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Kim G, Lee Y, Park JH, Kim D, Lee W. Beta-Meta: a meta-analysis application considering heterogeneity among genome-wide association studies. Genomics Inform 2022; 20:e49. [PMID: 36617656 PMCID: PMC9847376 DOI: 10.5808/gi.22046] [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: 07/26/2022] [Accepted: 10/05/2022] [Indexed: 12/31/2022] Open
Abstract
Many packages for a meta-analysis of genome-wide association studies (GWAS) have beendeveloped to discover genetic variants. Although variations across studies must be considered, there are not many currently-accessible packages that estimate between-study heterogeneity. Thus, we propose a python based application called Beta-Meta which can easilyprocess a meta-analysis by automatically selecting between a fixed effects and a randomeffects model based on heterogeneity. Beta-Meta implements flexible input data manipulation to allow multiple meta-analyses of different genotype-phenotype associations in asingle process. It provides a step-by-step meta-analysis of GWAS for each association inthe following order: heterogeneity test, two different calculations of an effect size and ap-value based on heterogeneity, and the Benjamini-Hochberg p-value adjustment. Thesemethods enable users to validate the results of individual studies with greater statisticalpower and better estimation precision. We elaborate on these and illustrate them with examples from several studies of infertility-related disorders.
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Li T, Chen Y, Lai Y, He G, He G. The relationship between polymorphisms of microRNA and preeclampsia: A protocol for meta-analysis and bioinformatics prediction. Medicine (Baltimore) 2021; 100:e25477. [PMID: 33832165 PMCID: PMC8036089 DOI: 10.1097/md.0000000000025477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Preeclampsia has genetic correlation. Many studies have shown that microRNA (miRNA) polymorphism is highly associated with preeclampsia, but the results are inconsistent. The purpose of this study is to systematically evaluate the relationship between miRNA polymorphism and preeclampsia. METHODS In this study, the search time is set from the establishment of the database on January 2021. The search database include China National Knowledge Infrastructure (CNKI), Wanfang, VIP and China Biology Medicine disc (CBM), PubMed, EMBASE, and Web of Science, and the Cochrane Library. The subjects are case-control studies on the relationship between miRNA polymorphism and preeclampsia. The language is limited to English and Chinese. The data of the included study are extracted and the literature quality is evaluated by 2 researchers independently. The data are statistically analyzed through Stata 16.0 software. We also predicted the miRNA secondary structure and the binding sites of miRNA interaction with its target genes. RESULTS This review will be disseminated in print by peer-review. CONCLUSION This study will provide evidence-based medicine to elucidate the genetic tendency of preeclampsia. ETHICS AND DISSEMINATION Private information from individuals will not be published. This systematic review also does not involve endangering participant rights. Ethical approval will not be required. The results may be published in a peer-reviewed journal or disseminated at relevant conferences. OSF REGISTRATION NUMBER DOI 10.17605/OSF.IO/MJY2X.
