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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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Li X, Liu L, Whitehead C, Li J, Thierry B, Le TD, Winter M. OUP accepted manuscript. Brief Funct Genomics 2022; 21:296-309. [PMID: 35484822 PMCID: PMC9328024 DOI: 10.1093/bfgp/elac006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 11/24/2022] Open
Abstract
Preeclampsia is a pregnancy-specific disease that can have serious effects on the health of both mothers and their offspring. Predicting which women will develop preeclampsia in early pregnancy with high accuracy will allow for improved management. The clinical symptoms of preeclampsia are well recognized, however, the precise molecular mechanisms leading to the disorder are poorly understood. This is compounded by the heterogeneous nature of preeclampsia onset, timing and severity. Indeed a multitude of poorly defined causes including genetic components implicates etiologic factors, such as immune maladaptation, placental ischemia and increased oxidative stress. Large datasets generated by microarray and next-generation sequencing have enabled the comprehensive study of preeclampsia at the molecular level. However, computational approaches to simultaneously analyze the preeclampsia transcriptomic and network data and identify clinically relevant information are currently limited. In this paper, we proposed a control theory method to identify potential preeclampsia-associated genes based on both transcriptomic and network data. First, we built a preeclampsia gene regulatory network and analyzed its controllability. We then defined two types of critical preeclampsia-associated genes that play important roles in the constructed preeclampsia-specific network. Benchmarking against differential expression, betweenness centrality and hub analysis we demonstrated that the proposed method may offer novel insights compared with other standard approaches. Next, we investigated subtype specific genes for early and late onset preeclampsia. This control theory approach could contribute to a further understanding of the molecular mechanisms contributing to preeclampsia.
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Affiliation(s)
- Xiaomei Li
- UniSA STEM, University of South Australia, Mawson Lakes, 5095, SA, Australia
| | - Lin Liu
- UniSA STEM, University of South Australia, Mawson Lakes, 5095, SA, Australia
| | - Clare Whitehead
- Pregnancy Research Centre, Dept of Obstetrics & Gynaecology, University of Melbourne, Royal Women’s Hospital, Melbourne, 3052, VIC, Australia
| | - Jiuyong Li
- UniSA STEM, University of South Australia, Mawson Lakes, 5095, SA, Australia
| | - Benjamin Thierry
- Future Industries Institute, University of South Australia, Mawson Lakes, 5095, SA, Australia
| | - Thuc D Le
- Corresponding authors: Thuc D. Le, UniSA STEM, University of South Australia, Mawson Lakes, 5095, SA, Australia. E-mail: ; M. Winter, Future Industries Institute, University of South Australia, Mawson Lakes, 5095, SA, Australia. E-mail:
| | - Marnie Winter
- Corresponding authors: Thuc D. Le, UniSA STEM, University of South Australia, Mawson Lakes, 5095, SA, Australia. E-mail: ; M. Winter, Future Industries Institute, University of South Australia, Mawson Lakes, 5095, SA, Australia. E-mail:
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Tarca AL, Romero R, Erez O, Gudicha DW, Than NG, Benshalom-Tirosh N, Pacora P, Hsu CD, Chaiworapongsa T, Hassan SS, Gomez-Lopez N. Maternal whole blood mRNA signatures identify women at risk of early preeclampsia: a longitudinal study. J Matern Fetal Neonatal Med 2021; 34:3463-3474. [PMID: 31900005 PMCID: PMC10544754 DOI: 10.1080/14767058.2019.1685964] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 12/16/2022]
Abstract
PURPOSE To determine whether previously established mRNA signatures are predictive of early preeclampsia when evaluated by maternal cellular transcriptome analysis in samples collected before clinical manifestation. MATERIALS AND METHODS We profiled gene expression at exon-level resolution in whole blood samples collected longitudinally from 49 women with normal pregnancy (controls) and 13 with early preeclampsia (delivery <34 weeks of gestation). After preprocessing and removal of gestational age-related trends in gene expression, data were converted into Z-scores based on the mean and standard deviation among controls for six gestational-age intervals. The average Z-scores of mRNAs in each previously established signature considered herein were compared between cases and controls at 9-11, 11-17, 17-22, 22-28, 28-32, and 32-34 weeks of gestation.Results: (1) Average expression of the 