1
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Paquette A, Ahuna K, Hwang YM, Pearl J, Liao H, Shannon P, Kadam L, Lapehn S, Bucher M, Roper R, Funk C, MacDonald J, Bammler T, Baloni P, Brockway H, Mason WA, Bush N, Lewinn KZ, Karr CJ, Stamatoyannopoulos J, Muglia LJ, Jones H, Sadovsky Y, Myatt L, Sathyanarayana S, Price ND. A genome scale transcriptional regulatory model of the human placenta. SCIENCE ADVANCES 2024; 10:eadf3411. [PMID: 38941464 PMCID: PMC11212735 DOI: 10.1126/sciadv.adf3411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Gene regulation is essential to placental function and fetal development. We built a genome-scale transcriptional regulatory network (TRN) of the human placenta using digital genomic footprinting and transcriptomic data. We integrated 475 transcriptomes and 12 DNase hypersensitivity datasets from placental samples to globally and quantitatively map transcription factor (TF)-target gene interactions. In an independent dataset, the TRN model predicted target gene expression with an out-of-sample R2 greater than 0.25 for 73% of target genes. We performed siRNA knockdowns of four TFs and achieved concordance between the predicted gene targets in our TRN and differences in expression of knockdowns with an accuracy of >0.7 for three of the four TFs. Our final model contained 113,158 interactions across 391 TFs and 7712 target genes and is publicly available. We identified 29 TFs which were significantly enriched as regulators for genes previously associated with preterm birth, and eight of these TFs were decreased in preterm placentas.
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Affiliation(s)
- Alison Paquette
- University of Washington, Seattle, WA, USA
- Seattle Children’s Research Institute, Seattle, WA, USA
| | - Kylia Ahuna
- Oregon Health and Sciences University, Portland, OR, USA
| | | | | | - Hanna Liao
- University of Washington, Seattle, WA, USA
| | | | - Leena Kadam
- Oregon Health and Sciences University, Portland, OR, USA
| | | | - Matthew Bucher
- Oregon Health and Sciences University, Portland, OR, USA
| | - Ryan Roper
- Institute for Systems Biology, Seattle, WA, USA
| | - Cory Funk
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | | | - Heather Brockway
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
| | - W. Alex Mason
- University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Nicole Bush
- University of California San Francisco, San Francisco, CA, USA
| | - Kaja Z. Lewinn
- University of California San Francisco, San Francisco, CA, USA
| | | | | | - Louis J. Muglia
- The Burroughs Wellcome Fund, Research Triangle Park, NC, USA
- Cincinnati Children’s Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | | | - Yoel Sadovsky
- Magee Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
| | - Leslie Myatt
- Oregon Health and Sciences University, Portland, OR, USA
| | - Sheela Sathyanarayana
- University of Washington, Seattle, WA, USA
- Seattle Children’s Research Institute, Seattle, WA, USA
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, WA, USA
- Thorne HealthTech, New York City, NY, USA
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2
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Vasconcelos S, Moustakas I, Branco MR, Guimarães S, Caniçais C, van der Helm T, Ramalho C, Marques CJ, de Sousa Lopes SMC, Dória S. Syncytiotrophoblast Markers Are Downregulated in Placentas from Idiopathic Stillbirths. Int J Mol Sci 2024; 25:5180. [PMID: 38791219 PMCID: PMC11121380 DOI: 10.3390/ijms25105180] [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: 04/01/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The trophoblast cells are responsible for the transfer of nutrients between the mother and the foetus and play a major role in placental endocrine function by producing and releasing large amounts of hormones and growth factors. Syncytiotrophoblast cells (STB), formed by the fusion of mononuclear cytotrophoblasts (CTB), constitute the interface between the foetus and the mother and are essential for all of these functions. We performed transcriptome analysis of human placental samples from two control groups-live births (LB), and stillbirths (SB) with a clinically recognised cause-and from our study group, idiopathic stillbirths (iSB). We identified 1172 DEGs in iSB, when comparing with the LB group; however, when we compared iSB with the SB group, only 15 and 12 genes were down- and upregulated in iSB, respectively. An assessment of these DEGs identified 15 commonly downregulated genes in iSB. Among these, several syncytiotrophoblast markers, like genes from the PSG and CSH families, as well as ALPP, KISS1, and CRH, were significantly downregulated in placental samples from iSB. The transcriptome analysis revealed underlying differences at a molecular level involving the syncytiotrophoblast. This suggests that defects in the syncytial layer may underlie unexplained stillbirths, therefore offering insights to improve clinical obstetrics practice.
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Affiliation(s)
- Sara Vasconcelos
- Genetics Service, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal (C.J.M.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Ioannis Moustakas
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands (T.v.d.H.); (S.M.C.d.S.L.)
- Sequencing Analysis Support Core, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Miguel R. Branco
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK
| | - Susana Guimarães
- Department of Pathology, Faculty of Medicine and Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | - Carla Caniçais
- Genetics Service, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal (C.J.M.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Talia van der Helm
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands (T.v.d.H.); (S.M.C.d.S.L.)
| | - Carla Ramalho
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Centro Hospitalar Universitário São João, 4200-319 Porto, Portugal
| | - Cristina Joana Marques
- Genetics Service, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal (C.J.M.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
| | - Susana M. Chuva de Sousa Lopes
- Department of Anatomy and Embryology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands (T.v.d.H.); (S.M.C.d.S.L.)
| | - Sofia Dória
- Genetics Service, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal (C.J.M.)
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal
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3
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Gonzalez TL, Wertheimer S, Flowers AE, Wang Y, Santiskulvong C, Clark EL, Jefferies CA, Lawrenson K, Chan JL, Joshi NV, Zhu Y, Tseng HR, Karumanchi SA, Williams III J, Pisarska MD. High-throughput mRNA-seq atlas of human placenta shows vast transcriptome remodeling from first to third trimester†. Biol Reprod 2024; 110:936-949. [PMID: 38271627 PMCID: PMC11094392 DOI: 10.1093/biolre/ioae007] [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: 06/30/2023] [Revised: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 01/27/2024] Open
Abstract
The placenta, composed of chorionic villi, changes dramatically across gestation. Understanding differences in ongoing pregnancies are essential to identify the role of chorionic villi at specific times in gestation and develop biomarkers and prognostic indicators of maternal-fetal health. The normative mRNA profile is established using next-generation sequencing of 124 first trimester and 43 third trimester human placentas from ongoing healthy pregnancies. Stably expressed genes (SEGs) not different between trimesters and with low variability are identified. Differential expression analysis of first versus third trimester adjusted for fetal sex is performed, followed by a subanalysis with 23 matched pregnancies to control for subject variability using the same genetic and environmental background. Placenta expresses 14,979 polyadenylated genes above sequencing noise (transcripts per million > 0.66), with 10.7% SEGs across gestation. Differentially expressed genes (DEGs) account for 86.7% of genes in the full cohort [false discovery rate (FDR) < 0.05]. Fold changes highly correlate between the full cohort and subanalysis (Pearson = 0.98). At stricter thresholds (FDR < 0.001, fold change > 1.5), there remains 50.1% DEGs (3353 upregulated in first and 4155 upregulated in third trimester). This is the largest mRNA atlas of healthy human placenta across gestation, controlling for genetic and environmental factors, demonstrating substantial changes from first to third trimester in chorionic villi. Specific differences and SEGs may be used to understand the specific role of the chorionic villi throughout gestation and develop first trimester biomarkers of placental health that transpire across gestation, which can be used for future development of biomarkers for maternal-fetal health.
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Affiliation(s)
- Tania L Gonzalez
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sahar Wertheimer
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Amy E Flowers
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yizhou Wang
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chintda Santiskulvong
- CS Cancer Applied Genomics Shared Resource, CS Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ekaterina L Clark
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Caroline A Jefferies
- Division of Rheumatology, Department of Medicine, Kao Autoimmune Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Women’s Cancer Research Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica L Chan
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nikhil V Joshi
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yazhen Zhu
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - John Williams III
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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4
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Inohaya A, Chigusa Y, Takakura M, Io S, Kim MA, Matsuzaka Y, Yasuda E, Ueda Y, Kawamura Y, Takamatsu S, Mogami H, Takashima Y, Mandai M, Kondoh E. Shear stress in the intervillous space promotes syncytial formation of iPS cells-derived trophoblasts†. Biol Reprod 2024; 110:300-309. [PMID: 37930227 DOI: 10.1093/biolre/ioad143] [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: 06/06/2023] [Revised: 10/01/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
The intervillous space of human placenta is filled with maternal blood, and villous trophoblasts are constantly exposed to the shear stress generated by maternal blood pressure and flow throughout the entire gestation period. However, the effects of shear stress on villous trophoblasts and their biological significance remain unknown. Here, using our recently established naïve human pluripotent stem cells-derived cytotrophoblast stem cells (nCTs) and a device that can apply arbitrary shear stress to cells, we investigated the impact of shear stress on early-stage trophoblasts. After 72 h of exposure to 10 dyn/cm2 shear stress, nCTs became fused and multinuclear, and mRNA expression of the syncytiotrophoblast (ST) markers, such as glial cell missing 1, endogenous retrovirus group W member 1 envelope, chorionic gonadotropin subunit beta 3, syndecan 1, pregnancy specific beta-1-glycoprotein 3, placental growth factor, and solute carrier family 2 member 1 were significantly upregulated compared to static conditions. Immunohistochemistry showed that shear stress increased fusion index, human chorionic gonadotropin secretion, and human placental lactogen secretion. Increased microvilli formation on the surface of nCTs under flow conditions was detected using scanning electron microscopy. Intracellular cyclic adenosine monophosphate significantly increased under flow conditions. Moreover, transcriptome analysis of nCTs subjected to shear stress revealed that shear stress upregulated ST-specific genes and downregulated CT-specific genes. Collectively, these findings indicate that shear stress promotes the differentiation of nCTs into ST.
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Affiliation(s)
- Asako Inohaya
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshitsugu Chigusa
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahito Takakura
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shingo Io
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Min-A Kim
- Department of Obstetrics and Gynecology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Yu Matsuzaka
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eriko Yasuda
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Ueda
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawamura
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shiro Takamatsu
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Haruta Mogami
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuhiro Takashima
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, Kyoto Japan
| | - Masaki Mandai
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Eiji Kondoh
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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5
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Elkin ER, Campbell KA, Lapehn S, Harris SM, Padmanabhan V, Bakulski KM, Paquette AG. Placental single cell transcriptomics: Opportunities for endocrine disrupting chemical toxicology. Mol Cell Endocrinol 2023; 578:112066. [PMID: 37690473 PMCID: PMC10591899 DOI: 10.1016/j.mce.2023.112066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
The placenta performs essential biologic functions for fetal development throughout pregnancy. Placental dysfunction is at the root of multiple adverse birth outcomes such as intrauterine growth restriction, preeclampsia, and preterm birth. Exposure to endocrine disrupting chemicals during pregnancy can cause placental dysfunction, and many prior human studies have examined molecular changes in bulk placental tissues. Placenta-specific cell types, including cytotrophoblasts, syncytiotrophoblasts, extravillous trophoblasts, and placental resident macrophage Hofbauer cells play unique roles in placental development, structure, and function. Toxicant-induced changes in relative abundance and/or impairment of these cell types likely contribute to placental pathogenesis. Although gene expression insights gained from bulk placental tissue RNA-sequencing data are useful, their interpretation is limited because bulk analysis can mask the effects of a chemical on individual populations of placental cells. Cutting-edge single cell RNA-sequencing technologies are enabling the investigation of placental cell-type specific responses to endocrine disrupting chemicals. Moreover, in situ bioinformatic cell deconvolution enables the estimation of cell type proportions in bulk placental tissue gene expression data. These emerging technologies have tremendous potential to provide novel mechanistic insights in a complex heterogeneous tissue with implications for toxicant contributions to adverse pregnancy outcomes.
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Affiliation(s)
- Elana R Elkin
- School of Public Health, San Diego State University, San Diego, CA, USA.
| | - Kyle A Campbell
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Samantha Lapehn
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sean M Harris
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, Michigan Medicine, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Alison G Paquette
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
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6
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Bulka CM, Everson TM, Burt AA, Marsit CJ, Karagas MR, Boyle KE, Niemiec S, Kechris K, Davidson EJ, Yang IV, Feinberg JI, Volk HE, Ladd-Acosta C, Breton CV, O’Shea TM, Fry RC. Sex-based differences in placental DNA methylation profiles related to gestational age: an NIH ECHO meta-analysis. Epigenetics 2023; 18:2179726. [PMID: 36840948 PMCID: PMC9980626 DOI: 10.1080/15592294.2023.2179726] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 12/08/2022] [Accepted: 12/21/2022] [Indexed: 02/26/2023] Open
Abstract
The placenta undergoes many changes throughout gestation to support the evolving needs of the foetus. There is also a growing appreciation that male and female foetuses develop differently in utero, with unique epigenetic changes in placental tissue. Here, we report meta-analysed sex-specific associations between gestational age and placental DNA methylation from four cohorts in the National Institutes of Health (NIH) Environmental influences on Child Health Outcomes (ECHO) Programme (355 females/419 males, gestational ages 23-42 weeks). We identified 407 cytosine-guanine dinucleotides (CpGs) in females and 794 in males where placental methylation levels were associated with gestational age. After cell-type adjustment, 55 CpGs in females and 826 in males were significant. These were enriched for biological processes critical to the immune system in females and transmembrane transport in males. Our findings are distinct between the sexes: in females, associations with gestational age are largely explained by differences in placental cellular composition, whereas in males, gestational age is directly associated with numerous alterations in methylation levels.
