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Ning J, Yan J, Wang S, Cui Z, Xue Y, Juan J, Yang H. Demethylase FTO-mediated m6A modification of SIK1 modulates placental cytotrophoblast syncytialization in type 2 diabetes mellitus. iScience 2024; 27:109900. [PMID: 38883837 PMCID: PMC11177141 DOI: 10.1016/j.isci.2024.109900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 02/24/2024] [Accepted: 05/01/2024] [Indexed: 06/18/2024] Open
Abstract
Type 2 diabetes mellitus (T2DM) represents a common complication during pregnancy that affects fetoplacental development. We demonstrated the existence of impaired trophoblast syncytialization under hyperglycemic conditions. However, the exact mechanism remains unknown. RNA N6-methyladenosine (m6A) is an emerging regulatory mechanism of mRNA and participates in various biological processes. We described the global m6A modification pattern in T2DM placenta by the combined analysis of methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and RNA sequencing (RNA-Seq). Both the m6A modification and expression of SIK1, which is critical for syncytialization, were significantly decreased in trophoblast exposed to hyperglycemic conditions. In addition, the m6A demethylase fat mass and obesity-associated protein (FTO) affects the expression and mRNA stability of SIK1 by binding to its 3'-untranslated region (UTR) m6A site. This work reveals that the FTO-m6A-SIK1 axis plays critical roles in regulating syncytialization in the placenta.
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Affiliation(s)
- Jie Ning
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Jie Yan
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Shuxian Wang
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Yiwei Xue
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Juan Juan
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Huixia Yang
- Department of Obstetrics and Gynecology and Reproductive Medicine, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
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Golden TN, Mani S, Linn RL, Leite R, Trigg NA, Wilson A, Anton L, Mainigi M, Conine CC, Kaufman BA, Strauss JF, Parry S, Simmons RA. Extracellular vesicles alter trophoblast function in pregnancies complicated by COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.17.580824. [PMID: 38464046 PMCID: PMC10925147 DOI: 10.1101/2024.02.17.580824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and resulting coronavirus disease (COVID-19) causes placental dysfunction, which increases the risk of adverse pregnancy outcomes. While abnormal placental pathology resulting from COVID-19 is common, direct infection of the placenta is rare. This suggests that pathophysiology associated with maternal COVID-19, rather than direct placental infection, is responsible for placental dysfunction and alteration of the placental transcriptome. We hypothesized that maternal circulating extracellular vesicles (EVs), altered by COVID-19 during pregnancy, contribute to placental dysfunction. To examine this hypothesis, we characterized maternal circulating EVs from pregnancies complicated by COVID-19 and tested their effects on trophoblast cell physiology in vitro . We found that the gestational timing of COVID-19 is a major determinant of circulating EV function and cargo. In vitro trophoblast exposure to EVs isolated from patients with an active infection at the time of delivery, but not EVs isolated from Controls, altered key trophoblast functions including hormone production and invasion. Thus, circulating EVs from participants with an active infection, both symptomatic and asymptomatic cases, can disrupt vital trophoblast functions. EV cargo differed between participants with COVID-19 and Controls, which may contribute to the disruption of the placental transcriptome and morphology. Our findings show that COVID-19 can have effects throughout pregnancy on circulating EVs and circulating EVs are likely to participate in placental dysfunction induced by COVID-19.
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You G, Li Z, Li L, Xu C. Overexpression of RBM15 modulated the effect of trophoblast cells by promoting the binding ability between YTHDF2 and the CD82 3'UTR to decrease the expression of CD82. Heliyon 2024; 10:e30702. [PMID: 38765115 PMCID: PMC11098837 DOI: 10.1016/j.heliyon.2024.e30702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 05/21/2024] Open
Abstract
Background Pre-eclampsia (PE) is a syndrome with no specific pathological mechanism and is specific to pregnancy. The combined analysis of proteomics and transcriptomics possesses many benefits for treating this disease. m6A modification plays a major role in PE; however, mechanism have not been studied clearly. This study investigated the potential mechanism underlying the role of m6A in PE. Methods Mass spectrometry-based label-free quantitative proteomics and transcriptomics experiments were conducted on the placenta of patients with pre-eclampsia and normal pregnancies, and the two omics were followed by joint analysis. Total m6A modification in placental tissues, HTR8/SVneo cells, and JEG-3 cells was measured by dot blot. The levels of RBM15 and CD82 in tissues and cells were detected using qPCR. The protein levels of G3BP1, RBM15, MMP-2, YTHDF2, and MMP-9 were measured by western blotting. The function, migration, and invasion characteristics of HTR8/SVneo and JEG-3 cells were measured using Transwell assays. SRAMP predicted the m6A modification site in the CD82 mRNA 3'UTR, and this was confirmed using luciferase activity and YTHDF2-RIP. Results m6A modification was promoted in the PE group, and the RBM15 abundance was increased. Overexpression of RBM15 increased m6A modification. However, overexpression of RBM15 suppressed the expression of MMP-2 and MMP-9 and also the migratory and invasive capabilities of HTR8/SVneo and JEG-3 cells. CD82 expression levels were decreased in PE, and CD82 expression was confirmed via qPCR, western blotting and immunofluorescence. Furthermore, RBM15 overexpression reduced CD82 mRNA and protein levels. Luciferase activity and YTHDF2-RIP results verified that overexpression of RBM15 promoted the binding ability between YTHDF2 and the CD82 3'UTR, thereby decreasing CD82 expression. Finally, CD82 overexpression reversed the effect of RBM15 overexpression on the expression of MMP-2 and MMP-9 and on the migratory and invasive capabilities of the cells. Conclusions Overexpression of RBM15 hindered the migratory and invasive capabilities of trophoblasts, while concurrently enhancing m6A modification. The potential mechanism was that overexpression of RBM15 promoted the binding capability between YTHDF2 and CD82 3'UTR and decrease the expression of CD82. Thus, this study provides a theoretical basis for the treatment of PE.