16-gene untargeted cellular mRNA signature was higher in women diagnosed with early preeclampsia at 32-34 weeks of gestation, yet more importantly, also prior to diagnosis at 28-32 weeks and 22-28 weeks of gestation, compared to controls (all, p < .05). (2) A combination of four genes from this signature, including a long non-protein coding RNA [H19 imprinted maternally expressed transcript (H19)], fibronectin 1 (FN1), tubulin beta-6 class V (TUBB6), and formyl peptide receptor 3 (FPR3) had a sensitivity of 0.85 (0.55-0.98) and a specificity of 0.92 (0.8-0.98) for prediction of early preeclampsia at 22-28 weeks of gestation. (3) H19, FN1, and TUBB6 were increased in women with early preeclampsia as early as 11-17 weeks of gestation (all, p < .05). (4) After diagnosis at 32-34 weeks, but also prior to diagnosis at 11-17 weeks, women destined to have early preeclampsia showed a coordinated increase in whole blood expression of several single-cell placental signatures, including the 20-gene signature of extravillous trophoblast (all, p < .05). (5) A combination of three mRNAs from the extravillous trophoblast signature (MMP11, SLC6A2, and IL18BP) predicted early preeclampsia at 11-17 weeks of gestation with a sensitivity of 0.83 (0.52-0.98) and specificity of 0.94 (0.79-0.99). CONCLUSIONS Circulating early transcriptomic markers for preeclampsia can be found either by untargeted profiling of the cellular transcriptome or by focusing on placental cell-specific mRNAs. The untargeted cellular mRNA signature was consistently increased in early preeclampsia after 22 weeks of gestation, and individual mRNAs of this signature were significantly increased as early as 11-17 weeks of gestation. Several single-cell placental signatures predicted future development of the disease at 11-17 weeks and were also increased in women already diagnosed at 32-34 weeks of gestation.
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Affiliation(s)
- Adi L. Tarca
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Computer Science, Wayne State University College of Engineering, Detroit, Michigan, USA
| | - Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan, USA
- Detroit Medical Center, Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - Offer Erez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Maternity Department “D,” Division of Obstetrics and Gynecology, Soroka University Medical Center, School of Medicine, Faculty of Health Sciences, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Dereje W. Gudicha
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
| | - Nandor Gabor Than
- Systems Biology of Reproduction Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
- First Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Maternity Private Department, Kutvolgyi Clinical Block, Semmelweis University, Budapest, Hungary
| | - Neta Benshalom-Tirosh
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Percy Pacora
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Chaur-Dong Hsu
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Tinnakorn Chaiworapongsa
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Sonia S. Hassan
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, Michigan, USA
- Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, and Detroit, Michigan, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, Michigan, USA
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, Michigan, USA
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Yong HEJ, Chan SY. Current approaches and developments in transcript profiling of the human placenta. Hum Reprod Update 2021; 26:799-840. [PMID: 33043357 PMCID: PMC7600289 DOI: 10.1093/humupd/dmaa028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The placenta is the active interface between mother and foetus, bearing the molecular marks of rapid development and exposures in utero. The placenta is routinely discarded at delivery, providing a valuable resource to explore maternal-offspring health and disease in pregnancy. Genome-wide profiling of the human placental transcriptome provides an unbiased approach to study normal maternal–placental–foetal physiology and pathologies. OBJECTIVE AND RATIONALE To date, many studies have examined the human placental transcriptome, but often within a narrow focus. This review aims to provide a comprehensive overview of human placental transcriptome studies, encompassing those from the cellular to tissue levels and contextualize current findings from a broader perspective. We have consolidated studies into overarching themes, summarized key research findings and addressed important considerations in study design, as a means to promote wider data sharing and support larger