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Xu X, Yang A, Tian P, Zhang K, Liu Y, Wang Y, Wang Z, Wu Y, Zhao Z, Li Q, Shi B, Huang X, Hao GM. Expression profile analysis of LncRNAs and mRNAs in pre-receptive endometrium of women with polycystic ovary syndrome undergoing in vitro fertilization-embryo transfer. BMC Med Genomics 2024; 17:26. [PMID: 38243290 PMCID: PMC10799537 DOI: 10.1186/s12920-024-01806-w] [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: 02/05/2023] [Accepted: 01/11/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND To compare the expression levels of long non-coding RNA (lncRNA) and messenger RNA (mRNA) in pre-receptive endometrium between patients with Polycystic Ovary Syndrome (PCOS)and normal ovulation undergoing in vitro fertilization-embryo transfer (IVF-ET). METHODS Endometrial tissues were collected with endometrial vacuum curette in pre-receptive phase (3 days after oocytes retrieval) from PCOS and control groups. LncRNAs and mRNAs of endometrium were identified via RNA sequencing and alignments. A subset of 9 differentially expressed lncRNAs and 11 mRNAs were validated by quantitative reverse transcription polymerase chain reaction(qRT-PCR)in 22 PCOS patients and 18 ovulation patients. The function of mRNAs with differential expression patterns were explored using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). RESULTS We found out 687 up-regulated and 680 down-regulated mRNAs, as well as 345 up-regulated and 63 down-regulated lncRNAs in the PCOS patients in contrast to normal ovulation patients. qRT-PCR was used to detect the expression of 11 mRNAs, and validated that the expression of these 6 mRNAs CXCR4, RABL6, OPN3, SYBU, IDH1, NOP10 were significantly elevated among PCOS patients, and the expression of ZEB1 was significantly decreased. qRT-PCR was performed to detect the expression of 9 lncRNAs, and validated that the expression of these 7 lncRNAs IDH1-AS1, PCAT14, FTX, DANCR, PRKCQ-AS1, SNHG8, TPT1-AS1 were significantly enhanced among PCOS patients. Bioinformatics analysis showed that differentially expressed genes (DEGs) involved KEGG pathway were tyrosine metabolism, PI3K-Akt pathway, metabolic pathway, Jak-STAT pathway, pyruvate metabolism, protein processing in endoplasmic reticulum, oxidative phosphorylation and proteasome. The up-regulation of GO classification was involved in ATP metabolic process, oxidative phosphorylation, RNA catabolic process, and down-regulation of GO classification was response to corticosteroid, steroid hormone, and T cell activation. CONCLUSION Our results determined the characteristics and expression profile of endometrial lncRNAs and mRNAs in PCOS patients in pre-receptive phase, which is the day 3 after oocytes retrival. The possible pathways and related genes of endometrial receptivity disorders were found, and those lncRNAs may be developed as a predictive biomarker of endometrium in pre-receptive phase.
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Affiliation(s)
- Xiuhua Xu
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Cardiovascular platform, Institute of Health and Disease, Hebei Medical University, Shijiazhuang, 050000, China
| | - Aimin Yang
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
- Department of Gynecology and Obstetrics, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Pengxiang Tian
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Kun Zhang
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yuanyuan Liu
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yizhuo Wang
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Ziwei Wang
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Yanjing Wu
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Zhiming Zhao
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Qian Li
- Cardiovascular platform, Institute of Health and Disease, Hebei Medical University, Shijiazhuang, 050000, China
| | - Baojun Shi
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Xianghua Huang
- Department of Gynecology and Obstetrics, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
| | - Gui-Min Hao
- Hebei Key Laboratory of Infertility and Genetics, Hebei Clinical Research Center for Birth Defects, Hebei Medical Key Discipline of Reproductive Medicine, Hebei Collaborative Innovation Center of Integrated Traditional and Western Medicine on Reproductive Disease, Department of Reproductive Medicine, Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
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Luo J, Huang R, Xiao P, Xu A, Dong Z, Zhang L, Wu R, Qiu Y, Zhu L, Zhang R, Tang L. Construction of hub transcription factor-microRNAs-messenger RNA regulatory network in recurrent implantation failure. J Assist Reprod Genet 2024; 41:3-13. [PMID: 37878219 PMCID: PMC10789703 DOI: 10.1007/s10815-023-02947-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/14/2023] [Indexed: 10/26/2023] Open
Abstract
PURPOSE Recurrent implantation failure (RIF) affects up to 10% of in vitro fertilization (IVF) patients worldwide. However, the pathogenesis of RIF remains unclear. This study was aimed at identifying hub transcription factors (TFs) of RIF in bioinformatics approaches. METHODS The GSE111974 (mRNA), GSE71332 (miRNA), and GSE103465 (mRNA) datasets were downloaded from the Gene Expression Omnibus database from human endometrial tissue using R version 4.2.1 and used to identify differentially expressed TFs (DETFs), differentially expressed miRNAs, and differentially expressed genes for RIF, respectively. DETFs were subjected to functional enrichment analysis and the protein-protein interaction network analysis using the Search Tool for the Retrieval of Interacting Genes (version 11.5) database. Hub TFs were identified using the cytoHubb plug-in, after which a hub TF-miRNA-mRNA network was constructed using Cytoscape v3.8.2. RESULTS Fifty-seven DETFs were identified, in which Gene Ontology analysis revealed to be mainly involved in the regulation of transcription. Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that DETFs were enriched in transcriptional misregulation in cancer, aldosterone synthesis and secretion, AMPK signaling pathway, and cGMP-PKG signaling pathway. EOMES, NKX2-1, and POU5F1 were identified as hub TFs, and a hub TF-miRNA-mRNA regulatory network was constructed using these three hub TFs, four miRNAs, and four genes. CONCLUSION Collectively, we identified three promising molecular biomarkers for the diagnosis of RIF, which may further be potential therapeutic targets. This study provides novel insights into the molecular mechanisms underlying RIF. However, further experiments are required to verify these results.
