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Hur YM, Yoo JY, You YA, Park S, Kim SM, Lee G, Kim YJ. A genome-wide and candidate gene association study of preterm birth in Korean pregnant women. PLoS One 2023; 18:e0294948. [PMID: 38019868 PMCID: PMC10686439 DOI: 10.1371/journal.pone.0294948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/12/2023] [Indexed: 12/01/2023] Open
Abstract
Preterm birth (PTB) refers to delivery before 37 weeks of gestation. Premature neonates exhibit higher neonatal morbidity and mortality rates than term neonates; therefore, it is crucial to predict and prevent PTB. Advancements enable the prediction and prevention of PTB using genetic approaches, especially by investigating its correlation with single nucleotide polymorphisms (SNPs). We aimed to identify impactive and relevant SNPs for the prediction of PTB via whole-genome sequencing analyses of the blood of 31 pregnant women with PTB (n = 13) and term birth (n = 18) who visited the Ewha Womans University Mokdong Hospital from November 1, 2018 to February 29, 2020. A genome-wide association study was performed using PLINK 1.9 software and 256 SNPs were selected and traced through protein-protein interactions. Moreover, a validation study by genotyping was performed on 60 other participants (preterm birth, n = 30; term birth, n = 30) for 25 SNPs related to ion channel binding and receptor complex pathways. Odds ratios were calculated using additive, dominant, and recessive genetic models. The risk of PTB in women with the AG allele of rs2485579 (gene name: RYR2) was significantly 4.82-fold increase, and the risk of PTB in women with the AG allele of rs7903957 (gene name: TBX5) was significantly 0.25-fold reduce. Our results suggest that rs2485579 (in RYR2) can be a genetic marker of PTB, which is considered through the association with abnormal cytoplasmic Ca2+ concentration and dysfunctional uterine contraction due to differences of RYR2 in the sarcoplasmic reticulum.
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Affiliation(s)
- Young Min Hur
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Jae Young Yoo
- Division of Biobank, Korea National Institute of Health (KNIH), Korea Disease Control and Prevention Agency (KDCA), Cheongju, Korea
| | - Young Ah You
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Sunwha Park
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Soo Min Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Gain Lee
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
| | - Young Ju Kim
- Department of Obstetrics and Gynecology, College of Medicine, Ewha Medical Research Institute, Ewha Womans University Mokdong Hospital, Seoul, Korea
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2
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Eltoukhy A, Jia Y, Lamraoui I, Abo-Kadoum MA, Atta OM, Nahurira R, Wang J, Yan Y. Transcriptome analysis and cytochrome P450 monooxygenase reveal the molecular mechanism of Bisphenol A degradation by Pseudomonas putida strain YC-AE1. BMC Microbiol 2022; 22:294. [PMID: 36482332 PMCID: PMC9733184 DOI: 10.1186/s12866-022-02689-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/02/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Bisphenol A (BPA) is a rapid spreading organic pollutant that widely used in many industries especially as a plasticizer in polycarbonate plastic and epoxy resins. BPA reported as a prominent endocrine disruptor compound that possesses estrogenic activity and fulminant toxicity. Pseudomonas putida YC-AE1 was isolated in our previous study and exerted a strong degradation capacity toward BPA at high concentrations; however, the molecular degradation mechanism is still enigmatic. RESULTS We employed RNA sequencing to analyze the differentially expressed genes (DEGs) in the YC-AE1 strain upon BPA induction. Out of 1229 differentially expressed genes, 725 genes were positively regulated, and 504 genes were down-regulated. The pathways of microbial metabolism in diverse environments were significantly enriched among DEGs based on KEGG enrichment analysis. qRT-PCR confirm the involvement of BPA degradation relevant genes in accordance with RNA Seq data. The degradation pathway of BPA in YC-AE1 was proposed with specific enzymes and encoded genes. The role of cytochrome P450 (CYP450) in BPA degradation was further verified. Sever decrease in BPA degradation was recorded by YC-AE1 in the presence of CYP450 inhibitor. Subsequently, CYP450bisdB deficient YC-AE1 strain △ bisdB lost its ability toward BPA transformation comparing with the wild type. Furthermore, Transformation of E. coli with pET-32a-bisdAB empowers it to degrade 66 mg l-1 of BPA after 24 h. Altogether, the results showed the role of CYP450 in biodegradation of BPA by YC-AE1. CONCLUSION In this study we propose the molecular basis and the potential role of YC-AE1cytochrome P450 monooxygenase in BPA catabolism.
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Affiliation(s)
- Adel Eltoukhy
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt ,grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yang Jia
- grid.412899.f0000 0000 9117 1462National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, and Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou, 325035 China
| | - Imane Lamraoui
- Higher National School of Biotechnology “Toufik Khaznadar” (ENSB), 25000 Constantine, Algeria
| | - M. A. Abo-Kadoum
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt
| | - Omar Mohammad Atta
- grid.411303.40000 0001 2155 6022Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, 71524 Egypt
| | - Ruth Nahurira
- grid.449527.90000 0004 0534 1218Faculty of Science, Kabale University, Kabale, Uganda
| | - Junhuan Wang
- grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yanchun Yan
- grid.410727.70000 0001 0526 1937Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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3
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Protein interaction networks define the genetic architecture of preterm birth. Sci Rep 2022; 12:438. [PMID: 35013336 PMCID: PMC8748950 DOI: 10.1038/s41598-021-03427-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 02/10/2021] [Indexed: 11/20/2022] Open
Abstract
The likely genetic architecture of complex diseases is that subgroups of patients share variants in genes in specific networks sufficient to express a shared phenotype. We combined high throughput sequencing with advanced bioinformatic approaches to identify such subgroups of patients with variants in shared networks. We performed targeted sequencing of patients with 2 or 3 generations of preterm birth on genes, gene sets and haplotype blocks that were highly associated with preterm birth. We analyzed the data using a multi-sample, protein–protein interaction (PPI) tool to identify significant clusters of patients associated with preterm birth. We identified shared protein interaction networks among preterm cases in two statistically significant clusters, p < 0.001. We also found two small control-dominated clusters. We replicated these data on an independent, large birth cohort. Separation testing showed significant similarity scores between the clusters from the two independent cohorts of patients. Canonical pathway analysis of the unique genes defining these clusters demonstrated enrichment in inflammatory signaling pathways, the glucocorticoid receptor, the insulin receptor, EGF and B-cell signaling, These results support a genetic architecture defined by subgroups of patients that share variants in genes in specific networks and pathways which are sufficient to give rise to the disease phenotype.
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4
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Couceiro J, Matos I, Mendes JJ, Baptista PV, Fernandes AR, Quintas A. Inflammatory factors, genetic variants, and predisposition for preterm birth. Clin Genet 2021; 100:357-367. [PMID: 34013526 DOI: 10.1111/cge.14001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/11/2021] [Accepted: 05/17/2021] [Indexed: 12/21/2022]
Abstract
Preterm birth is a major clinical and public health challenge, with a prevalence of 11% worldwide. It is the leading cause of death in children younger than 5 years old and represents 70% of neonatal deaths and 75% of neonatal morbidity. Despite the clinical and public health significance, this condition's etiology is still unclear, and most of the cases are spontaneous. There are several known preterm birth risk factors, including inflammatory diseases and the genetic background, although the underlying molecular mechanisms are far from understood. The present review highlights the research advances on the association between inflammatory-related genes and the increased risk for preterm delivery. The most associated genetic variants are the TNFα rs1800629, the IL1α rs17561, and the IL1RN rs2234663. Moreover, many of the genes discussed in this review are also implicated in pathologies involving inflammatory or autoimmune systems, such as periodontal disease, bowel inflammatory disease, and autoimmune rheumatic diseases. This review presents evidence suggesting a common genetic background to preterm birth, autoimmune and inflammatory diseases susceptibility.
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Affiliation(s)
- Joana Couceiro
- Centro de Investigação Interdisciplinar Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal.,UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal
| | - Irina Matos
- Centro de Investigação Interdisciplinar Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal
| | - José João Mendes
- Centro de Investigação Interdisciplinar Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal
| | - Pedro V Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Campus de Caparica, Caparica, Portugal
| | - Alexandre Quintas
- Centro de Investigação Interdisciplinar Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal.,Laboratório de Ciências Forenses e Psicológicas Egas Moniz, Campus Universitário Quinta da Granja, Caparica, Portugal
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5
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Tong M, Smith AH, Abrahams VM. Activated Neutrophils Propagate Fetal Membrane Inflammation and Weakening through ERK and Neutrophil Extracellular Trap-Induced TLR-9 Signaling. THE JOURNAL OF IMMUNOLOGY 2021; 206:1039-1045. [PMID: 33472905 DOI: 10.4049/jimmunol.2001268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022]
Abstract
Preterm birth is associated with significant neonatal mortality and morbidity worldwide. Chorioamnionitis, inflammation of the fetal membranes (FMs), is a major risk factor and is characterized by neutrophil infiltration. However, the role of neutrophils at the FMs remains unclear. We recently reported that FMs exposed to bacterial LPS recruited more neutrophils compared with resting FMs and activated them to degranulate and release reactive oxygen species, chemokines/cytokines, and neutrophil extracellular traps. We posit that under resting conditions, neutrophils play a protective surveillance role, whereas during infection/inflammation, they induce FM tissue injury. To test this, human FM explants were exposed to neutrophil conditioned media (CM). We demonstrate that CM from neutrophils exposed to resting FM-CM did not affect FM viability or function. Conversely, CM from neutrophils activated by LPS-stimulated FM-CM significantly increased FM secretion of inflammatory IL-6, IL-8, GRO-α, and the markers of membrane weakening, MMP-9 and PGE2 This FM response was partially mediated by ERK signaling and neutrophil extracellular traps through the activation of the DNA sensor, TLR-9. Thus, neutrophils recruited by FMs during infection can propagate FM inflammation and weakening, acting in a feed-forward mechanism to propagate tissue injury at the maternal-fetal interface, increasing the risk of premature FM rupture and preterm birth in women with intrauterine infection.