meta-analysis of already available data and greater collaboration between researchers in order to fully capitalize on the potential of transcript profiling in future studies. SEARCH METHODS The PubMed database, National Center for Biotechnology Information and European Bioinformatics Institute dataset repositories were searched, to identify all relevant human studies using ‘placenta’, ‘decidua’, ‘trophoblast’, ‘transcriptome’, ‘microarray’ and ‘RNA sequencing’ as search terms until May 2019. Additional studies were found from bibliographies of identified studies. OUTCOMES The 179 identified studies were classifiable into four broad themes: healthy placental development, pregnancy complications, exposures during pregnancy and in vitro placental cultures. The median sample size was 13 (interquartile range 8–29). Transcriptome studies prior to 2015 were predominantly performed using microarrays, while RNA sequencing became the preferred choice in more recent studies. Development of fluidics technology, combined with RNA sequencing, has enabled transcript profiles to be generated of single cells throughout pregnancy, in contrast to previous studies relying on isolated cells. There are several key study aspects, such as sample selection criteria, sample processing and data analysis methods that may represent pitfalls and limitations, which need to be carefully considered as they influence interpretation of findings and conclusions. Furthermore, several areas of growing importance, such as maternal mental health and maternal obesity are understudied and the profiling of placentas from these conditions should be prioritized. WIDER IMPLICATIONS Integrative analysis of placental transcriptomics with other ‘omics’ (methylome, proteome and metabolome) and linkage with future outcomes from longitudinal studies is crucial in enhancing knowledge of healthy placental development and function, and in enabling the underlying causal mechanisms of pregnancy complications to be identified. Such understanding could help in predicting risk of future adversity and in designing interventions that can improve the health outcomes of both mothers and their offspring. Wider collaboration and sharing of placental transcriptome data, overcoming the challenges in obtaining sufficient numbers of quality samples with well-defined clinical characteristics, and dedication of resources to understudied areas of pregnancy will undoubtedly help drive the field forward.
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Affiliation(s)
- Hannah E J Yong
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
| | - Shiao-Yng Chan
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Serebrova VN, Trifonova EA, Stepanov VA. Natural Selection as a Driver for the Genetic Component of Preeclampsia. Mol Biol 2021. [DOI: 10.1134/s0026893321020308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ren Z, Gao Y, Gao Y, Liang G, Chen Q, Jiang S, Yang X, Fan C, Wang H, Wang J, Shi YW, Xiao C, Zhong M, Yang X. Distinct placental molecular processes associated with early-onset and late-onset preeclampsia. Am J Cancer Res 2021; 11:5028-5044. [PMID: 33754042 PMCID: PMC7978310 DOI: 10.7150/thno.56141] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Patients with preeclampsia display a spectrum of onset time and severity of clinical presentation, yet the underlying molecular bases for the early-onset and late-onset clinical subtypes are not known. Although several transcriptome studies have been done on placentae from PE patients, only a small number of differentially expressed genes have been identified due to very small sample sizes and no distinguishing of clinical subtypes. Methods: We carried out RNA-seq on 65 high-quality placenta samples, including 33 from 30 patients and 32 from 30 control subjects, to search for dysregulated genes and the molecular network and pathways they are involved in. Results: We identified two functionally distinct sets of dysregulated genes in the two major subtypes: 2,977 differentially expressed genes in early-onset severe preeclampsia, which are enriched with metabolism-related pathways, notably transporter functions; and 375 differentially expressed genes in late-onset severe preeclampsia, which are enriched with immune-related pathways. We also identified some key transcription factors, which may drive the widespread gene dysregulation in both early-onset and late-onset patients. Conclusion: These results suggest that early-onset and late-onset severe preeclampsia have different molecular mechanisms, whereas the late-onset mild preeclampsia may have no placenta-specific causal factors. A few regulators may be the key drivers of the dysregulated molecular pathways.