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Affiliation(s)
- Catherine M. Bulka
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- College of Public Health, University of South Florida, Tampa, FL, USA
| | - Todd M. Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Kristen E. Boyle
- Section of Nutrition, Department of Pediatrics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
| | - Sierra Niemiec
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
| | - Katerina Kechris
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
- Department of Biostatistics & Informatics, Colorado School of Public Health, Aurora, CO, USA
| | | | - Ivana V. Yang
- Colorado School of Public Health, The Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO, USA
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jason I. Feinberg
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Heather E. Volk
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, ML, USA
| | - Carrie V. Breton
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - T. Michael O’Shea
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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7
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Chelslín F, Lodefalk M, Kruse R. Smoking during pregnancy is associated with the placental proteome. Reprod Toxicol 2023; 119:108409. [PMID: 37209868 DOI: 10.1016/j.reprotox.2023.108409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 05/22/2023]
Abstract
Maternal smoking during pregnancy (MSDP) is a significant risk factor for the development of foetal, neonatal, and childhood morbidities. We hypothesized that infants exposed to MSDP have a distinct proteomic expression in their term placentas compared to infants without such an exposure. A total of 39 infants exposed (cord blood cotinine levels of >1 ng/mL) and 44 infants not exposed to MSDP were included in the study. Women with chronic disease, body mass index of > 30, or a history of uterine surgery were excluded. Total proteome abundance was analysed with quantitative mass spectrometry. For univariate analysis of differences in placental protein levels between groups, ANOVA with multiple testing corrections by the Benjamini-Hochberg method was used. For multivariate analysis, we used principal component analysis, partial least squares, lasso, random forest, and neural networks. The univariate analyses showed four differentially abundant proteins (PXDN, CYP1A1, GPR183, and KRT81) when heavy and moderate smoking groups were compared to non-smokers. With the help of machine learning, we found that an additional six proteins (SEPTIN3, CRAT, NAAA, CD248, CADM3, and ZNF648) were discriminants of MSDP. The placental abundance of these ten proteins together explained 74.1% of the variation in cord blood cotinine levels (p = 0.002). Infants exposed to MSDP showed differential abundance of proteins in term placentas. We report differential placental abundance of several proteins for the first time in the setting of MSDP. We believe that these findings supplement the current understanding of how MSDP affects the placental proteome.
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Affiliation(s)
- Felix Chelslín
- University Health Care Research Centre, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden.
| | - Maria Lodefalk
- University Health Care Research Centre, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; Department of Paediatrics, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Robert Kruse
- Department of Clinical Research Laboratory, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; Inflammatory Response and Infection Susceptibility Centre (iRiSC) and X-HiDE Consortium, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
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8
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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9
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Hussey MR, Enquobahrie DA, Loftus CT, MacDonald JW, Bammler TK, Paquette AG, Marsit CJ, Szpiro AA, Kaufman JD, LeWinn KZ, Bush NR, Tylavsky F, Zhao Q, Karr CJ, Sathyanarayana S. Associations of prenatal exposure to NO 2 and near roadway residence with placental gene expression. Placenta 2023; 138:75-82. [PMID: 37216796 PMCID: PMC10349584 DOI: 10.1016/j.placenta.2023.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
INTRODUCTION Traffic-related air pollution (TRAP), a common exposure, potentially impacts pregnancy through altered placental function. We investigated associations between prenatal TRAP exposure and placental gene expression. METHODS Whole transcriptome sequencing was performed on placental samples from CANDLE (Memphis, TN) (n = 776) and GAPPS (Seattle and Yakima, WA) (n = 205), cohorts of the ECHO-PATHWAYS Consortium. Residential NO2 exposures were computed via spatiotemporal models for full-pregnancy, each trimester, and the first/last months of pregnancy. Individual cohort-specific, covariate-adjusted linear models were fit for 10,855 genes and respective exposures (NO2 or roadway proximity [≤150 m]). Infant-sex/exposure interactions on placental gene expression were tested with interaction terms in separate models. Significance was based on false discovery rate (FDR<0.10). RESULTS In GAPPS, final-month NO2 exposure was positively associated with MAP1LC3C expression (FDR p-value = 0.094). Infant-sex interacted with second-trimester NO2 on STRIP2 expression (FDR interaction p-value = 0.011, inverse and positive associations among male and female infants, respectively) and roadway proximity on CEBPA expression (FDR interaction p-value = 0.045, inverse among females). In CANDLE, infant-sex interacted with first-trimester and full-pregnancy NO2 on RASSF7 expression (FDR interaction p-values = 0.067 and 0.013, respectively, positive among male infants and inverse among female infants). DISCUSSION Overall, pregnancy NO2 exposure and placental gene expression associations were primarily null, with exception of final month NO2 exposure and placental MAP1LC3C association. We found several interactions of infant sex and TRAP exposures on placental expression of STRIP2, CEBPA, and RASSF7. These highlighted genes suggest influence of TRAP on placental cell proliferation, autophagy, and growth, though additional replication and functional studies are required for validation.
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Affiliation(s)
- Michael R Hussey
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Daniel A Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Health Systems and Population Health, School of Public Health, University of Washington, Seattle, WA, USA
| | - Christine T Loftus
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Alison G Paquette
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Adam A Szpiro
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Joel D Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kaja Z LeWinn
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, School of Medicine, University of California, San Francisco, San, Francisco, CA, USA
| | - Frances Tylavsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Qi Zhao
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Catherine J Karr
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Sheela Sathyanarayana
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
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10
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Gonzalez TL, Wertheimer S, Flowers AE, Wang Y, Santiskulvong C, Clark EL, Jefferies CA, Lawrenson K, Chan JL, Joshi NV, Zhu Y, Tseng HR, Karumanchi SA, Williams J, Pisarska MD. High-throughput mRNA-seq atlas of human placenta shows vast transcriptome remodeling from first to third trimester. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543972. [PMID: 37333287 PMCID: PMC10274746 DOI: 10.1101/2023.06.06.543972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Background The placenta, composed of chorionic villi, changes dramatically across gestation. Understanding differences in ongoing pregnancies are essential to identify the role of chorionic villi at specific times in gestation and develop biomarkers and prognostic indicators of maternal- fetal health. Methods The normative mRNA profile is established using next-generation sequencing of 124 first trimester and 43 third trimester human placentas from ongoing healthy pregnancies. Stably expressed genes not different between trimesters and with low variability are identified. Differential expression analysis of first versus third trimester adjusted for fetal sex is performed, followed by a subanalysis with 23 matched pregnancies to control for subject variability using the same genetic and environmental background. Results Placenta expresses 14,979 mRNAs above sequencing noise (TPM>0.66), with 1,545 stably expressed genes across gestation. Differentially expressed genes account for 86.7% of genes in the full cohort (FDR<0.05). Fold changes highly correlate between the full cohort and subanalysis (Pearson = 0.98). At stricter thresholds (FDR<0.001, fold change>1.5), there are 6,941 differentially expressed protein coding genes (3,206 upregulated in first and 3,735 upregulated in third trimester). Conclusion This is the largest mRNA atlas of healthy human placenta across gestation, controlling for genetic and environmental factors, demonstrating substantial changes from first to third trimester in chorionic villi. Specific differences and stably expressed genes may be used to understand the specific role of the chorionic villi throughout gestation and develop first trimester biomarkers of placental health that transpire across gestation, which can be used for future development of biomarkers in maternal-fetal disease.
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11
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Olney KC, Plaisier SB, Phung TN, Silasi M, Perley L, O'Bryan J, Ramirez L, Kliman HJ, Wilson MA. Sex differences in early and term placenta are conserved in adult tissues. Biol Sex Differ 2022; 13:74. [PMID: 36550527 PMCID: PMC9773522 DOI: 10.1186/s13293-022-00470-y] [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: 08/08/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Pregnancy complications vary based on the fetus's genetic sex, which may, in part, be modulated by the placenta. Furthermore, developmental differences early in life can have lifelong health outcomes. Yet, sex differences in gene expression within the placenta at different timepoints throughout pregnancy and comparisons to adult tissues remains poorly characterized. METHODS Here, we collect and characterize sex differences in gene expression in term placentas (≥ 36.6 weeks; 23 male XY and 27 female XX). These are compared with sex differences in previously collected first trimester placenta samples and 42 non-reproductive adult tissues from GTEx. RESULTS We identify 268 and 53 sex-differentially expressed genes in the uncomplicated late first trimester and term placentas, respectively. Of the 53 sex-differentially expressed genes observed in the term placentas, 31 are also sex-differentially expressed genes in the late first trimester placentas. Furthermore, sex differences in gene expression in term placentas are highly correlated with sex differences in the late first trimester placentas. We found that sex-differential gene expression in the term placenta is significantly correlated with sex differences in gene expression in 42 non-reproductive adult tissues (correlation coefficient ranged from 0.892 to 0.957), with the highest correlation in brain tissues. Sex differences in gene expression were largely driven by gene expression on the sex chromosomes. We further show that some gametologous genes (genes with functional copies on X and Y) will have different inferred sex differences if the X-linked gene expression in females is compared to the sum of the X-linked and Y-linked gene expression in males. CONCLUSIONS We find that sex differences in gene expression are conserved in late first trimester and term placentas and that these sex differences are conserved in adult tissues. We demonstrate that there are sex differences associated with innate immune response in late first trimester placentas but there is no significant difference in gene expression of innate immune genes between sexes in healthy full-term placentas. Finally, sex differences are predominantly driven by expression from sex-linked genes.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Seema B Plaisier
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Tanya N Phung
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Michelle Silasi
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Mercy Hospital St. Louis, St. Louis, MO, 63141, USA
| | - Lauren Perley
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Jane O'Bryan
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Lucia Ramirez
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85282, USA.
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA.
- The Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85282, USA.
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12
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LeWinn KZ, Karr CJ, Hazlehurst M, Carroll K, Loftus C, Nguyen R, Barrett E, Swan SH, Szpiro AA, Paquette A, Moore P, Spalt E, Younglove L, Sullivan A, Colburn T, Byington N, Sims Taylor L, Moe S, Wang S, Cordeiro A, Mattias A, Powell J, Johnson T, Norona-Zhou A, Mason A, Bush NR, Sathyanarayana S. Cohort profile: the ECHO prenatal and early childhood pathways to health consortium (ECHO-PATHWAYS). BMJ Open 2022; 12:e064288. [PMID: 36270755 PMCID: PMC9594508 DOI: 10.1136/bmjopen-2022-064288] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
PURPOSE Exposures early in life, beginning in utero, have long-term impacts on mental and physical health. The ECHO prenatal and early childhood pathways to health consortium (ECHO-PATHWAYS) was established to examine the independent and combined impact of pregnancy and childhood chemical exposures and psychosocial stressors on child neurodevelopment and airway health, as well as the placental mechanisms underlying these associations. PARTICIPANTS The ECHO-PATHWAYS consortium harmonises extant data from 2684 mother-child dyads in three pregnancy cohort studies (CANDLE [Conditions Affecting Neurocognitive Development and Learning in Early Childhood], TIDES [The Infant Development and Environment Study] and GAPPS [Global Alliance to Prevent Prematurity and Stillbirth]) and collects prospective data under a unified protocol. Study participants are socioeconomically diverse and include a large proportion of Black families (38% Black and 51% White), often under-represented in research. Children are currently 5-15 years old. New data collection includes multimodal assessments of primary outcomes (airway health and neurodevelopment) and exposures (air pollution, phthalates and psychosocial stress) as well as rich covariate characterisation. ECHO-PATHWAYS is compiling extant and new biospecimens in a central biorepository and generating the largest placental transcriptomics data set to date (N=1083). FINDINGS TO DATE Early analyses demonstrate adverse associations of prenatal exposure to air pollution, phthalates and maternal stress with early childhood airway outcomes and neurodevelopment. Placental transcriptomics work suggests that phthalate exposure alters placental gene expression, pointing to mechanistic pathways for the developmental toxicity of phthalates. We also observe associations between prenatal maternal stress and placental corticotropin releasing hormone, a marker of hormonal activation during pregnancy relevant for child health. Other publications describe novel methods for examining exposure mixtures and the development of a national spatiotemporal model of ambient outdoor air pollution. FUTURE PLANS The first wave of data from the unified protocol (child age 8-9) is nearly complete. Future work will leverage these data to examine the combined impact of early life social and chemical exposures on middle childhood health outcomes and underlying placental mechanisms.