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Affiliation(s)
| | | | - Ling Li
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, PR China
| | - Chengfang Xu
- Department of Gynecology and Obstetrics, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong Province, PR China
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Ren ZR, Luo SS, Qin XY, Huang HF, Ding GL. Sex-Specific Alterations in Placental Proteomics Induced by Intrauterine Hyperglycemia. J Proteome Res 2024; 23:1272-1284. [PMID: 38470452 DOI: 10.1021/acs.jproteome.3c00735] [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] [Indexed: 03/13/2024]
Abstract
Gestational diabetes mellitus (GDM) with intrauterine hyperglycemia induces a series of changes in the placenta, which have adverse effects on both the mother and the fetus. The aim of this study was to investigate the changes in the placenta in GDM and its gender differences. In this study, we established an intrauterine hyperglycemia model using ICR mice. We collected placental specimens from mice before birth for histological observation, along with tandem mass tag (TMT)-labeled proteomic analysis, which was stratified by sex. When the analysis was not segregated by sex, the GDM group showed 208 upregulated and 225 downregulated proteins in the placenta, primarily within the extracellular matrix and mitochondria. Altered biological processes included cholesterol metabolism and oxidative stress responses. After stratification by sex, the male subgroup showed a heightened tendency for immune-related pathway alterations, whereas the female subgroup manifested changes in branched-chain amino acid metabolism. Our study suggests that the observed sex differences in placental protein expression may explain the differential impact of GDM on offspring.
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Affiliation(s)
- Zhuo-Ran Ren
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai 200032, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China
| | - Si-Si Luo
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China
- Shanghai First Maternity and Infant Hospital, Shanghai 201204, China
| | - Xue-Yun Qin
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai 200032, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China
| | - He-Feng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai 200032, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Guo-Lian Ding
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai 200011, China
- Shanghai Key Laboratory of Reproduction and Development, Shanghai 200032, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences, Shanghai 200032, China
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Ning J, Yan J, Yang H. Exploring the role of m6A modification in the great obstetrical syndromes. J Matern Fetal Neonatal Med 2023; 36:2234541. [PMID: 37474299 DOI: 10.1080/14767058.2023.2234541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND N6-methyladenosine (m6A) is one of the predominant RNA epigenetic modifications that modify RNAs reversibly and dynamically by "writers" (methyltransferase), "erasers" (demethylase), and "readers." OBJECTIVE This review aimed to provide a comprehensive understanding of the complexity of m6A regulation in the great obstetrical syndromes to understand its pathogenesis and potential therapeutic targets. METHODS The terms "placenta or trophoblast" and "m6A or N6-methyladenosine" were searched in PubMed databases (June 2023). RESULTS In this review, we discuss the regulatory role of m6A in the great obstetrical syndromes such as preeclampsia (PE), spontaneous abortion (SA), hyperglycemia in pregnancy (HIP) and fetal growth to emphasize the clinical relevance of m6A dysregulation in pregnancy. We also describe mechanisms that potentially involve the participation of m6A methylation, such as proliferation, invasion, migration, apoptosis, autophagy, endoplasmic reticulum stress, macrophage polarization, and inflammation. CONCLUSION We summarize the recent research progress on the role of m6A modification in the great obstetrical syndromes and placental function and provide a brief perspective on its prospective applications.
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Affiliation(s)
- Jie Ning
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
| | - Jie Yan
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
| | - Huixia Yang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing, China
- Beijing Key Laboratory of Maternal Fetal Medicine of Gestational Diabetes Mellitus, Beijing, China
- Peking University, Beijing, China
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Zhang Y, Guo X, Chen Z, Guo R. Low m6A modification-mediated upregulation of PLAC8 promotes trophoblast cell invasion and migration in preeclampsia. Eur J Med Res 2023; 28:466. [PMID: 37885015 PMCID: PMC10605972 DOI: 10.1186/s40001-023-01442-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND The main symptoms of preeclampsia (PE), a specific ailment that develops during pregnancy, are proteinuria and hypertension. The pathological root of the onset and progression of PE is widely regarded as abnormal placental trophoblast cell function. This study aimed to look into the character and mechanism of Placenta-specific 8 (PLAC8) in trophoblast cell invasion and migration. METHODS Expressions of PLAC8 and AlkB homologue 5 (ALKBH5) were examined by western blot and quantitative real-time PCR. The m6A level of PLAC8 mRNA was detected by methylated RNA Immunoprecipitation. Using Transwell experiments, cell invasion and migration were examined. The enzyme-linked immunosorbent assay was utilized to analyze the MMP-2 and MMP-9 secretion levels. RNA pull-down and RNA immunoprecipitation were conducted to detect the binding between ALKBH5 and PLAC8. RESULTS In PE tissue and hypoxia-treated HTR-8/SVneo cells, levels of ALKBH5 and PLAC8 were increased, and PLAC8 m6A methylation levels were decreased. There was a positive correlation between PLAC8 and ALKBH5 expression in clinical tissues. In addition, overexpressing PLAC8 promoted HTR-8/SVneo cell migration and invasion, and so as the levels of MMP-2 and MMP-9; while interference with PLAC8 reduced the migration and invasion of hypoxia-treated HTR-8/SVneo cells, and so as the levels of MMP-2 and MMP-9. Moreover, the PLAC8 mRNA's m6A modification site was GAACU (Position 1449, Site 2). Increased levels of MMP-2 and MMP-9, as well as migration and invasion of HTR-8/SVneo cells exposed to hypoxia, were all facilitated by the m6A Site2 mutation. Furthermore, ALKBH5 could bind to PLAC8, reduce its m6A modification, and promote its expression. CONCLUSION High-expressed ALKBH5 inhibits the m6A level of PLAC8 mRNA and promotes PLAC8 expression, while PLAC8 overexpression can promote hypoxia-induced invasion and migration of HTR-8/Svneo cells, indicating its potential protective function in PE.