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Feng Y, Chen X, Wang H, Chen X, Lan Z, Li P, Cao Y, Liu M, Lv J, Chen Y, Wang Y, Sheng C, Huang Y, Zhong M, Wang Z, Yue X, Huang L. Collagen I Induces Preeclampsia-Like Symptoms by Suppressing Proliferation and Invasion of Trophoblasts. Front Endocrinol (Lausanne) 2021; 12:664766. [PMID: 34421817 PMCID: PMC8378400 DOI: 10.3389/fendo.2021.664766] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/14/2021] [Indexed: 11/15/2022] Open
Abstract
Preeclampsia is a common obstetric disorder affecting 2-8% of pregnancy worldwide. Fibrosis is an important histological change occurring in preeclamptic placenta, and might depend on the excess deposition of collagen I. However, the role of fibrotic placenta and collagen I in the pathogenesis of preeclampsia remains unclear. Therefore, we analyzed the collagen deposition and the expression of Collagen I in human placenta by Masson staining, Sirius red staining and western blotting. Further, the role of collagen I in preeclampsia pathogenesis was studied in C57BL/6 mice. HTR-8/SVneo cells were used to investigate the mechanisms underlying the effects of collagen I in trophoblasts by transcriptome sequencing and pharmacological agonists. Human preeclamptic placenta exhibited a significantly higher degree of fibrosis in stem villi and terminal villi than normal placenta, and was characterized by collagen I deposition. In vivo, a single injection of collagen I on gestational day 0.5 led to an increase in systolic pressure of pregnant mice from gestational days 4.5-17.5, to a decrease in weight and number of embryos, and to enhanced placental collagen I expression and degree of fibrosis compared with control mice. In vitro, collagen I attenuated the proliferation and invasion of HTR-8SV/neo cells. This effect could be reversed by treatment with agonists of ERK and β-catenin. Moreover, transcriptome sequencing demonstrated that signaling pathways related to cell proliferation and invasion were significantly downregulated in HTR-8SV/neo cells. Thus, we propose that collagen I induced preeclampsia-like symptoms by suppressing the proliferation and invasion of trophoblasts through inhibition of the ERK phosphorylation and WNT/β-catenin signaling pathways. Our findings could pave the way to the discovery of small-molecule inhibitors for preeclampsia treatment and future studies with larger sample size are required.
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Affiliation(s)
- Yinglin Feng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xia Chen
- Department of Obstetrics and Gynecology, Foshan First People’s Hospital, Foshan, China
| | - Huiqiao Wang
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Xueping Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zixin Lan
- Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Pan Li
- Microbiome Research Center, University of New South Wales, Sydney, NSW, Australia
| | - Yingshi Cao
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mian Liu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jin Lv
- Department of Pathology, Foshan First People’s Hospital, Foshan, China
| | - Yun Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Chao Sheng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingying Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhijian Wang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaojing Yue
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Liping Huang, ; Xiaojing Yue,
| | - Liping Huang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- *Correspondence: Liping Huang, ; Xiaojing Yue,
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Szilagyi A, Gelencser Z, Romero R, Xu Y, Kiraly P, Demeter A, Palhalmi J, Gyorffy BA, Juhasz K, Hupuczi P, Kekesi KA, Meinhardt G, Papp Z, Draghici S, Erez O, Tarca AL, Knöfler M, Than NG. Placenta-Specific Genes, Their Regulation During Villous Trophoblast Differentiation and Dysregulation in Preterm Preeclampsia. Int J Mol Sci 2020; 21:ijms21020628. [PMID: 31963593 PMCID: PMC7013556 DOI: 10.3390/ijms21020628] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 12/15/2022] Open
Abstract
The human placenta maintains pregnancy and supports the developing fetus by providing nutrition, gas-waste exchange, hormonal regulation, and an immunological barrier from the maternal immune system. The villous syncytiotrophoblast carries most of these functions and provides the interface between the maternal and fetal circulatory systems. The syncytiotrophoblast is generated by the biochemical and morphological differentiation of underlying cytotrophoblast progenitor cells. The dysfunction of the villous trophoblast development is implicated in placenta-mediated pregnancy complications. Herein, we describe gene modules and clusters involved in the dynamic differentiation of villous cytotrophoblasts into the syncytiotrophoblast. During this process, the immune defense functions are first established, followed by structural and metabolic changes, and then by peptide hormone synthesis. We describe key transcription regulatory molecules that regulate gene modules involved in placental functions. Based on transcriptomic evidence, we infer how villous trophoblast differentiation and functions are dysregulated in preterm preeclampsia, a life-threatening placenta-mediated obstetrical syndrome for the mother and fetus. In the conclusion, we uncover the blueprint for villous trophoblast development and its impairment in preterm preeclampsia, which may aid in the future development of non-invasive biomarkers for placental functions and early identification of women at risk for preterm preeclampsia as well as other placenta-mediated pregnancy complications.