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Affiliation(s)
- Tao Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yihong Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Yi Lai
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guoqian He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guolin He
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
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Overexpression of PTEN regulated by miR-19b and miR-494 in the villous of recurrent spontaneous abortion patients. J Reprod Immunol 2020; 140:103133. [DOI: 10.1016/j.jri.2020.103133] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/07/2020] [Accepted: 04/09/2020] [Indexed: 11/19/2022]
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Asadi-Tarani M, Saravani M, Teimoori B, Ghasemi M, Salimi S. The relationships between maternal and placental polymorphisms of miR-196a2 and miRNA-499 genes and preeclampsia. Br J Biomed Sci 2020; 77:191-195. [DOI: 10.1080/09674845.2020.1769331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- M Asadi-Tarani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - M Saravani
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - B Teimoori
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - M Ghasemi
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Pregnancy Health Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - S Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
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Salimi S, Eskandari F, Rezaei M, Narooei-nejad M, Teimoori B, Yazdi A, Yaghmaei M. The effect of miR-146a rs2910164 and miR-149 rs2292832 polymorphisms on preeclampsia susceptibility. Mol Biol Rep 2019; 46:4529-4536. [DOI: 10.1007/s11033-019-04908-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 06/07/2019] [Indexed: 01/05/2023]
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Wang XQ, Wang H, Zhang L, Liu HN, Gao J, Wang YY, Ma X, Xia HF. Haplotype-based association of two SNPs in miR-423 with unexplained recurrent pregnancy loss in a Chinese Han population. Exp Cell Res 2019; 374:210-220. [DOI: 10.1016/j.yexcr.2018.11.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/22/2018] [Accepted: 11/28/2018] [Indexed: 12/25/2022]
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Cai H, Zhu XX, Li ZF, Zhu YP, Lang JH. MicroRNA Dysregulation and Steroid Hormone Receptor Expression in Uterine Tissues of Rats with Endometriosis during the Implantation Window. Chin Med J (Engl) 2018; 131:2193-2204. [PMID: 30203794 PMCID: PMC6144856 DOI: 10.4103/0366-6999.240808] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: Estrogen receptor (ER) and progesterone receptor (PR) are involved in endometriosis, but the involvement of microRNAs (miRNAs) is unknown. The aim of the study was to explore the correlation between miRNA and ER/PR in uterine tissues of rats with endometriosis during the implantation window. Methods: Twenty female Sprague-Dawley rats were randomized in three groups: endometriosis (n = 7), fat tissue control (n = 6), and normal (n = 7) groups. The female rats were mated and sacrificed on day 5 (implantation). Uterine tissues were obtained for hematoxylin-eosin staining, immunohistochemistry, and miRNA expression. Reverse transcription polymerase chain reaction (RT-PCR) was used to validate the expression of rno-miR-29c-3p, rno-miR-34c-5p, rno-miR-141-5p, rno-miR-24-1-5p, and rno-miR-490-5p. Results: The 475 miRNAs were found to differentially express between the endometriosis and normal control groups, with 127 being upregulated and 348 being downregulated. Expression of five miRNAs (rno-miR-29c-3p, rno-miR-34c-5p, rno-miR-141-5p, rno-miR-24-1-5p, and rno-miR-490-5p) were validated by RT-PCR and found to be differentially expressed among the three groups. Expression of ER and PR proteins (immunohistochemistry) in the glandular epithelium and endometrial stroma was significantly different among the three groups (all P < 0.05). Five miRNAs were involved in pathways probably taking part in implantation and fertility. Conclusions: The results suggested that miRNAs, ER, and PR could play important roles in the embryo implantation period of rats with endometriosis. These miRNAs might play a role in endometrial receptivity in endometriosis.
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Affiliation(s)
- Han Cai
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing 100005, China
| | - Xin-Xin Zhu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing 100005, China
| | - Zhan-Fei Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing 100005, China
| | - Ya-Pei Zhu
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing 100005, China
| | - Jing-He Lang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Beijing 100005, China
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Abstract
There are several known causes of recurrent pregnancy loss (RPL) in a couple, which include endocrine abnormalities, immunologic abnormalities, structural uterine abnormalities and karyotype abnormalities. The evaluation largely focuses on the female. The male contribution to RPL remains understudied. With the exception of the karyotype analysis, there is currently no other recommended testing for the male partner of a woman who has suffered multiple pregnancy losses. Chromosomal abnormalities are well defined causes of pregnancy losses in the literature. However, despite the fact that abnormal DNA fragmentation has been implicated in the pathogenesis of unexplained RPL, it is not routinely checked during the evaluation of RPL. This is likely due to the fact that abnormal DNA fragmentation is the end result of multiple different mechanisms including environmental exposures, varicoceles, gene alteration and epigenetic changes resulting in an inherent susceptibility to DNA damage? We are just beginning to scratch the surface of our understanding of the male contribution to RPL and more studies especially focusing on epigenetic modifications and gene alterations are needed.
