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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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2
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Wang J, Hua G, Chen J, Cui K, Yang Z, Han D, Yang X, Dong X, Ma Y, Cai G, Zhang Y, Li J, Tai Y, Da L, Li X, Ma L, Ma Q, Li R, Liu J, Darwish HYA, Wu K, Rong W, Liu W, Zhao Y, Deng X. Epigenetic mechanism of Gtl2-miRNAs causes the primitive sheep characteristics found in purebred Merino sheep. Cell Biosci 2023; 13:190. [PMID: 37828606 PMCID: PMC10571318 DOI: 10.1186/s13578-023-01142-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 10/05/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND It is not uncommon for some individuals to retain certain primitive characteristics even after domestication or long-term intensive selection. Wild ancestors or original varieties of animals typically possess strong adaptability to environmental preservation, a trait that is often lacking in highly artificially selected populations. In the case of the Merino population, a world-renowned fine wool sheep breed, a phenotype with primitive coarse wool characteristic has re-emerged. It is currently unclear whether this characteristic is detrimental to the production of fine wool or whether it is linked to the adaptability of sheep. The underlying genetic/epigenetic mechanisms behind this trait are also poorly understood. RESULTS This study identified lambs with an ancestral-like coarse (ALC) wool type that emerged during the purebred breeding of Merino fine wool sheep. The presence of this primitive sheep characteristic resulted in better environmental adaptability in lambs, as well as improved fine wool yield in adulthood. Reciprocal cross experiments revealed that the ALC phenotype exhibited maternal genetic characteristics. Transcriptomic SNP analysis indicated that the ALC phenotype was localized to the imprinted Gtl2-miRNAs locus, and a significant correlation was found between the ALC wool type and a newly identified short Interstitial Telomeric Sequences (s-ITSs) at this locus. We further confirmed that a novel 38-nt small RNA transcribed from these s-ITSs, in combination with the previously reported 22-nt small RNAs cluster from the Gtl2-miRNAs locus, synergistically inhibited PI3K/AKT/Metabolic/Oxidative stress and subsequent apoptotic pathways in wool follicle stem cells, resulting in the ALC wool type. The necessity of Gtl2-miRNAs in controlling primary hair follicle morphogenesis, as well as the wool follicle type for ALC wool lambs, was verified using intergenic differentially methylated region-knockout mice. CONCLUSION The ALC wool type of Merino sheep, which does not reduce wool quality but increases yield and adaptability, is regulated by epigenetic mechanisms in the imprinted Gtl2-miRNAs region on sheep chromosome 18, with the maternally expressed imprinted gene responsible for the ALC phenotype. This study highlights the significance of epigenetic regulation during embryonic and juvenile stages and emphasizes the advantages of early adaptation breeding for maternal parents in enhancing the overall performance of their offspring.
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Affiliation(s)
- Jiankui Wang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Guoying Hua
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jianfei Chen
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Kai Cui
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100086, China
| | - Zu Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Deping Han
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xue Yang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xianggui Dong
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuhao Ma
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Ganxian Cai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yuanyuan Zhang
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Jinnan Li
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Yurong Tai
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Lai Da
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Xinhai Li
- College of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Qing Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Hesham Y A Darwish
- Department of Applied Biotechnology, Molecular Biology Researches & Studies Institute, Assiut University, Assiut, 71526, Egypt
| | - Keliang Wu
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Weiheng Rong
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Huhhot, 010031, China
| | - Wansheng Liu
- Department of Animal Science, Center for Reproductive Biology and Health, College of Agricultural Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Yaofeng Zhao
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
| | - Xuemei Deng
- Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
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3
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Hou KC, Tsai MH, Akbarian S, Huang HS. Mir125b-1 is Not Imprinted in Human Brain and Shows Developmental Expression Changes in Mouse Brain. Neuroscience 2023; 529:99-106. [PMID: 37598835 DOI: 10.1016/j.neuroscience.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Genomic imprinting is a predominantly brain and placenta-specific epigenetic process that contributes to parent-of-origin-specific gene expression. While microRNAs are highly expressed in the brain, their imprinting status in this tissue remains poorly studied. Previous research demonstrated that Mir125b-2 is imprinted in the human brain and regulates hippocampal circuits and functions in mice. However, the imprinting status of another isoform of miR125b, Mir125b-1, in the human brain, as well as its spatiotemporal expression patterns in mice, have not been elucidated. Here, we show MIR125B1 is not imprinted in the human brain. Moreover, miR-125b-1 was highly expressed in the brains of mice. Furthermore, miR-125b-1 was down-regulated during brain development in mice. Specifically, miR-125b-1 displayed preferential expression in the olfactory bulb, thalamus, and hypothalamus of the mouse brain. Notably, miR-125b-1 was enriched in GABAergic neurons, particularly somatostatin-expressing GABAergic neurons, compared with glutamatergic neurons. Taken together, our findings provide the imprinting status and comprehensive spatiotemporal expression profiling of Mir125b-1 in the brain.
