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Liu H, Wang Z, Li Y, Chen Q, Jiang S, Gao Y, Wang J, Chi Y, Liu J, Wu X, Chen Q, Xiao C, Zhong M, Chen C, Yang X. Hierarchical lncRNA regulatory network in early-onset severe preeclampsia. BMC Biol 2024; 22:159. [PMID: 39075446 PMCID: PMC11287949 DOI: 10.1186/s12915-024-01959-1] [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: 04/12/2023] [Accepted: 07/15/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Recent studies have shown that several long non-coding RNAs (lncRNAs) in the placenta are associated with preeclampsia (PE). However, the extent to which lncRNAs may contribute to the pathological progression of PE is unclear. RESULTS Here, we report a hierarchical regulatory network involved in early-onset severe PE (EOSPE). We have carried out transcriptome sequencing on the placentae from patients and normal subjects to identify the differentially expressed genes (DEGs), including some lncRNAs (DElncRNAs). We then constructed a high-quality hierarchical regulatory network of lncRNAs, transcription factors (TFs), and target DEGs, containing 1851 lncRNA-TF interactions and 6901 TF-promoter interactions. The lncRNA-to-target regulatory interactions were further validated by the triplex structures between the DElncRNAs and the promoters of the target DEGs. The DElncRNAs in the regulatory network were clustered into 3 clusters, one containing DElncRNAs correlated with the blood pressure, including FLNB-AS1 with targeting 27.89% (869/3116) DEGs in EOSPE. We further demonstrated that FLNB-AS1 could bind the transcription factor JUNB to regulate a series members of the HIF-1 signaling pathway in trophoblast cells. CONCLUSIONS Our results suggest that the differential expression of lncRNAs may perturb the lncRNA-TF-DEG hierarchical regulatory network, leading to the dysregulation of many genes involved in EOSPE. Our study provides a new strategy and a valuable resource for studying the mechanism underlying gene dysregulation in EOSPE patients.
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Affiliation(s)
- Haihua Liu
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Zhijian Wang
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yanjun Li
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Qian Chen
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Sijia Jiang
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yue Gao
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jing Wang
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Yali Chi
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jie Liu
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xiaoli Wu
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Qiong Chen
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Chaoqun Xiao
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Mei Zhong
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Chunlin Chen
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Xinping Yang
- Center for Genetics and Developmental Systems Biology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Obstetrics & Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Key Laboratory of Psychiatric Disorders, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Department of Psychology, School of Public Health, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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2
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Chen H, Li T, Gao R, Cheng M, Zhang Q, Liu X, Chen M, Liao X, Qin L. RNA editing landscape of adipose tissue in polycystic ovary syndrome provides insight into the obesity-related immune responses. Front Endocrinol (Lausanne) 2024; 15:1379293. [PMID: 38978626 PMCID: PMC11229675 DOI: 10.3389/fendo.2024.1379293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/03/2024] [Indexed: 07/10/2024] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is the most common reproductive-endocrine disorder with wide-ranging metabolic implications, including obesity. RNA editing, a post-transcriptional modification, can fine-tune protein function and introduce heterogeneity. However, the role of RNA editing and its impact on adipose tissue function in PCOS remain poorly understood. Methods This study aimed to comprehensively analyze RNA-editing events in abdominal and subcutaneous adipose tissue of PCOS patients and healthy controls using high-throughput whole-genome sequencing (WGS) and RNA sequencing. Results Our results revealed that PCOS patients exhibited more RNA-editing sites, with adenosine-to-inosine (A-to-I) editing being prevalent. The expression of ADAR genes, responsible for A-to-I editing, was also higher in PCOS. Aberrant RNA-editing sites in PCOS adipose tissue was enriched in immune responses, and interleukin-12 biosynthetic process. Tumor necrosis factor (TNF) signaling, nuclear factor kappa B (NF-κB) signaling, Notch signaling, terminal uridylyl transferase 4 (TUT4), hook microtubule tethering protein 3 (HOOK3), and forkhead box O1 (FOXO1) were identified to be of significant differences. Differentially expressed genes (DEGs) in PCOS adipose tissue were enriched in immune responses compared with controls, and the DEGs between subcutaneous and abdominal adipose tissue were also enriched in immune responses suggesting the important role of subcutaneous adipose tissue. Furthermore, we identified the correlations between RNA editing levels and RNA expression levels of specific genes, such as ataxia-telangiectasia mutated (ATM) and mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) in inflammation pathways and ATM, TUT4, and YTH N6-methyladenosine RNA-binding protein C2 (YTHDC2) in oocyte development pathway. Conclusions These findings suggest that RNA-editing dysregulation in PCOS adipose tissue may contribute to inflammatory dysregulations. Understanding the interplay between RNA editing and adipose tissue function may unveil potential therapeutic targets for PCOS management. However, further research and validation are required to fully elucidate the molecular mechanisms underlying these associations.