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Affiliation(s)
- Yetunde Ibrahim
- Utah Center for Reproductive Medicine, Department of Obstetrics and Gynecology, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Erica Johnstone
- Utah Center for Reproductive Medicine, Department of Obstetrics and Gynecology, University of Utah, School of Medicine, Salt Lake City, UT, USA
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Ahn TK, Kim JO, Kumar H, Choi H, Jo MJ, Sohn S, Ropper AE, Kim NK, Han IB. Polymorphisms of miR-146a, miR-149, miR-196a2, and miR-499 are associated with osteoporotic vertebral compression fractures in Korean postmenopausal women. J Orthop Res 2018; 36:244-253. [PMID: 28741852 DOI: 10.1002/jor.23640] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/21/2017] [Indexed: 02/04/2023]
Abstract
Genetic factors have been shown to be a small but significant predictor for osteoporosis and osteoporotic fracture risk. We performed a case-control association study to determine the association between miR-146a, miR-149, miR-196a2, and miR-499 polymorphisms and osteoporotic vertebral compression fracture (OVCF) susceptibility. In total, 286 unrelated postmenopausal Korean women (57 with OVCFs, 55 with non-OVCFs, and 174 healthy controls) were recruited. All subjects underwent dual energy X-ray absorptiometry to determine BMD at the lumbar spine and femoral neck. We focused on four single nucleotide polymorphisms (SNPs) of pre-miRNA sequences including miR-146aC>G (rs2910164), miR-149T>C (rs2292832), miR-196a2T>C (rs11614913), and miR-499A>G (rs3746444). Genotype frequencies of these four SNPs were determined using polymerase chain reaction-restriction fragment length polymorphism analysis. The TT genotype of miR-149aT>C was less frequent in subjects with OVCFs, suggesting a protective effect against OVCF risk (Odds ratio [OR], 0.435; 95% confidence interval [CI], 0.22-0.85, p = 0.014), whereas the miR-146aCG/ miR-196a2TC combined genotype was more frequent in OVCF patients (OR, 5.163; 95%CI, 1.057-25.21, p = 0.043), suggesting an increase in OVCF risk. Additionally, combinations of miR-146a, -149, -196a2, and -449 showed a significant association with increased prevalence of OVCFs in postmenopausal women. In particular, the miR-146aG/-149T/-196a2C/-449G allele combination was significantly associated with an increased risk of OVCF (OR, 35.01; 95% CI, 1.919-638.6, p = 0.001). Our findings suggest that the TT genotype of miR-149aT>C may contribute to decreased susceptibility to OVCF in Korean postmenopausal women. Conversely, the miR-146aCG/ miR-196a2TC combined genotype and the miR-146aG/-149T/-196a2C/-449G allele combination may contribute to increased susceptibility to OVCF. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:244-253, 2018.
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Affiliation(s)
- Tae-Keun Ahn
- Department of Orthopedic Surgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
| | - Jung-Oh Kim
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, 13488, Korea
| | - Hemant Kumar
- Department of Neurosurgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
| | - Hyemi Choi
- Department of Neurosurgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
| | - Min-Jae Jo
- Department of Neurosurgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
| | - Seil Sohn
- Department of Neurosurgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
| | | | - Nam-Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam-si, 13488, Korea
| | - In-Bo Han
- Department of Neurosurgery, CHA University, CHA Bundang Medical Center, 59 Yaptapro, Seongnam-si, 13496, South Korea