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Affiliation(s)
- Yajuan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1st Jianshe East Road, Zhengzhou, Henan, 450000, China
| | - Xiaoguang Guo
- Department of Anesthesiology, Pain and Perioperative Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450000, China
| | - Zhimin Chen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1st Jianshe East Road, Zhengzhou, Henan, 450000, China
| | - Ruixia Guo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1st Jianshe East Road, Zhengzhou, Henan, 450000, China.
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Argentato PP, Guerra JVDS, Luzia LA, Ramos ES, Maschietto M, Rondó PHDC. Excessive Gestational Weight Gain Alters DNA Methylation and Influences Foetal and Neonatal Body Composition. EPIGENOMES 2023; 7:18. [PMID: 37606455 PMCID: PMC10443290 DOI: 10.3390/epigenomes7030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Changes in body weight are associated with the regulation of DNA methylation (DNAm). In this study, we investigated the associations between maternal gestational weight gain-related DNAm and foetal and neonatal body composition. METHODS Brazilian pregnant women from the Araraquara Cohort Study were followed up during pregnancy, delivery, and after hospital discharge. Women with normal pre-pregnancy BMI were allocated into two groups: adequate gestational weight gain (AGWG, n = 45) and excessive gestational weight gain (EGWG, n = 30). Foetal and neonatal body composition was evaluated via ultrasound and plethysmography, respectively. DNAm was assessed in maternal blood using Illumina Infinium MethylationEPIC BeadChip arrays. Linear regression models were used to explore the associations between DNAm and foetal and neonatal body composition. RESULTS Maternal weight, GWG, neonatal weight, and fat mass were higher in the EGWG group. Analysis of DNAm identified 46 differentially methylated positions and 11 differentially methylated regions (DMRs) between the EGWG and AGWG groups. Nine human phenotypes were enriched for these 11 DMRs located in 13 genes (EMILIN1, HOXA5, CPT1B, CLDN9, ZFP57, BRCA1, POU5F1, ANKRD33, HLA-B, RANBP17, ZMYND11, DIP2C, TMEM232), highlighting the terms insulin resistance, and hyperglycaemia. Maternal DNAm was associated with foetal total thigh and arm tissues and subcutaneous thigh and arm fat, as well as with neonatal fat mass percentage and fat mass. CONCLUSION The methylation pattern in the EGWG group indicated a risk for developing chronic diseases and involvement of maternal DNAm in foetal lean and fat mass and in neonatal fat mass.
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Affiliation(s)
- Perla Pizzi Argentato
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
| | - João Victor da Silva Guerra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM) and Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Rua Giuseppe Máximo Scolfaro 10.000, Cidade Universitária, Campinas 13083-970, SP, Brazil;
| | - Liania Alves Luzia
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto 14049-900, SP, Brazil;
| | - Mariana Maschietto
- Boldrini Children’s Hospital, University of Campinas, Rua Márcia Mendes 619, Cidade Universitária, Campinas 13083-884, SP, Brazil;
| | - Patrícia Helen de Carvalho Rondó
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
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Huang E, Chen L. RNA N 6-methyladenosine modification in female reproductive biology and pathophysiology. Cell Commun Signal 2023; 21:53. [PMID: 36894952 PMCID: PMC9996912 DOI: 10.1186/s12964-023-01078-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/12/2023] [Indexed: 03/11/2023] Open
Abstract
Gene expression and posttranscriptional regulation can be strongly influenced by epigenetic modifications. N6-methyladenosine, the most extensive RNA modification, has been revealed to participate in many human diseases. Recently, the role of RNA epigenetic modifications in the pathophysiological mechanism of female reproductive diseases has been intensively studied. RNA m6A modification is involved in oogenesis, embryonic growth, and foetal development, as well as preeclampsia, miscarriage, endometriosis and adenomyosis, polycystic ovary syndrome, premature ovarian failure, and common gynaecological tumours such as cervical cancer, endometrial cancer, and ovarian cancer. In this review, we provide a summary of the research results of m6A on the female reproductive biology and pathophysiology in recent years and aim to discuss future research directions and clinical applications of m6A-related targets. Hopefully, this review will add to our understanding of the cellular mechanisms, diagnostic biomarkers, and underlying therapeutic strategies of female reproductive system diseases. Video Abstract.
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Affiliation(s)
- Erqing Huang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Lijuan Chen
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Zhang T, Tang X, Zhu Y, Wang C, Jiang Z, Yang N, Wang T, Shu L, Xu Y, Sun L. IGF2BP2 enhances LincRNA01116 stability via m 6 A: A potential biomarker and therapeutic target for patients with pre-eclampsia. J Cell Biochem 2023; 124:239-253. [PMID: 36538649 DOI: 10.1002/jcb.30358] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 02/24/2023]
Abstract
Pre-eclampsia (PE) is a serious complication in pregnant women characterized by failure of placental remodeling and is one of the primary causes of changes in the placental structure and function. The aberrant expression of long noncoding RNA is associated with the occurrence and progression of PE. This study found that linc01116 expression was significantly downregulated in PE patients and was related to poor uterine spiral artery remodeling. Knockdown of linc01116 remarkably decreased the angiogenesis of trophoblast cells in vitro and in vivo. Mechanistically, IGF2BP2 regulated linc01116 RNA stability via m6 A methylation. Bioinformatics and other experiments further revealed that linc01116 upregulates AAMP expression by adsorbing miR-210-3p in trophoblast cells. In conclusion, this study revealed the critical role of linc01116 in regulating trophoblast angiogenesis. Furthermore, the study provides new clues for detecting placental pathology in PE.