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Affiliation(s)
- Hanxiao Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Tongtong Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Department of Physiology School of Basic Medical Sciences, Cheeloo College of Medicine Shandong University, Jinan, Shandong, China
| | - Rui Gao
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- The Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Meng Cheng
- Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Qiong Zhang
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Xiumei Liu
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Mingli Chen
- Department of Obstetrics and Gynecology, Sichuan Province Ziyang Maternal and Child Health Care Hospital, Ziyang, China
| | - Xin Liao
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- Department of Operation Room, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lang Qin
- Key Laboratory of Birth Defects and Related of Women and Children of Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
- The Reproductive Medical Center, Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China
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Gong X, He W, Jin W, Ma H, Wang G, Li J, Xiao Y, Zhao Y, Chen Q, Guo H, Yang J, Qi Y, Dong W, Fu M, Li X, Liu J, Liu X, Yin A, Zhang Y, Wei Y. Disruption of maternal vascular remodeling by a fetal endoretrovirus-derived gene in preeclampsia. Genome Biol 2024; 25:117. [PMID: 38715110 PMCID: PMC11075363 DOI: 10.1186/s13059-024-03265-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Preeclampsia, one of the most lethal pregnancy-related diseases, is associated with the disruption of uterine spiral artery remodeling during placentation. However, the early molecular events leading to preeclampsia remain unknown. RESULTS By analyzing placentas from preeclampsia, non-preeclampsia, and twin pregnancies with selective intrauterine growth restriction, we show that the pathogenesis of preeclampsia is attributed to immature trophoblast and maldeveloped endothelial cells. Delayed epigenetic reprogramming during early extraembryonic tissue development leads to generation of excessive immature trophoblast cells. We find reduction of de novo DNA methylation in these trophoblast cells results in selective overexpression of maternally imprinted genes, including the endoretrovirus-derived gene PEG10 (paternally expressed gene 10). PEG10 forms virus-like particles, which are transferred from the trophoblast to the closely proximate endothelial cells. In normal pregnancy, only a low amount of PEG10 is transferred to maternal cells; however, in preeclampsia, excessive PEG10 disrupts maternal vascular development by inhibiting TGF-beta signaling. CONCLUSIONS Our study reveals the intricate epigenetic mechanisms that regulate trans-generational genetic conflict and ultimately ensure proper maternal-fetal interface formation.
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Affiliation(s)
- Xiaoli Gong
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Wei He
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wan Jin
- Euler Technology, Beijing, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongwei Ma
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Gang Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiaxin Li
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | - Yu Xiao
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
- Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
- Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yangyu Zhao
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
| | | | | | - Jiexia Yang
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yiming Qi
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wei Dong
- Maternity Ward, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Meng Fu
- Department of Obstetrics and Gynecology, Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiaojuan Li
- Euler Technology, Beijing, China
- Present Address: International Max Planck Research School for Genome Science, and University of Göttingen, Göttingen Center for Molecular Biosciences, Göttingen, Germany
| | | | - Xinghui Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, China.
- Department Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Aihua Yin
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, China.
| | - Yi Zhang
- Euler Technology, Beijing, China.
| | - Yuan Wei
- Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.