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Toraih EA, Ismail NM, Toraih AA, Hussein MH, Fawzy MS. Precursor miR-499a Variant but not miR-196a2 is Associated with Rheumatoid Arthritis Susceptibility in an Egyptian Population. Mol Diagn Ther 2017; 20:279-95. [PMID: 27002721 DOI: 10.1007/s40291-016-0194-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Rheumatoid arthritis (RA) has a complex component induced by several genes that interact together with environmental and hormonal factors. We aimed to investigate the association of miR-196a2 rs11614913 (C/T) and miR-499a rs3746444 (A/G) polymorphisms and their combination with RA susceptibility and disease activity in an Egyptian population, and to evaluate their impact on methotrexate drug response and toxicity. MATERIALS AND METHODS Bioinformatics databases were searched to select potential micro RNA (miRNA)-messenger RNA (mRNA) interactions involved in RA pathogenesis. Ninety-five RA patients diagnosed according to the American College of Rheumatology and 200 healthy controls were genotyped using real-time polymerase chain reaction technology. RESULTS In overall and stratified analysis, miR-499a, but not miR-196a2, was associated with RA risk. Heterozygote carriers with rs3746444*A/G displayed protection against developing RA (p = 0.005) with an odds ratio of 0.2 (95 % confidence interval 0.17-0.62). The carriage of the combinations (miR499a*AG + miR196a2*CC) and (miR499a*AA + miR196a2*TT) were 3 and 7.5 times more likely to develop RA, respectively, while the combinations (miR499a*GG + miR196a2*CC), (miR499a*AG + miR196a2*TT) and (miR499a*AA + miR196a2*CT) show less susceptibility to have RA disease (all p < 0.05). rs3746444*AA genotype had a higher disease activity score (DAS28) [p = 0.023], tender joint count (TJC) (p = 0.007), and methotrexate-induced gastrointestinal toxicity (p = 0.043) compared with both AG/GG genotypes. rs11614913*C carriers were associated with higher DAS28 activity (p = 0.021). Homozygote male patients (CC and TT) had higher TJC (p = 0.046) and higher rheumatoid factor levels (p = 0.026), whereas, TT homozygote females had higher levels of ALT (p = 0.022). CONCLUSIONS Different genotypes of miR-499a rs3746444 single nucleotide polymorphisms (SNPs) are associated with RA risk, disease activity, and methotrexate toxicity in our population. In combination with specific miR-196a2 rs11614913 genotypes, this risk could increase or decrease according to the type of combination. Further functional analysis of the SNP and its impact on mRNA targets is required to confirm the relationship between genotype and phenotype.
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Affiliation(s)
- Eman A Toraih
- Department of Histology and Cell Biology (Genetics Unit), Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Nesreen M Ismail
- Department of Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Ahmed A Toraih
- Department of Orthopedic Surgery, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Mohammad H Hussein
- Department of Chest Disease, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Manal S Fawzy
- Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, PO 41522, Ismailia, Egypt.
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Tang L, Zheng S, Wang Y, Li F, Bao M, Zeng J, Xiang J, Luo H, Li J. Rs4265085 in GPER1 gene increases the risk for unexplained recurrent spontaneous abortion in Dai and Bai ethnic groups in China. Reprod Biomed Online 2017; 34:399-405. [PMID: 28126236 DOI: 10.1016/j.rbmo.2017.01.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/06/2017] [Accepted: 01/06/2017] [Indexed: 11/24/2022]
Abstract
Oestrogen receptors are implicated in the pathogenesis of recurrent spontaneous abortion (RSA). Non-genomic oestrogen responses can be mediated by GPER. The prevalence of polymorphisms in GPER1 gene in RSA was assessed in 747 Chinese women from Yunnan province (171 Bai, 258 Chinese Han, 234 Dai, 33 Achang and 51 Jingpo patients). Snapshot technology was used for genotyping the polymorphisms of the GPER1 gene. The rs4265085G was significantly increased in the Dai and Bai groups versus controls (Dai: P < 0.0001, Padj < 0.0001, OR 95% CI 2.34 [1.79 to 3.05]; Bai: P = 0.0004, Padj = 0.0012, OR 95% CI 1.71 [1.27 to 2.31]); recessive model of rs4265085 in the Dai (P = 0.003, Padj = 0.009, OR 95% CI 2.71 [1.38 to 5.30]); Bai (P < 0.0001, Padj < 0.0001, OR 95% CI 3.37 [1.93 to 5.91]). Haplotype frequencies containing rs10269151G-rs4265085G-rs11544331C were separately significantly different in Dai and Bai ethnic groups (Dai: P = 0.0002, Padj = 0.001, OR 95% CI = 2.12 [1.43 to 3.17]; Bai: P = 0.005, Padj = 0.025, OR 95% CI = 1.82 [1.18 to 2.78]) compared with controls. The intron variant rs4265085 may confer risk for RSA in Dai and Bai ethnic groups.