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Affiliation(s)
- Tingting Zhang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaotong Tang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yuanyuan Zhu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Cong Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Ziyan Jiang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Nana Yang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Tianjun Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lijun Shu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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Omit SBS, Akhter S, Rana HK, Rana ARMMH, Podder NK, Rakib MI, Nobi A. Identification of Comorbidities, Genomic Associations, and Molecular Mechanisms for COVID-19 Using Bioinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6996307. [PMID: 36685671 PMCID: PMC9848821 DOI: 10.1155/2023/6996307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Several studies have been done to identify comorbidities of COVID-19. In this work, we developed an analytical bioinformatics framework to reveal COVID-19 comorbidities, their genomic associations, and molecular mechanisms accomplishing transcriptomic analyses of the RNA-seq datasets provided by the Gene Expression Omnibus (GEO) database, where normal and infected tissues were evaluated. Using the framework, we identified 27 COVID-19 correlated diseases out of 7,092 collected diseases. Analyzing clinical and epidemiological research, we noticed that our identified 27 diseases are associated with COVID-19, where hypertension, diabetes, obesity, and lung cancer are observed several times in COVID-19 patients. Therefore, we selected the above four diseases and performed assorted analyses to demonstrate the association between COVID-19 and hypertension, diabetes, obesity, and lung cancer as comorbidities. We investigated genomic associations with the cross-comparative analysis and Jaccard's similarity index, identifying shared differentially expressed genes (DEGs) and linking DEGs of COVID-19 and the comorbidities, in which we identified hypertension as the most associated illness. We also revealed molecular mechanisms by identifying statistically significant ten pathways and ten ontologies. Moreover, to understand cellular physiology, we did protein-protein interaction (PPI) analyses among the comorbidities and COVID-19. We also used the degree centrality method and identified ten biomarker hub proteins (IL1B, CXCL8, FN1, MMP9, CXCL10, IL1A, IRF7, VWF, CXCL9, and ISG15) that associate COVID-19 with the comorbidities. Finally, we validated our findings by searching the published literature. Thus, our analytical approach elicited interconnections between COVID-19 and the aforementioned comorbidities in terms of remarkable DEGs, pathways, ontologies, PPI, and biomarker hub proteins.
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Affiliation(s)
- Shudeb Babu Sen Omit
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Salma Akhter
- Department of Environmental Science and Disaster Management, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Dhaka 1207, Bangladesh
| | - A. R. M. Mahamudul Hasan Rana
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Nitun Kumar Podder
- Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh
| | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ashadun Nobi
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
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Wang Y, Bai X, Guo X, Gao X, Chen Y, Li H, Fan W, Han C. Bioinformatics analysis combined with clinical sample screening reveals that leptin may be a biomarker of preeclampsia. Front Physiol 2023; 13:1031950. [PMID: 36685185 PMCID: PMC9846503 DOI: 10.3389/fphys.2022.1031950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction: Preeclampsia (PE) is a gestational hypertensive disease with unclear pathogenesis. This study aimed to identify the genes that play an important role in determining the pathogenesis of PE using bioinformatics analysis and fundamental researches. Materials and methods: Datasets from the Gene Expression Omnibus (GEO) database were used to screen for differentially expressed genes (DEGs). The NCBI, SangerBox, and other databases were used to analyze the functions of the DEGs. Targetscan7, miRWalk, ENCORI, DIANA TOOLS, CircBank databases, and the Cytoscape tool were used to construct the lncRNA/circRNA-miRNA- LEP network. SRAMP, RPISeq, RBPsuite, and catRPAID were used to analyze the RNA modifications of LEP. Immune cell infiltration was analyzed using the dataset GSE75010. Placental tissues from normal pregnant women and PE patients were collected, screened for gene expression using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and western blotting. The results were further verified in HTR-8/SVneo cell line hypoxia model and PE mouse model. Results: Our analyses revealed that LEP was significantly upregulated in eight datasets. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses indicated that LEP was involved in the JAK/STAT signaling pathway, angiogenesis, and placental development. Immune cell infiltration analysis showed that M1 and M2 macrophages differed between normal pregnancies and those in PE patients. A competing endogenous RNA (ceRNA) network was constructed, and proteins interacting with LEP were identified. RNA modification sites of LEP were also identified. Finally, the overexpression of LEP in PE was confirmed in clinical samples, HTR-8/SVneo cell line and PE mouse model. Conclusion: Our results indicate that LEP overexpression is associated with PE and may be a potential diagnostic marker and therapeutic target.