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4
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Azmi MB, Nasir MF, Asif U, Kazi M, Uddin MN, Qureshi SA. Analyzing molecular signatures in preeclampsia and fetal growth restriction: Identifying key genes, pathways, and therapeutic targets for preterm birth. Front Mol Biosci 2024; 11:1384214. [PMID: 38712342 PMCID: PMC11070483 DOI: 10.3389/fmolb.2024.1384214] [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: 02/08/2024] [Accepted: 03/22/2024] [Indexed: 05/08/2024] Open
Abstract
Background Intrauterine growth restriction (IUGR) and preeclampsia (PE) are intricately linked with specific maternal health conditions, exhibit shared placental abnormalities, and play pivotal roles in precipitating preterm birth (PTB) incidences. However, the molecular mechanism underlying the association between PE and IUGR has not been determined. Therefore, we aimed to analyze the data of females with PE and those with PE + IUGR to identify the key gene(s), their molecular pathways, and potential therapeutic interactions. Methods In this study, a comprehensive relationship analysis of both PE and PE + IUGR was conducted using RNA sequence datasets. Using two datasets (GSE148241 and GSE114691), differential gene expression analysis via DESeq2 through R-programming was performed. Gene set enrichment analysis was performed using ClusterProfiler, protein‒protein interaction (PPI) networks were constructed, and cluster analyses were conducted using String and MCODE in Cytoscape. Functional enrichment analyses of the resulting subnetworks were performed using ClueGO software. The hub genes were identified under both conditions using the CytoHubba method. Finally, the most common hub protein was docked against a library of bioactive flavonoids and PTB drugs using the PyRx AutoDock tool, followed by molecular dynamic (MD) simulation analysis. Pharmacokinetic analysis was performed to determine the ADMET properties of the compounds using pkCSM. Results We identified eight hub genes highly expressed in the case of PE, namely, PTGS2, ENG, KIT, MME, CGA, GAPDH, GPX3, and P4HA1, and the network of the PE + IUGR gene set demonstrated that nine hub genes were overexpressed, namely, PTGS2, FGF7, FGF10, IL10, SPP1, MPO, THBS1, CYBB, and PF4. PTGS2 was the most common hub gene found under both conditions (PE and PEIUGR). Moreover, the greater (-9.1 kcal/mol) molecular binding of flavoxate to PTGS2 was found to have satisfactory pharmacokinetic properties compared with those of other compounds. The flavoxate-bound PTGS2 protein complex remained stable throughout the simulation; with a ligand fit to protein, i.e., a RMSD ranging from ∼2.0 to 4.0 Å and a RMSF ranging from ∼0.5 to 2.9 Å, was observed throughout the 100 ns analysis. Conclusion The findings of this study may be useful for treating PE and IUGR in the management of PTB.
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Affiliation(s)
- Muhammad Bilal Azmi
- Computational Biochemistry Research Laboratory, Department of Biochemistry, Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan
| | - Mushyeda Fatima Nasir
- Department of Biosciences, Faculty of Life Sciences, Mohammad Ali Jinnah University, Karachi, Pakistan
| | - Uzma Asif
- Department of Biochemistry, Medicine Program, Batterjee Medical College, Jeddah, Saudi Arabia
| | - Mohsin Kazi
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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Fitzgerald E, Shen M, Yong HEJ, Wang Z, Pokhvisneva I, Patel S, O'Toole N, Chan SY, Chong YS, Chen H, Gluckman PD, Chan J, Lee PKM, Meaney MJ. Hofbauer cell function in the term placenta associates with adult cardiovascular and depressive outcomes. Nat Commun 2023; 14:7120. [PMID: 37963865 PMCID: PMC10645763 DOI: 10.1038/s41467-023-42300-8] [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: 11/24/2022] [Accepted: 10/05/2023] [Indexed: 11/16/2023] Open
Abstract
Pathological placental inflammation increases the risk for several adult disorders, but these mediators are also expressed under homeostatic conditions, where their contribution to adult health outcomes is unknown. Here we define an inflammation-related expression signature, primarily expressed in Hofbauer cells of the term placenta and use expression quantitative trait loci to create a polygenic score (PGS) predictive of its expression. Using this PGS in the UK Biobank we conduct a phenome-wide association study, followed by Mendelian randomization and identify protective, sex-dependent effects of the placental module on cardiovascular and depressive outcomes. Genes differentially regulated by intra-amniotic infection and preterm birth are over-represented within the module. We also identify aspirin as a putative modulator of this inflammation-related signature. Our data support a model where disruption of placental Hofbauer cell function, due to preterm birth or prenatal infection, contributes to the increased risk of depression and cardiovascular disease observed in these individuals.