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Affiliation(s)
- Mancy Tong
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510
| | - Abigail H Smith
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510
| | - Vikki M Abrahams
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510
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6
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Gaining a deeper understanding of social determinants of preterm birth by integrating multi-omics data. Pediatr Res 2021; 89:336-343. [PMID: 33188285 PMCID: PMC7898277 DOI: 10.1038/s41390-020-01266-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/13/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
In the US, high rates of preterm birth (PTB) and profound Black-White disparities in PTB have persisted for decades. This review focuses on the role of social determinants of health (SDH), with an emphasis on maternal stress, in PTB disparity and biological embedding. It covers: (1) PTB disparity in US Black women and possible contributors; (2) the role of SDH, highlighting maternal stress, in the persistent racial disparity of PTB; (3) epigenetics at the interface between genes and environment; (4) the role of the genome in modifying maternal stress-PTB associations; (5) recent advances in multi-omics studies of PTB; and (6) future perspectives on integrating multi-omics with SDH to elucidate the Black-White disparity in PTB. Available studies have indicated that neither environmental exposures nor genetics alone can adequately explain the Black-White PTB disparity. Preliminary yet promising findings of epigenetic and gene-environment interaction studies underscore the value of integrating SDH with multi-omics in prospective birth cohort studies, especially among high-risk Black women. In an era of rapid advancements in biomedical sciences and technologies and a growing number of prospective birth cohort studies, we have unprecedented opportunities to advance this field and finally address the long history of health disparities in PTB. IMPACT: This review provides an overview of social determinants of health (SDH) with a focus on maternal stress and its role on Black-White disparity in preterm birth (PTB). It summarizes the available literature on the interplay of maternal stress with key biological layers (e.g., individual genome and epigenome in response to environmental stressors) and significant knowledge gaps. It offers perspectives that such knowledge may provide deeper insight into how SDH affects PTB and why some women are more vulnerable than others and underscores the critical need for integrating SDH with multi-omics in prospective birth cohort studies, especially among high-risk Black women.
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7
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Park B, Khanam R, Vinayachandran V, Baqui AH, London SJ, Biswal S. Epigenetic biomarkers and preterm birth. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa005. [PMID: 32551139 PMCID: PMC7293830 DOI: 10.1093/eep/dvaa005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 05/06/2023]
Abstract
Preterm birth (PTB) is a major public health challenge, and novel, sensitive approaches to predict PTB are still evolving. Epigenomic markers are being explored as biomarkers of PTB because of their molecular stability compared to gene expression. This approach is also relatively new compared to gene-based diagnostics, which relies on mutations or single nucleotide polymorphisms. The fundamental principle of epigenome diagnostics is that epigenetic reprogramming in the target tissue (e.g. placental tissue) might be captured by more accessible surrogate tissue (e.g. blood) using biochemical epigenome assays on circulating DNA that incorporate methylation, histone modifications, nucleosome positioning, and/or chromatin accessibility. Epigenomic-based biomarkers may hold great potential for early identification of the majority of PTBs that are not associated with genetic variants or mutations. In this review, we discuss recent advances made in the development of epigenome assays focusing on its potential exploration for association and prediction of PTB. We also summarize population-level cohort studies conducted in the USA and globally that provide opportunities for genetic and epigenetic marker development for PTB. In addition, we summarize publicly available epigenome resources and published PTB studies. We particularly focus on ongoing genome-wide DNA methylation and epigenome-wide association studies. Finally, we review the limitations of current research, the importance of establishing a comprehensive biobank, and possible directions for future studies in identifying effective epigenome biomarkers to enhance health outcomes for pregnant women at risk of PTB and their infants.
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Affiliation(s)
- Bongsoo Park
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Vinesh Vinayachandran
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Shyam Biswal
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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8
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Stress During Pregnancy and Epigenetic Modifications to Offspring DNA: A Systematic Review of Associations and Implications for Preterm Birth. J Perinat Neonatal Nurs 2020; 34:134-145. [PMID: 32332443 PMCID: PMC7185032 DOI: 10.1097/jpn.0000000000000471] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Offspring born preterm (ie, before 37 weeks of gestation) are more likely to die or experience long-standing illness than full-term offspring. Maternal genetic variants (ie, heritable, stable variations in the genetic code) and epigenetic modifications (ie, chemical modifications to the genetic code that can affect which genes are turned on or off) in response to stress have been implicated in preterm birth. Fetal genetic variants have been linked to preterm birth though the role of offspring epigenetics in preterm birth remains understudied. This systematic review synthesizes the literature examining associations among stress during pregnancy and epigenetic modifications to offspring DNA, with 25 reports identified. Ten reports examined DNA methylation (ie, addition/removal of methyl groups to/from DNA) across the epigenome. The remainder examined DNA methylation near genes of interest, primarily genes linked to hypothalamic-pituitary-adrenal axis function (NR3C1, FKBP51), growth/immune function (IGF2), and socioemotional regulation (SLC6A4, OXTR). The majority of reports noted associations among stress and offspring DNA methylation, primarily when perceived stress, anxiety, or depression served as the predictor. Findings suggest that differences in offspring epigenetic patterns may play a role in stress-associated preterm birth and serve as targets for novel interventions.
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9
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Del Gobbo GF, Konwar C, Robinson WP. The significance of the placental genome and methylome in fetal and maternal health. Hum Genet 2019; 139:1183-1196. [PMID: 31555906 DOI: 10.1007/s00439-019-02058-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 08/29/2019] [Indexed: 01/15/2023]
Abstract
The placenta is a crucial organ for supporting a healthy pregnancy, and defective development or function of the placenta is implicated in a number of complications of pregnancy that affect both maternal and fetal health, including maternal preeclampsia, fetal growth restriction, and spontaneous preterm birth. In this review, we highlight the role of the placental genome in mediating fetal and maternal health by discussing the impact of a variety of genetic alterations, from large whole-chromosome aneuploidies to single-nucleotide variants, on placental development and function. We also discuss the placental methylome in relation to its potential applications for refining diagnosis, predicting pathology, and identifying genetic variants with potential functional significance. We conclude that understanding the influence of the placental genome on common placental-mediated pathologies is critical to improving perinatal health outcomes.
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Affiliation(s)
- Giulia F Del Gobbo
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Chaini Konwar
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada
| | - Wendy P Robinson
- BC Children's Hospital Research Institute, 950 West 28th Ave, Vancouver, BC, V5Z 4H4, Canada. .,Department of Medical Genetics, University of British Columbia, 4500 Oak Street, Vancouver, BC, V6H 3N1, Canada.
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10
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Liu X, Helenius D, Skotte L, Beaumont RN, Wielscher M, Geller F, Juodakis J, Mahajan A, Bradfield JP, Lin FTJ, Vogelezang S, Bustamante M, Ahluwalia TS, Pitkänen N, Wang CA, Bacelis J, Borges MC, Zhang G, Bedell BA, Rossi RM, Skogstrand K, Peng S, Thompson WK, Appadurai V, Lawlor DA, Kalliala I, Power C, McCarthy MI, Boyd HA, Marazita ML, Hakonarson H, Hayes MG, Scholtens DM, Rivadeneira F, Jaddoe VWV, Vinding RK, Bisgaard H, Knight BA, Pahkala K, Raitakari O, Helgeland Ø, Johansson S, Njølstad PR, Fadista J, Schork AJ, Nudel R, Miller DE, Chen X, Weirauch MT, Mortensen PB, Børglum AD, Nordentoft M, Mors O, Hao K, Ryckman KK, Hougaard DM, Kottyan LC, Pennell CE, Lyytikainen LP, Bønnelykke K, Vrijheid M, Felix JF, Lowe WL, Grant SFA, Hyppönen E, Jacobsson B, Jarvelin MR, Muglia LJ, Murray JC, Freathy RM, Werge TM, Melbye M, Buil A, Feenstra B. Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Nat Commun 2019; 10:3927. [PMID: 31477735 PMCID: PMC6718389 DOI: 10.1038/s41467-019-11881-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 08/05/2019] [Indexed: 12/17/2022] Open
Abstract
The duration of pregnancy is influenced by fetal and maternal genetic and non-genetic factors. Here we report a fetal genome-wide association meta-analysis of gestational duration, and early preterm, preterm, and postterm birth in 84,689 infants. One locus on chromosome 2q13 is associated with gestational duration; the association is replicated in 9,291 additional infants (combined P = 3.96 × 10-14). Analysis of 15,588 mother-child pairs shows that the association is driven by fetal rather than maternal genotype. Functional experiments show that the lead SNP, rs7594852, alters the binding of the HIC1 transcriptional repressor. Genes at the locus include several interleukin 1 family members with roles in pro-inflammatory pathways that are central to the process of parturition. Further understanding of the underlying mechanisms will be of great public health importance, since giving birth either before or after the window of term gestation is associated with increased morbidity and mortality.