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Affiliation(s)
- Yajuan Wang
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xuening Bai
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xin Guo
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoli Gao
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Yuanyuan Chen
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Huanrong Li
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Wenjun Fan
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China
| | - Cha Han
- Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China,Tianjin Key Laboratory of Female Reproductive Health and Eugenics, Tianjin Medical University General Hospital, Tianjin, China,*Correspondence: Cha Han,
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12
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Bian Y, Li J, Shen H, Li Y, Hou Y, Huang L, Song G, Qiao C. WTAP dysregulation-mediated HMGN3-m6A modification inhibited trophoblast invasion in early-onset preeclampsia. FASEB J 2022; 36:e22617. [PMID: 36412513 DOI: 10.1096/fj.202200700rr] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/30/2022] [Accepted: 10/07/2022] [Indexed: 11/23/2022]
Abstract
Early-onset preeclampsia (ePE) originates from abnormal implantation and placentation that involves trophoblast invasion, but its pathophysiology is not entirely understood. N6-methyladenosine (m6A) regulators mediate the progression of various cancers. The invasiveness of trophoblast cells is similar to that of tumor cells. However, little is known regarding the potential role of m6A modification in ePE and the underlying mechanism. This study aimed to explore the m6A level in placental tissue samples collected from ePE patients and to investigate whether m6A modification was an essential part of PE pathogenesis. The m6A level in placental tissue samples of 80 PE participants was examined. MeRIP-microarray, RNA-Seq, luciferase reporter assay, and RNA immunoprecipitation chip (RIP) assay were performed. The m6A level in the ePE group was significantly reduced compared with the control group. Wilms' tumor 1-associating protein (WTAP) regulated trophoblast cell migration and invasion. Mechanistically, the high mobility group nucleosomal binding domain 3 (HMGN3) gene was a target gene of WTAP in trophoblast (p < .05). WTAP enhanced the stability of HMGN3 mRNA through binding with its 3'-UTR m6A site(+485A, +522A). HMGN3 was recognized by m6A recognition protein insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), which was inhibited when knocking down WTAP. Both m6A and WTAP levels were downregulated in ePE. The m6A modification mediated by WTAP/IGF2BP1/HMGN3 axis might contribute to abnormal trophoblast invasion. Our work provided a foundation for further exploration of RNA epigenetic regulatory patterns in ePE, and indicated a new treatment strategy for ePE.
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Affiliation(s)
- Yue Bian
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Jiapo Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Hongfei Shen
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Yuanyuan Li
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Yue Hou
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Ling Huang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Guiyu Song
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
| | - Chong Qiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Shenyang, China.,Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China.,Research Center of China Medical University Birth Cohort, Shenyang, China
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13
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Ouyang Y, Tu Y, Chen S, Min H, Wen Z, Zheng G, Wan T, Fan H, Yang W, Sun G. Characterization of immune microenvironment infiltration and m 6A regulator-mediated RNA methylation modification patterns in osteoarthritis. Front Immunol 2022; 13:1018701. [PMID: 36505479 PMCID: PMC9728527 DOI: 10.3389/fimmu.2022.1018701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/31/2022] [Indexed: 11/24/2022] Open
Abstract
Background Few studies have been reported the potential role of N6-methyladenosine (m6A) modification in osteoarthritis (OA). We investigated the patterns of m6A modification in the immune microenvironment of OA. Methods We evaluated the m6A modification patterns based on 22 m6A regulators in 139 OA samples and systematically associated these modification patterns with immune cell infiltration characteristics. The function of m6A phenotype-related differentially expressed genes (DEGs) was investigated using gene enrichment analysis. An m6A score model was constructed using principal component analysis (PCA), and an OA prediction model was established based on the key m6A regulators. We used real-time PCR analysis to detect the changes of gene expression in the cell model of OA. Results Healthy and OA samples showed significant differences in the expression of m6A regulators. Nine key m6A regulators, two m6A modification patterns, m6A-related genes and two gene clusters were identified. Some m6A regulators had a strong correlation with each other. Gene clusters and m6A clusters have high similarity, and cluster A corresponds to a high m6A score. Immunocytes infiltration differed significantly between the two clusters, with the m6A cluster B and gene cluster B having more types of infiltrating immunocytes than cluster A. The predictive model can also predict the progression of OA through m6A regulators expression. The results of real-time PCR analysis showed that the gene expression in the cell model of OA is similar to that of the m6A cluster B. Conclusions Our study reveals for the first time the potential regulatory mechanism of m6A modification in the immune microenvironment of OA. This study also sheds new light on the pathogenesis of OA.
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Affiliation(s)
| | - Yuanqing Tu
- Nanchang University, Nanchang, Jiangxi, China
| | | | - Huan Min
- Jiangxi Provincial People’s Hospital, Nanchang, Jiangxi, China
| | - Zhexu Wen
- The Fourth Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Guihao Zheng
- Shangrao People’s Hospital, Shangrao, Jiangxi, China
| | - Ting Wan
- Nanchang University, Nanchang, Jiangxi, China
| | - Hao Fan
- Nanchang University, Nanchang, Jiangxi, China
| | | | - Guicai Sun
- The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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14
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Zhou W, Xue P, Yang Y, Xia L, Yu B. Research progress on N6-methyladenosine in the human placenta. J Perinat Med 2022; 50:1115-1123. [PMID: 35606944 DOI: 10.1515/jpm-2021-0665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/25/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES N6-methyladenosine (m6A) is one of the most common epigenetic modifications of eukaryotic RNA. Under the jointly reversible regulation of related enzymes, m6A regulates many aspects of RNA, such as translation, stability and degradation. The aim of this study is to investigate the role of m6A in placenta-related diseases. METHODS Data were compiled from 2018 to 2021 citations in PubMed and Google Scholar using the keywords: placenta AND N6-methyladenosine. Seven studies were included. RESULTS In this study, we introduced some conventional methods to detect m6A modification at the whole RNA, region (peak) and single base levels. We also summarized the current studies of m6A modification in the placenta and briefly describe m6A in placental-related diseases, including recurrent miscarriage (RM), preeclampsia (PE) and gestational diabetes mellitus (GDM). CONCLUSIONS Although the relevant reports are still in the preliminary stage and some results are inconsistent, studies on methylation m6A modification have contributed new ideas for the research of reproductive diseases, providing a new basis for the diagnosis, treatment, prognosis and monitoring of related diseases.