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Affiliation(s)
- Eamon Fitzgerald
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montréal, Canada.
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, Canada.
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada.
| | - Mojun Shen
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore
| | - Hannah Ee Juen Yong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore
| | - Zihan Wang
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada
| | - Irina Pokhvisneva
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada
| | - Sachin Patel
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada
| | - Nicholas O'Toole
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montréal, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montréal, Canada
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Helen Chen
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke-National University of Singapore, Singapore, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore
- The University of Auckland, Auckland, New Zealand
| | - Jerry Chan
- KK Women's and Children's Hospital, Singapore, Singapore
- Duke-National University of Singapore, Singapore, Singapore
| | - Patrick Kia Ming Lee
- Brain - Body Initiative, Agency for Science, Technology & Research, Singapore, Singapore
| | - Michael J Meaney
- Sackler Program for Epigenetics and Psychobiology, McGill University, Montréal, Canada.
- Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montréal, Canada.
- Singapore Institute for Clinical Sciences, Agency for Science, Technology & Research, Singapore, Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Brain - Body Initiative, Agency for Science, Technology & Research, Singapore, Singapore.
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6
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Gao Y, Wu Z, Liu S, Chen Y, Zhao G, Lin HP. Identification of key genes in the pathogenesis of preeclampsia via bioinformatic analysis and experimental verification. Front Endocrinol (Lausanne) 2023; 14:1190012. [PMID: 37576963 PMCID: PMC10420078 DOI: 10.3389/fendo.2023.1190012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Background Preeclampsia (PE) is the primary cause of perinatal maternal-fetal mortality and morbidity. The exact molecular mechanisms of PE pathogenesis are largely unknown. This study aims to identify the hub genes in PE and explore their potential molecular regulatory network. Methods We downloaded the GSE148241, GSE190971, GSE74341, and GSE114691 datasets for the placenta and performed a differential expression analysis to identify hub genes. We performed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO), Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) Analysis to determine functional roles and regulatory networks of differentially expressed genes (DEGs). We then verified the DEGs at transcriptional and translational levels by analyzing the GSE44711 and GSE177049 datasets and our clinical samples, respectively. Results We identified 60 DEGs in the discovery phase, consisting of 7 downregulated genes and 53 upregulated genes. We then identified seven hub genes using Cytoscape software. In the verification phase, 4 and 3 of the seven genes exhibited the same variation patterns at the transcriptional level in the GSE44711 and GSE177049 datasets, respectively. Validation of our clinical samples showed that CADM3 has the best discriminative performance for predicting PE. Conclusion These findings may enhance the understanding of PE and provide new insight into identifying potential therapeutic targets for PE.