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Affiliation(s)
- Kaja Z LeWinn
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Catherine J Karr
- Department of Environmental and Occupational Health Sciences and Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, Washington, USA
| | - Marnie Hazlehurst
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Kecia Carroll
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christine Loftus
- Department of Environmental Health and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Ruby Nguyen
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota System, Minneapolis, Minnesota, USA
| | - Emily Barrett
- Department of Biostatistics and Epidemiology, Environmental and Occupational Health Sciences Institute (EOHSI), Rutgers School of Public Health, Rutgers University, Piscataway, New Jersey, USA
| | - Shanna H Swan
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Adam A Szpiro
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Alison Paquette
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, Washington, USA
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Paul Moore
- Division of Allergy, Immunology, and Pulmonology and the Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Elizabeth Spalt
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Lisa Younglove
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Alexis Sullivan
- Center for Health and Community, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Trina Colburn
- Center for Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Nora Byington
- Center for Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Lauren Sims Taylor
- Department of Preventive Medicine, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Stacey Moe
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota System, Minneapolis, Minnesota, USA
| | - Sarah Wang
- Center for Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Alana Cordeiro
- Center for Health and Community, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Aria Mattias
- Department of Envrionmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jennifer Powell
- Center for Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Tye Johnson
- Department of Obstetrics and Gynecology, University of Rochester Medical Center, Rochester, New York, USA
| | - Amanda Norona-Zhou
- Center for Health and Community, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Alex Mason
- Department of Preventive Medicine, College of Medicine, The University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences and the Department of Pediatrics, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sheela Sathyanarayana
- Center for Child Health, Behavior, and Development, Seattle Children's Research Institute, Seattle, Washington, USA
- Department of Environmental and Occupational Health Sciences, School of Public Health; Department of Pediatrics, School of Medicine, University of Washington, Seattle, Washington, USA
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13
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Gil GP, Ananina G, Maschietto M, Lima SCS, da Silva Costa SM, Baptista LDC, Ito MT, Costa FF, Costa ML, de Melo MB. Epigenetic analysis in placentas from sickle cell disease patients reveals a hypermethylation profile. PLoS One 2022; 17:e0274762. [PMID: 36129958 PMCID: PMC9491616 DOI: 10.1371/journal.pone.0274762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/05/2022] [Indexed: 11/25/2022] Open
Abstract
Pregnancy in Sickle Cell Disease (SCD) women is associated to increased risk of clinical and obstetrical complications. Placentas from SCD pregnancies can present increased abnormal findings, which may lead to placental insufficiency, favoring adverse perinatal outcome. These placental abnormalities are well known and reported, however little is known about the molecular mechanisms, such as epigenetics. Thus, our aim was to evaluate the DNA methylation profile in placentas from women with SCD (HbSS and HbSC genotypes), compared to uncomplicated controls (HbAA). We included in this study 11 pregnant women with HbSS, 11 with HbSC and 21 with HbAA genotypes. Illumina Methylation EPIC BeadChip was used to assess the whole placental DNA methylation. Pyrosequencing was used for array data validation and qRT-PCR was applied for gene expression analysis. Our results showed high frequency of hypermethylated CpGs sites in HbSS and HbSC groups with 73.5% and 76.2% respectively, when compared with the control group. Differentially methylated regions (DMRs) also showed an increased hypermethylation status for the HbSS (89%) and HbSC (86%) groups, when compared with the control group methylation data. DMRs were selected for methylation validation (4 DMRs-HbSS and 3 DMRs the HbSC groups) and after analyses three were validated in the HbSS group, and none in the HbSC group. The gene expression analysis showed differential expression for the PTGFR (-2.97-fold) and GPR56 (3.0-fold) genes in the HbSS group, and for the SPOCK1 (-2.40-fold) and ADCY4 (1.80-fold) genes in the HbSC group. Taken together, these data strongly suggest that SCD (HbSS and HbSC genotypes) can alter placental DNA methylation and lead to gene expression changes. These changes possibly contribute to abnormal placental development and could impact in the clinical course, especially for the fetus, possibly leading to increased risk of abortion, fetal growth restriction (FGR), stillbirth, small for gestational age newborns and prematurity.
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Affiliation(s)
- Gislene Pereira Gil
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - Galina Ananina
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | | | | | - Sueli Matilde da Silva Costa
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - Leticia de Carvalho Baptista
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | - Mirta Tomie Ito
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
| | | | - Maria Laura Costa
- Department of Obstetrics and Gynecology, University of Campinas, Campinas, São Paulo, Brazil
| | - Mônica Barbosa de Melo
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas-UNICAMP, Campinas, São Paulo, Brazil
- * E-mail:
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14
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Meyrueix LP, Gharaibeh R, Xue J, Brouwer C, Jones C, Adair L, Norris SA, Ideraabdullah F. Gestational diabetes mellitus placentas exhibit epimutations at placental development genes. Epigenetics 2022; 17:2157-2177. [DOI: 10.1080/15592294.2022.2111751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Affiliation(s)
| | - Raad Gharaibeh
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
- Bioinformatics Service Division, University of North Carolina, Charlotte, NC, USA
- Department of Medicine, Division of Gastroenterology, University of Florida, Gainesville, FL, USA
| | - Jing Xue
- Genetics Department, University of North Carolina, Chapel Hill, NC, USA
| | - Cory Brouwer
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA
- Bioinformatics Service Division, University of North Carolina, Charlotte, NC, USA
| | - Corbin Jones
- Department of Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Linda Adair
- Nutrition Department, University of North Carolina, Chapel Hill, NC, USA
| | - Shane A. Norris
- SAMRC Developmental Health Pathways for Health Research Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Folami Ideraabdullah
- Nutrition Department, University of North Carolina, Chapel Hill, NC, USA
- Genetics Department, University of North Carolina, Chapel Hill, NC, USA
- SAMRC Developmental Health Pathways for Health Research Unit, University of Witwatersrand, Johannesburg, South Africa
- Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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15
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Enquobahrie DA, MacDonald J, Hussey M, Bammler TK, Loftus CT, Paquette AG, Byington N, Marsit CJ, Szpiro A, Kaufman JD, LeWinn KZ, Bush NR, Tylavsky F, Karr CJ, Sathyanarayana S. Prenatal exposure to particulate matter and placental gene expression. ENVIRONMENT INTERNATIONAL 2022; 165:107310. [PMID: 35653832 PMCID: PMC9235522 DOI: 10.1016/j.envint.2022.107310] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 04/13/2022] [Accepted: 05/16/2022] [Indexed: 05/30/2023]
Abstract
BACKGROUND While strong evidence supports adverse maternal and offspring consequences of air pollution, mechanisms that involve the placenta, a key part of the intrauterine environment, are largely unknown. Previous studies of air pollution and placental gene expression were small candidate gene studies that rarely considered prenatal windows of exposure or the potential role of offspring sex. We examined overall and sex-specific associations of prenatal exposure to fine particulate matter (PM2.5) with genome-wide placental gene expression. METHODS Participants with placenta samples, collected at birth, and childhood health outcomes from CANDLE (Memphis, TN) (n = 776) and GAPPS (Seattle, WA) (n = 205) cohorts of the ECHO-PATHWAYS Consortium were included in this study. PM2.5 exposures during trimesters 1, 2, 3, and the first and last months of pregnancy, were estimated using a spatiotemporal model. Cohort-specific linear adjusted models were fit for each exposure window and expression of >11,000 protein coding genes from paired end RNA sequencing data. Models with interaction terms were used to examine PM2.5-offspring sex interactions. False discovery rate (FDR < 0.10) was used to correct for multiple testing. RESULTS Mean PM2.5 estimate was 10.5-10.7 μg/m3 for CANDLE and 6.0-6.3 μg/m3 for GAPPS participants. In CANDLE, expression of 13 (11 upregulated and 2 downregulated), 20 (11 upregulated and 9 downregulated) and 3 (2 upregulated and 1 downregulated) genes was associated with PM2.5 in the first trimester, second trimester, and first month, respectively. While we did not find any statistically significant association, overall, between PM2.5 and gene expression in GAPPS, we found offspring sex and first month PM2.5 interaction for DDHD1 expression (positive association among males and inverse association among females). We did not observe PM2.5 and offspring sex interactions in CANDLE. CONCLUSION In CANDLE, but not GAPPS, we found that prenatal PM2.5 exposure during the first half of pregnancy is associated with placental gene expression.
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Affiliation(s)
- Daniel A Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States; Department of Health Systems and Population Health, School of Public Health, University of Washington, Seattle, WA, United States.
| | - James MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Michael Hussey
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Christine T Loftus
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Alison G Paquette
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, United States; Seattle Children's Research Institute, Seattle, WA, United States
| | - Nora Byington
- Seattle Children's Research Institute, Seattle, WA, United States
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Adam Szpiro
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, United States
| | - Joel D Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Kaja Z LeWinn
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, United States; Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Frances Tylavsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Catherine J Karr
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, United States
| | - Sheela Sathyanarayana
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, United States; Seattle Children's Research Institute, Seattle, WA, United States
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16
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Lapehn S, Paquette AG. The Placental Epigenome as a Molecular Link Between Prenatal Exposures and Fetal Health Outcomes Through the DOHaD Hypothesis. Curr Environ Health Rep 2022; 9:490-501. [PMID: 35488174 PMCID: PMC9363315 DOI: 10.1007/s40572-022-00354-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/08/2022] [Indexed: 12/31/2022]
Abstract
Purpose of Review The developmental origins of health and disease (DOHaD) hypothesis posits that the perinatal environment can impact fetal and later life health. The placenta is uniquely situated to assess prenatal exposures in the context of DOHaD because it is an essential ephemeral fetal organ that manages the transport of oxygen, nutrients, waste, and endocrine signals between the mother and fetus. The purpose of this review is to summarize recent studies that evaluated the DOHaD hypothesis in human placentas using epigenomics, including DNA methylation and transcriptomic studies of mRNA, lncRNA, and microRNAs. Recent Findings Between 2016 and 2021, 28 articles evaluated associations between prenatal exposures and placental epigenomics across broad exposure categories including maternal smoking, psychosocial stressors, chemicals, air pollution, and metals. Sixteen of these studies connected exposures to health outcome such as birth weight, fetal growth, or infant neurobehavior through mediation analysis, identification of shared associations between exposure and outcome, or network analysis. These aspects of infant and childhood health serve as a foundation for future studies that aim to use placental epigenetics to understand relationships between the prenatal environment and perinatal complications (such as preterm birth or fetal growth restriction) or later life childhood health. Summary Placental DNA methylation and RNA expression have been linked to numerous prenatal exposures, such as PM2.5 air pollution, metals, and maternal smoking, as well as infant and childhood health outcomes, including fetal growth and birth weight. Placental epigenomics provides a unique opportunity to expand the DOHaD premise, particularly if research applies novel methodologies such as multi-omics analysis, sequencing of non-coding RNAs, mixtures analysis, and assessment of health outcomes beyond early childhood.
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Affiliation(s)
- Samantha Lapehn
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA, 98101, USA
| | - Alison G Paquette
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 9th Avenue, Seattle, WA, 98101, USA. .,Department of Pediatrics, University of Washington, Seattle, WA, USA.
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17
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Bogias KJ, Pederson SM, Leemaqz S, Smith MD, McAninch D, Jankovic-Karasoulos T, McCullough D, Wan Q, Bianco-Miotto T, Breen J, Roberts CT. Placental Transcription Profiling in 6-23 Weeks' Gestation Reveals Differential Transcript Usage in Early Development. Int J Mol Sci 2022; 23:ijms23094506. [PMID: 35562897 PMCID: PMC9105363 DOI: 10.3390/ijms23094506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/13/2022] Open
Abstract
The human placenta is a rapidly developing transient organ that is key to pregnancy success. Early development of the conceptus occurs in a low oxygen environment before oxygenated maternal blood begins to flow into the placenta at ~10-12 weeks' gestation. This process is likely to substantially affect overall placental gene expression. Transcript variability underlying gene expression has yet to be profiled. In this study, accurate transcript expression profiles were identified for 84 human placental chorionic villus tissue samples collected across 6-23 weeks' gestation. Differential gene expression (DGE), differential transcript expression (DTE) and differential transcript usage (DTU) between 6-10 weeks' and 11-23 weeks' gestation groups were assessed. In total, 229 genes had significant DTE yet no significant DGE. Integration of DGE and DTE analyses found that differential expression patterns of individual transcripts were commonly masked upon aggregation to the gene-level. Of the 611 genes that exhibited DTU, 534 had no significant DGE or DTE. The four most significant DTU genes ADAM10, VMP1, GPR126, and ASAH1, were associated with hypoxia-responsive pathways. Transcript usage is a likely regulatory mechanism in early placentation. Identification of functional roles will facilitate new insight in understanding the origins of pregnancy complications.
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Affiliation(s)
- Konstantinos J. Bogias
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Stephen M. Pederson
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia;
| | - Shalem Leemaqz
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Melanie D. Smith
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dale McAninch
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
| | - Tanja Jankovic-Karasoulos
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Dylan McCullough
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Qianhui Wan
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute (Adelaide Office), Adelaide, SA 5000, Australia;
- College of Health & Medicine, Australian National University, Canberra, ACT 2600, Australia
| | - Claire T. Roberts
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia; (K.J.B.); (S.L.); (D.M.); (T.J.-K.)
- Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia;
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia; (M.D.S.); (D.M.); (Q.W.)
- Correspondence:
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18
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Paquette AG, MacDonald J, Lapehn S, Bammler T, Kruger L, Day DB, Price ND, Loftus C, Kannan K, Marsit C, Mason WA, Bush NR, LeWinn KZ, Enquobahrie DA, Prasad B, Karr CJ, Sathyanarayana S. A Comprehensive Assessment of Associations between Prenatal Phthalate Exposure and the Placental Transcriptomic Landscape. ENVIRONMENTAL HEALTH PERSPECTIVES 2021; 129:97003. [PMID: 34478338 PMCID: PMC8415559 DOI: 10.1289/ehp8973] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
BACKGROUND Phthalates are commonly used endocrine-disrupting chemicals that are ubiquitous in the general population. Prenatal phthalate exposure may alter placental physiology and fetal development, leading to adverse perinatal and childhood health outcomes. OBJECTIVE We examined associations between prenatal phthalate exposure in the second and third trimesters and the placental transcriptome at birth, including genes and long noncoding RNAs (lncRNAs), to gain insight into potential mechanisms of action during fetal development. METHODS The ECHO PATHWAYs consortium quantified 21 urinary phthalate metabolites from 760 women enrolled in the CANDLE study (Shelby County, TN) using high-performance liquid chromatography-tandem mass spectrometry. Placental transcriptomic data were obtained using paired-end RNA sequencing. Linear models were fitted to estimate separate associations between maternal urinary phthalate metabolite concentration during the second and third trimester and placental gene expression at birth, adjusted for confounding variables. Genes were considered differentially expressed at a Benjamini-Hochberg false discovery rate (FDR) p<0.05. Associations between phthalate metabolites and biological pathways were identified using self-contained gene set testing and considered significantly altered with an FDR-adjusted p<0.2. RESULTS We observed significant associations between second-trimester phthalate metabolites mono (carboxyisooctyl) phthalate (MCIOP), mono-2-ethyl-5-carboxypentyl phthalate, and mono-2-ethyl-5-oxohexyl phthalate and 18 genes in total, including four lncRNAs. Specifically, placental expression of NEAT1 was associated with multiple phthalate metabolites. Third-trimester MCIOP and mono-isobutyl phthalate concentrations were significantly associated with placental expression of 18 genes and two genes, respectively. Expression of genes within 27 biological pathways was associated with mono-methyl phthalate, MCIOP, and monoethyl phthalate concentrations. DISCUSSION To our knowledge, this is the first genome-wide assessment of the relationship between the placental transcriptome at birth and prenatal phthalate exposure in a large and diverse birth cohort. We identified numerous genes and lncRNAs associated with prenatal phthalate exposure. These associations mirror findings from other epidemiological and in vitro analyses and may provide insight into biological pathways affected in utero by phthalate exposure. https://doi.org/10.1289/EHP8973.
