able to reproduce naturally, which is inconsistent with previous reports. Ultrastructural analysis revealed severe asthenozoospermia associated with absence of the mitochondrial sheath and annulus in spermatozoa from both the probands, and both structural defects were verified by HSP60 and SEPT4 immunofluorescence analysis. SLC26A8 levels were significantly reduced in spermatozoa from patients harboring biallelic SLC26A8 mutations, and both patients achieved good prognosis following intracytoplasmic sperm injection. Our findings indicate that mutations in SLC26A8 could manifest as a recessive genetic cause of severe asthenozoospermia and male infertility.
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Affiliation(s)
- Yang Gao
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Huan Wu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Yuping Xu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Qunshan Shen
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Chuan Xu
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Hao Geng
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Mingrong Lv
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, China
| | - Qing Tan
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Anhui Provincial Human Sperm Bank, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Kuokuo Li
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Anhui Province Key Laboratory of Reproductive Health and Genetics, Hefei, China
| | - Dongdong Tang
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Bing Song
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Ping Zhou
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Zhaolian Wei
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Xiaojin He
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
| | - Yunxia Cao
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, China.,Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, Hefei, China
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9
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Bataglia L, Simões ZLP, Nunes FMF. Active genic machinery for epigenetic RNA modifications in bees. INSECT MOLECULAR BIOLOGY 2021; 30:566-579. [PMID: 34291855 DOI: 10.1111/imb.12726] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m6 A (N6-methyladenine) and m5 C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m6 A and m5 C measured in the fat body and brain of adult workers differ significantly. Also, m6 A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m5 C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.
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Affiliation(s)
- L Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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10
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Averina OA, Permyakov OA, Grigorieva OO, Starshin AS, Mazur AM, Prokhortchouk EB, Dontsova OA, Sergiev PV. Comparative Analysis of Genome Editors Efficiency on a Model of Mice Zygotes Microinjection. Int J Mol Sci 2021; 22:10221. [PMID: 34638562 PMCID: PMC8508852 DOI: 10.3390/ijms221910221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Genome editing is an indispensable tool for functional genomics. The caveat of the genome-editing pipeline is a prevalence of error-prone non-homologous end joining over homologous recombination, while only the latter is suitable to introduce particularly desired genetic variants. To overcome this problem, a toolbox of genome engineering was appended by a variety of improved instruments. In this work, we compared the efficiency of a number of recently suggested improved systems for genome editing applied to the same genome regions on a murine zygote model via microinjection. As a result, we observed that homologous recombination utilizing an ssDNA template following sgRNA directed Cas9 cleavage is still the method of choice for the creation of animals with precise genome alterations.
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Affiliation(s)
- Olga A. Averina
- Institute of Functional Genomics, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.A.); (O.A.P.); (O.O.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119899 Moscow, Russia
| | - Oleg A. Permyakov
- Institute of Functional Genomics, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.A.); (O.A.P.); (O.O.G.)
| | - Olga O. Grigorieva
- Institute of Functional Genomics, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.A.); (O.A.P.); (O.O.G.)
| | - Alexey S. Starshin
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.S.S.); (A.M.M.); (E.B.P.)
| | - Alexander M. Mazur
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.S.S.); (A.M.M.); (E.B.P.)
| | - Egor B. Prokhortchouk
- Research Center of Biotechnology of the Russian Academy of Sciences, Institute of Bioengineering, 119071 Moscow, Russia; (A.S.S.); (A.M.M.); (E.B.P.)
| | - Olga A. Dontsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Petr V. Sergiev
- Institute of Functional Genomics, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.A.); (O.A.P.); (O.O.G.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
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11
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Azhar M, Altaf S, Uddin I, Cheng J, Wu L, Tong X, Qin W, Bao J. Towards Post-Meiotic Sperm Production: Genetic Insight into Human Infertility from Mouse Models. Int J Biol Sci 2021; 17:2487-2503. [PMID: 34326689 PMCID: PMC8315030 DOI: 10.7150/ijbs.60384] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/16/2021] [Indexed: 02/06/2023] Open
Abstract
Declined quality and quantity of sperm is currently the major cause of patients suffering from infertility. Male germ cell development is spatiotemporally regulated throughout the whole developmental process. While it has been known that exogenous factors, such as environmental exposure, diet and lifestyle, et al, play causative roles in male infertility, recent progress has revealed abundant genetic mutations tightly associated with defective male germline development. In mammals, male germ cells undergo dramatic morphological change (i.e., nuclear condensation) and chromatin remodeling during post-meiotic haploid germline development, a process termed spermiogenesis; However, the molecular machinery players and functional mechanisms have yet to be identified. To date, accumulated evidence suggests that disruption in any step of haploid germline development is likely manifested as fertility issues with low sperm count, poor sperm motility, aberrant sperm morphology or combined. With the continually declined cost of next-generation sequencing and recent progress of CRISPR/Cas9 technology, growing studies have revealed a vast number of disease-causing genetic variants associated with spermiogenic defects in both mice and humans, along with mechanistic insights partially attained and validated through genetically engineered mouse models (GEMMs). In this review, we mainly summarize genes that are functional at post-meiotic stage. Identification and characterization of deleterious genetic variants should aid in our understanding of germline development, and thereby further improve the diagnosis and treatment of male infertility.