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Affiliation(s)
- Liang Tang
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; School of Basic Medical Science, Changsha Medical University, Changsha, China.
| | - Shui Zheng
- Key Laboratory for Fertility Regulation and Berth Heath of Minority Nationalities of Yunnan Province, Judicial Expertise Center, Yunnan Population and Family Planning Research Institute, Kunming, China
| | - Yan Wang
- School of Basic Medical Science, Changsha Medical University, Changsha, China; Experiment Center for Function, Changsha Medical University, Changsha, China
| | - Fang Li
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; School of Basic Medical Science, Changsha Medical University, Changsha, China
| | - Meihua Bao
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; School of Basic Medical Science, Changsha Medical University, Changsha, China
| | - Jie Zeng
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; School of Basic Medical Science, Changsha Medical University, Changsha, China
| | - Ju Xiang
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; School of Basic Medical Science, Changsha Medical University, Changsha, China
| | - Huaiqing Luo
- School of Basic Medical Science, Changsha Medical University, Changsha, China; Experiment Center for Function, Changsha Medical University, Changsha, China
| | - Jianming Li
- Department of Human Anatomy, Histology and Embryology, Institute of Neuroscience, Changsha Medical University, Changsha, China; Department of Neurology, Xiang-ya Hospital, Central South University, Changsha, China
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Amin-Beidokhti M, Mirfakhraie R, Zare-Karizi S, Karamoddin F. The role of parental microRNA alleles in recurrent pregnancy loss: an association study. Reprod Biomed Online 2016; 34:325-330. [PMID: 28012790 DOI: 10.1016/j.rbmo.2016.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/13/2016] [Accepted: 12/08/2016] [Indexed: 01/19/2023]
Abstract
The medical evaluation of recurrent pregnancy loss (RPL), the occurrence of two or more consecutive pregnancy losses prior to 20th week of gestation, is mainly focused on maternal factors. However, paternally expressed genes may also play a role in implantation and placenta quality. This study aimed to investigate the possible association between parental miR-196a2C>T and miR-499aT>C polymorphisms and RPL in a case-control study including 200 RPL couples and 400 healthy men and women. Genotyping was performed using Tetra-ARMS-PCR and PCR-RFLP for miR-196a2C>T and miR-499aT>C polymorphisms, respectively. In men, the association was observed between miR-499a and RPL under dominant (P = 0.006; odds ratio [OR] = 2.36; 95% confidence interval [CI], 1.28-4.37), recessive (P < 0.0001; OR = 2.89; 95% CI, 1.92-4.36) and additive (P < 0.001; OR = 2.77; 95% CI, 1.52-5.10) models. In women, the association was found between miR-196a2 and RPL under recessive (P = 0.02; OR = 2.19; 95% CI, 1.16-4.14) and additive (P = 0.03; OR = 1.53; 95% CI, 1.04-2.27) models. Hence, evidence was provided for association of genetic variation in parental microRNA polymorphisms with RPL. Further studies are required to validate the significance of the studied genetic variations in diverse ethnic populations.