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Affiliation(s)
- Alison G. Paquette
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
| | | | - Samantha Lapehn
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Theo Bammler
- University of Washington, Seattle, Washington, USA
| | - Laken Kruger
- Washington State University, Spokane, Washington, USA
| | - Drew B. Day
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Nathan D. Price
- Institute For Systems Biology, Seattle, Washington, USA
- Onegevity Health, New York City, New York, USA
| | | | | | | | - W. Alex Mason
- University of Tennessee Health Sciences Center, Memphis, Tennessee, USA
| | - Nicole R. Bush
- University of California San Francisco, San Francisco California, USA
| | - Kaja Z. LeWinn
- University of California San Francisco, San Francisco California, USA
| | | | | | | | - Sheela Sathyanarayana
- Seattle Children’s Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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19
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Li H, Huang Q, Liu Y, Garmire LX. Single cell transcriptome research in human placenta. Reproduction 2021; 160:R155-R167. [PMID: 33112783 PMCID: PMC7707799 DOI: 10.1530/rep-20-0231] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 09/22/2020] [Indexed: 12/30/2022]
Abstract
Human placenta is a complex and heterogeneous organ interfacing between the mother and the fetus that supports fetal development. Alterations to placental structural components are associated with various pregnancy complications. To reveal the heterogeneity among various placenta cell types in normal and diseased placentas, as well as elucidate molecular interactions within a population of placental cells, a new genomics technology called single cell RNA-seq (or scRNA-seq) has been employed in the last couple of years. Here we review the principles of scRNA-seq technology, and summarize the recent human placenta studies at scRNA-seq level across gestational ages as well as in pregnancy complications, such as preterm birth and preeclampsia. We list the computational analysis platforms and resources available for the public use. Lastly, we discuss the future areas of interest for placenta single cell studies, as well as the data analytics needed to accomplish them.
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Affiliation(s)
- Hui Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Qianhui Huang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Yu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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20
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Proteome profiling of human placenta reveals developmental stage-dependent alterations in protein signature. Clin Proteomics 2021; 18:18. [PMID: 34372761 PMCID: PMC8351416 DOI: 10.1186/s12014-021-09324-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 08/01/2021] [Indexed: 12/26/2022] Open
Abstract
Introduction Placenta is a complex organ that plays a significant role in the maintenance of pregnancy health. It is a dynamic organ that undergoes dramatic changes in growth and development at different stages of gestation. In the first-trimester, the conceptus develops in a low oxygen environment that favors organogenesis in the embryo and cell proliferation and angiogenesis in the placenta; later in pregnancy, higher oxygen concentration is required to support the rapid growth of the fetus. This oxygen transition, which appears unique to the human placenta, must be finely tuned through successive rounds of protein signature alterations. This study compares placental proteome in normal first-trimester (FT) and term human placentas (TP). Methods Normal human first-trimester and term placental samples were collected and differentially expressed proteins were identified using two-dimensional liquid chromatography-tandem mass spectrometry. Results Despite the overall similarities, 120 proteins were differently expressed in first and term placentas. Out of these, 72 were up-regulated and 48 were down-regulated in the first when compared with the full term placentas. Twenty out of 120 differently expressed proteins were sequenced, among them seven showed increased (GRP78, PDIA3, ENOA, ECH1, PRDX4, ERP29, ECHM), eleven decreased (TRFE, ALBU, K2C1, ACTG, CSH2, PRDX2, FABP5, HBG1, FABP4, K2C8, K1C9) expression in first-trimester compared to the full-term placentas and two proteins exclusively expressed in first-trimester placentas (MESD, MYDGF). Conclusion According to Reactome and PANTHER softwares, these proteins were mostly involved in response to chemical stimulus and stress, regulation of biological quality, programmed cell death, hemostatic and catabolic processes, protein folding, cellular oxidant detoxification, coagulation and retina homeostasis. Elucidation of alteration in protein signature during placental development would provide researchers with a better understanding of the critical biological processes of placentogenesis and delineate proteins involved in regulation of placental function during development. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-021-09324-y.
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21
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Bartho LA, O'Callaghan JL, Fisher JJ, Cuffe JSM, Kaitu'u-Lino TJ, Hannan NJ, Clifton VL, Perkins AV. Analysis of mitochondrial regulatory transcripts in publicly available datasets with validation in placentae from pre-term, post-term and fetal growth restriction pregnancies. Placenta 2021; 112:162-171. [PMID: 34364121 DOI: 10.1016/j.placenta.2021.07.303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The human placenta has a defined lifespan and placental aging is a key feature as pregnancy progresses. Placental aging and mitochondrial dysfunction are known to play a key role in pregnancy pathophysiology. Premature aging of the placenta has also been linked with placental dysfunction resulting in poor fetal development and premature birth. METHODS The expression of key mitochondrial-related genes were analysed in a series of publicly available databases then expression changes were validated in placental samples collected from term, pre-term, post-term pregnancies and pregnancies complicated by fetal growth restriction (FGR). Gene and protein expression levels of MFN1, MFN2, TFAM, TOMM20, OPA3 and SIRT4 were measured in placental tissues via qPCR and western blotting. RESULTS Initial analysis found that key mitochondrial transcripts related to biogenesis, bioenergetics and mitophagy clustered by pregnancy trimester. A refined list of 13 mitochondrial-related genes were investigated in additional external datasets of pregnancy complications. In the new cohort, protein expression of MFN1 was decreased in FGR and MFN2 is decreased in post-term placenta. Analysis of placental tissues revealed that TOMM20 gene and protein expression was altered in FGR and post-term placenta. DISCUSSION MFN1 and MFN2 play a major role in mitochondrial dynamics, and alterations in these markers have been highlighted in early unexplained miscarriage. TOMM20 is an importer protein that plays a major role in mitophagy and changes have also been identified in age-related diseases. Significant changes in MFN1, MFN2 and TOMM20 indicate that mitochondrial regulators play a critical role in placental aging and placental pathophysiology.
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Affiliation(s)
- Lucy A Bartho
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, Queensland, Australia
| | - Jessica L O'Callaghan
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Qld, Australia
| | - Joshua J Fisher
- Hunter Medical Research Institute and School of Medicine and Public Health, University of Newcastle, Newcastle, New South Wales, Australia
| | - James S M Cuffe
- School of Biomedical Sciences, University of Queensland, St. Lucia, Queensland, Australia
| | - Tu'uhevaha J Kaitu'u-Lino
- Translational Obstetrics Group, Dept of Obstetrics and Gynaecology University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Natalie J Hannan
- Translational Obstetrics Group, Dept of Obstetrics and Gynaecology University of Melbourne, Mercy Hospital for Women, Heidelberg, Victoria, Australia
| | - Vicki L Clifton
- Pregnancy and Development Group, Mater Research, Translational Research Institute, The University of Queensland, Brisbane, Qld, Australia
| | - Anthony V Perkins
- School of Pharmacy and Medical Science, Griffith University, Gold Coast Campus, Southport, Queensland, Australia.
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22
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Bazhenov DO, Khokhlova EV, Viazmina LP, Furaeva KN, Mikhailova VA, Kostin NA, Selkov SA, Sokolov DI. Characteristics of Natural Killer Cell Interaction with Trophoblast Cells During Pregnancy. Curr Mol Med 2021; 20:202-219. [PMID: 31393246 DOI: 10.2174/1566524019666190808103227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/19/2019] [Accepted: 07/30/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Maternal natural killer cells (NK cells) are a prevailing leukocyte population in the uteroplacental bed. Current descriptions of the effect of cytokines from the placental microenvironment on the expression of receptors by trophoblast and NK cells are inadequate and contradictory. There is insufficient information about the ability of NK cells to migrate through trophoblast cells. OBJECTIVE To assess the impact of conditioned media obtained during culturing of placentas from the first and the third trimesters of healthy pregnancies on the phenotype of trophoblast and NK cells and impact on adhesion and transmigration of NK cells through trophoblast cell layer. RESULTS We established that conditioned media obtained from both first and third trimester placentas increased the intensity of CD106, CD49e, CD49a, CD31, CD51/61, and integrin β6 expression by trophoblast cells. Conditioned media obtained from first trimester placentas increased the intensity of CD11a, CD29, CD49d, CD58, CD29 expression by NK cells. The presence of conditioned media from third trimester placentas resulted in more intense CD29, CD49d, CD11a, CD29, CD49d, and CD58 expression by NK cells. Migration of NK cells through trophoblast cells in the presence of conditioned media from first trimester placentas was increased compared with the migration level in the presence of conditioned media from third trimester placentas. This may be associated with increased expression of CD18 by NK cells. CONCLUSION First trimester placental secretory products increase adhesion receptor expression by both trophoblast and NK cells. Under these conditions, trophoblast is capable of ensuring NK cell adhesion and transmigration.
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Affiliation(s)
- Dmitry Olegovich Bazhenov
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation.,Federal State Budgetary Scientific Institution Research Institute of Experimental Medicine, Russian Federation
| | - Evgeniya Valerevna Khokhlova
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation
| | - Larisa Pavlovna Viazmina
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation
| | - Kseniya Nikolaevna Furaeva
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation
| | - Valentina Anatolievna Mikhailova
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation
| | - Nikolay Anatolievich Kostin
- Resource Centre for the Molecular and Cell Technologies Development, Saint Petersburg State University, Saint- Petersburg, Russian Federation
| | - Sergey Alekseevich Selkov
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation
| | - Dmitry Igorevich Sokolov
- Federal State Budgetary Scientific Institution Research Institute of Obstetrics, Gynecology and Reproductology named after D.O. Ott, Mendeleevskya line, 199034, Saint-Petersburg, Russian Federation.,Federal State Budgetary Scientific Institution Research Institute of Experimental Medicine, Russian Federation
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23
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Prater M, Hamilton RS, Wa Yung H, Sharkey AM, Robson P, Abd Hamid NE, Jauniaux E, Charnock-Jones DS, Burton GJ, Cindrova-Davies T. RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first-second trimester transition. Biol Open 2021; 10:268993. [PMID: 34100896 PMCID: PMC8214423 DOI: 10.1242/bio.058222] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
The human placenta is exposed to major environmental changes towards the end of the first trimester associated with full onset of the maternal arterial placental circulation. Changes include a switch from histotrophic to hemotrophic nutrition, and a threefold rise in the intraplacental oxygen concentration. We evaluated their impact on trophoblast development and function using RNA-sequencing (RNA-Seq) and DNA-methylation analyses performed on the same chorionic villous samples at 7-8 (n=8) and 13-14 (n=6) weeks of gestation. Reads were adjusted for fetal sex. Most DEGs were associated with protein processing in the endoplasmic reticulum (ER), hormone secretion, transport, extracellular matrix, vasculogenesis, and reactive oxygen species metabolism. Transcripts higher in the first trimester were associated with synthesis and ER processing of peptide hormones, and glycolytic pathways. Transcripts encoding proteins mediating transport of oxygen, lipids, protein, glucose, and ions were significantly increased in the second trimester. The motifs of CBX3 and BCL6 were significantly overrepresented, indicating the involvement of these transcription factor networks in the regulation of trophoblast migration, proliferation and fusion. These findings are consistent with a high level of cell proliferation and hormone secretion by the early placenta to secure implantation in a physiological low-oxygen environment.