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Affiliation(s)
- Muhammad Azhar
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
| | - Saba Altaf
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
| | - Islam Uddin
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
| | - Jinbao Cheng
- The 901th hospital of Joint logistics support Force of PLA, Anhui, China
| | - Limin Wu
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
| | - Xianhong Tong
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
| | - Weibing Qin
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, China
| | - Jianqiang Bao
- Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Anhui, China
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12
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Mojarrad M, Saburi E, Golshan A, Moghbeli M. Genetics and molecular biology of male infertility among Iranian population: an update. Am J Transl Res 2021; 13:5767-5785. [PMID: 34306325 PMCID: PMC8290737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/19/2021] [Indexed: 06/13/2023]
Abstract
Infertility is one of the main social and health problems among young couples. Although a noticeable ratio of infertilities are asymptomatic, about half of the cases are observed among males. Various environmental factors such as life style, dietary patterns, and pathogens are associated with male infertility. Mutations and chromosomal abnormalities are also the most important genetic risk factors of male infertility. Similar to other populations, there is a dramatically rising trend of male infertility among Iranian. Regarding the high ratio of asymptomatic cases, it is required to clarify the molecular biology and cellular processes involved in male infertility in this population to suggest an efficient panel of diagnostic markers. In this review, we have summarized all of the cellular and molecular processes which have been reported among Iranian infertile males to clarify the molecular biology of male infertility in this population. It was observed that the stress response, cellular detoxification, and DNA repair processes were the most common aberrant cellular mechanisms among Iranian infertile males. This review paves the way of introducing a population-based diagnostic panel of genetic markers among Iranian infertile males.
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Affiliation(s)
- Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical SciencesMashhad, Iran
| | - Ehsan Saburi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical SciencesMashhad, Iran
| | - Alireza Golshan
- Department of Urology, School of Medicine, Mashhad University of Medical SciencesMashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical SciencesMashhad, Iran
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13
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Tsukanov AS, Barinov AA, Shubin VP, Loginova AN, Savelieva TA, Pikunov DY, Kuzminov AM, Kashnikov VN, Polyakov AV, Shelygin YA. Finding the Cause of Hereditary Disease in a Family with Adenomatous Polyposis: Why It Is Important to Accumulate Whole Exome Sequencing Data in the Russian Population. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421060120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA. Translational adaptation to heat stress is mediated by RNA 5-methylcytosine in Caenorhabditis elegans. EMBO J 2021; 40:e105496. [PMID: 33283887 PMCID: PMC7957426 DOI: 10.15252/embj.2020105496] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 12/31/2022] Open
Abstract
Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5 C-methyltransferases have been studied, the impact of the global cytosine-5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5 C in RNA, demonstrating that this modification is non-essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5 C sites in the RNome in vivo. We find that NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5 C34-modified tRNA. This leads to reduced translation efficiency of UUG-rich transcripts and impaired fertility, suggesting a role of m5 C tRNA wobble methylation in the adaptation to higher temperatures.
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Affiliation(s)
- Isabela Cunha Navarro
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Francesca Tuorto
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
- Division of BiochemistryMannheim Institute for Innate Immunoscience (MI3)Medical Faculty MannheimHeidelberg UniversityMannheimGermany
- Center for Molecular Biology of Heidelberg University (ZMBH)DKFZ‐ZMBH AllianceHeidelbergGermany
| | - David Jordan
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Carine Legrand
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
| | - Jonathan Price
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Fabian Braukmann
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
| | - Alan G Hendrick
- STORM Therapeutics LimitedBabraham Research CampusCambridgeUK
| | - Alper Akay
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- School of Biological SciencesUniversity of East AngliaNorwichUK
| | - Annika Kotter
- Institute of Pharmacy and BiochemistryJohannes Gutenberg‐University MainzMainzGermany
| | - Mark Helm
- Institute of Pharmacy and BiochemistryJohannes Gutenberg‐University MainzMainzGermany
| | - Frank Lyko
- Division of EpigeneticsDKFZ‐ZMBH AllianceGerman Cancer Research CenterHeidelbergGermany
| | - Eric A Miska
- Gurdon InstituteUniversity of CambridgeCambridgeUK
- Department of GeneticsUniversity of CambridgeCambridgeUK
- Wellcome Sanger InstituteWellcome Genome CampusCambridgeUK
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15
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NSUN2-mediated RNA 5-methylcytosine promotes esophageal squamous cell carcinoma progression via LIN28B-dependent GRB2 mRNA stabilization. Oncogene 2021; 40:5814-5828. [PMID: 34345012 PMCID: PMC8484015 DOI: 10.1038/s41388-021-01978-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 07/18/2021] [Accepted: 07/21/2021] [Indexed: 02/07/2023]
Abstract
5-Methylcytosine (m5C) is a posttranscriptional RNA modification participating in many critical bioprocesses, but its functions in human cancer remain unclear. Here, by detecting the transcriptome-wide m5C profiling in esophageal squamous cell carcinoma (ESCC), we showed increased m5C methylation in ESCC tumors due to the overexpressed m5C methyltransferase NSUN2. Aberrant expression of NSUN2 was positively regulated by E2F Transcription Factor 1 (E2F1). High NSUN2 levels predicted poor survival of ESCC patients. Moreover, silencing NSUN2 suppressed ESCC tumorigenesis and progression in Nsun2 knockout mouse models. Mechanistically, NSUN2 induced m5C modification of growth factor receptor-bound protein 2 (GRB2) and stabilized its mRNA, which was mediated by a novel m5C mediator, protein lin-28 homolog B (LIN28B). Elevated GRB2 levels increased the activation of PI3K/AKT and ERK/MAPK signalling. These results demonstrate that NSUN2 enhances the initiation and progression of ESCC via m5C-LIN28B dependent stabilization of GRB2 transcript, providing a promising epitranscriptomic-targeted therapeutic strategy for ESCC.