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Affiliation(s)
- Mona Amin-Beidokhti
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Shohreh Zare-Karizi
- Department of Biology, Varamin Islamic Azad University, Pishva-Varamin, Iran
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Association of miR-146a, miR-149, miR-196a2, and miR-499 Polymorphisms with Ossification of the Posterior Longitudinal Ligament of the Cervical Spine. PLoS One 2016; 11:e0159756. [PMID: 27454313 PMCID: PMC4959720 DOI: 10.1371/journal.pone.0159756] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/07/2016] [Indexed: 12/31/2022] Open
Abstract
Background Ossification of the posterior longitudinal ligament (OPLL) of the spine is considered a multifactorial and polygenic disease. We aimed to investigate the association between four single nucleotide polymorphisms (SNPs) of pre-miRNAs [miR-146aC>G (rs2910164), miR-149T>C (rs2292832), miR-196a2T>C (rs11614913), and miR-499A>G (rs3746444)] and the risk of cervical OPLL in the Korean population. Methods The genotypic frequencies of these four SNPs were analyzed in 207 OPLL patients and 200 controls by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. Findings For four SNPs in pre-miRNAs, no significant differences were found between OPLL patients and controls. However, subgroup analysis based on OPLL subgroup (continuous: continuous type plus mixed type, segmental: segmental and localized type) showed that miR-499GG genotype was associated with an increased risk of segmental type OPLL (adjusted odds ratio = 4.314 with 95% confidence interval: 1.109–16.78). In addition, some allele combinations (C-T-T-G, G-T-T-A, and G-T-C-G of miR-146a/-149/-196a2/-499) and combined genotypes (miR-149TC/miR-196a2TT) were associated with increased OPLL risk, whereas the G-T-T-G and G-C-C-G allele combinations were associated with decreased OPLL risk. Conclusion The results indicate that GG genotype of miR-499 is associated with significantly higher risks of OPLL in the segmental OPLL group. The miR-146a/-149/-196a2/-499 allele combinations may be a genetic risk factor for cervical OPLL in the Korean population.
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Li D, Li J. Association of miR-34a-3p/5p, miR-141-3p/5p, and miR-24 in Decidual Natural Killer Cells with Unexplained Recurrent Spontaneous Abortion. Med Sci Monit 2016; 22:922-9. [PMID: 26996957 PMCID: PMC4805134 DOI: 10.12659/msm.895459] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The specific causes of recurrent spontaneous abortion (RSA) remain unknown in 37-79% of affected women. The aim of this study was to explore the expression levels of 6 miRNAs in natural killer (NK) cells from the decidua of patients with unexplained RSA (URSA) and to predict the target genes of 3 miRNAs. MATERIAL/METHODS Two groups were examined: URSA (n=20) and controls (n=20). Flow cytometry analysis was used to identify NK cells isolated from the decidua. Transcriptional levels of miRNA were monitored using quantitative real-time reverse transcription-polymerase chain reaction. Prediction and analysis of mRNA targets of differentially expressed miRNAs were performed using bioinformatics methods. RESULTS Five miRNAs [miR-34a (+281%, P<0.001), miR-155 (+396%, P<0.001), miR-141 (+142%, P<0.01), miR-125a (+279%, P<0.001), and miR-125b (+185%, P<0.001)] were up-regulated, while miR-24 was down-regulated (-64%, P<0.01) in the URSA group, compared to the control group. This study identified potential miRNA targets: miR-34a-3p/5p, 585/1718 (targets of miR-34a-3p/targets of miR-34a-5p), miR-141-3p/5p, 2270/629 (targets of miR-141-3p/targets of miR-141-5p), and miR-24, 2320 target genes. A total of 140 pathways related to target genes were identified including PI3K-Akt, focal adhesion, MAPK, Wnt, regulation of the actin cytoskeleton, T cell receptor, TGF-β, and estrogen signaling pathways. CONCLUSIONS This study suggests that miR-34a-3p/5p, miR-141-3p/5p, and miR-24 in decidual NK cells could be associated with URSA. These findings might contribute to the panel of diagnostic and prognostic biomarkers with clinical utility, and facilitate the development of new strategies for targeted therapy against URSA.