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Affiliation(s)
- Malwina Prater
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
| | - Russell S Hamilton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Hong Wa Yung
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
| | - Andrew M Sharkey
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Paul Robson
- The Jackson Laboratory, The JAX Center for Genetics of Fertility and Reproduction, 10 Discovery Drive, Farmington, CT 06032, USA.,Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Eric Jauniaux
- Department of Obstetrics and Gynaecology, EGA Institute for Women's Health, Faculty of Population Health Sciences, University College London, London, WC1E 6BT, UK
| | - D Stephen Charnock-Jones
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.,Department of Obstetrics and Gynaecology, University of Cambridge, The Rosie Hospital, Cambridge, CB2 0SW, UK.,National Institute for Health Research, Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, UK
| | - Graham J Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
| | - Tereza Cindrova-Davies
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK
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Napso T, Zhao X, Lligoña MI, Sandovici I, Kay RG, George AL, Gribble FM, Reimann F, Meek CL, Hamilton RS, Sferruzzi-Perri AN. Placental secretome characterization identifies candidates for pregnancy complications. Commun Biol 2021; 4:701. [PMID: 34103657 PMCID: PMC8187406 DOI: 10.1038/s42003-021-02214-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 05/12/2021] [Indexed: 11/09/2022] Open
Abstract
Alterations in maternal physiological adaptation during pregnancy lead to complications, including abnormal birthweight and gestational diabetes. Maternal adaptations are driven by placental hormones, although the full identity of these is lacking. This study unbiasedly characterized the secretory output of mouse placental endocrine cells and examined whether these data could identify placental hormones important for determining pregnancy outcome in humans. Secretome and cell peptidome analyses were performed on cultured primary trophoblast and fluorescence-activated sorted endocrine trophoblasts from mice and a placental secretome map was generated. Proteins secreted from the placenta were detectable in the circulation of mice and showed a higher relative abundance in pregnancy. Bioinformatic analyses showed that placental secretome proteins are involved in metabolic, immune and growth modulation, are largely expressed by human placenta and several are dysregulated in pregnancy complications. Moreover, proof-of-concept studies found that secreted placental proteins (sFLT1/MIF and ANGPT2/MIF ratios) were increased in women prior to diagnosis of gestational diabetes. Thus, placental secretome analysis could lead to the identification of new placental biomarkers of pregnancy complications.
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Affiliation(s)
- Tina Napso
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Xiaohui Zhao
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Marta Ibañez Lligoña
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Ionel Sandovici
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, UK
| | - Richard G Kay
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Amy L George
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Fiona M Gribble
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Frank Reimann
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Claire L Meek
- Wellcome-MRC Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Russell S Hamilton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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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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Ayala-Ramírez P, Gámez T, Castro-Pontón DL, Silva J, García-Robles R, Olaya-C M. Expression of tissue factor and thrombomodulin in the placentas of pregnancies affected by early-onset and late-onset preeclampsia. J Obstet Gynaecol Res 2021; 47:2307-2317. [PMID: 33876519 DOI: 10.1111/jog.14793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/17/2021] [Accepted: 03/20/2021] [Indexed: 11/26/2022]
Abstract
AIM To analyze the differential genetic expression and protein localization of thrombomodulin (THBD) and tissue factor (F3) in the placentas of pregnancies affected by preeclampsia. METHODS We assessed the expression of THBD and F3 by immunohistochemistry and real-time polymerase chain reaction (PCR) in placentas from 20 PE cases: 10 early-onset PE placentas, 10 late-onset PE placentas, and 10 control cases (normal pregnancies). RESULTS In cases, we found higher THBD and F3 RNA levels in placental tissue. Protein expression in controls differed from that in late-onset PE placentas, which had lower THBD levels in syncytiotrophoblasts and amniotic cells. Likewise, late-onset PE placentas exhibited comparatively lower F3 expression in the perivillous fibrin. In contrast, early-onset PE had high F3 expression in the subdecidual fibrin. We found no significant differences in the F3/THBD ratio between the groups. CONCLUSION Our study supports evidence that shows the involvement of F3 and THBD in placental disorders. Furthermore, this finding contributes to a better understanding of the physio-pathological role that these molecules may play in the development of this heterogeneous disease.
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Affiliation(s)
- Paola Ayala-Ramírez
- Human Genetics Institute. Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Tatiana Gámez
- Human Genetics Institute. Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Derna L Castro-Pontón
- Department of Pathology. Faculty of Medicine, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Jaime Silva
- Department of Obstetrics and Gynecology. Faculty of Medicine - Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá, Colombia
| | - Reggie García-Robles
- Department of Physiological Sciences. Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Mercedes Olaya-C
- Department of Pathology. Faculty of Medicine, Pontificia Universidad Javeriana, Hospital Universitario San Ignacio, Bogotá, Colombia
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Liu F, Simasotchi C, Vibert F, Zhu W, Gil S, Degrelle SA, Fournier T. Age and Sex-Related Changes in Human First-Trimester Placenta Transcriptome and Insights into Adaptative Responses to Increased Oxygen. Int J Mol Sci 2021; 22:ijms22062901. [PMID: 33809345 PMCID: PMC8001632 DOI: 10.3390/ijms22062901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/17/2022] Open
Abstract
Physiological oxygen tension rises dramatically in the placenta between 8 and 14 weeks of gestation. Abnormalities in this period can lead to gestational diseases, whose underlying mechanisms remain unclear. We explored the changes at mRNA level by comparing the transcriptomes of human placentas at 8–10 gestational weeks and 12–14 gestational weeks. A total of 20 samples were collected and divided equally into four groups based on sex and age. Cytotrophoblasts were isolated and sequenced using RNAseq. Key genes were identified using two different methods: DESeq2 and weighted gene co-expression network analysis (WGCNA). We also constructed a local database of known targets of hypoxia-inducible factor (HIF) subunits, alpha and beta, to investigate expression patterns likely linked with changes in oxygen. Patterns of gene enrichment in and among the four groups were analyzed based on annotations of gene ontology (GO) and KEGG pathways. We characterized the similarities and differences between the enrichment patterns revealed by the two methods and the two conditions (age and sex), as well as those associated with HIF targets. Our results provide a broad perspective of the processes that are active in cytotrophoblasts during the rise in physiological oxygen, which should benefit efforts to discover possible drug-targeted genes or pathways in the human placenta.
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Affiliation(s)
- Fulin Liu
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
| | - Christelle Simasotchi
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Fondation PremUp, F-75006 Paris, France
| | - Françoise Vibert
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
| | - Wencan Zhu
- UMR Applied Mathematics & Informatics, AgroParisTech-Université Paris-Saclay, F-75005 Paris, France;
| | - Sophie Gil
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Fondation PremUp, F-75006 Paris, France
| | - Séverine A. Degrelle
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Inovarion, F-75005 Paris, France
| | - Thierry Fournier
- Pathophysiology & Pharmacotoxicology of the Human Placenta, Pre & Postnatal Microbiota, Université de Paris, INSERM, 3PHM, F-75006 Paris, France; (F.L.); (C.S.); (F.V.); (S.G.); (S.A.D.)
- Correspondence:
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Trumpff C, Sturm G, Picard M, Foss S, Lee S, Feng T, Cardenas A, McCormack C, Champagne FA, Monk C. Added sugar intake during pregnancy: Fetal behavior, birth outcomes, and placental DNA methylation. Dev Psychobiol 2021; 63:878-889. [PMID: 33415750 DOI: 10.1002/dev.22088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 11/23/2020] [Accepted: 12/20/2020] [Indexed: 12/11/2022]
Abstract
Pregnancy is a critical time for the effects of environmental factors on children's development. The effect of added sugar intake on fetal development and pregnancy outcomes remains understudied despite increasing dietary intake in the United States. This study investigated the effect of added sugar on fetal programming by examining the association between maternal added sugar consumption, fetal movement, birth outcomes, and placental DNA methylation. Further, primary human fibroblasts were cultured under normal or high glucose conditions to assess the effect of high glucose exposure on cells' DNA methylation. We found that higher added sugar intake across pregnancy was associated with reduced 3rd-trimester fetal movement (p < .05) and shorter gestation (p < .01). Our sample size was not powered to detect the alteration of individual placental CpG with genome-wide significance. However, a secondary analysis suggested that added sugar consumption was associated with differential methylation of functionally related gene families across pregnancy. Consistent with this, high glucose exposure in primary cultured human fibroblasts altered the methylation of 17% of all CpGs, providing converging evidence for an effect of sugar on DNA methylation. Our results suggest that diets high in added sugar during pregnancy may have implications for offspring health via prenatal programming effects measurable before birth.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA.,Department of Neurology, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY, USA
| | - Sophie Foss
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA
| | - Seonjoo Lee
- Division of Mental Health Data Science, New York State Psychiatric Institute, New York, NY, USA.,Research Foundation for Mental Hygiene Inc, New York, NY, USA.,Department of Biostatistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Tianshu Feng
- Research Foundation for Mental Hygiene Inc, New York, NY, USA.,Department of Biostatistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Andrès Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Clare McCormack
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA
| | - Frances A Champagne
- Department of Psychology, The University of Texas at Austin, Austin, TX, USA
| | - Catherine Monk
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA.,Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY, USA.,New York State Psychiatric Institute, New York, NY, USA
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29
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Karahoda R, Abad C, Horackova H, Kastner P, Zaugg J, Cerveny L, Kucera R, Albrecht C, Staud F. Dynamics of Tryptophan Metabolic Pathways in Human Placenta and Placental-Derived Cells: Effect of Gestation Age and Trophoblast Differentiation. Front Cell Dev Biol 2020; 8:574034. [PMID: 33072756 PMCID: PMC7530341 DOI: 10.3389/fcell.2020.574034] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022] Open
Abstract
L-Tryptophan is an essential amino acid and a precursor of several physiologically active metabolites. In the placenta, the serotonin and kynurenine metabolic pathways of tryptophan metabolism have been identified, giving rise to various molecules of neuroactive or immunoprotective properties, such as serotonin, melatonin, kynurenine, kynurenic acid, or quinolinic acid. Current literature suggests that optimal levels of these molecules in the fetoplacental unit are crucial for proper placenta functions, fetal development and programming. Placenta is a unique endocrine organ that, being equipped with a battery of biotransformation enzymes and transporters, precisely orchestrates homeostasis of tryptophan metabolic pathways. However, because pregnancy is a dynamic process and placental/fetal needs are continuously changing throughout gestation, placenta must adapt to these changes and ensure proper communication in the feto-placental unit. Therefore, in this study we investigated alterations of placental tryptophan metabolic pathways throughout gestation. Quantitative polymerase chain reaction (PCR) analysis of 21 selected genes was carried out in first trimester (n = 13) and term (n = 32) placentas. Heatmap analysis with hierarchical clustering revealed differential gene expression of serotonin and kynurenine pathways across gestation. Subsequently, digital droplet PCR, Western blot, and functional analyses of the rate-limiting enzymes suggest preferential serotonin synthesis early in pregnancy with a switch to kynurenine production toward term. Correspondingly, increased function and/or protein expression of serotonin degrading enzyme and transporters at term indicates efficient placental uptake and metabolic degradation of serotonin. Lastly, gene expression analysis in choriocarcinoma-derived cell lines (BeWo, BeWo b30, JEG-3) revealed dissimilar expression patterns and divergent effect of syncytialization compared to primary trophoblast cells isolated from human term placentas; these findings show that the commonly used in vitro placental models are not suitable to study placental handling of tryptophan. Altogether, our data provide the first comprehensive evidence of changes in placental homeostasis of tryptophan and its metabolites as a function of gestational age, which is critical for proper placental function and fetal development.
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Affiliation(s)
- Rona Karahoda
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Cilia Abad
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Hana Horackova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Petr Kastner
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Jonas Zaugg
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.,Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Lukas Cerveny
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Radim Kucera
- Department of Pharmaceutical Chemistry and Pharmaceutical Analysis, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Christiane Albrecht
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.,Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Frantisek Staud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Kralove, Charles University, Hradec Kralove, Czechia
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30
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Jang HY, Lim SM, Lee HJ, Hong JS, Kim GJ. Identification of microRNAs and their target genes in the placenta as biomarkers of inflammation. Clin Exp Reprod Med 2020; 47:42-53. [PMID: 32146774 PMCID: PMC7127901 DOI: 10.5653/cerm.2019.03013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE Recently, microRNA (miRNA) has been identified both as a powerful regulator involved in various biological processes through the regulation of numerous genes and as an effective biomarker for the prediction and diagnosis of various disease states. The objective of this study was to identify and validate miRNAs and their target genes involved in inflammation in placental tissue. METHODS Microarrays were utilized to obtain miRNA and gene expression profiles from placentas with or without inflammation obtained from nine normal pregnant women and 10 preterm labor patients. Quantitative real-time polymerase chain reaction and Western blots were performed to validate the miRNAs and differentially-expressed genes in the placentas with inflammation. Correlations between miRNA and target gene expression were confirmed by luciferase assays in HTR-8/SVneo cells. RESULTS We identified and validated miRNAs and their target genes that were differentially expressed in placentas with inflammation. We also demonstrated that several miRNAs (miR-371a-5p, miR-3065-3p, miR-519b-3p, and miR-373-3p) directly targeted their target genes (LEF1, LOX, ITGB4, and CD44). However, some miRNAs and their direct target genes showed no correlation in tissue samples. Interestingly, miR-373-3p and miR-3065-3p were markedly regulated by lipopolysaccharide (LPS) treatment, although the expression of their direct targets CD44 and LOX was not altered by LPS treatment. CONCLUSION These results provide candidate miRNAs and their target genes that could be used as placental biomarkers of inflammation. These candidates may be useful for further miRNA-based biomarker development.