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16
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Xiang S, Ma Y, Shen J, Zhao Y, Wu X, Li M, Yang X, Kaboli PJ, Du F, Ji H, Zheng Y, Li X, Li J, Wen Q, Xiao Z. m 5C RNA Methylation Primarily Affects the ErbB and PI3K-Akt Signaling Pathways in Gastrointestinal Cancer. Front Mol Biosci 2020; 7:599340. [PMID: 33365328 PMCID: PMC7750483 DOI: 10.3389/fmolb.2020.599340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/28/2020] [Indexed: 12/22/2022] Open
Abstract
5-Methylcytosine (m5C) is a kind of methylation modification that occurs in both DNA and RNA and is present in the highly abundant tRNA and rRNA. It has an important impact on various human diseases including cancer. The function of m5C is modulated by regulatory proteins, including methyltransferases (writers) and special binding proteins (readers). This study aims at comprehensive study of the m5C RNA methylation-related genes and the main pathways under m5C RNA methylation in gastrointestinal (GI) cancer. Our result showed that the expression of m5C writers and reader was mostly up-regulated in GI cancer. The NSUN2 gene has the highest proportion of mutations found in GI cancer. Importantly, in liver cancer, higher expression of almost all m5C regulators was significantly associated with lower patient survival rate. In addition, the expression level of m5C-related genes is significantly different at various pathological stages. Finally, we have found through bioinformatics analysis that m5C regulatory proteins are closely related to the ErbB/PI3K–Akt signaling pathway and GSK3B was an important target for m5C regulators. Besides, the compound termed streptozotocin may be a key candidate drug targeting on GSK3B for molecular targeted therapy in GI cancer.
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Affiliation(s)
- Shixin Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yongshun Ma
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xiao Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yuan Zheng
- Neijiang Health and Health Vocational College, Neijiang, China
| | - Xiang Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M.) Affiliated to Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
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17
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Jiao SY, Yang YH, Chen SR. Molecular genetics of infertility: loss-of-function mutations in humans and corresponding knockout/mutated mice. Hum Reprod Update 2020; 27:154-189. [PMID: 33118031 DOI: 10.1093/humupd/dmaa034] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Infertility is a major issue in human reproductive health, affecting an estimated 15% of couples worldwide. Infertility can result from disorders of sex development (DSD) or from reproductive endocrine disorders (REDs) with onset in infancy, early childhood or adolescence. Male infertility, accounting for roughly half of all infertility cases, generally manifests as decreased sperm count (azoospermia or oligozoospermia), attenuated sperm motility (asthenozoospermia) or a higher proportion of morphologically abnormal sperm (teratozoospermia). Female infertility can be divided into several classical types, including, but not limited to, oocyte maturation arrest, premature ovarian insufficiency (POI), fertilization failure and early embryonic arrest. An estimated one half of infertility cases have a genetic component; however, most genetic causes of human infertility are currently uncharacterized. The advent of high-throughput sequencing technologies has greatly facilitated the identification of infertility-associated gene mutations in patients over the past 20 years. OBJECTIVE AND RATIONALE This review aims to conduct a narrative review of the genetic causes of human infertility. Loss-of-function mutation discoveries related to human infertility are summarized and further illustrated in tables. Corresponding knockout/mutated animal models of causative genes for infertility are also introduced. SEARCH METHODS A search of the PubMed database was performed to identify relevant studies published in English. The term 'mutation' was combined with a range of search terms related to the core focus of the review: infertility, DSD, REDs, azoospermia or oligozoospermia, asthenozoospermia, multiple morphological abnormalities of the sperm flagella (MMAF), primary ciliary dyskinesia (PCD), acephalic spermatozoa syndrome (ASS), globozoospermia, teratozoospermia, acrosome, oocyte maturation arrest, POI, zona pellucida, fertilization defects and early embryonic arrest. OUTCOMES Our search generated ∼2000 records. Overall, 350 articles were included in the final review. For genetic investigation of human infertility, the traditional candidate gene approach is proceeding slowly, whereas high-throughput sequencing technologies in larger cohorts of individuals is identifying an increasing number of causative genes linked to human infertility. This review provides a wide panel of gene mutations in several typical forms of human infertility, including DSD, REDs, male infertility (oligozoospermia, MMAF, PCD, ASS and globozoospermia) and female infertility (oocyte maturation arrest, POI, fertilization failure and early embryonic arrest). The causative genes, their identified mutations, mutation rate, studied population and their corresponding knockout/mutated mice of non-obstructive azoospermia, MMAF, ASS, globozoospermia, oocyte maturation arrest, POI, fertilization failure and early embryonic arrest are further illustrated by tables. In this review, we suggest that (i) our current knowledge of infertility is largely obtained from knockout mouse models; (ii) larger cohorts of clinical cases with distinct clinical characteristics need to be recruited in future studies; (iii) the whole picture of genetic causes of human infertility relies on both the identification of more mutations for distinct types of infertility and the integration of known mutation information; (iv) knockout/mutated animal models are needed to show whether the phenotypes of genetically altered animals are consistent with findings in human infertile patients carrying a deleterious mutation of the homologous gene; and (v) the molecular mechanisms underlying human infertility caused by pathogenic mutations are largely unclear in most current studies. WILDER IMPLICATIONS It is important to use our current understanding to identify avenues and priorities for future research in the field of genetic causes of infertility as well as to apply mutation knowledge to risk prediction, genetic diagnosis and potential treatment for human infertility.