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Affiliation(s)
- Jiahuan Luo
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- First Clinical Medical College, Kunming Medical University, Kunming, China
| | - Rongxia Huang
- Department of Gynecology, Kunming Maternal and Child Health Hospital, Kunming, China
| | - Pengying Xiao
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China
| | - Anli Xu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Zhaomei Dong
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Lirong Zhang
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Rui Wu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Yunlin Qiu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China
| | - Li Zhu
- Department of Reproductive Medicine, The First Affiliated Hospital of Dali University, Dali, China.
- Innovation Team in Reproductive Medicine, Dali University, No. 32, Carlsberg Avenue, Dali, Yunnan, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Ruopeng Zhang
- Reproductive Medicine Center, Dongguan Songshan Lake Central Hospital, Dongguan, 523429, China.
- Reproductive Medicine Center, Kunming Maternal and Child Health Hospital, No. 43, Huashan West Road, Huashan Street, Wuhua District, Kunming, China.
| | - Li Tang
- Department of Reproductive Genetics, The First Affiliated Hospital of Kunming Medical University, No. 295, Xichang Road, Wuhua District, Kunming, China.
- First Clinical Medical College, Kunming Medical University, Kunming, China.
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Zheng Y, Pan J, Xia C, Chen H, Zhou H, Ju W, Wegiel J, Myatt L, Roberts JM, Guo X, Zhong N. Characterization of placental and decidual cell development in early pregnancy loss by single-cell RNA sequencing. Cell Biosci 2022; 12:168. [PMID: 36209198 PMCID: PMC9548121 DOI: 10.1186/s13578-022-00904-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022] Open
Abstract
Background Early pregnancy loss (EPL) presents as sporadic or recurrent miscarriage during the first trimester. In addition to chromosomal defects, EPL may result from impairment of the placental-decidual interface at early gestational age due to gene-environmental interactions. Methods To better understand the pathogenesis associated with this impairment, cell development in chorionic villi and decidua of different forms of EPL (sporadic or recurrent) was investigated with single-cell RNA sequencing and compared to that of normal first-trimester tissue. Results Unique gene expression signatures were obtained for the different forms of EPL and for normal tissue and the composition of placental and decidual cell clusters in each form was established. In particular, the involvement of macrophages in the EPL phenotypes was identified revealing an immunoactive state. Conclusion Differential gene expression and unique marker genes among cell clusters from chorionic villi and decidua of miscarried and normal pregnancies, may lead to identification of biomarker for EPL. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00904-5.
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Affiliation(s)
- Yuhua Zheng
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Jing Pan
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Chenglai Xia
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Haiying Chen
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Huadong Zhou
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Weina Ju
- grid.420001.70000 0000 9813 9625New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Jerzy Wegiel
- grid.420001.70000 0000 9813 9625New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
| | - Leslie Myatt
- grid.5288.70000 0000 9758 5690Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239 USA
| | - James M. Roberts
- grid.5288.70000 0000 9758 5690Oregon Health and Science University, 3181 SW Sam Jackson Park Rd, Portland, OR 97239 USA ,grid.460217.60000 0004 0387 4432Department of Obstetrics, Gynecology and Reproductive Sciences, Epidemiology and Clinical and Translational Research University of Pittsburgh, Magee-Womens Research Institute, 204 Craft Avenue, Pittsburgh, PA 15213 USA
| | - Xiaoling Guo
- Maternity and Child Healthcare Hospital, Foshan Women and Children, 11 W. Renmin Lu, Foshan, 528000 China
| | - Nanbert Zhong
- grid.420001.70000 0000 9813 9625New York State Institute for Basic Research in Developmental Disabilities, 1050 Forest Hill Road, Staten Island, NY 10314 USA
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