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Affiliation(s)
- Andras Szilagyi
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Zsolt Gelencser
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20692, and Detroit, MI 48201, USA; (R.R.); (Y.X.); (O.E.); (A.L.T.)
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Detroit Medical Center, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Florida International University, Miami, FL 33199, USA
| | - Yi Xu
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20692, and Detroit, MI 48201, USA; (R.R.); (Y.X.); (O.E.); (A.L.T.)
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Peter Kiraly
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Amanda Demeter
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Janos Palhalmi
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Balazs A. Gyorffy
- Laboratory of Proteomics, Institute of Biology, Eotvos Lorand University, H-1117 Budapest, Hungary; (B.A.G.); (K.A.K.)
| | - Kata Juhasz
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
| | - Petronella Hupuczi
- Maternity Private Clinic of Obstetrics and Gynecology, H-1126 Budapest, Hungary; (P.H.); (Z.P.)
| | - Katalin Adrienna Kekesi
- Laboratory of Proteomics, Institute of Biology, Eotvos Lorand University, H-1117 Budapest, Hungary; (B.A.G.); (K.A.K.)
- Department of Physiology and Neurobiology, Eotvos Lorand University, H-1117 Budapest, Hungary
| | - Gudrun Meinhardt
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, Vienna A-1090, Austria; (G.M.); (M.K.)
| | - Zoltan Papp
- Maternity Private Clinic of Obstetrics and Gynecology, H-1126 Budapest, Hungary; (P.H.); (Z.P.)
- Department of Obstetrics and Gynecology, Semmelweis University, H-1088 Budapest, Hungary
| | - Sorin Draghici
- Department of Computer Science, Wayne State University College of Engineering, Detroit, MI 48202, USA;
| | - Offer Erez
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20692, and Detroit, MI 48201, USA; (R.R.); (Y.X.); (O.E.); (A.L.T.)
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel
| | - Adi Laurentiu Tarca
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20692, and Detroit, MI 48201, USA; (R.R.); (Y.X.); (O.E.); (A.L.T.)
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Martin Knöfler
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, Vienna A-1090, Austria; (G.M.); (M.K.)
| | - Nandor Gabor Than
- Systems Biology of Reproduction Lendulet Group, Institute of Enzymology, Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (A.S.); (Z.G.); (P.K.); (A.D.); (J.P.); (K.J.)
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20692, and Detroit, MI 48201, USA; (R.R.); (Y.X.); (O.E.); (A.L.T.)
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Maternity Private Clinic of Obstetrics and Gynecology, H-1126 Budapest, Hungary; (P.H.); (Z.P.)