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Affiliation(s)
- Shi-Ya Jiao
- Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
| | - Yi-Hong Yang
- Reproduction Medical Center of West China Second University Hospital, Key Laboratory of Obstetric, Gynecologic and Pediatric Diseases and Birth Defects of Ministry of Education, Sichuan University, 610041 Chengdu, China
| | - Su-Ren Chen
- Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 100875 Beijing, China
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18
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Jiang Z, Li S, Han MJ, Hu GM, Cheng P. High expression of NSUN5 promotes cell proliferation via cell cycle regulation in colorectal cancer. Am J Transl Res 2020; 12:3858-3870. [PMID: 32774740 PMCID: PMC7407745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
NSUN5, a gene encodes a cytosine-5 RNA methyltransferase, is rarely mentioned in cancers. Our study is the first one to evaluate the role of NSUN5 in the progression of colorectal cancer. Data from TCGA was used to show the different expression of NSUN5 between CRC tumor tissues and adjacent normal ones. The NSUN5 expression in the tissue microarray was detected by immunohistochemistry (IHC). qRT-PCR was conducted for NSUN5 expression examination in CRC cell lines. Cell proliferation was analyzed by the Celigo machine. GESA and correlation analysis were performed to reveal the possible underlying mechanism. The effects of NSUN5 expression on CRC cell behavior in vitro were analyzed by flow cytometry and β-galactosidase staining. The expression of cell-cycle related proteins were evaluated by western blot. Subcutaneously implanted tumor model was carried out for animal experiment. NSUN5 expression was up-regulated in CRC tumor tissues and cells, and associated with advanced tumor stages (III, IV). NSUN5 could promote cell proliferation, trigger cell cycle arrest in vitro and boost tumor growth in vivo. In addition, knockdown of NSUN5 could lead to a higher expression of Rb and a lower expression of CDK4, CDK6, p-Rb and CCNE1, but made no difference on P21, Bcl-2, caspase3 and C-Caspase3 of CRC cells. Taken together, we identify NSUN5 as a promoter in CRC development via cell cycle regulation.
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Affiliation(s)
- Zhou Jiang
- Department of Oncology, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang UniversityHangzhou 310009, China
| | - Shu Li
- Department of Hematology, Second Affiliated Hospital, Zhejiang University School of MedicineHangzhou, China
| | - Meng-Jiao Han
- Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhou, Zhejiang Province, China
| | - Guo-Ming Hu
- Department of General Surgery (Breast and Thyroid Surgery), Shaoxing People’s Hospital (Shaoxing Hospital, Zhejiang University School of Medicine)Shaoxing 312000, Zhejiang, China
| | - Pu Cheng
- Department of Gynecology, Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang UniversityHangzhou 310009, China
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19
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Hiltpold M, Niu G, Kadri NK, Crysnanto D, Fang ZH, Spengeler M, Schmitz-Hsu F, Fuerst C, Schwarzenbacher H, Seefried FR, Seehusen F, Witschi U, Schnieke A, Fries R, Bollwein H, Flisikowski K, Pausch H. Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility. PLoS Genet 2020; 16:e1008804. [PMID: 32407316 PMCID: PMC7252675 DOI: 10.1371/journal.pgen.1008804] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 05/27/2020] [Accepted: 04/28/2020] [Indexed: 12/30/2022] Open
Abstract
Cattle are ideally suited to investigate the genetics of male reproduction, because semen quality and fertility are recorded for all ejaculates of artificial insemination bulls. We analysed 26,090 ejaculates of 794 Brown Swiss bulls to assess ejaculate volume, sperm concentration, sperm motility, sperm head and tail anomalies and insemination success. The heritability of the six semen traits was between 0 and 0.26. Genome-wide association testing on 607,511 SNPs revealed a QTL on bovine chromosome 6 that was associated with sperm motility (P = 2.5 x 10−27), head (P = 2.0 x 10−44) and tail anomalies (P = 7.2 x 10−49) and insemination success (P = 9.9 x 10−13). The QTL harbors a recessive allele that compromises semen quality and male fertility. We replicated the effect of the QTL on fertility (P = 7.1 x 10−32) in an independent cohort of 2481 Brown Swiss bulls. The analysis of whole-genome sequencing data revealed that a synonymous variant (BTA6:58373887C>T, rs474302732) in WDR19 encoding WD repeat-containing protein 19 was in linkage disequilibrium with the fertility-associated haplotype. WD repeat-containing protein 19 is a constituent of the intraflagellar transport complex that is essential for the physiological function of motile cilia and flagella. Bioinformatic and transcription analyses revealed that the BTA6:58373887 T-allele activates a cryptic exonic splice site that eliminates three evolutionarily conserved amino acids from WDR19. Western blot analysis demonstrated that the BTA6:58373887 T-allele decreases protein expression. We make the remarkable observation that, in spite of negative effects on semen