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Affiliation(s)
- Xueping Liu
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Dorte Helenius
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Line Skotte
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Jonathan P Bradfield
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Quantinuum Research, LLC, San Diego, CA, USA
| | - Frederick T J Lin
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Suzanne Vogelezang
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Niina Pitkänen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
| | - Carol A Wang
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW, Australia
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria C Borges
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
| | - Bruce A Bedell
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Robert M Rossi
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kristin Skogstrand
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Statens Serum Institut, Center for Neonatal Screening, Department for Congenital Disorders, Copenhagen, Denmark
| | - Shouneng Peng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Wesley K Thompson
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Vivek Appadurai
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Ilkka Kalliala
- Department of Surgery and Cancer, IRDB, Faculty of Medicine, Imperial College, London, W12 0NN, UK
- Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu, 200029 HUS, Finland
| | - Christine Power
- Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College London, London, UK
| | - Mark I McCarthy
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, OX3 7LJ, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, Oxford, OX3 7LJ, UK
| | - Heather A Boyd
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Anthropology, Northwestern University, Evanston, IL, USA
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Denise M Scholtens
- Division of Biostatistics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Fernando Rivadeneira
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Vincent W V Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Rebecca K Vinding
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bridget A Knight
- NIHR Exeter Clinical Research Facility, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
| | - Katja Pahkala
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Paavo Nurmi Centre, Sports & Exercise Medicine Unit, Department of Health and Physical Activity, University of Turku, 20520, Turku, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521, Turku, Finland
| | - Øyvind Helgeland
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
- Norwegian Institute of Public Health, Division of Health data and Digitalization, Department of Genetic Research and Bioinformatics, Oslo, Norway
| | - Stefan Johansson
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | - Pål R Njølstad
- K. G. Jebsen Center for Diabetes Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - João Fadista
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Andrew J Schork
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Ron Nudel
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Daniel E Miller
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- iSEQ, Centre for Integrative Sequencing, Aarhus University, Aarhus, Denmark
- Department of Biomedicine-Human Genetics, Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Center Copenhagen, Mental Health Services in the Capital Region of Denmark, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Kelli K Ryckman
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Epidemiology, University of Iowa, Iowa City, IA, USA
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Statens Serum Institut, Center for Neonatal Screening, Department for Congenital Disorders, Copenhagen, Denmark
| | - Leah C Kottyan
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Craig E Pennell
- School of Medicine and Public Health, Faculty of Medicine and Health, The University of Newcastle, Newcastle, NSW, Australia
| | - Leo-Pekka Lyytikainen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, 33520, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center-Tampere, Faculty of Medicine and Life Sciences, University of Tampere, 33014, Tampere, Finland
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - William L Lowe
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Struan F A Grant
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Elina Hyppönen
- Population, Policy and Practice, Great Ormond Street Institute for Child Health, University College London, London, UK
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, Adelaide, Australia
- South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
| | - Marjo-Riitta Jarvelin
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, School of Public Health, Medical Research Council-Health Protection Agency Centre for Environment and Health, Faculty of Medicine, Imperial College London, London, UK
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Jeffrey C Murray
- Department of Pediatrics, University of Iowa, Iowa City, IA, USA
| | - Rachel M Freathy
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Royal Devon and Exeter Hospital, Barrack Road, Exeter, EX2 5DW, UK
- Medical Research Council Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Thomas M Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alfonso Buil
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.
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11
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Schuster J, Uzun A, Stablia J, Schorl C, Mori M, Padbury JF. Effect of prematurity on genome wide methylation in the placenta. BMC MEDICAL GENETICS 2019; 20:116. [PMID: 31253109 PMCID: PMC6599230 DOI: 10.1186/s12881-019-0835-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Abstract
Background Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns. Despite decades of research, the molecular mechanism underlying its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The “fetal origins” hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility. Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages. We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs). Results Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p < 0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p < 0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth. Conclusion These studies form the basis for future studies on the epigenetics of preterm birth, “fetal programming” and the impact of environment exposures on this important clinical challenge. Electronic supplementary material The online version of this article (10.1186/s12881-019-0835-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Schuster
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Alper Uzun
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA
| | - Joan Stablia
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, 02906, USA
| | - Mari Mori
- Pediatrics and Genetics, Hasbro Children's Hospital, Providence, Rhode Island, 02905, USA
| | - James F Padbury
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA. .,, Providence, USA.
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12
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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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13
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Abstract
Preterm birth (PTB) complications are the leading cause of long-term morbidity and mortality in children. By using whole blood samples, we integrated whole-genome sequencing (WGS), RNA sequencing (RNA-seq), and DNA methylation data for 270 PTB and 521 control families. We analyzed this combined dataset to identify genomic variants associated with PTB and secondary analyses to identify variants associated with very early PTB (VEPTB) as well as other subcategories of disease that may contribute to PTB. We identified differentially expressed genes (DEGs) and methylated genomic loci and performed expression and methylation quantitative trait loci analyses to link genomic variants to these expression and methylation changes. We performed enrichment tests to identify overlaps between new and known PTB candidate gene systems. We identified 160 significant genomic variants associated with PTB-related phenotypes. The most significant variants, DEGs, and differentially methylated loci were associated with VEPTB. Integration of all data types identified a set of 72 candidate biomarker genes for VEPTB, encompassing genes and those previously associated with PTB. Notably, PTB-associated genes RAB31 and RBPJ were identified by all three data types (WGS, RNA-seq, and methylation). Pathways associated with VEPTB include EGFR and prolactin signaling pathways, inflammation- and immunity-related pathways, chemokine signaling, IFN-γ signaling, and Notch1 signaling. Progress in identifying molecular components of a complex disease is aided by integrated analyses of multiple molecular data types and clinical data. With these data, and by stratifying PTB by subphenotype, we have identified associations between VEPTB and the underlying biology.
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14
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Hallman M, Haapalainen A, Huusko JM, Karjalainen MK, Zhang G, Muglia LJ, Rämet M. Spontaneous premature birth as a target of genomic research. Pediatr Res 2019; 85:422-431. [PMID: 30353040 DOI: 10.1038/s41390-018-0180-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/20/2018] [Accepted: 08/23/2018] [Indexed: 01/23/2023]
Abstract
Spontaneous preterm birth is a serious and common pregnancy complication associated with hormonal dysregulation, infection, inflammation, immunity, rupture of fetal membranes, stress, bleeding, and uterine distention. Heredity is 25-40% and mostly involves the maternal genome, with contribution of the fetal genome. Significant discoveries of candidate genes by genome-wide studies and confirmation in independent replicate populations serve as signposts for further research. The main task is to define the candidate genes, their roles, localization, regulation, and the associated pathways that influence the onset of human labor. Genomic research has identified some candidate genes that involve growth, differentiation, endocrine function, immunity, and other defense functions. For example, selenocysteine-specific elongation factor (EEFSEC) influences synthesis of selenoproteins. WNT4 regulates decidualization, while a heat-shock protein family A (HSP70) member 1 like, HSPAIL, influences expression of glucocorticoid receptor and WNT4. Programming of pregnancy duration starts before pregnancy and during placentation. Future goals are to understand the interactive regulation of the pathways in order to define the clocks that influence the risk of prematurity and the duration of pregnancy. Premature birth has a great impact on the duration and the quality of life. Intensification of focused research on causes, prediction and prevention of prematurity is justified.
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Affiliation(s)
- Mikko Hallman
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland.
| | - Antti Haapalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Johanna M Huusko
- 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, OH, USA
| | - Minna K Karjalainen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Ge Zhang
- 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, OH, USA
| | - 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, OH, USA
| | - Mika Rämet
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, and Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
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15
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Schuster J, Superdock M, Agudelo A, Stey P, Padbury J, Sarkar IN, Uzun A. Machine learning approach to literature mining for the genetics of complex diseases. Database (Oxford) 2019; 2019:baz124. [PMID: 31768545 PMCID: PMC6877776 DOI: 10.1093/database/baz124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/03/2019] [Accepted: 09/23/2019] [Indexed: 11/14/2022]
Abstract
To generate a parsimonious gene set for understanding the mechanisms underlying complex diseases, we reasoned it was necessary to combine the curation of public literature, review of experimental databases and interpolation of pathway-associated genes. Using this strategy, we previously built the following two databases for reproductive disorders: The Database for Preterm Birth (dbPTB) and The Database for Preeclampsia (dbPEC). The completeness and accuracy of these databases is essential for supporting our understanding of these complex conditions. Given the exponential increase in biomedical literature, it is becoming increasingly difficult to manually maintain these databases. Using our curated databases as reference data sets, we implemented a machine learning-based approach to optimize article selection for manual curation. We used logistic regression, random forests and neural networks as our machine learning algorithms to classify articles. We examined features derived from abstract text, annotations and metadata that we hypothesized would best classify articles with genetically relevant content associated to the disorder of interest. Combinations of these features were used build the classifiers and the performance of these feature sets were compared to a standard 'Bag-of-Words'. Several combinations of these genetic based feature sets outperformed 'Bag-of-Words' at a threshold such that 95% of the curated gene set obtained from the original manual curation of all articles were extracted from the articles classified by machine learning as 'considered'. The performance was superior in terms of the reduction of required manual curation and two measures of the harmonic mean of precision and recall. The reduction in workload ranged from 0.814 to 0.846 for the dbPTB and 0.301 to 0.371 for the dbPEC. Additionally, a database of metadata and annotations is generated which allows for rapid query of individual features. Our results demonstrate that machine learning algorithms can identify articles with relevant data for databases of genes associated with complex diseases.
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Affiliation(s)
- Jessica Schuster
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, 02905, USA
| | - Michael Superdock
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
| | - Anthony Agudelo
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, 02905, USA
| | - Paul Stey
- Computing and Information Services, Brown University, Providence, RI, 02903, USA
| | - James Padbury
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, 02905, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02906, USA
| | - Indra Neil Sarkar
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
- Center for Biomedical Informatics, Brown University, Providence, RI, 02912, USA
- Rhode Island Quality Institute, Providence, RI, 02908, USA
| | - Alper Uzun
- Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, 02903, USA
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, 02905, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, 02906, USA
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16
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Preda A, Caracostea G, Ona D, Zaharie G, Stamatian F. Association between maternal/newborn genetic variants, placental pathology and spontaneous preterm birth risk: a Romanian population-based study. J Matern Fetal Neonatal Med 2018; 33:1171-1177. [PMID: 30249138 DOI: 10.1080/14767058.2018.1517311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Objective: The objective of this study was to determine the association between maternal/newborn single-nucleotide polymorphisms (SNPs) in three candidate genes, placental pathology and the risk of spontaneous preterm birth (SPTB) in a Romanian population.Methods: We performed a prospective case-control study in a tertiary maternity in Romania, including 79 mother-newborn pairs with SPTB and 81 mother-newborn pairs with term delivery. Using real-time Polymerase Chain Reaction (PCR), three SNPs rs8192282 A > G, rs2277698 C > T and rs34003 A > C located on interleukin 6 receptor (IL6R), tissue inhibitor of matrix metalloproteinase-2 (TIMP2) and fibroblast growth factor 1 (FGF1) genes were assessed. The minor allele and genotype frequencies were compared between groups. Multilocus genetic association analyses were performed. From pathology reports, the morphological and histopathological examination of the placentas were extracted.Results: The rs34003 C/C genotype frequency in newborns FGF1 gene was significantly higher in the spontaneous preterm birth (SPTB) group compared to the control group (p = .045). In single-locus analyses, C/C genotype was associated with an increased risk of spontaneous preterm birth (OR = 2.59, 95%CI: 1.02-6.58). Additionally, this homozygote genotype was correlated with the presence of placental pathology, especially with the inflammatory and vascular lesions (p < .01). The prediction model based on rs34003 C/C genotype - placental pathology joint influence had a statistically significant regression coefficient (p < .01, OR = 7.76, 95%CI: 4.03-14.93). Single nucleotide polymorphisms related to IL6R gene in maternal samples and FGF1 gene in newborns were associated with spontaneous preterm delivery in multilocus genetic association analyses (p = .028, OR of 2.375).Conclusions: Our results indicate that rs34003 C/C genotype in newborns FGF1gene is correlated with the occurrence of placental pathological lesions and with an increased SPTB risk. The association of two SNPs in maternal and fetal genes doubled the risk of spontaneous preterm birth in our population.
