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Weeding E, Coit P, Yalavarthi S, Kaplan MJ, Knight JS, Sawalha AH. Genome-wide DNA methylation analysis in primary antiphospholipid syndrome neutrophils. Clin Immunol 2018; 196:110-116. [PMID: 30471352 DOI: 10.1016/j.clim.2018.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 01/07/2023]
Abstract
Antiphospholipid syndrome (APS) is a systemic autoimmune disease characterized by thromboembolic events and pregnancy loss. We sought to characterize the DNA methylation profile of primary APS in comparison to healthy controls and individuals with SLE. In primary APS neutrophils compared to controls, 17 hypomethylated and 25 hypermethylated CpG sites were identified. Notable hypomethylated genes included ETS1, a genetic risk locus for SLE, and PTPN2, a genetic risk locus for other autoimmune diseases. Gene ontology analysis of hypomethylated genes revealed enrichment of genes involved in pregnancy. None of the differentially methylated sites in primary APS were differentially methylated in SLE neutrophils, and there was no demethylation of interferon signature genes in primary APS as is seen in SLE. Hypomethylation within a single probe in the IFI44L promoter (cg06872964) was able to distinguish SLE from primary APS with a sensitivity of 93.3% and specificity of 80.0% at a methylation fraction of 0.329.
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Affiliation(s)
- Emma Weeding
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Srilakshmi Yalavarthi
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Jason S Knight
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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2
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hnRNPDL extensively regulates transcription and alternative splicing. Gene 2018; 687:125-134. [PMID: 30447347 DOI: 10.1016/j.gene.2018.11.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 08/30/2018] [Accepted: 11/08/2018] [Indexed: 01/31/2023]
Abstract
RNA binding proteins (RBPs) are key players of genome regulation. Here we report the transcriptome study of HnRNP D-Like protein, which belongs to the hnRNP family. We used RNA-seq to analyze the global transcript level and alternative splicing on hnRNPDL shRNA-treated cells and control. Sh-hnRNPDL extensively increased in the expression of genes involved in female pregnancy, cell apoptosis, cell proliferation and cell migration. HnRNPDL regulated alternative splicing of hundreds of genes enriched in transcription regulation and signaling pathways including NOD-like receptor signaling, Notch signaling, and TNF signaling. This study provides the first transcriptome-wide analysis of hnRNPDL regulation of gene expression, which adds to the understanding of critical hnRNPDL functions.
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Robinson JF, Kapidzic M, Gormley M, Ona K, Dent T, Seifikar H, Hamilton EG, Fisher SJ. Transcriptional Dynamics of Cultured Human Villous Cytotrophoblasts. Endocrinology 2017; 158:1581-1594. [PMID: 28323933 PMCID: PMC5460928 DOI: 10.1210/en.2016-1635] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 01/30/2017] [Indexed: 12/11/2022]
Abstract
During human pregnancy, cytotrophoblasts (CTBs) play key roles in uterine invasion, vascular remodeling, and anchoring of the feto-placental unit. Due to the challenges associated with studying human placentation in utero, cultured primary villous CTBs are used as a model of the differentiation pathway that leads to invasion of the uterine wall. In vitro, CTBs emulate in vivo cell behaviors, such as migration, aggregation, and substrate penetration. Although some of the molecular features related to these cell behaviors have been described, the underlying mechanisms, at a global level, remain undefined at midgestation. Thus, in this study, we characterized second-trimester CTB differentiation/invasion in vitro, correlating the major morphological transitions with the transcriptional changes that occurred at these steps. After plating on Matrigel as individual cells, CTBs migrated toward each other and formed multicellular aggregates. In parallel, using a microarray approach, we observed differentially expressed (DE) genes across time, which were enriched for numerous functions, including cell migration, vascular remodeling, morphogenesis, cell communication, and inflammatory signaling. DE genes encoded several molecules that we and others previously linked to critical CTB function in vivo, suggesting that the novel DE molecules we discovered played important roles. Immunolocalization confirmed that CTBs in situ gave a signal for two of the most highly expressed genes in vitro. In summary, we characterized, at a global level, the temporal dynamics of primary human CTB gene expression in culture. These data will enable future analyses of various types of in vitro perturbations-for example, modeling disease processes and environmental exposures.