quality and bull fertility, the BTA6:58373887 T-allele has a frequency of 24% in the Brown Swiss population. Our findings are the first to uncover a variant that is associated with quantitative variation in semen quality and male fertility in cattle. In cattle farming, artificial insemination is the most common method of breeding. To ensure high fertilization rates, ejaculate quality and insemination success are closely monitored in artificial insemination bulls. We analyse semen quality, insemination success and microarray-called genotypes at more than 600,000 genome-wide SNP markers of 794 bulls to identify a recessive allele that compromises semen quality. We take advantage of whole-genome sequencing to pinpoint a variant in the coding sequence of WDR19 encoding WD repeat-containing protein 19 that activates a novel exonic splice site. Our results indicate that cryptic splicing in WDR19 is associated with reduced male reproductive performance. This is the first report of a variant that contributes to quantitative variation in bovine semen quality.
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Affiliation(s)
| | - Guanglin Niu
- Livestock Biotechnology, TU München, Freising, Germany
| | | | | | - Zih-Hua Fang
- Animal Genomics, ETH Zürich, Lindau, Switzerland
| | | | | | | | | | | | - Frauke Seehusen
- Institute of Veterinary Pathology, University of Zurich, Zurich, Switzerland
| | | | | | - Ruedi Fries
- Animal Breeding, TU München, Freising, Germany
| | - Heinrich Bollwein
- Clinic of Reproductive Medicine, University of Zurich, Zürich, Switzerland
| | | | - Hubert Pausch
- Animal Genomics, ETH Zürich, Lindau, Switzerland
- * E-mail:
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20
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Begik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures. Genome Biol 2020; 21:97. [PMID: 32375858 PMCID: PMC7204298 DOI: 10.1186/s13059-020-02009-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 04/03/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized and poorly annotated, and we currently lack integrative studies that identify which RNA modification-related proteins (RMPs) may be dysregulated in each cancer type. RESULTS Here, we perform a comprehensive annotation and evolutionary analysis of human RMPs, as well as an integrative analysis of their expression patterns across 32 tissues, 10 species, and 13,358 paired tumor-normal human samples. Our analysis reveals an unanticipated heterogeneity of RMP expression patterns across mammalian tissues, with a vast proportion of duplicated enzymes displaying testis-specific expression, suggesting a key role for RNA modifications in sperm formation and possibly intergenerational inheritance. We uncover many RMPs that are dysregulated in various types of cancer, and whose expression levels are predictive of cancer progression. Surprisingly, we find that several commonly studied RNA modification enzymes such as METTL3 or FTO are not significantly upregulated in most cancer types, whereas several less-characterized RMPs, such as LAGE3 and HENMT1, are dysregulated in many cancers. CONCLUSIONS Our analyses reveal an unanticipated heterogeneity in the expression patterns of RMPs across mammalian tissues and uncover a large proportion of dysregulated RMPs in multiple cancer types. We provide novel targets for future cancer research studies targeting the human epitranscriptome, as well as foundations to understand cell type-specific behaviors that are orchestrated by RNA modifications.
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Affiliation(s)
- Oguzhan Begik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Morghan C Lucas
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Huanle Liu
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
| | - Jose Miguel Ramirez
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - John S Mattick
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- UNSW, Sydney, Sydney, NSW, 2052, Australia
| | - Eva Maria Novoa
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.
- Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia.
- UNSW, Sydney, Sydney, NSW, 2052, Australia.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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21
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Kuznetsova SA, Petrukov KS, Pletnev FI, Sergiev PV, Dontsova OA. RNA (C5-cytosine) Methyltransferases. BIOCHEMISTRY (MOSCOW) 2019; 84:851-869. [PMID: 31522668 DOI: 10.1134/s0006297919080029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The review summarizes the data on pro- and eukaryotic RNA (C5-cytosine) methyltransferases. The structure, intracellular location, RNA targets, and catalytic mechanisms of these enzymes, as well as the functional role of methylated cytosine residues in RNA are presented. The functions of RNA (C5-cytosine) methyltransferases unassociated with their methylation activity are discussed. Special attention is given to the similarities and differences in the structures and mechanisms of action of RNA and DNA methyltransferases. The data on the association of mutations in the RNA (C5-cytosine) methyltransferases genes and human diseases are presented.