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Affiliation(s)
- Kuan-Chu Hou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Meng-Han Tsai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
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4
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Baines KJ, West RC. Sex differences in innate and adaptive immunity impact fetal, placental, and maternal health†. Biol Reprod 2023; 109:256-270. [PMID: 37418168 DOI: 10.1093/biolre/ioad072] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/08/2023] Open
Abstract
The differences between males and females begin shortly after birth, continue throughout prenatal development, and eventually extend into childhood and adult life. Male embryos and fetuses prioritize proliferation and growth, often at the expense of the fetoplacental energy reserves. This singular focus on growth over adaptability leaves male fetuses and neonates vulnerable to adverse outcomes during pregnancy and birth and can have lasting impacts throughout life. Beyond this prioritization of growth, male placentas and fetuses also respond to infection and inflammation differently than female counterparts. Pregnancies carrying female fetuses have a more regulatory immune response, whereas pregnancies carrying male fetuses have a stronger inflammatory response. These differences can be seen as early as the innate immune response with differences in cytokine and chemokine signaling. The sexual dimorphism in immunity then continues into the adaptive immune response with differences in T-cell biology and antibody production and transfer. As it appears that these sex-specific differences are amplified in pathologic pregnancies, it stands to reason that differences in the placental, fetal, and maternal immune responses in pregnancy contribute to increased male perinatal morbidity and mortality. In this review, we will describe the genetic and hormonal contributions to the sexual dimorphism of fetal and placental immunity. We will also discuss current research efforts to describe the sex-specific differences of the maternal-fetal interface and how it impacts fetal and maternal health.
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Affiliation(s)
- Kelly J Baines
- Anatomy, Physiology, Pharmacology Department, Auburn University, Auburn, AL 36849, USA
| | - Rachel C West
- Anatomy, Physiology, Pharmacology Department, Auburn University, Auburn, AL 36849, USA
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5
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Martin C, Ligat G, Malnou CE. The Yin and the Yang of extracellular vesicles during viral infections. Biomed J 2023:100659. [PMID: 37690583 DOI: 10.1016/j.bj.2023.100659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023] Open
Abstract
The role of extracellular vesicles (EVs) as key players in the intercellular communication is a subject of growing interest in all areas of physiology and pathophysiology, and the field of viral infections is no exception to the rule. In this review, we focus on the current state of knowledge and remaining gaps regarding the entanglement of viruses and EVs during infections. These two entities share many similarities, mainly due to their intricated biogenesis pathways that are in constant interaction. EVs can promote the replication and dissemination of viruses within the organism, through the dysregulation of their cargo and the modulation of the innate and adaptive immune response that occurs upon infection, but they can also promote the mitigation of viral infections. Here, we will examine how viruses hijack EV biogenesis pathways and describe the consequences of dysregulated EV secretion during viral infections, beneficial or not for viruses, revealing the duality of their possible effects.
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Affiliation(s)
- Charlène Martin
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
| | - Gaëtan Ligat
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
| | - Cécile E Malnou
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France.