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Affiliation(s)
- Hee Yeon Jang
- Department of Biomedical Science, CHA University, Seongnam, Korea
| | - Seung Mook Lim
- Department of Biomedical Science, CHA University, Seongnam, Korea
| | - Hyun Jung Lee
- Non-Clinical Evaluation Center, CHA Advanced Research Institute, Seongnam, Korea
| | - Joon-Seok Hong
- Department of Obstetrics and Gynecology, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Gi Jin Kim
- Department of Biomedical Science, CHA University, Seongnam, Korea
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31
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Li Y, Cui S, Shi W, Yang B, Yuan Y, Yan S, Li Y, Xu Y, Zhang Z, Linlin Zhang. Differential placental methylation in preeclampsia, preterm and term pregnancies. Placenta 2020; 93:56-63. [PMID: 32250740 DOI: 10.1016/j.placenta.2020.02.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Preeclampsia (PE) is one of the leading causes of maternal mortality and morbidity worldwide. Recently, the role of epigenetic modifications in preeclampsia has been a focus of research. This study was to identified genes or pathways that may be associated with PE, and discuss whether the changes in the methylation level of these genes is related to the pathogenesis of PE. METHODS The methylation levels of placental tissues between PE (n = 4), preterm birth (PB, n = 4) and term birth (TB, n = 4) were detected by Illumina Infinium HumanMethylation850 K BeadChip. Pyrosequencing and qRT-PCR were used to validated the methylation and expression levels of the genes with the most significant differences. RESULTS The global methylation levels of placenta tissues in PE and PB were both higher compared to TB. After eliminated the effect of gestational age, there were 808 gene probes differentially methylated in PE compared to PB. We found 137 genes with 130 genes hypermethylated and 7 genes hypomethylated. CMIP, BLCAP and MICA genes were with the most significant differential methylation. The expression level of CMIP and BLCAP were both negatively correlated to the methylation levels, while the expression level of MICA was not related to its methylation levels. CONCLUSION The methylation levels in placenta tissues were associated with gestational ages. We indicated the expression levels of the significantly methylated genes were negatively correlated with the methylation levels, further functional researches were still needed to find out whether they are associated with the onset of preeclampsia.
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Affiliation(s)
- Yingying Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shihong Cui
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Wenli Shi
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Bo Yang
- Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yangyang Yuan
- Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shujun Yan
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ying Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yajuan Xu
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Zhan Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China; Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Linlin Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China; Department of Medical Research Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
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32
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Adams AD, Guedj F, Bianchi DW. Placental development and function in trisomy 21 and mouse models of Down syndrome: Clues for studying mechanisms underlying atypical development. Placenta 2020; 89:58-66. [PMID: 31683073 PMCID: PMC10040210 DOI: 10.1016/j.placenta.2019.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/30/2019] [Accepted: 10/04/2019] [Indexed: 12/17/2022]
Abstract
Down syndrome (DS) is the most common genetic disorder leading to developmental disability. The phenotypes associated with DS are complex and vary between affected individuals. Placental abnormalities in DS include differences in cytotrophoblast fusion that affect subsequent conversion to syncytiotrophoblast, atypical oxidative stress/antioxidant balance, and increased expression of genes that are also upregulated in the brains of individuals with Alzheimer's disease. Placentas in DS are prematurely senescent, showing atypical evidence of mineralization. Fetuses with DS are especially susceptible to adverse obstetric outcomes, including early in utero demise, stillbirth and growth restriction, all of which are related to placental function. The placenta, therefore, may provide key insights towards understanding the phenotypic variability observed in individuals with DS and aid in identifying biomarkers that can be used to evaluate phenotypic severity and prenatal treatments in real time. To address these issues, many different mouse models of DS have been generated to identify the mechanisms underlying developmental changes in many organ systems. Little is known, however, regarding placental development in the currently available mouse models of DS. Based upon the relative paucity of data on placental development in preclinical mouse models of DS, we recommend that future evaluation of new and existing models routinely include histologic and functional assessments of the placenta. In this paper we summarize studies performed in the placentas of both humans and mouse models with DS, highlighting gaps in knowledge and suggesting directions for future research.
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Affiliation(s)
- April D Adams
- Medical Genetics Branch (Prenatal Genomics and Therapy Section), National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Faycal Guedj
- Medical Genetics Branch (Prenatal Genomics and Therapy Section), National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Diana W Bianchi
- Medical Genetics Branch (Prenatal Genomics and Therapy Section), National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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33
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DNA methylation at LRP1 gene locus mediates the association between maternal total cholesterol changes in pregnancy and cord blood leptin levels. J Dev Orig Health Dis 2019; 11:369-378. [PMID: 31753053 DOI: 10.1017/s204017441900076x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Placental lipids transfer is essential for optimal fetal development, and alterations of these mechanisms could lead to a higher risk of adverse birth outcomes. Low-density lipoprotein receptor (LDLR), LDL receptor-related protein 1 (LRP1), and scavenger receptor class B type 1 (SCARB1) genes are encoding lipoprotein receptors expressed in the placenta where they participate in cholesterol exchange from maternal to fetal circulation. The aim of this study was thus to investigate the association between maternal lipid changes occurring in pregnancy, placental DNA methylation (DNAm) variations at LDLR, LRP1, and SCARB1 gene loci, and newborn's anthropometric profile at birth. Sixty-nine normoglycemic women were followed from the first trimester of pregnancy until delivery. Placental DNAm was quantified at 43 Cytosine-phosphate-Guanines (CpGs) at LDLR, LRP1, and SCARB1 gene loci using pyrosequencing: 4 CpGs were retained for further analysis. Maternal clinical data were collected at each trimester of pregnancy. Newborns' data were collected from medical records. Statistical models included minimally newborn sex and gestational and maternal age. Maternal total cholesterol changes during pregnancy (ΔT3-T1) were correlated with DNAm variations at LDLR (r = -0.32, p = 0.01) and LRP1 (r = 0.34, p = 0.007). DNAm at these loci was also correlated with newborns' cord blood triglyceride and leptin levels. Mediation analysis supports a causal relationship between maternal cholesterol changes, DNAm levels at LRP1 locus, and cord blood leptin concentration (pmediation = 0.02). These results suggest that LRP1 DNAm link maternal blood cholesterol changes in pregnancy and offspring adiposity at birth, which provide support for a better follow-up of blood lipids in pregnancy.
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Tekola-Ayele F, Workalemahu T, Gorfu G, Shrestha D, Tycko B, Wapner R, Zhang C, Louis GMB. Sex differences in the associations of placental epigenetic aging with fetal growth. Aging (Albany NY) 2019; 11:5412-5432. [PMID: 31395791 PMCID: PMC6710059 DOI: 10.18632/aging.102124] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/21/2019] [Indexed: 12/15/2022]
Abstract
Identifying factors that influence fetal growth in a sex-specific manner can help unravel mechanisms that explain sex differences in adverse neonatal outcomes and in-utero origins of cardiovascular disease disparities. Premature aging of the placenta, a tissue that supports fetal growth and exhibits sex-specific epigenetic changes, is associated with pregnancy complications. Using DNA methylation-based age estimator, we investigated the sex-specific relationship of placental epigenetic aging with fetal growth across 13-40 weeks gestation, neonatal size, and risk of low birth weight. Placental epigenetic age acceleration (PAA), the difference between DNA methylation age and gestational age, was associated with reduced fetal weight among males but with increased fetal weight among females. PAA was inversely associated with fetal weight, abdominal circumference, and biparietal diameter at 32-40 weeks among males but was positively associated with all growth measures among females across 13-40 weeks. A 1-week increase in PAA was associated with 2-fold (95% CI 1.2, 3.2) increased odds for low birth weight and 1.5-fold (95% CI 1.1, 2.0) increased odds for small-for-gestational age among males. In all, fetal growth was significantly reduced in males but not females exposed to a rapidly aging placenta. Epigenetic aging of the placenta may underlie sex differences in neonatal outcomes.
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Affiliation(s)
- Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gezahegn Gorfu
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC 20059, USA
| | - Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation and the Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Germaine M. Buck Louis
- Dean’s Office, College of Health and Human Services, George Mason University, Fairfax, VA 22030, USA
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Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, Marsit C, Lu AT, Ritz B, Bohlin J, Gjessing HK, Harris JR, Magnus P, Binder AM, Robinson WP, Jugessur A, Horvath S. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY) 2019; 11:4238-4253. [PMID: 31235674 PMCID: PMC6628997 DOI: 10.18632/aging.102049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
The human pan-tissue epigenetic clock is widely used for estimating age across the entire lifespan, but it does not lend itself well to estimating gestational age (GA) based on placental DNAm methylation (DNAm) data. We replicate previous findings demonstrating a strong correlation between GA and genome-wide DNAm changes. Using substantially more DNAm arrays (n=1,102 in the training set) than a previous study, we present three new placental epigenetic clocks: 1) a robust placental clock (RPC) which is unaffected by common pregnancy complications (e.g., gestational diabetes, preeclampsia), and 2) a control placental clock (CPC) constructed using placental samples from pregnancies without known placental pathology, and 3) a refined RPC for uncomplicated term pregnancies. These placental clocks are highly accurate estimators of GA based on placental tissue; e.g., predicted GA based on RPC is highly correlated with actual GA (r>0.95 in test data, median error less than one week). We show that epigenetic clocks derived from cord blood or other tissues do not accurately estimate GA in placental samples. While fundamentally different from Horvath's pan-tissue epigenetic clock, placental clocks closely track fetal age during development and may have interesting applications.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samantha L. Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Victor Yuan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amber Burt
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Carmen Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra M. Binder
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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Tiensuu H, Haapalainen AM, Karjalainen MK, Pasanen A, Huusko JM, Marttila R, Ojaniemi M, Muglia LJ, Hallman M, Rämet M. Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. PLoS Genet 2019; 15:e1008107. [PMID: 31194736 PMCID: PMC6563950 DOI: 10.1371/journal.pgen.1008107] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
Spontaneous preterm birth (SPTB) is the leading cause of neonatal death and morbidity worldwide. Both maternal and fetal genetic factors likely contribute to SPTB. We performed a genome-wide association study (GWAS) on a population of Finnish origin that included 247 infants with SPTB (gestational age [GA] < 36 weeks) and 419 term controls (GA 38-41 weeks). The strongest signal came within the gene encoding slit guidance ligand 2 (SLIT2; rs116461311, minor allele frequency 0.05, p = 1.6×10-6). Pathway analysis revealed the top-ranking pathway was axon guidance, which includes SLIT2. In 172 very preterm-born infants (GA <32 weeks), rs116461311 was clearly overrepresented (odds ratio 4.06, p = 1.55×10-7). SLIT2 variants were associated with SPTB in another European population that comprised 260 very preterm infants and 9,630 controls. To gain functional insight, we used immunohistochemistry to visualize SLIT2 and its receptor ROBO1 in placentas from spontaneous preterm and term births. Both SLIT2 and ROBO1 were located in villous and decidual trophoblasts of embryonic origin. Based on qRT-PCR, the mRNA levels of SLIT2 and ROBO1 were higher in the basal plate of SPTB placentas compared to those from term or elective preterm deliveries. In addition, in spontaneous term and preterm births, placental SLIT2 expression was correlated with variations in fetal growth. Knockdown of ROBO1 in trophoblast-derived HTR8/SVneo cells by siRNA indicated that it regulate expression of several pregnancy-specific beta-1-glycoprotein (PSG) genes and genes involved in inflammation. Our results show that the fetal SLIT2 variant and both SLIT2 and ROBO1 expression in placenta and trophoblast cells may be correlated with susceptibility to SPTB. SLIT2-ROBO1 signaling was linked with regulation of genes involved in inflammation, PSG genes, decidualization and fetal growth. We propose that this receptor-ligand couple is a component of the signaling network that promotes SPTB.
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Affiliation(s)
- Heli Tiensuu
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Antti M. Haapalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Minna K. Karjalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Anu Pasanen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Johanna M. Huusko
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States of America
| | - Riitta Marttila
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Marja Ojaniemi
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Louis J. Muglia
- Division of Human Genetics, Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, Ohio, United States of America
| | - Mikko Hallman
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Mika Rämet
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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Paquette A, Baloni P, Holloman AB, Nigam S, Bammler T, Mao Q, Price ND. Temporal transcriptomic analysis of metabolic genes in maternal organs and placenta during murine pregnancy. Biol Reprod 2018; 99:1255-1265. [PMID: 29939228 PMCID: PMC6692859 DOI: 10.1093/biolre/ioy148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/22/2018] [Accepted: 06/22/2018] [Indexed: 01/11/2023] Open
Abstract
Maternal pregnancy adaptation is crucial for fetal development and long-term health. Complex interactions occur between maternal digestive and excretory systems as they interface with the developing fetus through the placenta, and transcriptomic regulation in these organs throughout pregnancy is poorly understood. Our objective is to characterize transcriptomic changes across gestation in maternal organs and placenta. Gene expression was quantified in the kidney, liver, and small intestine harvested from nonpregnant and pregnant FVB mice at four time points and placenta at three time points (N = 5/time point) using Affymetrix Mouse Gene 1.0 ST arrays. In maternal organs, we identified 476 genes in the liver, 207 genes in the kidney, and 27 genes in the small intestine that were differentially expressed across gestation (False Discovery Rate [FDR] adjusted q < 0.05). The placenta had a total of 1576 differentially expressed genes between the placenta at either/gd15 or gd19 compared to gd10. We identified a number of pathways enriched for genes differentially expressed across gestation, including 5 pathways in the placenta, 9 pathways in the kidney, and 28 pathways in the liver, including the citrate cycle, retinol metabolism, bile acid synthesis, and steroid bile synthesis, which play functional roles in fetal development and pregnancy maintenance. Characterization of normal longitudinal changes that occur in pregnancy provides context to understand how perturbations in these biochemical pathways and perturbations in nutrient signaling may impact pregnancy.