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Affiliation(s)
- S A Kuznetsova
- Lomonosov Moscow State University, Institute of Functional Genomics, Moscow, 119234, Russia.
| | - K S Petrukov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia
| | - F I Pletnev
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - P V Sergiev
- Lomonosov Moscow State University, Institute of Functional Genomics, Moscow, 119234, Russia.,Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Petrov National Medical Research Center of Oncology, St. Petersburg, 197758, Russia
| | - O A Dontsova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Skolkovo Institute of Science and Technology, Skolkovo, 121205, Moscow Region, Russia.,Institute of Bioorganic Chemistry, Moscow, 117997, Russia
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22
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Bohnsack KE, Höbartner C, Bohnsack MT. Eukaryotic 5-methylcytosine (m⁵C) RNA Methyltransferases: Mechanisms, Cellular Functions, and Links to Disease. Genes (Basel) 2019; 10:genes10020102. [PMID: 30704115 PMCID: PMC6409601 DOI: 10.3390/genes10020102] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 01/04/2023] Open
Abstract
5-methylcytosine (m⁵C) is an abundant RNA modification that's presence is reported in a wide variety of RNA species, including cytoplasmic and mitochondrial ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), as well as messenger RNAs (mRNAs), enhancer RNAs (eRNAs) and a number of non-coding RNAs. In eukaryotes, C5 methylation of RNA cytosines is catalyzed by enzymes of the NOL1/NOP2/SUN domain (NSUN) family, as well as the DNA methyltransferase homologue DNMT2. In recent years, substrate RNAs and modification target nucleotides for each of these methyltransferases have been identified, and structural and biochemical analyses have provided the first insights into how each of these enzymes achieves target specificity. Functional characterizations of these proteins and the modifications they install have revealed important roles in diverse aspects of both mitochondrial and nuclear gene expression. Importantly, this knowledge has enabled a better understanding of the molecular basis of a number of diseases caused by mutations in the genes encoding m⁵C methyltransferases or changes in the expression level of these enzymes.
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Affiliation(s)
- Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany.
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.
- Göttingen Centre for Molecular Biosciences, University of Göttingen, Göttingen, Justus-von-Liebig-Weg 11, 37077 Germany.
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23
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García-Vílchez R, Sevilla A, Blanco S. Post-transcriptional regulation by cytosine-5 methylation of RNA. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1862:240-252. [PMID: 30593929 DOI: 10.1016/j.bbagrm.2018.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/04/2018] [Accepted: 12/07/2018] [Indexed: 02/02/2023]
Abstract
The recent advent of high-throughput sequencing technologies coupled with RNA modifications detection methods has allowed the detection of RNA modifications at single nucleotide resolution giving a more comprehensive landscape of post-transcriptional gene regulation pathways. In this review, we focus on the occurrence of 5-methylcytosine (m5C) in the transcriptome. We summarise the main findings of the molecular role in post-transcriptional regulation that governs m5C deposition in RNAs. Functionally, m5C deposition can regulate several cellular and physiological processes including development, differentiation and survival to stress stimuli. Despite many aspects concerning m5C deposition in RNA, such as position or sequence context and the fact that many readers and erasers still remain elusive, the overall recent findings indicate that RNA cytosine methylation is a powerful mechanism to post-transcriptionally regulate physiological processes. In addition, mutations in RNA cytosine-5 methyltransferases are associated to pathological processes ranging from neurological syndromes to cancer.
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Affiliation(s)
| | - Ana Sevilla
- Physiology, Cellular Biology and Immunology Department - Biology Faculty. University of Barcelona, Avda. Diagonal 643, 08028 Barcelona. Spain
| | - Sandra Blanco
- CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain; Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca, 37007 Salamanca, Spain..
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24
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Mohammad‐Hasani A, Hosseinzadeh Colagar A, Fallah A. Association of the human aryl hydrocarbon receptor repressor (
AhRR
)‐c.565C>G transversion with male infertility: A case‐control study from Iran. J Cell Biochem 2018; 120:8999-9005. [DOI: 10.1002/jcb.28171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Azadeh Mohammad‐Hasani
- Department of Molecular and Cell Biology Faculty of Basic Sciences, University of Mazandaran Babolsar Iran
| | | | - Ali Fallah
- Department of Molecular and Cell Biology Faculty of Basic Sciences, University of Mazandaran Babolsar Iran
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25
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Mayeur A, Ahdad N, Hesters L, Brisset S, Romana S, Tosca L, Tachdjian G, Frydman N. Chromosomal translocations and semen quality: A study on 144 male translocation carriers. Reprod Biomed Online 2018; 38:46-55. [PMID: 30518499 DOI: 10.1016/j.rbmo.2018.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 11/30/2022]
Abstract
RESEARCH QUESTION Chromosomal translocations are known genetic causes of male infertility. Are certain translocations or chromosomal regions more directly associated with sperm defects? Is there a threshold of sperm impairment that can be relevant for detection of translocations? DESIGN This is a monocentric retrospective observational study covering a 10-year period. Eighty-one patients carrying a reciprocal translocation (RCT) and 63 carrying a Robertsonian translocation (ROBT) were compared with 105 fertile patients. Semen quality before and after sperm migration was compared. The aims were to define whether a threshold based on sperm analysis could be proposed for detection of translocations and to identify whether some redundant chromosomal regions might be associated with sperm quality defects. RESULTS The number of progressive spermatozoa retrieved after sperm preparation (NPS-ASP) was altered in both RCT and ROBT carriers compared with controls, with a stronger alteration in ROBT. Based on the NPS-ASP results in this large group of translocation carriers, a relatively robust threshold, fixed at less than 5 million, may be proposed for detection of translocations. The alteration of NPS-ASP was independent of the chromosome involved in ROBT, while in RCT, four redundant chromosomal regions (1q21, 6p21, 16q21, 17q11.2) were associated with poor or very poor NPS-ASP. CONCLUSIONS The NPS-ASP appears to be a good parameter to assess sperm function and would be a useful tool to detect chromosomal translocations. Four redundant regions have been identified on four chromosomes, suggesting that they may contain genes of interest to study sperm functions.