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6
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Di Michele F, Chillón I, Feil R. Imprinted Long Non-Coding RNAs in Mammalian Development and Disease. Int J Mol Sci 2023; 24:13647. [PMID: 37686455 PMCID: PMC10487962 DOI: 10.3390/ijms241713647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/10/2023] Open
Abstract
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic expression controls in cis the expression of protein-coding genes, often developmentally regulated. Some imprinted lncRNAs act in trans as well, controlling target gene expression elsewhere in the genome. The regulation of imprinted gene expression-including that of imprinted lncRNAs-is susceptible to stochastic and environmentally triggered epigenetic changes in the early embryo. These aberrant changes persist during subsequent development and have long-term phenotypic consequences. This review focuses on the expression and the cis- and trans-regulatory roles of imprinted lncRNAs and describes human disease syndromes associated with their perturbed expression.
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Affiliation(s)
- Flavio Di Michele
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Isabel Chillón
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), CNRS, 1919 Route de Mende, 34093 Montpellier, France
- University of Montpellier, 163 Rue Auguste Broussonnet, 34090 Montpellier, France
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7
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Wickramage I, VanWye J, Max K, Lockhart JH, Hortu I, Mong EF, Canfield J, Lamabadu Warnakulasuriya Patabendige HM, Guzeloglu-Kayisli O, Inoue K, Ogura A, Lockwood CJ, Akat KM, Tuschl T, Kayisli UA, Totary-Jain H. SINE RNA of the imprinted miRNA clusters mediates constitutive type III interferon expression and antiviral protection in hemochorial placentas. Cell Host Microbe 2023; 31:1185-1199.e10. [PMID: 37315561 PMCID: PMC10524649 DOI: 10.1016/j.chom.2023.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 03/23/2023] [Accepted: 05/17/2023] [Indexed: 06/16/2023]
Abstract
Hemochorial placentas have evolved defense mechanisms to prevent the vertical transmission of viruses to the immunologically underdeveloped fetus. Unlike somatic cells that require pathogen-associated molecular patterns to stimulate interferon production, placental trophoblasts constitutively produce type III interferons (IFNL) through an unknown mechanism. We demonstrate that transcripts of short interspersed nuclear elements (SINEs) embedded in miRNA clusters within the placenta trigger a viral mimicry response that induces IFNL and confers antiviral protection. Alu SINEs within primate-specific chromosome 19 (C19MC) and B1 SINEs within rodent-specific microRNA cluster on chromosome 2 (C2MC) produce dsRNAs that activate RIG-I-like receptors (RLRs) and downstream IFNL production. Homozygous C2MC knockout mouse trophoblast stem (mTS) cells and placentas lose intrinsic IFN expression and antiviral protection, whereas B1 RNA overexpression restores C2MCΔ/Δ mTS cell viral resistance. Our results uncover a convergently evolved mechanism whereby SINE RNAs drive antiviral resistance in hemochorial placentas, placing SINEs as integral players in innate immunity.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Jeffrey VanWye
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Klaas Max
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - John H Lockhart
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ismet Hortu
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ezinne F Mong
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - John Canfield
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Ozlem Guzeloglu-Kayisli
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Kimiko Inoue
- Bioresource Engineering Division, BioResource Research Center, RIKEN, Tsukuba 305-0074, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, BioResource Research Center, RIKEN, Tsukuba 305-0074, Ibaraki, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| | - Charles J Lockwood
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Kemal M Akat
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA; Division of Cardiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
| | - Umit A Kayisli
- Department of Obstetrics and Gynecology, Morsani College of Medicine, University of South Florida, Tampa, FL 33602, USA
| | - Hana Totary-Jain
- Department of Molecular Pharmacology & Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Heart Institute, University of South Florida, Tampa, FL 33602, USA.