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Affiliation(s)
- Yongqi Gao
- Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Key Laboratory of Cardiovascular Diseases, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhongji Wu
- Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Key Laboratory of Cardiovascular Diseases, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Simin Liu
- Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Key Laboratory of Cardiovascular Diseases, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Yiwen Chen
- Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Key Laboratory of Cardiovascular Diseases, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Guojun Zhao
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan City People’s Hospital, Qingyuan, Guangdong, China
| | - Hui-Ping Lin
- Department of Basic Medical Research, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Key Laboratory of Cardiovascular Diseases, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
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7
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Ackerman WE, Buhimschi CS, Brown TL, Zhao G, Summerfield TL, Buhimschi IA. Transcriptomics-Based Subphenotyping of the Human Placenta Enabled by Weighted Correlation Network Analysis in Early-Onset Preeclampsia With and Without Fetal Growth Restriction. Hypertension 2023; 80:1363-1374. [PMID: 36987911 PMCID: PMC10192030 DOI: 10.1161/hypertensionaha.122.20807] [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: 12/14/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023]
Abstract
BACKGROUND Placental disorders contribute to pregnancy complications, including preeclampsia and fetal growth restriction (FGR), but debate regarding their specific pathobiology persists. Our objective was to apply transcriptomics with weighted gene correlation network analysis to further clarify the placental dysfunction in these conditions. METHODS We performed RNA sequencing with weighted gene correlation network analysis using human placental samples (n=30), separated into villous tissue and decidua basalis, and clinically grouped as follows: (1) early-onset preeclampsia (EOPE)+FGR (n=7); (2) normotensive, nonanomalous preterm FGR (n=5); (2) EOPE without FGR (n=8); (4) spontaneous idiopathic preterm birth (n=5) matched for gestational age; and (5) uncomplicated term births (n=5). Our data was compared with RNA sequencing data sets from public databases (GSE114691, GSE148241, and PRJEB30656; n=130 samples). RESULTS We identified 14 correlated gene modules in our specimens, of which most were significantly correlated with birthweight and maternal blood pressure. Of the 3 network modules consistently predictive of EOPE±FGR across data sets, we prioritized a coexpression gene group enriched for hypoxia-response and metabolic pathways for further investigation. Cluster analysis based on transcripts from this module and the glycolysis/gluconeogenesis metabolic pathway consistently distinguished a subset of EOPE±FGR samples with an expression signature suggesting modified tissue bioenergetics. We demonstrated that the expression ratios of LDHA/LDHB and PDK1/GOT1 could be used as surrogate indices for the larger panels of genes in identifying this subgroup. CONCLUSIONS We provide novel evidence for a molecular subphenotype consistent with a glycolytic metabolic shift that occurs more frequently but not universally in placental specimens of EOPE±FGR.
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Affiliation(s)
- William E. Ackerman
- University of Illinois College of Medicine - Chicago, Chicago, IL 60612, USA
| | | | - Thomas L. Brown
- Wright State University Boonshoft School of Medicine, Dayton, OH 45435, USA
| | - Guomao Zhao
- University of Illinois College of Medicine - Chicago, Chicago, IL 60612, USA
| | | | - Irina A. Buhimschi
- University of Illinois College of Medicine - Chicago, Chicago, IL 60612, USA
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Wang L, Yuan X, Zhou X. Expression pattern and clinical significance of microRNA-let-7a and IFN-gamma in placental tissue of patients with preeclampsia with severe features. J Perinat Med 2022; 50:1142-1149. [PMID: 35596257 DOI: 10.1515/jpm-2021-0133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 04/03/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Preeclampsia with severe features (PECsf) is a common disease in pregnant women. let-7a and IFN-gamma (interferon-gamma) are involved in diagnosis and prognosis of preeclampsia. This study explored effects of let-7a and IFN-gamma on PECsf patients. METHODS The placental tissue of 21 PECsf, 19 preeclampsia without severe features (PEC), and 20 normal pregnant women were collected, and clinical data were recorded. let-7a and IFN-gamma expressions in placental tissue were detected. The correlation between let-7a/IFN-gamma expression and clinical indexes was analyzed. According to let-7a and IFN-gamma expressions, PECsf patients were assigned into Hlet-7a group (let-7a high expression group), Llet-7a group (let-7a low expression group), HIFN-gamma group (IFN-gamma high expression group) and LIFN-gamma group (IFN-gamma low expression group). The incidence of adverse prognosis was compared. RESULTS let-7a and IFN-gamma were highly expressed in placental tissue of preeclampsia patients, with significant differences between PEC and PECsf. The high expressions of let-7a and IFN-gamma were positively correlated with mean arterial pressure, lactate dehydrogenase, and 24 h urinary protein in placental tissues of PECsf patients. High let-7a and IFN-gamma expressions were correlated with adverse outcomes of PECsf. CONCLUSIONS High let-7a and IFN-gamma expressions were correlated with clinical features, and could be used as biomarkers for treatment and poor prognosis of PECsf.