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Affiliation(s)
- Andreia Preda
- 1st Department of Obstetrics and Gynaecology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Gabriela Caracostea
- 1st Department of Obstetrics and Gynaecology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Dan Ona
- 1st Department of Obstetrics and Gynaecology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Gabriela Zaharie
- Department of Neonatology, Iuliu Haţieganu, University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Florin Stamatian
- 1st Department of Obstetrics and Gynaecology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Imogen Research Center, Cluj County Emergency Hospital, Cluj-Napoca, Romania
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17
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Silva LVCD, Javorski N, André Cavalcanti Brandão L, Lima MDC, Crovella S, Eickmann SH. Influence of MBL2 and NOS3 polymorphisms on spontaneous preterm birth in North East Brazil: genetics and preterm birth. J Matern Fetal Neonatal Med 2018; 33:127-135. [PMID: 29886784 DOI: 10.1080/14767058.2018.1487938] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Background: The mannose-binding lectin (MBL2) and nitric oxide synthase 3 (NOS3) genes are associated with the immune response against inflammatory processes, have been reported as possibly related with premature birth. Until now, most of the researches regarding the genetic influence of prematurity have revealed limited results because only investigating the child or the mothers' genotypes, thus not exploring the possible effects of interactions between these genotypes or the interactions with environmental factors related to the duration of pregnancy.Objective: We performed a replica study investigating the influence of single nucleotide polymorphisms (SNPs) in MBL2 and NOS3 genes on premature birth, also considering socioeconomic, demographic, and gestational factors.Materials and methods: We conducted a case-control study with 189 mother-infant dyads, with 104 spontaneous preterm births and 85 term births from Recife, Brazil. We used peripheral blood samples and umbilical cord samples to extract DNA. Functional SNPs at exon 1 and promoter region of MBL2 and NOS3 RS1799983 SNP were genotyped using direct sequencing and fluorescent allelic specific TaqMan® assays respectively. Data were analyzed using the Statistical Package for the Social Sciences (SPSS®) program with bivariate association and logistic multivariate regression tests.Results: We observed a prevalence of MBL2 wild-type genotype in the mother-infant dyad of the preterm group and polymorphic genotype in the mother-infant dyad of term birth. The haplotype LYA predominated in our sample, being more frequent in the preterm group, while the haplotype LYB, correlated with lower levels of MBL protein, was more frequent in the term birth group. About NOS3 RS1799983 SNP, the G/G genotype was more frequent throughout the sample. The heterozygous genotype predominated among women from the preterm group, showed a borderline difference between the groups. When MBL2 genotypes of the mother and son were analyzed together, codon 54 of MBL2 remained associated with prematurity. When the variables with p value lower than .20 in the bivariate analysis were analyzed by logistic regression, the low weight of the pregnant woman in relation to the gestational age, the occurrence of preterm premature rupture of membranes, urinary tract infection during birth and maternal history of other premature births were risk factors to prematurity. On the other hand, the presence of B allele at codon 54 of maternal MBL2 was a protective factor for the occurrence of spontaneous premature birth. In contrast, a borderline association was established between the maternal genetic variation within NOS3 gene and the outcome studied.Conclusions: Our study, limited by the small number of patients enrolled, indicates that MBL2 and NOS3 functional SNPs are associated with the occurrence of spontaneous prematurity and the regulation of the maternal inflammatory response. Despite these results are in agreement with previously reports, our findings do not replicate the ones reported in a large genome-wide association study performed on quite high number of subjects. Thus, we can conclude that MBL2 and NOS3 functional SNPs are plausible candidate risk factors just in few preterm birth cases, and consequently they cannot be included in the general diagnostic practice.
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Affiliation(s)
| | - Natassia Javorski
- Post-graduation in Genetics of Federal University of Pernambuco, Recife, Brazil
| | | | - Marília de Carvalho Lima
- Post-graduation in Child and Adolescent Health of Federal University of Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetics Department of Federal University of Pernambuco, Recife, Brazil
| | - Sophie Helena Eickmann
- Post-graduation in Child and Adolescent Health of Federal University of Pernambuco, Recife, Brazil
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18
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Glover AV, Manuck TA. Screening for spontaneous preterm birth and resultant therapies to reduce neonatal morbidity and mortality: A review. Semin Fetal Neonatal Med 2018; 23:126-132. [PMID: 29229486 PMCID: PMC6381594 DOI: 10.1016/j.siny.2017.11.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite considerable effort aimed at decreasing the incidence of spontaneous preterm birth, it remains the leading cause of perinatal morbidity and mortality. Screening strategies are imperfect. Approaches used to identify women considered by historical factors to be low risk for preterm delivery (generally considered to be women with singleton pregnancies without a history of a previous preterm birth) as well as those at high risk for preterm birth (those with a previous preterm birth, short cervix, or multiple gestation) continue to evolve. Herein, we review the current evidence and approaches to screening women for preterm birth, and examine future directions for clinical practice. Further research is necessary to better identify at-risk women and provide evidence-based management.
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Affiliation(s)
- Angelica V Glover
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tracy A Manuck
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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19
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Strauss JF, Romero R, Gomez-Lopez N, Haymond-Thornburg H, Modi BP, Teves ME, Pearson LN, York TP, Schenkein HA. Spontaneous preterm birth: advances toward the discovery of genetic predisposition. Am J Obstet Gynecol 2018; 218:294-314.e2. [PMID: 29248470 PMCID: PMC5834399 DOI: 10.1016/j.ajog.2017.12.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 02/08/2023]
Abstract
Evidence from family and twin-based studies provide strong support for a significant contribution of maternal and fetal genetics to the timing of parturition and spontaneous preterm birth. However, there has been only modest success in the discovery of genes predisposing to preterm birth, despite increasing sophistication of genetic and genomic technology. In contrast, DNA variants associated with other traits/diseases have been identified. For example, there is overwhelming evidence that suggests that the nature and intensity of an inflammatory response in adults and children are under genetic control. Because inflammation is often invoked as an etiologic factor in spontaneous preterm birth, the question of whether spontaneous preterm birth has a genetic predisposition in the case of pathologic inflammation has been of long-standing interest to investigators. Here, we review various genetic approaches used for the discovery of preterm birth genetic variants in the context of inflammation-associated spontaneous preterm birth. Candidate gene studies have sought genetic variants that regulate inflammation in the mother and fetus; however, the promising findings have often not been replicated. Genome-wide association studies, an approach to the identification of chromosomal loci responsible for complex traits, have also not yielded compelling evidence for DNA variants predisposing to preterm birth. A recent genome-wide association study that included a large number of White women (>40,000) revealed that maternal loci contribute to preterm birth. Although none of these loci harbored genes directly related to innate immunity, the results were replicated. Another approach to identify DNA variants predisposing to preterm birth is whole exome sequencing, which examines the DNA sequence of protein-coding regions of the genome. A recent whole exome sequencing study identified rare mutations in genes encoding for proteins involved in the negative regulation (dampening) of the innate immune response (eg, CARD6, CARD8, NLRP10, NLRP12, NOD2, TLR10) and antimicrobial peptide/proteins (eg, DEFB1, MBL2). These findings support the concept that preterm labor, at least in part, has an inflammatory etiology, which can be induced by pathogens (ie, intraamniotic infection) or "danger signals" (alarmins) released during cellular stress or necrosis (ie, sterile intraamniotic inflammation). These findings support the notion that preterm birth has a polygenic basis that involves rare mutations or damaging variants in multiple genes involved in innate immunity and host defense mechanisms against microbes and their noxious products. An overlap among the whole exome sequencing-identified genes and other inflammatory conditions associated with preterm birth, such as periodontal disease and inflammatory bowel disease, was observed, which suggests a shared genetic substrate for these conditions. We propose that whole exome sequencing, as well as whole genome sequencing, is the most promising approach for the identification of functionally significant genetic variants responsible for spontaneous preterm birth, at least in the context of pathologic inflammation. The identification of genes that contribute to preterm birth by whole exome sequencing, or whole genome sequencing, promises to yield valuable population-specific biomarkers to identify the risk for spontaneous preterm birth and potential strategies to mitigate such a risk.
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Affiliation(s)
- Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA.
| | - Roberto Romero
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD and Detroit, MI; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI.