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Affiliation(s)
| | | | | | - Sanjay Nigam
- Departments of Pediatrics and Medicine, University of California San Diego, San Diego, California, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health Science, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Qingcheng Mao
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA
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Gene Expression Profiling of Placenta from Normal to Pathological Pregnancies. Placenta 2018. [DOI: 10.5772/intechopen.80551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register]
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Paquette AG, Chu T, Wu X, Wang K, Price ND, Sadovsky Y. Distinct communication patterns of trophoblastic miRNA among the maternal-placental-fetal compartments. Placenta 2018; 72-73:28-35. [PMID: 30501878 DOI: 10.1016/j.placenta.2018.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/18/2018] [Accepted: 10/17/2018] [Indexed: 01/23/2023]
Abstract
INTRODUCTION The placenta produces microRNAs (miRNA) that may traffic to the maternal or fetal compartments and influence the physiology of pregnancy. The trafficking patterns of miRNA expressed from the large human chromosome 19 and chromosome 14 clusters (C19MC and C14MC), remains unclear. We interrogated the cross-sectional landscape of miRNA expression within the human placenta, fetal and maternal plasma to elucidate miRNA trafficking. We hypothesized that C19MC and C14MC miRNAs have similar expression patterns across the maternal-fetal compartments. METHODS Placental biopsies, maternal and fetal venous plasma were collected from 25 pregnancies, and RNA was quantified using next generation sequencing. We identified expression and correlations differences among the compartments, and uncovered distinct miRNA expression patterns using consensus clustering. RESULTS We found that the placenta exhibits the highest total abundance, average miRNA expression and lowest variance of both C19MC and C14MC miRNAs. The C19MC miRNAs had a comparable expression and variance in fetal and maternal plasma and higher expression in the placenta. In contrast, the C14MC miRNAs had comparable expression between the placenta and fetal plasma, which was higher than the maternal plasma. We also identified 5 distinct groups of trophoblastic miRNAs with different expression patterns in each compartment. DISCUSSION This is the first comprehensive analysis of C19MC and C14MC miRNA expression patterns in the human placental, maternal and fetal compartments. Our findings suggest that C14MC miRNAs are produced by both the fetus and placenta, but C19MC miRNAs are produced primarily in the placenta and are trafficked to the fetal and maternal compartments.
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Affiliation(s)
| | - Tianjiao Chu
- Magee-Womens Research Institute, USA; Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Xiaogang Wu
- Institute for Systems Biology, Seattle, WA, 98119, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA, 98119, USA
| | | | - Yoel Sadovsky
- Magee-Womens Research Institute, USA; Department of Obstetrics and Gynecology and Reproductive Science, University of Pittsburgh, Pittsburgh, PA, 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15213, USA.
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Vaswani K, Dekker Nitert M, Chan HW, B. Almughlliq F, Peiris HN, Wood-Bradley RJ, Armitage JA, Rice GE, Mitchell MD. Mid-to-Late Gestational Changes in Inflammatory Gene Expression in the Rat Placenta. Reprod Sci 2017; 25:222-229. [DOI: 10.1177/1933719117741375] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Kanchan Vaswani
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Marloes Dekker Nitert
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Hsiu-Wen Chan
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Fatema B. Almughlliq
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Hassendrini N. Peiris
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Ryan J. Wood-Bradley
- Faculty of Health, School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - James A. Armitage
- Faculty of Health, School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
- Department of Anatomy & Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Gregory E. Rice
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
| | - Murray D. Mitchell
- UQ Centre for Clinical Research, The University of Queensland, Herston, Queensland, Australia
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A complex association between DNA methylation and gene expression in human placenta at first and third trimesters. PLoS One 2017; 12:e0181155. [PMID: 28704530 PMCID: PMC5509291 DOI: 10.1371/journal.pone.0181155] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/27/2017] [Indexed: 11/24/2022] Open
Abstract
The human placenta is a maternal-fetal organ essential for normal fetal development and maternal health. During pregnancy, the placenta undergoes many structural and functional changes in response to fetal needs and environmental exposures. Previous studies have demonstrated widespread epigenetic and gene expression changes from early to late pregnancy. However, on the global level, how DNA methylation changes impact on gene expression in human placenta is not yet well understood. We performed DNA methylome analysis by reduced representation bisulfite sequencing (RRBS) and gene expression analysis by RNA-Seq for both first and third trimester human placenta tissues. From first to third trimester, 199 promoters (corresponding to 189 genes) and 2,297 gene bodies were differentially methylated, with a clear dominance of hypermethylation (96.8% and 93.0% for promoters and gene bodies, respectively). A total of 2,447 genes were differentially expressed, of which 77.2% were down-regulated. Gene ontology analysis using differentially expressed genes were enriched for cell cycle and immune response functions. The correlation between DNA methylation and gene expression was non-linear and complex, depending on the genomic context (promoter or gene body) and gene expression levels. A wide range of DNA methylation and gene expression changes were observed at different gestational ages. The non-linear association between DNA methylation and gene expression indicates that epigenetic regulation of placenta development is more complex than previously envisioned.
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Walker N, Filis P, Soffientini U, Bellingham M, O’Shaughnessy PJ, Fowler PA. Placental transporter localization and expression in the Human: the importance of species, sex, and gestational age differences†. Biol Reprod 2017; 96:733-742. [PMID: 28339967 PMCID: PMC5441296 DOI: 10.1093/biolre/iox012] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/22/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022] Open
Abstract
The placenta is a critical organ during pregnancy, essential for the provision of an optimal intrauterine environment, with fetal survival, growth, and development relying on correct placental function. It must allow nutritional compounds and relevant hormones to pass into the fetal bloodstream and metabolic waste products to be cleared. It also acts as a semipermeable barrier to potentially harmful chemicals, both endogenous and exogenous. Transporter proteins allow for bidirectional transport and are found in the syncytiotrophoblast of the placenta and endothelium of fetal capillaries. The major transporter families in the human placenta are ATP-binding cassette (ABC) and solute carrier (SLC), and insufficiency of these transporters may lead to deleterious effects on the fetus. Transporter expression levels are gestation-dependent and this is of considerable clinical interest as levels of drug resistance may be altered from one trimester to the next. This highlights the importance of these transporters in mediating correct and timely transplacental passage of essential compounds but also for efflux of potentially toxic drugs and xenobiotics. We review the current literature on placental molecular transporters with respect to their localization and ontogeny, the influence of fetal sex, and the relevance of animal models. We conclude that a paucity of information exists, and further studies are required to unlock the enigma of this dynamic organ.
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Affiliation(s)
- Natasha Walker
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Panagiotis Filis
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
| | - Ugo Soffientini
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Michelle Bellingham
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Peter J O’Shaughnessy
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Paul A Fowler
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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Altmäe S, Segura MT, Esteban FJ, Bartel S, Brandi P, Irmler M, Beckers J, Demmelmair H, López-Sabater C, Koletzko B, Krauss-Etschmann S, Campoy C. Maternal Pre-Pregnancy Obesity Is Associated with Altered Placental Transcriptome. PLoS One 2017; 12:e0169223. [PMID: 28125591 PMCID: PMC5268451 DOI: 10.1371/journal.pone.0169223] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022] Open
Abstract
Maternal obesity has a major impact on pregnancy outcomes. There is growing evidence that maternal obesity has a negative influence on placental development and function, thereby adversely influencing offspring programming and health outcomes. However, the molecular mechanisms underlying these processes are poorly understood. We analysed ten term placenta’s whole transcriptomes in obese (n = 5) and normal weight women (n = 5), using the Affymetrix microarray platform. Analyses of expression data were carried out using non-parametric methods. Hierarchical clustering and principal component analysis showed a clear distinction in placental transcriptome between obese and normal weight women. We identified 72 differentially regulated genes, with most being down-regulated in obesity (n = 61). Functional analyses of the targets using DAVID and IPA confirm the dysregulation of previously identified processes and pathways in the placenta from obese women, including inflammation and immune responses, lipid metabolism, cancer pathways, and angiogenesis. In addition, we detected new molecular aspects of obesity-derived effects on the placenta, involving the glucocorticoid receptor signalling pathway and dysregulation of several genes including CCL2, FSTL3, IGFBP1, MMP12, PRG2, PRL, QSOX1, SERPINE2 and TAC3. Our global gene expression profiling approach demonstrates that maternal obesity creates a unique in utero environment that impairs the placental transcriptome.
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Affiliation(s)
- Signe Altmäe
- Department of Women’s and Children’s Health, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm, Sweden
- Centre of Excellence for Paediatric Research EURISTIKOS and Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
- * E-mail: (SA); (CC)
| | - Maria Teresa Segura
- Centre of Excellence for Paediatric Research EURISTIKOS and Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
| | | | - Sabine Bartel
- Division of Experimental Asthma Research, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Member of the German Center for Lung Research (DZL), Borstel, Germany
| | - Pilar Brandi
- Centre of Excellence for Paediatric Research EURISTIKOS and Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, Neuherberg, Germany
- Technische Universität München, Chair of Experimental Genetics, Freising, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Hans Demmelmair
- Ludwig-Maximilians-University of Munich, Dr. Hauner Children’s Hospital, University of Munich Medical Centre, Munich, Germany
| | - Carmen López-Sabater
- Department of Nutrition and Bromatology, School of Pharmacy, University of Barcelona, Spain
| | - Berthold Koletzko
- Ludwig-Maximilians-University of Munich, Dr. Hauner Children’s Hospital, University of Munich Medical Centre, Munich, Germany
| | - Susanne Krauss-Etschmann
- Division of Experimental Asthma Research, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Member of the German Center for Lung Research (DZL), Borstel, Germany
- Institute for Experimental Medicine, Christian-Albrechts-Universitaet zu Kiel, Kiel, Germany
- Comprehensive Pneumology Center, Ludwig Maximilians University Hospital and Helmholtz Zentrum München, Großhadern, Germany
| | - Cristina Campoy
- Centre of Excellence for Paediatric Research EURISTIKOS and Department of Paediatrics, School of Medicine, University of Granada, Granada, Spain
- Biohealth Institute of Granada, Granada, Spain
- * E-mail: (SA); (CC)
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Rahat B, Najar RA, Hamid A, Bagga R, Kaur J. The role of aberrant methylation of trophoblastic stem cell origin in the pathogenesis and diagnosis of placental disorders. Prenat Diagn 2017; 37:133-143. [PMID: 27885689 DOI: 10.1002/pd.4974] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 10/10/2016] [Accepted: 11/18/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Beenish Rahat
- Department of Biochemistry; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Rauf Ahmad Najar
- Cancer Pharmacology Division; Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine; Jammu India
| | - Abid Hamid
- Cancer Pharmacology Division; Council of Scientific and Industrial Research-Indian Institute of Integrative Medicine; Jammu India
| | - Rashmi Bagga
- Department of Obstetrics and Gynecology; Postgraduate Institute of Medical Education and Research; Chandigarh India
| | - Jyotdeep Kaur
- Department of Biochemistry; Postgraduate Institute of Medical Education and Research; Chandigarh India
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45
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Buckberry S, Bianco-Miotto T, Bent SJ, Clifton V, Shoubridge C, Shankar K, Roberts CT. Placental transcriptome co-expression analysis reveals conserved regulatory programs across gestation. BMC Genomics 2017; 18:10. [PMID: 28049421 PMCID: PMC5209944 DOI: 10.1186/s12864-016-3384-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 12/07/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Mammalian development in utero is absolutely dependent on proper placental development, which is ultimately regulated by the placental genome. The regulation of the placental genome can be directly studied by exploring the underlying organisation of the placental transcriptome through a systematic analysis of gene-wise co-expression relationships. RESULTS In this study, we performed a comprehensive analysis of human placental co-expression using RNA sequencing and intergrated multiple transcriptome datasets spanning human gestation. We identified modules of co-expressed genes that are preserved across human gestation, and also identifed modules conserved in the mouse indicating conserved molecular networks involved in placental development and gene expression patterns more specific to late gestation. Analysis of co-expressed gene flanking sequences indicated that conserved co-expression modules in the placenta are regulated by a core set of transcription factors, including ZNF423 and EBF1. Additionally, we identified a gene co-expression module enriched for genes implicated in the pregnancy pathology preeclampsia. By using an independnet transcriptome dataset, we show that these co-expressed genes are differentially expressed in preeclampsia. CONCLUSIONS This study represents a comprehensive characterisation of placental co-expression and provides insight into potential transcriptional regulators that govern conserved molecular programs fundamental to placental development.
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Affiliation(s)
- Sam Buckberry
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,University of Western Australia, Harry Perkins Institute of Medical Research, Perth, 6009, Australia.,University of Western Australia, Australian Research Council Centre of Excellence in Plant Energy Biology, Perth, 6009, Australia
| | - Tina Bianco-Miotto
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.,The University of Adelaide, School of agriculture, food and wine, Adelaide, 5005, Australia
| | - Stephen J Bent
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Vicki Clifton
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Cheryl Shoubridge
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia
| | - Kartik Shankar
- University of Arkansas for Medical Sciences, The Department of Pediatrics, Little Rock, 72202, USA
| | - Claire T Roberts
- The Robinson Research Institute, The University of Adelaide, School of Paediatrics and Reproductive Health, Adelaide, 5005, Australia.
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Yaghi L, Poras I, Simoes RT, Donadi EA, Tost J, Daunay A, de Almeida BS, Carosella ED, Moreau P. Hypoxia inducible factor-1 mediates the expression of the immune checkpoint HLA-G in glioma cells through hypoxia response element located in exon 2. Oncotarget 2016; 7:63690-63707. [PMID: 27577073 PMCID: PMC5325396 DOI: 10.18632/oncotarget.11628] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 08/20/2016] [Indexed: 12/31/2022] Open
Abstract
HLA-G is an immune checkpoint molecule with specific relevance in cancer immunotherapy. It was first identified in cytotrophoblasts, protecting the fetus from maternal rejection. HLA-G tissue expression is very restricted but induced in numerous malignant tumors such as glioblastoma, contributing to their immune escape. Hypoxia occurs during placenta and tumor development and was shown to activate HLA-G. We aimed to elucidate the mechanisms of HLA-G activation under conditions combining hypoxia-mimicking treatment and 5-aza-2'deoxycytidine, a DNA demethylating agent used in anti-cancer therapy which also induces HLA-G. Both treatments enhanced the amount of HLA-G mRNA and protein in HLA-G negative U251MG glioma cells. Electrophoretic Mobility Shift Assays and luciferase reporter gene assays revealed that HLA-G upregulation depends on Hypoxia Inducible Factor-1 (HIF-1) and a hypoxia responsive element (HRE) located in exon 2. A polymorphic HRE at -966 bp in the 5'UT region may modulate the magnitude of the response mediated by the exon 2 HRE. We suggest that therapeutic strategies should take into account that HLA-G expression in response to hypoxic tumor environment is dependent on HLA-G gene polymorphism and DNA methylation state at the HLA-G locus.