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Affiliation(s)
- Wenbo Zhou
- International Genome Center, Jiangsu University, Zhenjiang, P.R. China
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, P.R. China
| | - Pingping Xue
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, P.R. China
| | - Yuqi Yang
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, P.R. China
| | - Lin Xia
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, P.R. China
| | - Bin Yu
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou, P.R. China
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15
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Biomarker screening in preeclampsia: an RNA-sequencing approach based on data from multiple studies. J Hypertens 2022; 40:2022-2036. [PMID: 36052525 DOI: 10.1097/hjh.0000000000003226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Biomarkers have become important in the prognosis and diagnosis of various diseases. High-throughput methods, such as RNA sequencing facilitate the detection of differentially expressed genes (DEGs), hence potential biomarker candidates. Individual studies suggest long lists of DEGs, hampering the identification of clinically relevant ones. Concerning preeclampsia - a major obstetric burden with high risk for adverse maternal and/or neonatal outcomes - limitations in diagnosis and prediction are still important issues. We, therefore, developed a workflow to facilitate the screening for biomarkers. METHODS On the basis of the tool DESeq2, a comprehensive workflow for identifying DEGs was established, analyzing data from several publicly available RNA-sequencing studies. We applied it to four RNA-sequencing datasets (one blood, three placenta) analyzing patients with preeclampsia and normotensive controls. We compared our results with other published approaches and evaluated their performance. RESULTS We identified 110 genes that are dysregulated in preeclampsia, observed in at least three of the studies analyzed, six even in all four studies. These included FLT-1, TREM-1, and FN1, which either represent established biomarkers at protein level, or promising candidates based on recent studies. For comparison, using a published meta-analysis approach, 5240 DEGs were obtained. CONCLUSION This study presents a data analysis workflow for preeclampsia biomarker screening, capable of identifying promising biomarker candidates, while drastically reducing the numbers of candidates. Moreover, we were also able to confirm its performance for heart failure. This approach can be applied to additional diseases for biomarker identification, and the set of DEGs identified in preeclampsia represents a resource for further studies.
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16
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Zhang B, Li D, Wang R. Transcriptome Profiling of N7-Methylguanosine Modification of Messenger RNA in Drug-Resistant Acute Myeloid Leukemia. Front Oncol 2022; 12:926296. [PMID: 35865472 PMCID: PMC9294171 DOI: 10.3389/fonc.2022.926296] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive hematological tumor caused by the malignant transformation of myeloid progenitor cells. Although intensive chemotherapy leads to an initial therapeutic response, relapse due to drug resistance remains a significant challenge. In recent years, accumulating evidence has suggested that post-transcriptional methylation modifications are strongly associated with tumorigenesis. However, the mRNA profile of m7G modification in AML and its role in drug-resistant AML are unknown. In this study, we used MeRIP-seq technology to establish the first transcriptome-wide m7G methylome profile for AML and drug-resistant AML cells, and differences in m7G between the two groups were analyzed. In addition, bioinformatics analysis was conducted to explore the function of m7G-specific methylated transcripts. We found significant differences in m7G mRNA modification between AML and drug-resistant AML cells. Furthermore, bioinformatics analysis revealed that differential m7G-modified mRNAs were associated with a wide range of cellular functions. Importantly, down-methylated m7G modification was significantly enriched in ABC transporter-related mRNAs, which are widely recognized to play a key role in multidrug resistance. Our results provide new insights into a novel function of m7G methylation in drug resistance progression of AML.
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Affiliation(s)
- Bing Zhang
- Department of Pediatrics, Qilu Hospital of Shandong University, Shandong, China
| | - Dong Li
- Department of Pediatrics, Qilu Hospital of Shandong University, Shandong, China
| | - Ran Wang
- Department of Hematology, Qilu Hospital of Shandong University, Shandong, China
- *Correspondence: Ran Wang,
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17
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Wang Q, Pan M, Zhang T, Jiang Y, Zhao P, Liu X, Gao A, Yang L, Hou J. Fear Stress During Pregnancy Affects Placental m6A-Modifying Enzyme Expression and Epigenetic Modification Levels. Front Genet 2022; 13:927615. [PMID: 35812725 PMCID: PMC9257140 DOI: 10.3389/fgene.2022.927615] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
As the hub connecting mother and offspring, the placenta’s normal development is vital for fetal growth. Fear stress can cause some structural alterations in the placenta and affect placental development and function. N6-methyladenosine (m6A) is the most common mRNA modification and is involved in regulating the development of the placenta and embryo. There are no reports on the potential role of m6A modification in placental damage caused by fear stress during pregnancy. In this study, we demonstrated that fear stress during pregnancy increases the levels of methylated enzymes (METTL3, METTL14, and WTAP), decreases the levels of demethylase FTO, and increases the overall methylation levels in the placenta of pregnant rats. MeRIP-seq data analysis revealed 22,010 m6A peaks associated with 12,219 genes in the placenta of the model and 21,060 m6A peaks associated with 11,730 genes in the placenta of the control. The peaks were mainly concentrated in the coding region and the 3ʹ untranslated region. In addition, 50 genes with abnormal modification and expression (double aberrant genes) were screened out by combining MeRIP-seq and RNA-seq data. Mefv, Erbb2, and Cgas were selected from 50 double aberrant genes, and MeRIP-qPCR and real-time quantitative polymerase chain reaction were used to verify their modification and expression levels. Our findings suggest that m6A modifications play an important role in placental dysfunction induced by fear stress during pregnancy.