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Affiliation(s)
- Joshua F. Robinson
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143
| | - Mirhan Kapidzic
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143
| | - Matthew Gormley
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143
| | - Katherine Ona
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
| | - Terrence Dent
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
| | - Helia Seifikar
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
| | - Emily G. Hamilton
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
| | - Susan J. Fisher
- Center for Reproductive Sciences, University of California, San Francisco, California 94143
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, California 94143
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, California 94143
- Division of Maternal Fetal Medicine, University of California, San Francisco, California 94143
- Department of Anatomy, University of California, San Francisco, California 94143
- Human Embryonic Stem Cell Program, University of California, San Francisco, California 94143
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Baines K, Renaud S. Transcription Factors That Regulate Trophoblast Development and Function. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 145:39-88. [DOI: 10.1016/bs.pmbts.2016.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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5
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Abstract
A possible role for the transcription factor v-ets avian erythroblastosis virus E26 oncogene homolog 1 (ETS1) in human trophoblast cell differentiation was examined using a highly enriched fraction of human mononuclear cytotrophoblast cells (CTBs) that differentiate spontaneously in vitro to a multinucleated syncytiotrophoblast cell (STB) phenotype. ETS1 mRNA and protein levels were abundant in freshly isolated CTBs and decreased as the cells differentiated. Silencing of ETS1 expression in freshly prepared CTBs markedly attenuated syncytialization, as demonstrated by desmoplakin staining, and blocked the induction of syncytin, the transcription factor activator protein-2α, placental lactogen, and other STB-specific genes. Conversely, overexpression of ETS1 in primary trophoblast cells induced STB marker gene mRNAs and transactivated each of the gene proximal promoters. Taken together, these findings strongly suggest a critical role for ETS1 in the induction of human villus CTB differentiation. The effect of ETS1 on syncytialization likely results, at least in part, from inhibition of syncytin expression, whereas the induction of STB marker genes likely results in part from transactivation by activator protein-2α.
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Affiliation(s)
- Cherie A Kessler
- Divisions of Endocrinology (C.A.K., S.H.) and Pathology (J.W.S., K.F.S.), Children's Hospital Medical Center, and Departments of Pediatrics (C.A.K., S.H.) and Pathology (J.W.S., K.F.S.), University of Cincinnati, Cincinnati, Ohio 45229
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Angiogenesis in the placenta: the role of reactive oxygen species signaling. BIOMED RESEARCH INTERNATIONAL 2015; 2015:814543. [PMID: 25705690 PMCID: PMC4325211 DOI: 10.1155/2015/814543] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/28/2014] [Indexed: 02/07/2023]
Abstract
Proper placental development and function are central to the health of both the mother and the fetus during pregnancy. A critical component of healthy placental function is the proper development of its vascular network. Poor vascularization of the placenta can lead to fetal growth restriction, preeclampsia, and in some cases fetal death. Therefore, understanding the mechanisms by which uterine stressors influence the development of the placental vasculature and contribute to placental dysfunction is of central importance to ensuring a healthy pregnancy. In this review we discuss how oxidative stress observed in maternal smoking, maternal obesity, and preeclampsia has been associated with aberrant angiogenesis and placental dysfunction resulting in adverse pregnancy outcomes. We also highlight that oxidative stress can influence the expression of a number of transcription factors important in mediating angiogenesis. Therefore, understanding how oxidative stress affects redox-sensitive transcription factors within the placenta may elucidate potential therapeutic targets for correcting abnormal placental angiogenesis and function.