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD and Detroit, MI; Department of Obstetrics and Gynecology and the Department of Immunology, Microbiology and Biochemistry, Wayne State University School of Medicine, Detroit, MI
| | - Hannah Haymond-Thornburg
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Bhavi P Modi
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Maria E Teves
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Laurel N Pearson
- Department of Anthropology, Pennsylvania State University, University Park, PA
| | - Timothy P York
- Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Harvey A Schenkein
- Department of Periodontics, Virginia Commonwealth University School of Dentistry, Richmond, VA
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20
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The biological basis and prevention of preterm birth. Best Pract Res Clin Obstet Gynaecol 2018; 52:13-22. [PMID: 29703554 DOI: 10.1016/j.bpobgyn.2018.01.022] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/30/2018] [Indexed: 12/11/2022]
Abstract
The time of birth is a critical determinant of perinatal and long-term outcomes. Preterm birth is still the first cause of infant mortality and morbidity; unfortunately, rates of preterm birth remain high in both high- and low-resource countries, ranging from 5% to 18%. Preterm parturition is a syndrome, which can be induced by various factors such as infection, cervical pathology, uterine overdistension, progesterone deficiency, vascular alterations (utero-placental ischemia, decidual hemorrhage), maternal and fetal stress, allograft reaction, allergic phenomena, and probably other several unknown factors. These various etiologies can lead to the pathological activation of a common pathway of decidua/fetal membranes, which causes uterine contractility, cervical ripening, and rupture of membranes. Moreover, the mechanisms responsible for these processes have been identified, which involve receptors, chemokines, and inflammatory cytokines. It is very important to understand the cellular and biochemical pathways responsible for preterm labor to identify, treat, and prevent negative outcome in a timely manner. Clinicians and researchers play a key role in improving biochemical knowledge on preterm delivery, identifying risk factors, and shaping interventions that can address this complex syndrome.
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21
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Quinney SK, Gullapelli R, Haas DM. Translational Systems Pharmacology Studies in Pregnant Women. CPT-PHARMACOMETRICS & SYSTEMS PHARMACOLOGY 2017; 7:69-81. [PMID: 29239132 PMCID: PMC5824114 DOI: 10.1002/psp4.12269] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 12/26/2022]
Abstract
Pregnancy involves rapid physiological adaptation and complex interplay between mother and fetus. New analytic technologies provide large amounts of genomic, proteomic, and metabolomics data. The integration of these data through bioinformatics, statistical, and systems pharmacology techniques can improve our understanding of the mechanisms of normal maternal physiologic changes and fetal development. New insights into the mechanisms of pregnancy‐related disorders, such as preterm birth (PTB), may lead to the development of new therapeutic interventions and novel biomarkers.
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Affiliation(s)
- Sara K Quinney
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Rakesh Gullapelli
- School of Informatics and Computing, Indiana University Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Division of Clinical Pharmacology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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22
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Fatahi N, Niknafs N, Kalani M, Dalili H, Shariat M, Amini E, Esmaeilnia Shirvani T, Hardani AK, Taheritafti R, Ghasemi-Fakhr N, Ghadami M, Tavakkoly-Bazzaz J, Rashidi-Nezhad R, Nayeri F, Rashidi-Nezhad A. Association of SP-B gene 9306 A/G polymorphism (rs7316) and risk of RDS. J Matern Fetal Neonatal Med 2017; 31:2965-2970. [PMID: 28738720 DOI: 10.1080/14767058.2017.1359829] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Respiratory distress syndrome (RDS) is a severe pulmonary disease predominantly affects preterm newborns. Polymorphisms of surfactant-protein genes have been mostly evaluated as the candidate contributors in genetics of RDS. However the results are divers in different studies. We aimed at investigating the association of surfactant protein B (SPB) gene 9306 A/G polymorphism (rs7316) with RDS development. METHOD Three hundred and eighty newborns with gestational age of less than 34 weeks were included in a multicenter case-control study. Respiratory distress (RD) was scored according to Downes' scoring system. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used for genotyping. RESULT One hundred and eighty-four neonates showed RDS and 196 did not. Gestational age (GA) was significantly lower in the RDS group compared with the controls. AA genotype and A allele were found more frequently in the RDS group than the controls (96.2% versus 63.8% and 98.1% versus 80.6%, respectively) (p =.0001). CONCLUSIONS This is the first report of association of SFTPB rs7316 polymorphism with RDS development in Iranian newborns. The current study suggests that GA <28-weeks is the most important factor in predisposition to RDS. Genetic background in terms of SP-B gene might be involved in predisposition to RDS in premature neonates.
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Affiliation(s)
- Neda Fatahi
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,b Ronash Medical Genetic Center , Tehran , Iran
| | - Nikoo Niknafs
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,c Breast feeding Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran
| | - Majid Kalani
- d Akbarabadi Hospital , Iran University of Medical Sciences , Tehran , Iran
| | - Hosein Dalili
- c Breast feeding Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran
| | - Mamak Shariat
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,c Breast feeding Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran
| | - Elaheh Amini
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,e Department of Pediatrics, Faculty of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Tahereh Esmaeilnia Shirvani
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,e Department of Pediatrics, Faculty of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Amir Kamal Hardani
- f Ahwaz Jundishapur University of Medical Sciences , School of Medicine , Ahwaz , Iran
| | - Roya Taheritafti
- g Department of Pediatrics, Faculty of Medicine , Shahid Beheshti University of Medical Sciences , Tehran , Iran
| | - Nasrin Ghasemi-Fakhr
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran
| | - Mohsen Ghadami
- h Department of Medical Genetics, Faculty of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Javad Tavakkoly-Bazzaz
- h Department of Medical Genetics, Faculty of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | | | - Fatemeh Nayeri
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,c Breast feeding Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran
| | - Ali Rashidi-Nezhad
- a Maternal, Fetal and Neonatal Research Center , Imam Khomeini Hospital Complex, Tehran University of Medical Sciences , Tehran , Iran.,b Ronash Medical Genetic Center , Tehran , Iran
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23
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Eidem HR, McGary KL, Capra JA, Abbot P, Rokas A. The transformative potential of an integrative approach to pregnancy. Placenta 2017; 57:204-215. [PMID: 28864013 DOI: 10.1016/j.placenta.2017.07.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 07/08/2017] [Accepted: 07/15/2017] [Indexed: 11/17/2022]
Abstract
BACKGROUND Complex traits typically involve diverse biological pathways and are shaped by numerous genetic and environmental factors. Pregnancy-associated traits and pathologies are further complicated by extensive communication across multiple tissues in two individuals, interactions between two genomes-maternal and fetal-that obscure causal variants and lead to genetic conflict, and rapid evolution of pregnancy-associated traits across mammals and in the human lineage. Given the multi-faceted complexity of human pregnancy, integrative approaches that synthesize diverse data types and analyses harbor tremendous promise to identify the genetic architecture and environmental influences underlying pregnancy-associated traits and pathologies. METHODS We review current research that addresses the extreme complexities of traits and pathologies associated with human pregnancy. RESULTS We find that successful efforts to address the many complexities of pregnancy-associated traits and pathologies often harness the power of many and diverse types of data, including genome-wide association studies, evolutionary analyses, multi-tissue transcriptomic profiles, and environmental conditions. CONCLUSION We propose that understanding of pregnancy and its pathologies will be accelerated by computational platforms that provide easy access to integrated data and analyses. By simplifying the integration of diverse data, such platforms will provide a comprehensive synthesis that transcends many of the inherent challenges present in studies of pregnancy.
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Affiliation(s)
- Haley R Eidem
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Kriston L McGary
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, 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; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37235, USA.
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24
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Time-Variant Genetic Effects as a Cause for Preterm Birth: Insights from a Population of Maternal Cousins in Sweden. G3-GENES GENOMES GENETICS 2017; 7:1349-1356. [PMID: 28250013 PMCID: PMC5386882 DOI: 10.1534/g3.116.038612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Preterm delivery (PTD) is the leading cause of neonatal mortality worldwide, yet its etiology remains largely unexplained. We propose that the genetic factors controlling this trait could act in a nonuniform manner during pregnancy, with each factor having a unique “window of sensitivity.” We test this hypothesis by modeling the distribution of gestational ages (GAs) observed in maternal cousins from the Swedish Medical Birth Register (MBR) (n = 35,541 pairs). The models were built using a time-to-event framework, with simulated genetic factors that increase the hazard of birth either uniformly across the pregnancy (constant effect) or only in particular windows (varying effect). By including various combinations of these factors, we obtained four models that were then optimized and compared. Best fit to the clinical data was observed when most of the factors had time-variant effects, independently of the number of loci simulated. Finally, power simulations were performed to assess the ability to discover varying-effect loci by usual methods for genome-wide association testing. We believe that the tools and concepts presented here should prove useful for the design of future studies of PTD and provide new insights into the genetic architecture determining human GA.