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8
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Vilimova M, Pfeffer S. Post-transcriptional regulation of polycistronic microRNAs. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1749. [PMID: 35702737 DOI: 10.1002/wrna.1749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 02/02/2023]
Abstract
An important proportion of microRNA (miRNA) genes tend to lie close to each other within animal genomes. Such genomic organization is generally referred to as miRNA clusters. Even though many miRNA clusters have been greatly studied, most attention has been usually focused on functional impacts of clustered miRNA co-expression. However, there is also another compelling aspect about these miRNA clusters, their polycistronic nature. Being transcribed on a single RNA precursor, polycistronic miRNAs benefit from common transcriptional regulation allowing their coordinated expression. And yet, numerous reports have revealed striking discrepancies in the accumulation of mature miRNAs produced from the same cluster. Indeed, the larger polycistronic transcripts can act as platforms providing unforeseen post-transcriptional regulatory mechanisms controlling individual miRNA processing, thus leading to differential miRNA expression, and sometimes even challenging the general assumption that polycistronic miRNAs are co-expressed. In this review, we aim to address the current knowledge about how miRNA polycistrons are post-transcriptionally regulated. In particular, we will focus on the mechanisms occurring at the level of the primary transcript, which are highly relevant for individual miRNA processing and as such have a direct repercussion on miRNA function within the cell. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Monika Vilimova
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Sébastien Pfeffer
- Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
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9
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Murrieta-Coxca JM, Barth E, Fuentes-Zacarias P, Gutiérrez-Samudio RN, Groten T, Gellhaus A, Köninger A, Marz M, Markert UR, Morales-Prieto DM. Identification of altered miRNAs and their targets in placenta accreta. Front Endocrinol (Lausanne) 2023; 14:1021640. [PMID: 36936174 PMCID: PMC10022468 DOI: 10.3389/fendo.2023.1021640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 02/07/2023] [Indexed: 03/06/2023] Open
Abstract
Placenta accreta spectrum (PAS) is one of the major causes of maternal morbidity and mortality worldwide with increasing incidence. PAS refers to a group of pathological conditions ranging from the abnormal attachment of the placenta to the uterus wall to its perforation and, in extreme cases, invasion into surrounding organs. Among them, placenta accreta is characterized by a direct adhesion of the villi to the myometrium without invasion and remains the most common diagnosis of PAS. Here, we identify the potential regulatory miRNA and target networks contributing to placenta accreta development. Using small RNA-Seq followed by RT-PCR confirmation, altered miRNA expression, including that of members of placenta-specific miRNA clusters (e.g., C19MC and C14MC), was identified in placenta accreta samples compared to normal placental tissues. In situ hybridization (ISH) revealed expression of altered miRNAs mostly in trophoblast but also in endothelial cells and this profile was similar among all evaluated degrees of PAS. Kyoto encyclopedia of genes and genomes (KEGG) analyses showed enriched pathways dysregulated in PAS associated with cell cycle regulation, inflammation, and invasion. mRNAs of genes associated with cell cycle and inflammation were downregulated in PAS. At the protein level, NF-κB was upregulated while PTEN was downregulated in placenta accreta tissue. The identified miRNAs and their targets are associated with signaling pathways relevant to controlling trophoblast function. Therefore, this study provides miRNA:mRNA associations that could be useful for understanding PAS onset and progression.
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Affiliation(s)
| | - Emanuel Barth
- Friedrich Schiller University Jena, Faculty of Mathematics and Computer Science, RNA Bioinformatics and High Throughput Analysis, Jena, Germany
- Faculty of Mathematics and Computer Science, Bioinformatics Core Facility, Friedrich Schiller University Jena, Jena, Germany
| | | | | | - Tanja Groten
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
| | - Alexandra Gellhaus
- Department of Gynecology and Obstetrics, University of Duisburg-Essen, Essen, Germany
| | - Angela Köninger
- Department of Gynecology and Obstetrics, University of Duisburg-Essen, Essen, Germany
- University Department of Gynecology and Obstetrics, Hospital St. Hedwig of the Order of St. John, University Medical Center Regensburg, Regensburg, Germany
| | - Manja Marz
- Friedrich Schiller University Jena, Faculty of Mathematics and Computer Science, RNA Bioinformatics and High Throughput Analysis, Jena, Germany
- Fritz Lipman Institute (FLI), Leibniz Institute for Age Research, Jena, Germany
| | - Udo R. Markert
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
- *Correspondence: Udo R. Markert, ; Diana M. Morales-Prieto,
| | - Diana M. Morales-Prieto
- Department of Obstetrics, Placenta Lab, Jena University Hospital, Jena, Germany
- *Correspondence: Udo R. Markert, ; Diana M. Morales-Prieto,
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10
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Placental extracellular vesicles in maternal-fetal communication during pregnancy. Biochem Soc Trans 2022; 50:1785-1795. [DOI: 10.1042/bst20220734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/13/2022]
Abstract
For several years, a growing number of studies have highlighted the pivotal role of placental extracellular vesicles (EVs) throughout pregnancy. These membrane nanovesicles, heterogeneous in nature, composition and origin, are secreted by several trophoblastic cell types and are found in both the maternal and fetal compartments. They can be uptaken by recipient cells and drive a wide variety of physiological and pathological processes. In this review, we provide an overview of the different described roles of placental EVs in various aspects of normal pregnancy, from placenta establishment to maternal immune tolerance towards the fetus and protection against viral infections. In the second part, we present selected examples of pathological pregnancies in which placental EVs are involved, such as gestational diabetes mellitus, pre-eclampsia, and congenital infections. Since the abundance and/or composition of placental EVs is deregulated in maternal serum during pathological pregnancies, this makes them interesting candidates as non-invasive biomarkers for gestational diseases and opens a wide field of translational perspectives.