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Murthi P, Kalionis B, Cocquebert M, Rajaraman G, Chui A, Keogh RJ, Evain-Brion D, Fournier T. Homeobox genes and down-stream transcription factor PPARγ in normal and pathological human placental development. Placenta 2013; 34:299-309. [PMID: 23484914 DOI: 10.1016/j.placenta.2013.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 01/07/2013] [Accepted: 01/10/2013] [Indexed: 01/12/2023]
Abstract
The placenta provides critical transport functions between the maternal and fetal circulations during intrauterine development. Formation of this interface is controlled by nuclear transcription factors including homeobox genes. Here we summarize current knowledge regarding the expression and function of homeobox genes in the placenta. We also describe the identification of target transcription factors including PPARγ, biological pathways regulated by homeobox genes and their role in placental development. The role of the nuclear receptor PPARγ, ligands and target genes in human placental development is also discussed. A better understanding of these pathways will improve our knowledge of placental cell biology and has the potential to reveal new molecular targets for the early detection and diagnosis of pregnancy complications including human fetal growth restriction.
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Affiliation(s)
- P Murthi
- Department of Perinatal Medicine Pregnancy Research Centre, Australia
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Lam KKW, Chiu PCN, Lee CL, Pang RTK, Leung CON, Koistinen H, Seppala M, Ho PC, Yeung WSB. Glycodelin-A protein interacts with Siglec-6 protein to suppress trophoblast invasiveness by down-regulating extracellular signal-regulated kinase (ERK)/c-Jun signaling pathway. J Biol Chem 2011; 286:37118-27. [PMID: 21880722 DOI: 10.1074/jbc.m111.233841] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During placentation, the cytotrophoblast differentiates into the villous cytotrophoblast and the extravillous cytotrophoblast. The latter invades the decidualized endometrium. Glycodelin-A (GdA) is abundantly synthesized by the decidua but not the trophoblast. Previous data indicate that GdA suppresses the invasion of trophoblast cell lines by down-regulating proteinase expression and activities. This study addresses the signaling pathway involved in the above phenomenon. GdA was found to suppress phosphorylation of ERKs and expression of their downstream effector c-Jun, a component of the transcription factor activator protein-1 (AP-1). The involvement of ERKs and c-Jun in suppressing trophoblast invasion and biosynthesis of proteinases was confirmed by using siRNA knockdown and pharmacological inhibitors. Desialylation reduced binding affinity of GdA toward and invasion suppressive activities on the trophoblast. Co-immunoprecipitation showed that Siglec-6 on the trophoblast was the binding protein of GdA. The binding of GdA to Siglec-6 was sialic acid-dependent. Treatment with anti-Siglec-6 antibody abolished the invasion suppressive activities of GdA. These results show that GdA interacts with Siglec-6 to suppress trophoblast invasiveness by down-regulating the ERK/c-Jun signaling pathway.
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Affiliation(s)
- Kevin K W Lam
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Queen Mary Hospital, Pokfulam Road, Hong Kong, China
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The role of placental homeobox genes in human fetal growth restriction. J Pregnancy 2011; 2011:548171. [PMID: 21547091 PMCID: PMC3087155 DOI: 10.1155/2011/548171] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 02/17/2011] [Indexed: 12/04/2022] Open
Abstract
Fetal growth restriction (FGR) is an adverse pregnancy outcome associated with significant perinatal and paediatric morbidity and mortality, and an increased risk of chronic disease later in adult life. One of the key causes of adverse pregnancy outcome is fetal growth restriction (FGR). While a number of maternal, fetal, and environmental factors are known causes of FGR, the majority of FGR cases remain idiopathic. These idiopathic FGR pregnancies are frequently associated with placental insufficiency, possibly as a result of placental maldevelopment. Understanding the molecular mechanisms of abnormal placental development in idiopathic FGR is, therefore, of increasing importance. Here, we review our understanding of transcriptional control of normal placental development and abnormal placental development associated with human idiopathic FGR. We also assess the potential for understanding transcriptional control as a means for revealing new molecular targets for the detection, diagnosis, and clinical management of idiopathic FGR.