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25
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Manuck TA, Watkins WS, Esplin MS, Biggio J, Bukowski R, Parry S, Zhan H, Huang H, Andrews W, Saade G, Sadovsky Y, Reddy UM, Ilekis J, Yandell M, Varner MW, Jorde LB. Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study. BJOG 2017; 125:343-350. [DOI: 10.1111/1471-0528.14485] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2016] [Indexed: 11/26/2022]
Affiliation(s)
- TA Manuck
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine; University of Utah School of Medicine; Salt Lake City UT USA
- Intermountain Healthcare Department of Maternal Fetal Medicine; Salt Lake City UT USA
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine; University of North Carolina-Chapel Hill; Chapel Hill NC USA
| | - WS Watkins
- Department of Human Genetics; University of Utah; Salt Lake City UT USA
| | - MS Esplin
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine; University of Utah School of Medicine; Salt Lake City UT USA
- Intermountain Healthcare Department of Maternal Fetal Medicine; Salt Lake City UT USA
| | - J Biggio
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine and Center for Women's Reproductive Health; University of Alabama at Birmingham; Birmingham AL USA
| | - R Bukowski
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; University of Texas Medical Branch; Galveston TX USA
| | - S Parry
- Department of Obstetrics and Gynecology; University of Pennsylvania School of Medicine; Philadelphia PA USA
| | - H Zhan
- Collaborative Center for Statistics in Science; Yale University School of Public Health; New Haven CT USA
| | - H Huang
- Collaborative Center for Statistics in Science; Yale University School of Public Health; New Haven CT USA
| | - W Andrews
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine and Center for Women's Reproductive Health; University of Alabama at Birmingham; Birmingham AL USA
| | - G Saade
- Department of Obstetrics and Gynecology; Division of Maternal-Fetal Medicine; University of Texas Medical Branch; Galveston TX USA
| | - Y Sadovsky
- Magee-Womens Research Institute; University of Pittsburgh School of Medicine; Pittsburgh PA USA
| | - UM Reddy
- Pregnancy and Perinatology Branch; Center for Developmental Biology and Perinatal Medicine; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Bethesda MD USA
| | - J Ilekis
- Pregnancy and Perinatology Branch; Center for Developmental Biology and Perinatal Medicine; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Bethesda MD USA
| | - M Yandell
- Department of Human Genetics; University of Utah; Salt Lake City UT USA
| | - MW Varner
- Department of Obstetrics and Gynecology; Division of Maternal Fetal Medicine; University of Utah School of Medicine; Salt Lake City UT USA
- Intermountain Healthcare Department of Maternal Fetal Medicine; Salt Lake City UT USA
| | - LB Jorde
- Department of Human Genetics; University of Utah; Salt Lake City UT USA
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26
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Abstract
BACKGROUND Runs of homozygosity (ROH) are consecutive homozygous genotypes, which may result from population inbreeding or consanguineous marriages. ROH enhance the expression of recessive traits. METHODS We mapped ROH in a case control study of women delivering at term compared with women delivering at or before 34 wk gestation. Gene sets known to be important in risk of preterm birth were examined for their overlap with identified ROH segments. RESULTS While we found no evidence of increased burden of ROH or copy number variations in mothers delivering at or before 34 wk compared with term, we identified 424 genome-wide 50 kb segments with significant difference in abundance of overlapping ROH segments in cases vs. controls, P < 0.05. These regions overlap 199 known genes. We found preterm birth associated genes (CXCR4, MYLK, PAK1) and genes shown to have an evolutionary link to preterm (CXCR4, PPP3CB, C6orf57, DUSP13, and SLC25A45) with significant differences in abundance of overlapping ROH blocks in cases vs. controls, P < 0.001. CONCLUSION We conclude, while we found no significant burden of ROH, we did identify genomic regions with significantly greater abundance of ROH blocks in women delivering preterm that overlapped genes known to be involved in preterm birth.
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27
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Harrison MS, Eckert LO, Cutland C, Gravett M, Harper DM, McClure EM, Nunes AP, Lazo S, Moore TM, Watson W, Kochhar S, Goldenberg RL. Pathways to preterm birth: Case definition and guidelines for data collection, analysis, and presentation of immunization safety data. Vaccine 2016; 34:6093-6101. [PMID: 27491689 PMCID: PMC5139807 DOI: 10.1016/j.vaccine.2016.03.054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 03/15/2016] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | - Michael Gravett
- Global Alliance to Prevent Prematurity and Stillbirth (GAPPS), an Initiative of Seattle Childrens, United States
| | | | | | | | - Suzette Lazo
- Philippine Society of Experimental and Clinical Pharmacology, Philippines
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28
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Fatahi N, Dalili H, Kalani M, Niknafs N, Shariat M, Tavakkoly-Bazzaz J, Amini E, Esmaeilnia Shirvani T, Hardani AK, Taheritafti R, Ghasemi-Fakhr N, Ghadami M, Nayeri F, Rashidi-Nezhad A. Association of SP-C gene codon 186 polymorphism (rs1124) and risk of RDS. J Matern Fetal Neonatal Med 2016; 30:2585-2589. [DOI: 10.1080/14767058.2016.1256994] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Neda Fatahi
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Ronash Medical Genetic Center, Tehran, Iran,
| | - Hosein Dalili
- Breast feeding Research Center, Tehran University of Medical Sciences, Tehran, Iran,
| | - Majid Kalani
- Akbarabadi Hospital, Iran University of Medical Sciences, Tehran, Iran,
| | - Nikoo Niknafs
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Breast feeding Research Center, Tehran University of Medical Sciences, Tehran, Iran,
| | - Mamak Shariat
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Breast feeding Research Center, Tehran University of Medical Sciences, Tehran, Iran,
| | - Javad Tavakkoly-Bazzaz
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Elaheh Amini
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Tahereh Esmaeilnia Shirvani
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Amir kamal Hardani
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- School of Medicine, Ahwaz Jundishapur University of Medical Sciences, Ahwaz, Iran, and
| | - Roya Taheritafti
- Breast feeding Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Department of Pediatrics, Faculty of Medicine, Shahid Beheshti University of medical Sciences, Tehran, Iran
| | - Nasrin Ghasemi-Fakhr
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
| | - Mohsen Ghadami
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran,
| | - Fatemeh Nayeri
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Breast feeding Research Center, Tehran University of Medical Sciences, Tehran, Iran,
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Tehran University of Medical Sciences, Tehran, Iran,
- Ronash Medical Genetic Center, Tehran, Iran,
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Kao PYP, Leung KH, Chan LWC, Yip SP, Yap MKH. Pathway analysis of complex diseases for GWAS, extending to consider rare variants, multi-omics and interactions. Biochim Biophys Acta Gen Subj 2016; 1861:335-353. [PMID: 27888147 DOI: 10.1016/j.bbagen.2016.11.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 10/17/2016] [Accepted: 11/19/2016] [Indexed: 12/20/2022]
Abstract
BACKGROUND Genome-wide association studies (GWAS) is a major method for studying the genetics of complex diseases. Finding all sequence variants to explain fully the aetiology of a disease is difficult because of their small effect sizes. To better explain disease mechanisms, pathway analysis is used to consolidate the effects of multiple variants, and hence increase the power of the study. While pathway analysis has previously been performed within GWAS only, it can now be extended to examining rare variants, other "-omics" and interaction data. SCOPE OF REVIEW 1. Factors to consider in the choice of software for GWAS pathway analysis. 2. Examples of how pathway analysis is used to analyse rare variants, other "-omics" and interaction data. MAJOR CONCLUSIONS To choose appropriate software tools, factors for consideration include covariate compatibility, null hypothesis, one- or two-step analysis required, curation method of gene sets, size of pathways, and size of flanking regions to define gene boundaries. For rare variants, analysis performance depends on consistency between assumed and actual effect distribution of variants. Integration of other "-omics" data and interaction can better explain gene functions. GENERAL SIGNIFICANCE Pathway analysis methods will be more readily used for integration of multiple sources of data, and enable more accurate prediction of phenotypes.
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Affiliation(s)
- Patrick Y P Kao
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Kim Hung Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Lawrence W C Chan
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Shea Ping Yip
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong SAR, China.
| | - Maurice K H Yap
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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Vora NL, Smeester L, Boggess K, Fry RC. Investigating the Role of Fetal Gene Expression in Preterm Birth. Reprod Sci 2016; 24:824-828. [PMID: 27678095 DOI: 10.1177/1933719116670038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Second-trimester amniotic fluid supernatant (AFS) contains cell-free fetal RNA (cffRNA) transcripts that can provide information about fetal gene expression. In a retrospective case-control study, we measured second-trimester fetal gene expression using cffRNA extracted from AFS in women who had spontaneous preterm birth (sPTB) <34 weeks and in women who delivered >37 weeks. We extracted cffRNA from AFS of women with singletons who had second-trimester genetic amniocenteses. Twenty-one gravidas who had sPTB and 21 term controls were matched 1:1 for maternal age, fetal sex, race, gestational age (GA) at the time of amniocentesis, and medication exposure. Cell-free fetal RNA was extracted and hybridized to a customized 65-gene NanoString panel containing genes related to oxidative stress, inflammation, and hypothalamic-pituitary-adrenal (HPA) axis and included 15 housekeeping genes. Two models were run, 1 examining sPTB in relation to case/control status and 1 examining sPTB in relation to GA as a continuous variable. Among cases, the gene expression of nitric oxide synthase 1 ( NOS1), d-aspartate oxidase ( DDO), and Beta-2-microglobulin ( B2M) was higher than controls ( P value < .05; false discovery rate-corrected Q value of ≤0.10). Nitric oxide synthase 1 and DDO are genes associated with oxidative stress; B2M is a marker of the fetal inflammatory response. Fetal HPA gene expression is not associated with GA at delivery or sPTB in second-trimester AFS. Alterations of fetal gene expression related to inflammation and oxidative stress antedate clinical symptoms and may be useful for early identification of patients at risk of having an sPTB.
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Affiliation(s)
- Neeta L Vora
- 1 Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lisa Smeester
- 2 Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Kim Boggess
- 1 Division of Maternal-Fetal Medicine, Department of Obstetrics & Gynecology, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Rebecca C Fry
- 2 Department of Environmental Sciences and Engineering, UNC Gillings School of Global Public Health, Chapel Hill, NC, USA
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Literature-Informed Analysis of a Genome-Wide Association Study of Gestational Age in Norwegian Women and Children Suggests Involvement of Inflammatory Pathways. PLoS One 2016; 11:e0160335. [PMID: 27490719 PMCID: PMC4973994 DOI: 10.1371/journal.pone.0160335] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/18/2016] [Indexed: 12/16/2022] Open
Abstract
Background Five-to-eighteen percent of pregnancies worldwide end in preterm birth, which is the major cause of neonatal death and morbidity. Approximately 30% of the variation in gestational age at birth can be attributed to genetic factors. Genome-wide association studies (GWAS) have not shown robust evidence of association with genomic loci yet. Methods We separately investigated 1921 Norwegian mothers and 1199 children from pregnancies with spontaneous onset of delivery. Individuals were further divided based on the onset of delivery: initiated by labor or prelabor rupture of membranes. Genetic association with ultrasound-dated gestational age was evaluated using three genetic models and adaptive permutations. The top-ranked loci were tested for enrichment in 12 candidate gene-sets generated by text-mining PubMed abstracts containing pregnancy-related keywords. Results The six GWAS did not reveal significant associations, with the most extreme empirical p = 5.1 × 10−7. The top loci from maternal GWAS with deliveries initiated by labor showed significant enrichment in 10 PubMed gene-sets, e.g., p = 0.001 and 0.005 for keywords "uterus" and "preterm" respectively. Enrichment signals were mainly caused by infection/inflammation-related genes TLR4, NFKB1, ABCA1, MMP9. Literature-informed analysis of top loci revealed further immunity genes: IL1A, IL1B, CAMP, TREM1, TFRC, NFKBIA, MEFV, IRF8, WNT5A. Conclusion Our analyses support the role of inflammatory pathways in determining pregnancy duration and provide a list of 32 candidate genes for a follow-up work. We observed that the top regions from GWAS in mothers with labor-initiated deliveries significantly more often overlap with pregnancy-related genes than would be expected by chance, suggesting that increased sample size would benefit similar studies.