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Affiliation(s)
- Layale Yaghi
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
- Lebanese University, School of Medicine, Hadath, Lebanon
| | - Isabelle Poras
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Renata T. Simoes
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
- Instituto de Ensino e Pesquisa da Santa Casa de Belo Horizonte, IEP/SCBH, Belo Horizonte, Minas Gerais, Brasil
| | - Eduardo A. Donadi
- Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Jörg Tost
- Centre d'Etude du Polymorphisme Humain, Fondation Jean-Dausset, Laboratory for Functional Genomics, Paris, France
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Centre National de Genotypage, Laboratory for Epigenetics and Environment, Evry, France
| | - Antoine Daunay
- Centre d'Etude du Polymorphisme Humain, Fondation Jean-Dausset, Laboratory for Functional Genomics, Paris, France
| | - Bibiana Sgorla de Almeida
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
- Divisão de Imunologia Clínica, Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil
| | - Edgardo D. Carosella
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
| | - Philippe Moreau
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Thérapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, Paris, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, Paris, France
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Marr AK, Boughorbel S, Presnell S, Quinn C, Chaussabel D, Kino T. A curated transcriptome dataset collection to investigate the development and differentiation of the human placenta and its associated pathologies. F1000Res 2016; 5:305. [PMID: 27303626 PMCID: PMC4897750 DOI: 10.12688/f1000research.8210.2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/06/2016] [Indexed: 02/02/2023] Open
Abstract
Compendia of large-scale datasets made available in public repositories provide a precious opportunity to discover new biomedical phenomena and to fill gaps in our current knowledge. In order to foster novel insights it is necessary to ensure that these data are made readily accessible to research investigators in an interpretable format. Here we make a curated, public, collection of transcriptome datasets relevant to human placenta biology available for further analysis and interpretation via an interactive data browsing interface. We identified and retrieved a total of 24 datasets encompassing 759 transcriptome profiles associated with the development of the human placenta and associated pathologies from the NCBI Gene Expression Omnibus (GEO) and present them in a custom web-based application designed for interactive query and visualization of integrated large-scale datasets (
http://placentalendocrinology.gxbsidra.org/dm3/landing.gsp). We also performed quality control checks using relevant biological markers. Multiple sample groupings and rank lists were subsequently created to facilitate data query and interpretation. Via this interface, users can create web-links to customized graphical views which may be inserted into manuscripts for further dissemination, or e-mailed to collaborators for discussion. The tool also enables users to browse a single gene across different projects, providing a mechanism for developing new perspectives on the role of a molecule of interest across multiple biological states. The dataset collection we created here is available at:
http://placentalendocrinology.gxbsidra.org/dm3.
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Affiliation(s)
| | | | - Scott Presnell
- Systems Immunology Division, Benaroya Research Institute, Seattle, WA, USA
| | - Charlie Quinn
- Systems Immunology Division, Benaroya Research Institute, Seattle, WA, USA
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Rouault C, Clément K, Guesnon M, Henegar C, Charles MA, Heude B, Evain-Brion D, Degrelle SA, Fournier T. Transcriptomic signatures of villous cytotrophoblast and syncytiotrophoblast in term human placenta. Placenta 2016; 44:83-90. [PMID: 27452442 DOI: 10.1016/j.placenta.2016.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
During pregnancy, the placenta ensures multiple functions, which are directly involved in the initiation, fetal growth and outcome of gestation. The placental tissue involved in maternal-fetal exchanges and in synthesis of pregnancy hormones is the mononucleated villous cytotrophoblast (VCT) which aggregates and fuses to form and renew the syncytiotrophoblast (ST). Knowledge of the gene expression pattern specific to this endocrine and exchanges tissue of human placenta is of major importance to understand functions of this heterogeneous and complex tissue. Therefore, we undertook a global analysis of the gene expression profiles of primary cultured-VCT (n = 6) and in vitro-differentiated-ST (n = 5) in comparison with whole term placental tissue from which mononucleated VCT were isolated. A total of 880 differentially expressed genes (DEG) were observed between VCT/ST compared to whole placenta, and a total of 37 and 137 genes were significantly up and down-regulated, respectively, in VCT compared to ST. The 37 VCT-genes were involved in cellular processes (assembly, organization, and maintenance), whereas the 137 ST-genes were associated with lipid metabolism and cell morphology. In silico, all networks were linked to 3 transcriptional regulators (PPARγ, RARα and NR2F1) which are known to be essential for trophoblast differentiation. A subset of six DEG was validated by RT-qPCR and four by immunohistochemistry. To conclude, recognition of these pathways is fundamental to increase our understanding of the molecular basis of human trophoblast differentiation. The present study provides for the first time a gene expression signature of the VCT and ST compared to their originated term human placental tissue.
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Affiliation(s)
- Christine Rouault
- INSERM, UMR-S 872, Centre de Recherche des Cordeliers, Equipe 7 Nutriomique, Paris, F-75006, France; Université Pierre et Marie Curie-Paris, Paris, F-75006, France; Fondation PremUp, Paris, F-75006, France
| | - Karine Clément
- INSERM, UMR-S 872, Centre de Recherche des Cordeliers, Equipe 7 Nutriomique, Paris, F-75006, France; Université Pierre et Marie Curie-Paris, Paris, F-75006, France; Fondation PremUp, Paris, F-75006, France; Assistance Publique-Hôpitaux de Paris (AP-HP), Pitié Salpétrière Hospital, Nutrition and Endocrinology Department, Paris, F-75013, France
| | - Mickael Guesnon
- INSERM, UMR-S1139, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France
| | - Corneliu Henegar
- INSERM, UMR-S 872, Centre de Recherche des Cordeliers, Equipe 7 Nutriomique, Paris, F-75006, France; Université Pierre et Marie Curie-Paris, Paris, F-75006, France
| | - Marie-Aline Charles
- Fondation PremUp, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France; INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center, Early ORigin of the Child's Health and Development Team (ORCHAD), Paris, F-75014, France
| | - Barbara Heude
- Fondation PremUp, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France; INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center, Early ORigin of the Child's Health and Development Team (ORCHAD), Paris, F-75014, France
| | - Danièle Evain-Brion
- Fondation PremUp, Paris, F-75006, France; INSERM, UMR-S1139, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France
| | - Séverine A Degrelle
- Fondation PremUp, Paris, F-75006, France; INSERM, UMR-S1139, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France
| | - Thierry Fournier
- Fondation PremUp, Paris, F-75006, France; INSERM, UMR-S1139, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, F-75006, France; Université Paris Descartes, Sorbonne Paris Cité, Paris, F-75006, France.
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Rasoulzadeh Z, Ghods R, Kazemi T, Mirzadegan E, Ghaffari-Tabrizi-Wizsy N, Rezania S, Kazemnejad S, Arefi S, Ghasemi J, Vafaei S, Mahmoudi AR, Zarnani AH. Placental Kisspeptins Differentially Modulate Vital Parameters of Estrogen Receptor-Positive and -Negative Breast Cancer Cells. PLoS One 2016; 11:e0153684. [PMID: 27101408 PMCID: PMC4839747 DOI: 10.1371/journal.pone.0153684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 04/01/2016] [Indexed: 11/28/2022] Open
Abstract
Kisspeptins (KPs) are major regulators of trophoblast and cancer invasion. Thus far, limited and conflicting data are available on KP-mediated modulation of breast cancer (BC) metastasis; mostly based on synthetic KP-10, the most active fragment of KP. Here, we report for the first time comprehensive functional effects of term placental KPs on proliferation, adhesion, Matrigel invasion, motility, MMP activity and pro-inflammatory cytokine production in MDA-MB-231 (estrogen receptor-negative) and MCF-7 (estrogen receptor-positive). KPs were expressed at high level by term placental syncytiotrophoblasts and released in soluble form. Placental explant conditioned medium containing KPs (CM) significantly reduced proliferation of both cell types compared to CM without (w/o) KP (CM-w/o KP) in a dose- and time-dependent manner. In MDA-MB-231 cells, placental KPs significantly reduced adhesive properties, while increased MMP9 and MMP2 activity and stimulated invasion. Increased invasiveness of MDA-MB-231 cells after CM treatment was inhibited by KP receptor antagonist, P-234. CM significantly reduced motility of MCF-7 cells at all time points (2–30 hr), while it stimulated motility of MDA-MB-231 cells. These effects were reversed by P-234. Co-treatment with selective ER modulators, Tamoxifen and Raloxifene, inhibited the effect of CM on motility of MCF-7 cells. The level of IL-6 in supernatant of MCF-7 cells treated with CM was higher compared to those treated with CM-w/o KP. Both cell types produced more IL-8 after treatment with CM compared to those treated with CM-w/o KP. Taken together, our observations suggest that placental KPs differentially modulate vital parameters of estrogen receptor-positive and -negative BC cells possibly through modulation of pro-inflammatory cytokine production.
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Affiliation(s)
- Zahra Rasoulzadeh
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 5165683146, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165683146, Iran
| | - Roya Ghods
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, IUMS, Tehran, 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, 1449614535, Iran
| | - Tohid Kazemi
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, 5165683146, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, 5165683146, Iran
- * E-mail: (AHZ); (TK)
| | - Ebrahim Mirzadegan
- Immunobiology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | | | - Simin Rezania
- Institute of Biophysics, Medical University of Graz, Graz, 8010, Austria
| | - Somaieh Kazemnejad
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | - Soheila Arefi
- Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | - Jamileh Ghasemi
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | - Sedigheh Vafaei
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | - Ahmad-Reza Mahmoudi
- Monoclonal Antibody Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
| | - Amir-Hassan Zarnani
- Nanobiotechnology Research Center, Avicenna Research Institute, ACECR, Tehran, 1177–19615, Iran
- Immunology Research Center, Iran University of Medical Sciences, Tehran, 81746–73461, Iran
- * E-mail: (AHZ); (TK)
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50
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Eidem HR, Rinker DC, Ackerman WE, Buhimschi IA, Buhimschi CS, Dunn-Fletcher C, Kallapur SG, Pavličev M, Muglia LJ, Abbot P, Rokas A. Comparing human and macaque placental transcriptomes to disentangle preterm birth pathology from gestational age effects. Placenta 2016; 41:74-82. [PMID: 27208410 DOI: 10.1016/j.placenta.2016.03.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 03/05/2016] [Accepted: 03/10/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION A major issue in the transcriptomic study of spontaneous preterm birth (sPTB) in humans is the inability to collect healthy control tissue at the same gestational age (GA) to compare with pathologic preterm tissue. Thus, gene expression differences identified after the standard comparison of sPTB and term tissues necessarily reflect differences in both sPTB pathology and GA. One potential solution is to use GA-matched controls from a closely related species to tease apart genes that are dysregulated during sPTB from genes that are expressed differently as a result of GA effects. METHODS To disentangle genes whose expression levels are associated with sPTB pathology from those linked to GA, we compared RNA sequencing data from human preterm placentas, human term placentas, and rhesus macaque placentas at 80% completed gestation (serving as healthy non-human primate GA-matched controls). We first compared sPTB and term human placental transcriptomes to identify significantly differentially expressed genes. We then overlaid the results of the comparison between human sPTB and macaque placental transcriptomes to identify sPTB-specific candidates. Finally, we overlaid the results of the comparison between human term and macaque placental transcriptomes to identify GA-specific candidates. RESULTS Examination of relative expression for all human genes with macaque orthologs identified 267 candidate genes that were significantly differentially expressed between preterm and term human placentas. 29 genes were identified as sPTB-specific candidates and 37 as GA-specific candidates. Altogether, the 267 differentially expressed genes were significantly enriched for a variety of developmental, metabolic, reproductive, immune, and inflammatory functions. Although there were no notable differences between the functions of the 29 sPTB-specific and 37 GA-specific candidate genes, many of these candidates have been previously shown to be dysregulated in diverse pregnancy-associated pathologies. DISCUSSION By comparing human sPTB and term transcriptomes with GA-matched control transcriptomes from a closely related species, this study disentangled the confounding effects of sPTB pathology and GA, leading to the identification of 29 promising sPTB-specific candidate genes and 37 genes potentially related to GA effects. The apparent similarity in functions of the sPTB and GA candidates may suggest that the effects of sPTB and GA do not correspond to biologically distinct processes. Alternatively, it may reflect the poor state of knowledge of the transcriptional landscape underlying placental development and disease.
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Affiliation(s)
- Haley R Eidem
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - David C Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Program in Human Genetics, Vanderbilt University, Nashville, TN 37235, USA.
| | - William E Ackerman
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH 43210, USA.
| | - Irina A Buhimschi
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH 43210, USA.
| | - Catalin S Buhimschi
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, OH 43210, USA.
| | - Caitlin Dunn-Fletcher
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Suhas G Kallapur
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH 43210, USA.
| | - Mihaela Pavličev
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Louis J Muglia
- Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH 45229, USA.
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Program in Human Genetics, Vanderbilt University, Nashville, TN 37235, USA.
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