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, H-1085 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-382-6788
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9
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Meta-analysis of gene expression profiles in preeclampsia. Pregnancy Hypertens 2020; 19:52-60. [DOI: 10.1016/j.preghy.2019.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
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10
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Paquette AG, Brockway HM, Price ND, Muglia LJ. Comparative transcriptomic analysis of human placentae at term and preterm delivery. Biol Reprod 2019; 98:89-101. [PMID: 29228154 PMCID: PMC5803773 DOI: 10.1093/biolre/iox163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/30/2017] [Indexed: 12/11/2022] Open
Abstract
Preterm birth affects 1 out of every 10 infants in the United States, resulting in substantial neonatal morbidity and mortality. Currently, there are few predictive markers and few treatment options to prevent preterm birth. A healthy, functioning placenta is essential to positive pregnancy outcomes. Previous studies have suggested that placental pathology may play a role in preterm birth etiology. Therefore, we tested the hypothesis that preterm placentae may exhibit unique transcriptomic signatures compared to term samples reflective of their abnormal biology leading to this adverse outcome. We aggregated publicly available placental villous microarray data to generate a preterm and term sample dataset (n = 133, 55 preterm placentae and 78 normal term placentae). We identified differentially expressed genes using the linear regression for microarray (LIMMA) package and identified perturbations in known biological networks using Differential Rank Conservation (DIRAC). We identified 129 significantly differentially expressed genes between term and preterm placenta with 96 genes upregulated and 33 genes downregulated (P-value <0.05). Significant changes in gene expression in molecular networks related to Tumor Protein 53 and phosphatidylinositol signaling were identified using DIRAC. We have aggregated a uniformly normalized transcriptomic dataset and have identified novel and established genes and pathways associated with developmental regulation of the placenta and potential preterm birth pathology. These analyses provide a community resource to integrate with other high-dimensional datasets for additional insights in normal placental development and its disruption.
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Affiliation(s)
| | - Heather M Brockway
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
| | | | - Louis J Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Cincinnati Children's, Hospital Medical Center, Cincinnati, Ohio, USA
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11
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Christians JK, Lennie KI, Huicochea Munoz MF, Binning N. PAPP-A2 deficiency does not exacerbate the phenotype of a mouse model of intrauterine growth restriction. Reprod Biol Endocrinol 2018; 16:58. [PMID: 29895300 PMCID: PMC5996520 DOI: 10.1186/s12958-018-0376-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/06/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Pregnancy-associated plasma protein-A2 (PAPP-A2) is consistently upregulated in the placentae of pregnancies complicated by preeclampsia and fetal growth restriction. The causes and significance of this upregulation remain unknown, but it has been hypothesized that it is a compensatory response to improve placental growth and development. We predicted that, if the upregulation of PAPP-A2 in pregnancy complications reflects a compensatory response, then deletion of Pappa2 in mice would exacerbate the effects of a gene deletion previously reported to impair placental development: deficiency of matrix metalloproteinase-9 (MMP9). METHODS We crossed mice carrying deletions in Pappa2 and Mmp9 to produce pregnancies deficient in one, both, or neither of these genes. We measured pregnancy rates, number of conceptuses, fetal and placental growth, and the histological structure of the placenta. RESULTS We found no evidence of reduced fertility, increased pregnancy loss, or increased fetal demise in Mmp9 -/- females. In pregnancies segregating for Mmp9, Mmp9 -/- fetuses were lighter than their siblings with a functional Mmp9 allele. However, deletion of Pappa2 did not exacerbate or reveal any effects of Mmp9 deficiency. We observed some effects of Pappa2 deletion on placental structure that were independent of Mmp9 deficiency, but no effects on fetal growth. At G16, male fetuses were heavier than female fetuses and had heavier placentae with larger junctional zones and smaller labyrinths. CONCLUSIONS Effects of Mmp9 deficiency were not exacerbated by the deletion of Pappa2. Our results do not provide evidence that upregulation of placental PAPP-A2 represents a mechanism to compensate for impaired fetal growth.
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Affiliation(s)
- Julian K. Christians
- 0000 0004 1936 7494grid.61971.38Department of Biological Sciences, Simon Fraser University, Burnaby, BC Canada
| | - Kendra I. Lennie
- 0000 0004 1936 7494grid.61971.38Department of Biological Sciences, Simon Fraser University, Burnaby, BC Canada
| | - Maria F. Huicochea Munoz
- 0000 0004 1936 7494grid.61971.38Department of Biological Sciences, Simon Fraser University, Burnaby, BC Canada
| | - Nimrat Binning
- 0000 0004 1936 7494grid.61971.38Department of Biological Sciences, Simon Fraser University, Burnaby, BC Canada
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