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Uzun A, Schuster J, McGonnigal B, Schorl C, Dewan A, Padbury J. Targeted Sequencing and Meta-Analysis of Preterm Birth. PLoS One 2016; 11:e0155021. [PMID: 27163930 PMCID: PMC4862658 DOI: 10.1371/journal.pone.0155021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 04/22/2016] [Indexed: 01/01/2023] Open
Abstract
Understanding the genetic contribution(s) to the risk of preterm birth may lead to the development of interventions for treatment, prediction and prevention. Twin studies suggest heritability of preterm birth is 36-40%. Large epidemiological analyses support a primary maternal origin for recurrence of preterm birth, with little effect of paternal or fetal genetic factors. We exploited an "extreme phenotype" of preterm birth to leverage the likelihood of genetic discovery. We compared variants identified by targeted sequencing of women with 2-3 generations of preterm birth with term controls without history of preterm birth. We used a meta-genomic, bi-clustering algorithm to identify gene sets coordinately associated with preterm birth. We identified 33 genes including 217 variants from 5 modules that were significantly different between cases and controls. The most frequently identified and connected genes in the exome library were IGF1, ATM and IQGAP2. Likewise, SOS1, RAF1 and AKT3 were most frequent in the haplotype library. Additionally, SERPINB8, AZU1 and WASF3 showed significant differences in abundance of variants in the univariate comparison of cases and controls. The biological processes impacted by these gene sets included: cell motility, migration and locomotion; response to glucocorticoid stimulus; signal transduction; metabolic regulation and control of apoptosis.
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Affiliation(s)
- Alper Uzun
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
- Brown Alpert Medical School, Providence, Rhode Island, United States of America
| | - Jessica Schuster
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
| | - Bethany McGonnigal
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
| | - Christoph Schorl
- Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Andrew Dewan
- Department of Epidemiology and Public Health, Yale University, New Haven, Connecticut, United States of America
| | - James Padbury
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, Rhode Island, United States of America
- Brown Alpert Medical School, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
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Uzun A, Triche EW, Schuster J, Dewan AT, Padbury JF. dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes. Database (Oxford) 2016; 2016:baw006. [PMID: 26946289 PMCID: PMC4779341 DOI: 10.1093/database/baw006] [Citation(s) in RCA: 8] [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: 11/19/2015] [Revised: 12/28/2015] [Accepted: 01/12/2016] [Indexed: 01/08/2023]
Abstract
Preeclampsia is one of the most common causes of fetal and maternal morbidity and mortality in the world. We built a Database for Preeclampsia (dbPEC) consisting of the clinical features, concurrent conditions, published literature and genes associated with Preeclampsia. We included gene sets associated with severity, concurrent conditions, tissue sources and networks. The published scientific literature is the primary repository for all information documenting human disease. We used semantic data mining to retrieve and extract the articles pertaining to preeclampsia-associated genes and performed manual curation. We deposited the articles, genes, preeclampsia phenotypes and other supporting information into the dbPEC. It is publicly available and freely accessible. Previously, we developed a database for preterm birth (dbPTB) using a similar approach. Using the gene sets in dbPTB, we were able to successfully analyze a genome-wide study of preterm birth including 4000 women and children. We identified important genes and pathways associated with preterm birth that were not otherwise demonstrable using genome-wide approaches. dbPEC serves not only as a resources for genes and articles associated with preeclampsia, it is a robust source of gene sets to analyze a wide range of high-throughput data for gene set enrichment analysis. Database URL: http://ptbdb.cs.brown.edu/dbpec/.
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Affiliation(s)
- Alper Uzun
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, USA Department of Pediatrics, Brown Alpert Medical School, Providence, RI, USA
| | - Elizabeth W Triche
- The Mandell Center for Multiple Sclerosis, Mount Sinai Rehabilitation Hospital, Hartford, CT, USA
| | - Jessica Schuster
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, USA Department of Pediatrics, Brown Alpert Medical School, Providence, RI, USA
| | - Andrew T Dewan
- Department of Epidemiology and Public Health, Yale University, New Haven, CT, USA
| | - James F Padbury
- Department of Pediatrics, Women & Infants Hospital of Rhode Island, Providence, RI, USA Department of Pediatrics, Brown Alpert Medical School, Providence, RI, USA Center for Computational Molecular Biology, Brown University, Providence, RI, USA
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Parets SE, Knight AK, Smith AK. Insights into genetic susceptibility in the etiology of spontaneous preterm birth. APPLICATION OF CLINICAL GENETICS 2015; 8:283-90. [PMID: 26715857 PMCID: PMC4685889 DOI: 10.2147/tacg.s58612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Preterm birth (PTB; <37 weeks of gestation) is a complex disorder, whose etiology is influenced by a variety of factors. A greater understanding of the biological mechanisms that contribute to PTB will facilitate identification of those at increased risk and may inform new treatments. To accomplish this, it is vital to elucidate the heritability patterns of this condition as well as the environment and lifestyle factors that increase risk for PTB. Identifying individual genes that contribute to the etiology of PTB presents particular challenges, and there has been little agreement among candidate gene and genome-wide studies performed to date. In this review we will evaluate recent genetic studies of spontaneous PTB, discuss common themes among their findings, and suggest approaches for future studies of PTB.
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Affiliation(s)
- Sasha E Parets
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna K Knight
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA ; Genetics and Molecular Biology Program, Emory University, Atlanta, GA, USA
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Haas DM, Lai D, Sharma S, Then J, Kho A, Flockhart DA, Tantisira K, Foroud T. Steroid Pathway Genes and Neonatal Respiratory Distress After Betamethasone Use in Anticipated Preterm Birth. Reprod Sci 2015; 23:680-6. [PMID: 26507871 DOI: 10.1177/1933719115612129] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To test several key glucocorticoid genes that are enhanced in lung development for associations with respiratory distress syndrome (RDS) after antenatal corticosteroid use. METHODS A prospective cohort of women received betamethasone to accelerate fetal lung maturity for threatened preterm delivery. DNA was obtained from mothers and newborns. Neonatal RDS was the primary outcome. Genotyping for single-nucleotide polymorphisms (SNPs) in 68 glucocorticoid genes found to be differentially expressed during lung development was performed. Multivariable analysis tested for associations of SNPs in the candidate genes with RDS. RESULTS Genotypic results for 867 SNPs in 96 mothers and 73 babies were included. Thirty-nine (53.4%) babies developed RDS. Maternal SNPs in the centromeric protein E (CENPE), GLRX, CD9, and AURKA genes provided evidence of association with RDS (P < .01). In newborns, SNPs in COL4A3, BHLHE40, and SRGN provided evidence of association with RDS (P < .01). CONCLUSION Single-nucleotide polymorphisms in several glucocorticoid responsive genes suggest association with neonatal RDS after antenatal corticosteroid use.
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Affiliation(s)
- David M Haas
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dongbing Lai
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sunita Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Jenny Then
- Indiana University School of Medicine, Indianapolis, IN, USA
| | - Alvin Kho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | - Kelan Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Tatiana Foroud
- Indiana University School of Medicine, Indianapolis, IN, USA
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Esplin MS, Manuck TA, Varner MW, Christensen B, Biggio J, Bukowski R, Parry S, Zhang H, Huang H, Andrews W, Saade G, Sadovsky Y, Reddy UM, Ilekis J. Cluster analysis of spontaneous preterm birth phenotypes identifies potential associations among preterm birth mechanisms. Am J Obstet Gynecol 2015; 213:429.e1-9. [PMID: 26070700 DOI: 10.1016/j.ajog.2015.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/13/2015] [Accepted: 06/02/2015] [Indexed: 01/23/2023]
Abstract
OBJECTIVE We sought to use an innovative tool that is based on common biologic pathways to identify specific phenotypes among women with spontaneous preterm birth (SPTB) to enhance investigators' ability to identify and to highlight common mechanisms and underlying genetic factors that are responsible for SPTB. STUDY DESIGN We performed a secondary analysis of a prospective case-control multicenter study of SPTB. All cases delivered a preterm singleton at SPTB ≤34.0 weeks' gestation. Each woman was assessed for the presence of underlying SPTB causes. A hierarchic cluster analysis was used to identify groups of women with homogeneous phenotypic profiles. One of the phenotypic clusters was selected for candidate gene association analysis with the use of VEGAS software. RESULTS One thousand twenty-eight women with SPTB were assigned phenotypes. Hierarchic clustering of the phenotypes revealed 5 major clusters. Cluster 1 (n = 445) was characterized by maternal stress; cluster 2 (n = 294) was characterized by premature membrane rupture; cluster 3 (n = 120) was characterized by familial factors, and cluster 4 (n = 63) was characterized by maternal comorbidities. Cluster 5 (n = 106) was multifactorial and characterized by infection (INF), decidual hemorrhage (DH), and placental dysfunction (PD). These 3 phenotypes were correlated highly by χ(2) analysis (PD and DH, P < 2.2e-6; PD and INF, P = 6.2e-10; INF and DH, (P = .0036). Gene-based testing identified the INS (insulin) gene as significantly associated with cluster 3 of SPTB. CONCLUSION We identified 5 major clusters of SPTB based on a phenotype tool and hierarch clustering. There was significant correlation between several of the phenotypes. The INS gene was associated with familial factors that were underlying SPTB.