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Rajaraman G, Murthi P, Pathirage N, Brennecke SP, Kalionis B. Downstream targets of homeobox gene HLX show altered expression in human idiopathic fetal growth restriction. THE AMERICAN JOURNAL OF PATHOLOGY 2009; 176:278-87. [PMID: 20008130 DOI: 10.2353/ajpath.2010.090187] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fetal growth restriction (FGR), a clinically significant pregnancy disorder, is poorly understood at the molecular level. This study investigates idiopathic FGR associated with placental insufficiency. Previously, we showed that the homeobox gene HLX is expressed in placental trophoblast cells and that HLX expression is significantly decreased in human idiopathic FGR. Here, we used the novel approach of identifying downstream targets of HLX in cell culture to detect potentially important genes involved in idiopathic FGR. Downstream targets were revealed by decreasing HLX expression in cultured trophoblast cells with HLX-specific small interfering RNAs to model human idiopathic FGR and comparing these levels with controls using a real-time PCR-based gene profiling system. Changes in candidate HLX target mRNA levels were verified in an independent trophoblast cell line, and candidate target gene expression was assessed in human idiopathic FGR-affected placentae (n = 25) compared with gestation-matched controls (n = 25). The downstream targets RB1 and MYC, cell cycle regulatory genes, showed significantly increased mRNA levels in FGR-affected tissues compared with gestation-matched controls, whereas CCNB1, ELK1, JUN, and CDKN1 showed significantly decreased mRNA levels (n = 25, P < 0.001, t-test). The changes for RB1 and CDKN1C were verified by Western blot analysis in FGR-affected placentae compared with gestation-matched controls (n = 6). We conclude that cell cycle regulatory genes RB1, MYC, CCNB1, ELK1, JUN, and CDKN1C, which control important trophoblast cell functions, are targets of HLX.
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Affiliation(s)
- Gayathri Rajaraman
- Department of Obstetrics and Gynaecology, University of Melbourne, RWH Campus, 20 Flemington Rd., Parkville, Victoria 3052, Australia.
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Laitem C, Leprivier G, Choul-Li S, Begue A, Monte D, Larsimont D, Dumont P, Duterque-Coquillaud M, Aumercier M. Ets-1 p27: a novel Ets-1 isoform with dominant-negative effects on the transcriptional properties and the subcellular localization of Ets-1 p51. Oncogene 2009; 28:2087-99. [PMID: 19377509 DOI: 10.1038/onc.2009.72] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The transcription factor Ets-1 is implicated in various physiological processes and invasive pathologies. We identified a novel variant of ets-1, ets-1Delta(III-VI), resulting from the alternative splicing of exons III to VI. This variant encodes a 27 kDa isoform, named Ets-1 p27. Ets-1 p27 lacks the threonine-38 residue, the Pointed domain and the transactivation domain, all of which are required for the transactivation of Ets-1 target genes. Both inhibitory domains surrounding the DNA-binding domain are conserved, suggesting that Ets-1 p27, like the full-length Ets-1 p51 isoform, is autoinhibited for DNA binding. We showed that Ets-1 p27 binds DNA in the same way as Ets-1 p51 does and that it acts both at a transcriptional and a subcellular localization level, thereby constituting a dual-acting dominant negative of Ets-1 p51. Ets-1 p27 blocks Ets-1 p51-mediated transactivation of target genes and induces the translocation of Ets-1 p51 from the nucleus to the cytoplasm. Furthermore, Ets-1 p27 overexpression represses the tumor properties of MDA-MB-231 mammary carcinoma cells in correlation with the known implication of Ets-1 in various cellular mechanisms. Thus the dual-acting dominant-negative function of Ets-1 p27 gives to the Ets-1 p27/Ets-1 p51 ratio a determining effect on cell fate.
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Affiliation(s)
- C Laitem
- CNRS Unité Mixte de Recherche 8161, Institut de Biologie de Lille, Institut Pasteur de Lille, Universités de Lille 1 and Lille 2, IFR 142, Lille, France
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