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Affiliation(s)
- Dandan Li
- Department of Family Planning, Beijing Obstetrics and Gynecology Hospital, Capital Medical Universityy, Beijing, China (mainland)
| | - Jian Li
- Department of Family Planning, Beijing Obstetrics and Gynecology Hospital, Capital Medical Universityy, Beijing, China (mainland)
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Kropp J, Khatib H. Characterization of microRNA in bovine in vitro culture media associated with embryo quality and development. J Dairy Sci 2015; 98:6552-63. [PMID: 26142856 DOI: 10.3168/jds.2015-9510] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/13/2015] [Indexed: 01/08/2023]
Abstract
Dairy cattle fertility has declined over time due to factors including reduced fertilization and early embryonic loss. To counter fertility problems and better study preimplantation embryonic development, in vitro production systems have been developed. These systems largely assess embryos based on their morphology, which is not a strong indicator of developmental potential. Currently, no biomarkers can be used to noninvasively survey an embryo's potential in terms of its development and ability to establish a pregnancy. Thus, the objective of this study was to characterize and identify microRNA (miRNA) in culture media of embryos of differing developmental competence for future development as noninvasive biomarkers of embryo quality. The MiRNA sequencing of media conditioned by blastocyst and degenerate (those that failed to develop from the morula to blastocyst stage) embryos, revealed 11 differentially expressed miRNA; all were higher in concentration in degenerate conditioned media. Differential expression of mature microRNA (miR)-24, miR-191, and miR-148a was further validated using quantitative real-time PCR. Functional analysis of miR-24 revealed that addition of a mimic miRNA to culture media of morulae embryos resulted in a 27.3% decrease in development to the blastocyst stage. Furthermore, expression of miR-24 was 44.29-fold higher in blastocysts cultured with a miR-24 mimic compared with control blastocysts. Interestingly, the expression of CDKN1b, a target gene of miR-24 was repressed in embryos grown in the presence of the miRNA mimic. Mimic supplementation experiments suggest that miRNA are taken up by the embryo and that extracellular miRNA affect embryonic development. Overall, identification of a rich extracellular milieu in conditioned media sets the framework for future studies to determine the long-term predictive ability of embryo-based miRNA biomarkers on pregnancy outcome.
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Affiliation(s)
- Jenna Kropp
- Department of Animal Sciences, University of Wisconsin, Madison 53706
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin, Madison 53706.
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16
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Chill HH, Dior UP, Kogan L, Revel A. microRNAs and Endometrial Pathophysiology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:143-55. [PMID: 26662990 DOI: 10.1007/978-3-319-22380-3_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Embryo implantation requires a reciprocal interaction between the blastocyst and endometrium and is associated with complex regulatory mechanisms. Since their discovery, microRNAs became prominent candidates providing missing links for many biological pathways. In recent years, microRNAs were implicated as one of the important players in regulation of various biological and physiological endometrial related processes. This chapter aims to present recent knowledge pertaining to the diverse aspects of microRNAs in the embryo-endometrial relationship. We will focus on the role of microRNAs in decidualization and their part in natural and stimulated cycles. Next, we will present recent studies deliberating the role of microRNAs in recurrent pregnancy loss and in the important phenomenon of recurrent implantation failure. Lastly, demonstrating an important aspect of embryo implantation and invasion, we will outline few microRNA related shared pathways of implantation and carcinogenesis.
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Affiliation(s)
- Henry H Chill
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel.
| | - Uri P Dior
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
| | - Liron Kogan
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
| | - Ariel Revel
- Department of Obstetrics and Gynecology, The Hebrew University-Hadassah Medical Center, POB 12272, Jerusalem, 91120, Israel
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17
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MicroRNA and gynecological reproductive diseases. Fertil Steril 2014; 101:1545-51. [PMID: 24882618 DOI: 10.1016/j.fertnstert.2014.04.044] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/29/2014] [Accepted: 04/29/2014] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs estimated to regulate the translation of mRNAs in 30% of all genes in animals by inhibiting translation. Aberrant miRNA expression is associated with many human diseases, including gynecological diseases, cancer, inflammatory diseases, and cardiovascular disorders. Abnormal expression of miRNAs has been observed in multiple human reproductive tract diseases including preeclampsia, endometrioid endometrial adenocarcinoma, uterine leiomyomata, ovarian carcinoma, endometriosis, and recurrent pregnancy loss. In the following review, an update of the role of microRNA and gynecological diseases is performed covering, not only impact of microRNA dysregulation in the origin of each disease, but also showing the potential useful diagnostic and therapeutic tool that miRNA may play in these gynecological pathologies.