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Affiliation(s)
- Anne Mayeur
- AP-HP, Reproductive Biology Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France.
| | - Naouel Ahdad
- AP-HP, Reproductive Medicine Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
| | - Laetitia Hesters
- AP-HP, Reproductive Biology Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
| | - Sophie Brisset
- AP-HP, Cytogenetic Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
| | - Serge Romana
- AP-HP, Cytogenetic Unit, Paris Descartes University, Necker-Enfants-Malades Hospital, Paris 75015, France
| | - Lucie Tosca
- AP-HP, Cytogenetic Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
| | - Gérard Tachdjian
- AP-HP, Cytogenetic Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
| | - Nelly Frydman
- AP-HP, Reproductive Biology Unit, Paris-Sud University, Paris-Saclay University, Antoine Béclère Hospital, Clamart 92140, France
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26
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Fallah A, Mohammad-Hasani A, Colagar AH. Zinc is an Essential Element for Male Fertility: A Review of Zn Roles in Men's Health, Germination, Sperm Quality, and Fertilization. J Reprod Infertil 2018; 19:69-81. [PMID: 30009140 PMCID: PMC6010824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Zinc (Zn) is the second most abundant trace element in human, which can't be stored in the body, thus regular dietary intake is required. This review explained the physiological and pathogenesis roles of zinc in men's health and its potentials in germination, quality of sperm, and fertilization. Our investigation showed that Zn contained many unique properties in human, especially males. The antioxidant quality is one of them. Also, the increased reactive oxygen species levels in the seminal plasma of men who are both infertile and smokers influence the Zn content of seminal plasma in a way that physiology of spermatozoa can be affected as well. Moreover, Zn acts as a toxic repercussionagainst heavy metals and cigarette inflammatory agents. Zinc as a hormone balancer helps hormones such as testosterone, prostate and sexual healthand functions as an antibacterial agent in men's urea system. It plays a role in epithelial integrity, showing that Zn is essential for maintaining the lining of the reproductive organs and may have a regulative role in the progress of capacitation and acrosome reaction. In contrast, Zn deficiency impedes spermatogenesis and is a reason for sperm abnormalities and has a negative effect on serum testosterone concentration. Based on these findings, Zn microelement is very essential for male fertility. It could be considered as a nutrient marker with many potentials in prevention, diagnosis, and treatment of male infertility.
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Affiliation(s)
| | | | - Abasalt Hosseinzadeh Colagar
- Corresponding Author: Abasalt Hosseinzadeh Colagar, Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Post Code: 47416-95447, Iran, E-mail:;
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27
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Liu RJ, Long T, Li J, Li H, Wang ED. Structural basis for substrate binding and catalytic mechanism of a human RNA:m5C methyltransferase NSun6. Nucleic Acids Res 2017; 45:6684-6697. [PMID: 28531330 PMCID: PMC5499824 DOI: 10.1093/nar/gkx473] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022] Open
Abstract
5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancers. However, no structural information for RNA-bound RNA:m5C methyltransferase was available until now, hindering elucidation of the catalytic mechanism behind RNA:m5C methylation. Here, we have solved the structures of NSun6, a human tRNA:m5C methyltransferase, in the apo form and in complex with a full-length tRNA substrate. These structures show a non-canonical conformation of the bound tRNA, rendering the base moiety of the target cytosine accessible to the enzyme for methylation. Further biochemical assays reveal the critical, but distinct, roles of two conserved cysteine residues for the RNA:m5C methylation. Collectively, for the first time, we have solved the complex structure of a RNA:m5C methyltransferase and addressed the catalytic mechanism of the RNA:m5C methyltransferase family, which may allow for structure-based drug design toward RNA:m5C methyltransferase–related diseases.