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Affiliation(s)
- Liping Wang
- Department of Obstetrics and Gynecology, Daqing Longnan Hospital, Daqing, Heilongjiang, P.R. China
| | - Xiaojie Yuan
- Department of Obstetrics and Gynecology, Daqing Longnan Hospital, Daqing, Heilongjiang, P.R. China
| | - Xuewu Zhou
- Department of Obstetrics and Gynecology, Daqing Longnan Hospital, Daqing, Heilongjiang, P.R. China
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9
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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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10
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Mani S, Ghosh J, Rhon-Calderon EA, Lan Y, Ord T, Kalliora C, Chan J, Schultz B, Vaughan-Williams E, Coutifaris C, Sapienza C, Senapati S, Bartolomei MS, Mainigi M. Embryo cryopreservation leads to sex-specific DNA methylation perturbations in both human and mouse placentas. Hum Mol Genet 2022; 31:3855-3872. [PMID: 35717573 PMCID: PMC9652110 DOI: 10.1093/hmg/ddac138] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/25/2022] Open
Abstract
In vitro fertilization (IVF) is associated with DNA methylation abnormalities and a higher incidence of adverse pregnancy outcomes. However, which exposure(s), among the many IVF interventions, contributes to these outcomes remains unknown. Frozen embryo transfer (ET) is increasingly utilized as an alternative to fresh ET, but reports suggest a higher incidence of pre-eclampsia and large for gestational age infants. This study examines DNA methylation in human placentas using the 850K Infinium MethylationEPIC BeadChip array obtained after 65 programmed frozen ET cycles, 82 fresh ET cycles and 45 unassisted conceptions. Nine patients provided placentas following frozen and fresh ET from consecutive pregnancies for a paired subgroup analysis. In parallel, eight mouse placentas from fresh and frozen ET were analyzed using the Infinium Mouse Methylation BeadChip array. Human and mouse placentas were significantly hypermethylated after frozen ET compared with fresh. Paired analysis showed similar trends. Sex-specific analysis revealed that these changes were driven by male placentas in humans and mice. Frozen and fresh ET placentas were significantly different from controls, with frozen samples hypermethylated compared with controls driven by males and fresh samples being hypomethylated compared with controls, driven by females. Sexually dimorphic epigenetic changes could indicate differential susceptibility to IVF-associated perturbations, which highlights the importance of sex-specific evaluation of adverse outcomes. Similarities between changes in mice and humans underscore the suitability of the mouse model in evaluating how IVF impacts the epigenetic landscape, which is valuable given limited access to human tissue and the ability to isolate specific interventions in mice.