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Norwitz ER, Bonney EA, Snegovskikh VV, Williams MA, Phillippe M, Park JS, Abrahams VM. Molecular Regulation of Parturition: The Role of the Decidual Clock. Cold Spring Harb Perspect Med 2015; 5:a023143. [PMID: 25918180 PMCID: PMC4632866 DOI: 10.1101/cshperspect.a023143] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The timing of birth is a critical determinant of perinatal outcome. Despite intensive research, the molecular mechanisms responsible for the onset of labor both at term and preterm remain unclear. It is likely that a "parturition cascade" exists that triggers labor at term, that preterm labor results from mechanisms that either prematurely stimulate or short-circuit this cascade, and that these mechanisms involve the activation of proinflammatory pathways within the uterus. It has long been postulated that the fetoplacental unit is in control of the timing of birth through a "placental clock." We suggest that it is not a placental clock that regulates the timing of birth, but rather a "decidual clock." Here, we review the evidence in support of the endometrium/decidua as the organ primarily responsible for the timing of birth and discuss the molecular mechanisms that prime this decidual clock.
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Affiliation(s)
- Errol R Norwitz
- Department of Obstetrics and Gynecology, Tufts Medical Center, Boston, Massachusetts 02111 Mother Infant Research Institute (MIRI), Tufts University School of Medicine, Boston, Massachusetts 02110
| | - Elizabeth A Bonney
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Vermont, Burlington, Vermont 05405
| | - Victoria V Snegovskikh
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Women and Infants Hospital of Rhode Island, Providence, Rhode Island 02905
| | - Michelle A Williams
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Mark Phillippe
- Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Joong Shin Park
- Department of Obstetrics and Gynecology, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Vikki M Abrahams
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510
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Abstract
The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms.
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Affiliation(s)
- Kayleigh A Swaggart
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229
| | - Mihaela Pavlicev
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229
| | - Louis J Muglia
- Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45229 Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229
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Capece A, Vasieva O, Meher S, Alfirevic Z, Alfirevic A. Pathway analysis of genetic factors associated with spontaneous preterm birth and pre-labor preterm rupture of membranes. PLoS One 2014; 9:e108578. [PMID: 25264875 PMCID: PMC4181300 DOI: 10.1371/journal.pone.0108578] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Background Pre-term birth (PTB) remains the leading cause of infant mortality and morbidity. Its etiology is multifactorial, with a strong genetic component. Genetic predisposition for the two subtypes, spontaneous PTB with intact membranes (sPTB) and preterm prelabor rapture of membranes (PPROM), and differences between them, have not yet been systematically summarised. Methods and findings Our literature search identified 15 association studies conducted in 3,600 women on 2175 SNPs in 274 genes. We used Ingenuity software to impute gene pathways and networks related to sPTB and PPROM. Detailed insight in the defined functional ontologies clearly separated integrated datasets for sPTB and PPROM. Our analysis of upstream regulators of genes suggests that glucocorticoid receptor (NR3C1), peroxisome proliferator activated receptor γ (PPARG) and interferon regulating factor 3 (IRF3) may be sPTB specific. PPROM-specific genes may be regulated by estrogen receptor2 (ESR2) and signal transducer and activator of transcription (STAT1). The inflammatory transcription factor NFκB is linked to both sPTB and PPROM, however, their inflammatory response is distinctly different. Conclusions Based on our analyses, we propose an autoimmune/hormonal regulation axis for sPTB, whilst pathways implicated in the etiology of PPROM include hematologic/coagulation function disorder, collagen metabolism, matrix degradation and local inflammation. Our hypothesis generating study has identified new candidate genes in the pathogenesis of PPROM and sPTB, which should be validated in large cohorts.
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Affiliation(s)
- Antonio Capece
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Olga Vasieva
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Shireen Meher
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Zarko Alfirevic
- Department of Women's and Children's Health, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Ana Alfirevic
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
- * E-mail:
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York TP, Eaves LJ, Neale MC, Strauss JF. The contribution of genetic and environmental factors to the duration of pregnancy. Am J Obstet Gynecol 2014; 210:398-405. [PMID: 24096276 DOI: 10.1016/j.ajog.2013.10.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/26/2013] [Accepted: 10/01/2013] [Indexed: 02/06/2023]
Abstract
This review describes how improvements in biometric-genetic studies of twin kinships, half-sibships, and cousinships have now demonstrated a sizeable fetal genetic and maternal genetic contribution to the spontaneous onset of labor. This is an important development because previous literature for the most part reports only an influence of the maternal genome. Current estimates of the percent of variation that is attributable to fetal genetic factors range from 11-35%; the range for the maternal genetic contribution is 13-20%. These same studies demonstrate an even larger influence of environmental sources over and above the influence of genetic sources and previously identified environmental risk factors. With these estimates in hand, a major goal for research on pregnancy duration is to identify specific allelic variation and environmental risk to account for this estimated genetic and environmental variation. A review of the current literature can serve as a guide for future research efforts.
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Affiliation(s)
- Timothy P York
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA.
| | - Lindon J Eaves
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Psychiatry, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Psychiatry, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Jerome F Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA; Department of Obstetrics and Gynecology, Virginia Commonwealth University School of Medicine, Richmond, VA
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Khadzhieva MB, Lutcenko NN, Volodin IV, Morozova KV, Salnikova LE. Association of oxidative stress-related genes with idiopathic recurrent miscarriage. Free Radic Res 2014; 48:534-41. [DOI: 10.3109/10715762.2014.891735] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Chun S, Plunkett J, Teramo K, Muglia LJ, Fay JC. Fine-mapping an association of FSHR with preterm birth in a Finnish population. PLoS One 2013; 8:e78032. [PMID: 24205076 PMCID: PMC3812121 DOI: 10.1371/journal.pone.0078032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 09/09/2013] [Indexed: 12/18/2022] Open
Abstract
Preterm birth is a complex disorder defined by gestations of less than 37 weeks. While preterm birth is estimated to have a significant genetic component, relative few genes have been associated with preterm birth. Polymorphism in one such gene, follicle-stimulating hormone receptor (FSHR), has been associated with preterm birth in Finnish and African American mothers but not other populations. To refine the genetic association of FSHR with preterm birth we conducted a fine-mapping study at the FSHR locus in a Finnish cohort. We sequenced a total of 44 kb, including protein-coding and conserved non-coding regions, in 127 preterm and 135 term mothers. Overall, we identified 288 single nucleotide variants and 65 insertion/deletions of 1-2 bp across all subjects. While no common SNPs in protein-coding regions were associated with preterm birth, including one previously associated with timing of fertilization, multiple SNPs spanning the first and second intron showed the strongest associations. Analysis of the associated SNPs revealed that they form both a protective (OR = 0.50, 95% CI = 0.25-0.93) as well as a risk (OR = 1.89, 95% CI = 1.08-3.39) haplotype with independent effects. In these haplotypes, two SNPs, rs12052281 and rs72822025, were predicted to disrupt ZEB1 and ELF3 transcription factor binding sites, respectively. Our results show that multiple haplotypes at FSHR are associated with preterm birth and we discuss the frequency and structure of these haplotypes outside of the Finnish population as a potential explanation for the absence of FSHR associations in some populations.
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Affiliation(s)
- Sung Chun
- Computational and Systems Biology Program, Washington University, St. Louis, Missouri, United States of America
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Atias N, Istrail S, Sharan R. Pathway-based analysis of genomic variation data. Curr Opin Genet Dev 2013; 23:622-6. [PMID: 24209906 DOI: 10.1016/j.gde.2013.09.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 09/18/2013] [Accepted: 09/18/2013] [Indexed: 02/02/2023]
Abstract
A holy grail of genetics is to decipher the mapping from genotype to phenotype. Recent advances in sequencing technologies allow the efficient genotyping of thousands of individuals carrying a particular phenotype in an effort to reveal its genetic determinants. However, the interpretation of these data entails tackling significant statistical and computational problems that stem from the complexity of human phenotypes and the huge genotypic search space. Recently, an alternative pathway-level analysis has been employed to combat these problems. In this review we discuss these developments, describe the challenges involved and outline possible solutions and future directions for improvement.
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Affiliation(s)
- Nir Atias
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
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Bezold KY, Karjalainen MK, Hallman M, Teramo K, Muglia LJ. The genomics of preterm birth: from animal models to human studies. Genome Med 2013; 5:34. [PMID: 23673148 PMCID: PMC3707062 DOI: 10.1186/gm438] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Preterm birth (delivery at less than 37 weeks of gestation) is the leading cause of infant mortality worldwide. So far, the application of animal models to understand human birth timing has not substantially revealed mechanisms that could be used to prevent prematurity. However, with amassing data implicating an important role for genetics in the timing of the onset of human labor, the use of modern genomic approaches, such as genome-wide association studies, rare variant analyses using whole-exome or genome sequencing, and family-based designs, holds enormous potential. Although some progress has been made in the search for causative genes and variants associated with preterm birth, the major genetic determinants remain to be identified. Here, we review insights from and limitations of animal models for understanding the physiology of parturition, recent human genetic and genomic studies to identify genes involved in preterm birth, and emerging areas that are likely to be informative in future investigations. Further advances in understanding fundamental mechanisms, and the development of preventative measures, will depend upon the acquisition of greater numbers of carefully phenotyped pregnancies, large-scale informatics approaches combining genomic information with information on environmental exposures, and new conceptual models for studying the interaction between the maternal and fetal genomes to personalize therapies for mothers and infants. Information emerging from these advances will help us to identify new biomarkers for earlier detection of preterm labor, develop more effective therapeutic agents, and/or promote prophylactic measures even before conception.
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Affiliation(s)
- Katherine Y Bezold
- Center for Prevention of Preterm Birth and Molecular and Developmental Biology Program, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Minna K Karjalainen
- Department of Pediatrics, Institute of Clinical Medicine, University of Oulu, Oulu, 90014, Finland
| | - Mikko Hallman
- Department of Pediatrics, Institute of Clinical Medicine, University of Oulu, Oulu, 90014, Finland
| | - Kari Teramo
- Department of Obstetrics and Gynecology, University Central Hospital, Helsinki, 00029 Finland
| | - Louis J Muglia
- Center for Prevention of Preterm Birth and Molecular and Developmental Biology Program, Cincinnati Children's Hospital Medical Center, and Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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