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18
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Huang N, Gao Y, Zhang M, Guo L, Qin L, Liao S, Wang H. METTL3-Mediated m6A RNA Methylation of ZBTB4 Interferes With Trophoblast Invasion and Maybe Involved in RSA. Front Cell Dev Biol 2022; 10:894810. [PMID: 35774226 PMCID: PMC9237410 DOI: 10.3389/fcell.2022.894810] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 05/03/2022] [Indexed: 11/14/2022] Open
Abstract
N6-methyladenosine (m6A) was the most abundant modification of mRNA and lncRNA in mammalian cells and played an important role in many biological processes. However, whether m6A modification was associated with recurrent spontaneous abortion (RSA) and its roles were still unclear. Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) was used to study the global m6A modification pattern in RSAs and controls. RNA sequencing (RNA-Seq) was used to study the level of global mRNA in two groups. Real-time quantitative PCR (RT-qPCR) was used to verify the level of mRNA of METTL3 and ZBTB4. MeRIP–qPCR was conducted to test the level of ZBTB4 m6A modification in two groups. In order to further explore whether ZBTB4 was the substrate of METTL3, the HTR-8/SVneo (HTR-8) cell line was selected for the knockdown and overexpression of METTL3. To study whether METTL3 regulated the ZBTB4 expression by recognizing ZBTB4 mRNA m6A motifs in coding sequences (CDS), dual-luciferase reporter assay was conducted. RNA stability assays using actinomycin D were conducted to study the RNA stability of the HTR-8 cell line with METTL3 overexpression and knockdown. To illustrate the role of METTL3 in the invasion of trophoblast, matrigel invasion assays and transwell migration assays were conducted using the HTR-8 cell line with METTL3 overexpression and knockdown. Results: A total of 65 genes were found with significant differences both in m6A modification and mRNA expression. We found m6A methyltransferase METTL3 was significantly down-regulated in the RSA group. Through gene function analysis, RT-qPCR, MeRIP–qPCR validation experiment, knockdown, and overexpression of METTL3 in the HTR-8 cell line, ZBTB4 was selected as one target of METTL3. Furthermore, we clarified that METTL3 regulated the expression of ZBTB4 by recognizing ZBTB4 mRNA m6A motifs in the CDS using the dual-luciferase reporter assay and METTL3 regulated the invasion of trophoblast by altering the stability and expression of ZBTB4 by RNA stability, matrigel invasion, and transwell migration assays. Conclusion: Our study revealed the mechanism by which METTL3 regulated the stability and expression of ZBTB4 and the trophoblast migration ability of RSA. A new perspective was provided for exploring the mechanism of embryonic development in RSA patients.
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Affiliation(s)
- Nana Huang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Yue Gao
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Mengting Zhang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Liangjie Guo
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Litao Qin
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
| | - Shixiu Liao
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
- *Correspondence: Shixiu Liao, ; Hongdan Wang,
| | - Hongdan Wang
- Henan Provincial People’s Hospital, Medical Genetics Institute of Henan Province, Zhengzhou University People’s Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Henan Institute of Reproduction Health Science and Technology, Zhengzhou, China
- *Correspondence: Shixiu Liao, ; Hongdan Wang,
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Li Y, Chen C, Diao M, Wei Y, Zhu Y, Hu W. Gene model-related m6A expression levels predict the risk of preeclampsia. BMC Med Genomics 2022; 15:103. [PMID: 35513840 PMCID: PMC9069853 DOI: 10.1186/s12920-022-01254-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 11/30/2022] Open
Abstract
Background This is the first study to explore the potential functions and expression patterns of RNA N6-methyladenosine (m6A) and potential related genes in preeclampsia. Methods We identified two m6A modification patterns through unsupervised cluster analysis and validated them by principal component analysis. We quantified the relative abundance of specific infiltrating immunocytes using single-sample gene set enrichment analysis (ssGSEA) and the Wilcoxon test. To screen hub genes related to m6A regulators, we performed weighted gene coexpression network analysis. Functional enrichment analysis was conducted for differential signalling pathways and cellular processes. Preeclampsia patients were grouped by consensus clustering based on differentially expressed hub genes and the relationship between different gene-mediated classifications and clinical features. Results Two m6A clusters in preeclampsia, cluster A and cluster B, were determined based on the expression of 17 m6A modification regulators; ssGSEA revealed seven significantly different immune cell subtypes between the two clusters. A total of 1393 DEGs and nine potential m6A-modified hub genes were screened. We divided the patients into two groups based on the expression of these nine genes. We found that almost all the patients in m6A cluster A were classified into hub gene cluster 1 and that a lower gestational age may be associated with more m6A-associated events. Conclusions This study revealed that hub gene-mediated classification is consistent with m6A modification clusters for predicting the clinical characteristics of patients with preeclampsia. Our results provide new insights into the molecular mechanisms of preeclampsia. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01254-4.
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Affiliation(s)
- Yiwei Li
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China
| | - Can Chen
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China
| | - Mengyuan Diao
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China
| | - Yanli Wei
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China
| | - Ying Zhu
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China.
| | - Wei Hu
- Department of Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, 216 Huansha Road, Hangzhou, 310006, Zhejiang, China.