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Affiliation(s)
- Sneha Mani
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jayashri Ghosh
- Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Eric A Rhon-Calderon
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yemin Lan
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Teri Ord
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charikleia Kalliora
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joe Chan
- Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Bryant Schultz
- Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Elaine Vaughan-Williams
- Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Carmen Sapienza
- Cancer and Cellular Biology, Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
| | - Suneeta Senapati
- Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Center for Research on Reproduction and Women’s Health, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Monica Mainigi
- To whom correspondence should be addressed at: Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, 3701 Market Street, 8th floor, Philadelphia, PA 19104, USA. Tel: +1 2156622972; Fax: +1 2153495512;
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11
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Zhou T, Wang W, Qi T, Ma S, Lu W. Expression and significance of let-7a and tumor necrosis factor-alpha in placenta of severe preeclampsia. J Matern Fetal Neonatal Med 2021; 35:7363-7367. [PMID: 34284684 DOI: 10.1080/14767058.2021.1949276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To investigate the expression and clinical significance of let-7a and tumor necrosis factor-alpha (TNF-α) in placental tissue of patients with severe preeclampsia (SPE). METHODS From January 2018 to October 2019, 64 cases of puerperal delivery at the First People's Hospital of Lianyungang City, 44 cases of SPE (SPE group), and 20 cases of healthy pregnant women (NC group) were selected. QRT-PCR and Western-blot were used to detect the expression levels of let-7a, TNF-αmRNA, and protein in the two groups of placental tissues. The correlation and the clinical significance of the two were statistically analyzed. RESULTS The relative expression of let-7a in the SPE group was significantly lower than that in the control group (0.06 ± 0.02 versus 0.25 ± 0.04, p < .05); the expression of TNF-αmRNA in the SPE group was significantly higher than that in the control group (0.48 ± 0.04 versus 0.17 ± 0.03, p < .05); TNF-α protein expression was significantly increased in the SPE group (1.09 ± 0.12 versus 0.56 ± 0.03, p < .05); let-7a and TNF-α were significantly negatively correlated (r = -0.41, p < .05); the blood pressure and birth weight of the pregnant women in the SPE group and the control group were significantly different [systolic blood pressure (164.27 ± 4.62) mmHg versus (125.01 ± 2.23)] mmHg, diastolic blood pressure (109.24 ± 2.97) mmHg versus (75.94 ± 2.74) mmHg, neonatal birth weight (2507.02 ± 161.46) g versus (3592.12 ± 153.05) g, p < .05]; the expression of TNF-α in placental tissue of SPE group was significantly positively correlated with systolic and diastolic blood pressure (r = 0.93 and 0.89, p < .05). CONCLUSION let-7a may participate in the occurrence and development of SPE by negatively regulating the expression of TNF-α.
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Affiliation(s)
- Tiantian Zhou
- Department of Obstetrics, Lianyungang First People's Hospital, Lianyungang, China
| | - Weijun Wang
- Department of Obstetrics, Lianyungang First People's Hospital, Lianyungang, China
| | - Ting Qi
- Department of Obstetrics, Lianyungang First People's Hospital, Lianyungang, China
| | - Shanduo Ma
- Department of Obstetrics, Lianyungang First People's Hospital, Lianyungang, China
| | - Wei Lu
- Department of Obstetrics, Lianyungang First People's Hospital, Lianyungang, China
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Naismith K, Cox B. Human placental gene sets improve analysis of placental pathologies and link trophoblast and cancer invasion genes. Placenta 2021; 112:9-15. [PMID: 34237528 DOI: 10.1016/j.placenta.2021.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/23/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Interpretation of gene expression uses set enrichment or overrepresentation methods that depend on sets of annotated genes, such as the popular Gene Ontology. The placenta is understudied relative to other major organs creating a deficit of molecular and functional knowledge about this organ. The lack of placental and trophoblast research significantly impacts our ability to interpret the results of high throughput experiments. METHODS Gene sets were generated by a semi-automated re-analysis of 330 microarray and 91 RNA sequencing experiments involving placental and trophoblast samples, excluding those related to pathology. Microarray data was obtained from the Gene Expression Omnibus and processed using the R package limma. RNA-sequencing data was extracted from the short read archive and processed using Kallisto and limma. The workflow consisted of quality control for experimental design and data. Sets were generated by pairwise differential expression with a maximum of 200 genes per set. RESULTS We created 235 human placenta and trophoblast specific gene sets and found unique subnetworks relative to Gene Ontology. We applied these new placental gene sets to the investigation of preeclampsia and fetal growth restriction as well as invasive tumors and cell models finding matching terms related to cell types and oxygen tension (hypoxia). DISCUSSION The human placental gene sets provide an improved context for interpretation of high throughput gene expression studies on placental pathologies beyond the Gene Ontology. Significant enrichment of placental gene sets to cancer samples and cell models indicates a utility beyond applications to placental and trophoblast cells.
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Affiliation(s)
- Kendra Naismith
- Department of Physiology, University of Toronto, Toronto, Canada
| | - Brian Cox
- Department of Physiology, University of Toronto, Toronto, Canada; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Canada.
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