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Affiliation(s)
- Ru-Juan Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China
| | - Tao Long
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Jing Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Hao Li
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P. R. China.,University of Chinese Academy of Sciences, Beijing 100039, P. R. China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, P. R. China
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28
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Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq. PLoS Genet 2016; 12:e1006398. [PMID: 27768696 PMCID: PMC5074504 DOI: 10.1371/journal.pgen.1006398] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/03/2016] [Indexed: 12/19/2022] Open
Abstract
A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy. SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome, an infant-onset epileptic encephalopathy. Dravet syndrome patients experience multiple seizures types that are often refractory to treatment, developmental delays, and elevated risk for SUDEP. The same sodium channel mutation can produce epilepsy phenotypes of varying clinical severity. This suggests that other factors, including genetic, modify the primary mutation and change disease severity. Mouse models provide a useful tool in studying the genetic basis of epilepsy. The mouse strain background can alter phenotype severity, supporting a contribution of genetic modifiers in epilepsy. The Scn1a+/- mouse model has a strain-dependent epilepsy phenotype. Scn1a+/- mice on the 129S6/SvEvTac (129) strain have a normal phenotype and lifespan, while [129xC57BL/6J]F1-Scn1a+/- mice experience spontaneous seizures, hyperthermia-induced seizures and high rates of premature death. We hypothesize the phenotypic differences are due to strain-specific genetic modifiers that influence expressivity of the Scn1a+/- phenotype. Low resolution mapping of Scn1a+/- identified several Dravet syndrome modifier (Dsm) loci responsible for the strain-dependent difference in survival. One locus of interest, Dsm1 located on chromosome 5, was fine mapped to a 9 Mb region using interval specific congenics. RNA-Seq was then utilized to identify candidate modifier genes within this narrowed region. Three genes with significant total gene expression differences between 129S6/SvEvTac and [129xC57BL/6J]F1 were identified, including the GABAA receptor subunit, Gabra2. Further analysis of Gabra2 demonstrated allele-specific expression. Pharmological manipulation by clobazam, a common anticonvulsant with preferential affinity for the GABRA2 receptor, revealed dose-dependent protection against hyperthermia-induced seizures in Scn1a+/- mice. These findings support Gabra2 as a genetic modifier of the Scn1a+/- mouse model of Dravet syndrome. Epilepsy is a neurological disorder affecting approximately 3 million Americans and 1% of the worldwide population. Approximately 70% of patients diagnosed with epilepsy have a genetic basis for their disease. The same genetic mutation can result in epilepsy with varying clinical severity in some individuals. This suggests that additional factors modify the effect of the primary mutation, resulting in the differences observed. Mouse models of epilepsy also exhibit variable severity depending on the inbred strain background. This is a useful model system that enables us to determine other genetic factors that influence phenotype presentation. This study investigates a mouse model of Dravet syndrome. Similar to Dravet syndrome patients, the mice experience a variety of seizure types and have increased risk for premature death. Interestingly, the Dravet syndrome phenotype is completely masked on one mouse strain background. Through a series of genetic and pharmacological techniques we were able to identify a gene that is likely responsible for the strain-dependent phenotype difference of Dravet mice. Identifying genes that modify diseases can help predict patient outcomes and suggest new therapies for the treatment of epilepsy.
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29
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Zhang S, Wang QM, Ding XP, Wang T, Mu XM, Chen ZY. Association of polymorphisms in PATE1 gene with idiopathic asthenozoospermia in Sichuan, China. J Reprod Immunol 2016; 118:54-60. [PMID: 27636828 DOI: 10.1016/j.jri.2016.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/16/2016] [Accepted: 08/22/2016] [Indexed: 12/14/2022]
Abstract
PURPOSE Idiopathic Asthenozoospermia (AZS) is a common symptom of male infertility described as reduced forward motility or absence of sperm motility. The PATE1 is generally expressed in male genital tract and related to sperm development, maturation and fertilization. However, the single nucleotide polymorphisms (SNPs) of the PATE1 gene which contribute to AZS were still unknown. For this reason, the possible association between the single nucleotide polymorphisms of the PATE1 gene and idiopathic asthenozoospermia was investigated in this research. METHODS 108 idiopathic asthenozoospermia were screened by karyotype analysis, detection of Y microdeletions and mutations in 5 other genes from 140 clinical AZS. The sequence analyses of the PATE1 gene were conducted in 108 idiopathic asthenozoospermia and 106 fertile men with normospermic parameters in Sichuan, China. RESULTS In this study, a total 108 patients without chromosomal abnormalities, Y microdeletions and selected genes mutation were confirmed. The 1423G (odds ratio [OR] 1.939, 95% confidence interval [CI] 1.320-2.848, P=0.001) was found to be increased significantly in idiopathic asthenozoospermic patients compared with their fertile counterparts. This mutation substitutes a highly conserved glutamic to arginine at the position of the 47th amino acid which was shown to be located on the flank of the pleated sheet domain in PATE1 protein by the 3D model given by the Protein Model Portal (PMP). Moreover, PolyPhen-2 analysis predicted that this variant was "probably damaging". CONCLUSIONS These results suggested that PATE1 variant (A1423G) was probably one of the high risk genetic factors for idiopathic asthenozoospermia among males in Sichuan, China.
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Affiliation(s)
- Shun Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China
| | - Qing-Ming Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China
| | - Xian-Ping Ding
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China; Institute of Medical Genetics, College of Life Science, Sichuan University, Chengdu 610064, China.
| | - Tao Wang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China
| | - Xue-Mei Mu
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China
| | - Zu-Yi Chen
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, School of Life Science, Institute of Medical Genetics, Sichuan University, Chengdu, China; Bio-resource Research and Utilization, Joint Key Laboratory of Sichuan and Chongqing, Chengdu, China
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