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18
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Kropp J, Salih SM, Khatib H. Expression of microRNAs in bovine and human pre-implantation embryo culture media. Front Genet 2014; 5:91. [PMID: 24795753 PMCID: PMC4006060 DOI: 10.3389/fgene.2014.00091] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/03/2014] [Indexed: 01/23/2023] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs which act to regulate expression of genes driving numerous cellular processes. These RNAs are secreted within exosomes from cells into the extracellular environment where they may act as signaling molecules. In addition, they are relatively stable and are specifically expressed in association to certain cancers making them strong candidates as biological markers. Moreover, miRNAs have been detected in body fluids including urine, milk, saliva, semen, and blood plasma. However, it is unknown whether they are secreted by embryonic cells into the culture media. Given that miRNAs are expressed throughout embryonic cellular divisions and embryonic genome activation, we hypothesized that they are secreted from the embryo into the extracellular environment and may play a role in the developmental competence of bovine embryos. To test this hypothesis, bovine embryos were cultured individually from day 5 to day 8 of development in an in vitro fertilization system and gene expression of 5 miRNAs was analyzed in both embryos and culture media. Differential miRNA gene expression was observed between embryos that developed to the blastocyst stage and those that failed to develop from the morula to blastocyst stage, deemed degenerate embryos. MiR-25, miR-302c, miR-196a2, and miR-181a expression was found to be higher in degenerate embryos compared to blastocyst embryos. Interestingly, these miRNAs were also found to be expressed in the culture media of both bovine and human pre-implantation embryos. Overall, our results show for the first time that miRNAs are secreted from pre-implantation embryos into culture media and that miRNA expression may correlate with developmental competence of the embryo. Expression of miRNAs in in vitro culture media could allow for the development of biological markers for selection of better quality embryos and for subsequent successful pregnancy.
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Affiliation(s)
- Jenna Kropp
- Department of Animal Sciences, University of Wisconsin-Madison Madison, WI, USA ; Department of Obstetrics and Gynecology, University of Wisconsin-Madison Madison, WI, USA
| | - Sana M Salih
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison Madison, WI, USA
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin-Madison Madison, WI, USA
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Dong F, Zhang Y, Xia F, Yang Y, Xiong S, Jin L, Zhang J. Genome-wide miRNA profiling of villus and decidua of recurrent spontaneous abortion patients. Reproduction 2014; 148:33-41. [PMID: 24686457 DOI: 10.1530/rep-14-0095] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules of about 22 nucleotides that involved in post-transcriptional gene regulation. Evidence indicates that miRNAs play essential roles in endometriosis, pre-eclampsia, infertility and other reproductive system diseases. However, whether miRNAs are involved in recurrent spontaneous abortion (RSA) is unclear. In this work, we analysed the miRNA expression profiles in six pairs of villus or decidua from RSA patients and normal pregnancy (NP) women using a human miRNA microarray. Some of the chip results were confirmed by RT-qPCR. In the villi of RSA patients, expression of hsa-miR-184, hsa-miR-187 and hsa-miR-125b-2 was significantly higher, while expression of hsa-miR-520f, hsa-miR-3175 and hsa-miR-4672 was significantly lower, comparing with those of NP control. As well, a total of five miRNAs (hsa-miR-517c, hsa-miR-519a-1, hsa-miR-522, hsa-miR-520h and hsa-miR-184) were upregulated in the decidua of RSA patients. The target genes of these differentially expressed miRNAs were predicted by miRWalk, and we speculate a network of miRNA regulating RSA by target genes function on adhesion, apoptosis and angiogenesis. Our study may help clarify the molecular mechanisms which are involved in the progression of RSA, and provide a reference for future research.
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Affiliation(s)
- Fulu Dong
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Yuan Zhang
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Fei Xia
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Yi Yang
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Sidong Xiong
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Liping Jin
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
| | - Jinping Zhang
- Institutes of Biology and Medical SciencesSoochow University, Suzhou, Jiangsu Province 215123, People's Republic of ChinaLaboratory for Reproductive ImmunologyHospital and Institute of Obstetrics and Gynecology, Fudan University Shanghai Medical College, No. 413, Zhaozhou Road, Shanghai 200011, People's Republic of China
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