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20
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Jedynak P, Tost J, Calafat AM, Bourova-Flin E, Broséus L, Busato F, Forhan A, Heude B, Jakobi M, Schwartz J, Slama R, Vaiman D, Lepeule J, Philippat C. Pregnancy exposure to phthalates and DNA methylation in male placenta - An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 160:107054. [PMID: 35032864 PMCID: PMC8972089 DOI: 10.1016/j.envint.2021.107054] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Exposure to phthalates during pregnancy may alter DNA methylation in the placenta, a crucial organ for the growth and development of the fetus. OBJECTIVES We studied associations between urinary concentrations of phthalate biomarkers during pregnancy and placental DNA methylation. METHODS We measured concentrations of 11 phthalate metabolites in maternal spot urine samples collected between 22 and 29 gestational weeks in 202 pregnant women. We analyzed DNA methylation levels in placental tissue (fetal side) collected at delivery. We first investigated changes in global DNA methylation of repetitive elements Alu and LINE-1. We then performed an adjusted epigenome-wide association study using IlluminaHM450 BeadChips and identified differentially methylated regions (DMRs) associated with phthalate exposure. RESULTS Monobenzyl phthalate concentration was inversely associated with placental methylation of Alu repeats. Moreover, all phthalate biomarkers except for monocarboxy-iso-octyl phthalate and mono(2-ethyl-5-hydroxyhexyl) phthalate were associated with at least one DMR. All but three DMRs showed increased DNA methylation with increased phthalate exposure. The largest identified DMR (22 CpGs) was positively associated with monocarboxy-iso-nonyl phthalate and encompassed heat shock proteins (HSPA1A, HSPA1L). The remaining DMRs encompassed transcription factors and nucleotide exchange factors, among other genes. CONCLUSIONS This is the first description of genome-wide modifications of placental DNA methylation in association with pregnancy exposure to phthalates. Our results suggest epigenetic mechanisms by which exposure to these compounds could affect fetal development. Of interest, four identified DMRs had been previously associated with maternal smoking, which may suggest particular sensitivity of these genomic regions to the effect of environmental contaminants.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ekaterina Bourova-Flin
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Lucile Broséus
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004 Paris, France
| | - Milan Jakobi
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Claire Philippat
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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21
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Li R, Qiu X, He M, Qiao J, He J, Zhong M. METTL3-mediated mature miR-497-5p/195-5p inhibits trophoblast migration and invasion by targeting WWP1 in preeclampsia. Cell Cycle 2021; 21:iii-xviii. [PMID: 34592887 DOI: 10.1080/15384101.2021.1982527] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Preeclampsia (PE) is a pregnancy-associated disorder caused by poor placentation. METTL3 as an RNA methyltransferase that plays an essential role in the regulation of the m6A modification. This work investigated the regulation of METTL3-mediated mature miR-497-5p/195-5p cluster in PE progression and identified the downstream mechanisms involved. Differentially expressed miRNAs in PE were obtained from the GSE96983 dataset. The miR-497-5p/195-5p levels in placental samples collected from 20 cases of PE patients and 18 cases of normal controls were measured by RT-qPCR. Effects of miR-497-5p/195-5p and WWP1 on trophoblast proliferation, migration, and invasion were analyzed by CCK8, EdU, wound healing and Transwell assays. Luciferase reporter and RIP experiments were conducted to verify the interaction of WWP1 with miR-497-5p/195-5p. Dot blot assay was performed to determine the m6A levels in PE. The m6A modification of pri-miR-497-5p/195-5p was determined by Me-RIP assay. Immunochemistry (IHC) and western blotting were used to examine the immunoreactivities and protein levels of METTL3 and WWP1 in placental samples from PE patients and normal controls. The miR-497-5p/195-5p levels were high in PE placenta. Functionally, overexpression of miR-497-5p/195-5p prevented trophoblast migration, invasion, and proliferation. WWP1 overexpression enhanced trophoblast migration, invasion, and proliferation. Mechanistically, WWP1 was verified to be targeted by miR-497-5p/195-5p. Moreover, METTL3 promoted the recognition of pri-miR-497-5p/195-5p by DGCR8 and enhanced the formation of mature miR-497-5p/195-5p in an m6A manner. We demonstrated that METTL3-mediated m6A modification promotes the transition of pri-miR-497-5p/195-5p to mature miRNAs, thereby upregulating miR-497-5p/195-5p to aggravate PE progression by targeting WWP1.
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Affiliation(s)
- Rui Li
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China.,Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Xia Qiu
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Mei He
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jing Qiao
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Jing He
- Department of Obstetrics and Gynecology, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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22
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Zhang L, Hao D, Ma P, Ma B, Qin J, Tian G, Liu Z, Zhou X. Epitranscriptomic Analysis of m6A Methylome After Peripheral Nerve Injury. Front Genet 2021; 12:686000. [PMID: 34306026 PMCID: PMC8301379 DOI: 10.3389/fgene.2021.686000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/04/2021] [Indexed: 12/02/2022] Open
Abstract
N6-methyladenosine (m6A) is one of the most plentiful internal RNA modifications, especially in eukaryotic messenger RNA (mRNA), which plays pivotal roles in the regulation of mRNA life cycle and nerve development. However, the mRNA m6A methylation pattern in peripheral nervous injury (PNI) has not been investigated. In this study, sciatic nerve samples were collected from 7 days after sciatic nerve injury (SNI) and control rats. Quantitative real-time PCR demonstrated that m6A-related methyltransferase/demethylase genes were remarkably upregulated in SNI group compared with control group. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was performed to reveal the m6A methylation landscape. The results showed that 4,014 m6A peaks were significantly altered, including 2,144 upregulated and 1,870 downregulated m6A peaks, which were corresponded to 1,858 genes. Moreover, 919 differentially expressed genes were identified by the conjoint analysis of MeRIP-seq and RNA-seq. GO and KEGG pathway analyses were performed to determine the biological functions and signaling pathways of the m6A-modified genes. Notably, these genes were mainly related to the immune system process, cell activation, and nervous system development in GO analysis. KEGG pathway analysis revealed that these genes were involved in the cell cycle, B cell receptor signaling pathway, axon guidance pathway, and calcium signaling pathway. Furthermore, the m6A methylation and protein expression levels of autophagy-related gene (Atg7) were increased, together with the activation of autophagy. These findings shed some light on the epigenetic regulation of gene expression, which may provide a new opinion to promote functional recovery after PNI.
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Affiliation(s)
- Lei Zhang
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Dingyu Hao
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Pengyi Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Boyuan Ma
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Jia Qin
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Guangyuan Tian
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Zihao Liu
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
| | - Xianhu Zhou
- Department of Orthopedics, Tianjin Medical University General Hospital, Tianjin, China
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