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11
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Wu X, He X, Liu Q, Li H. The developmental miR-17-92 cluster and the Sfmbt2 miRNA cluster cannot rescue the abnormal embryonic development generated using obstructive epididymal environment-producing sperm in C57BL/6 J mice. Reprod Biol Endocrinol 2022; 20:164. [PMID: 36451157 PMCID: PMC9710060 DOI: 10.1186/s12958-022-01025-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/16/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Sperm, during epididymal transit, acquires microRNAs(miRNAs), which are crucial for embryonic development. However, whether sperm miRNAs influenced by an obstructive epididymal environment affect embryonic development remains unknown. METHOD The sham operation and vasectomy were performed in C57BL/6 J mice to create the control group (CON) and the obstructive epididymal environment group(OEE) group, respectively. The morphology of the testis and epididymis was observed using hematoxylin and eosin staining (HE staining) to establish the OEE mice model. The sperm quality test, intracytoplasmic sperm injection (ICSI), and epididymosomes fusion were employed to observe the effect of the obstructive epididymal environment on sperm and resultant embryonic development. The alteration of the sperm small RNA (sRNA) profile was analyzed by sRNA sequencing. RT-qPCR and DNA methylation were applied to observe the effect of obstructive epididymis on the expression of sperm miRNAs. The miRNAs microinjection was used to explore the impacts of sperm miRNAs on embryonic development. RESULTS We confirmed postoperative 8-week mice as the OEE mice model by examining the morphology of the testis and epididymis. In the OEE group, we observed that sperm quality degraded and the development potential of embryos was reduced, which can be saved by the normal epididymal environment. The sperm sRNA sequencing revealed that the expression of the developmental miR-17-92 cluster and the Sfmbt2 miRNA cluster was downregulated in the OEE group. The expression of these two miRNA clusters in epididymis was also downregulated and regulated by DNA methylation. However, the downregulation of either the miR-17-92 cluster or the Sfmbt2 miRNA cluster in normal zygotes did not impair embryonic development. CONCLUSION The obstructive epididymal environment influences sperm quality and resultant embryonic development, as well as the abundance of the developmental miR-17-92 cluster and the Sfmbt2 miRNA cluster in sperm, but these miRNA clusters are not the cause of abnormal embryonic development. It implies that epididymis is important in early embryonic development and may play a potential role in sperm epigenome.
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Affiliation(s)
- Xunwei Wu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xiaomei He
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Qian Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Honggang Li
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China.
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12
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Jaszczuk I, Winkler I, Koczkodaj D, Skrzypczak M, Filip A. The Role of Cluster C19MC in Pre-Eclampsia Development. Int J Mol Sci 2022; 23:ijms232213836. [PMID: 36430313 PMCID: PMC9699419 DOI: 10.3390/ijms232213836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/03/2022] [Accepted: 11/06/2022] [Indexed: 11/12/2022] Open
Abstract
Pre-eclampsia is a placenta-related complication occurring in 2-10% of all pregnancies. miRNAs are a group of non-coding RNAs regulating gene expression. There is evidence that C19MC miRNAs are involved in the development of the placenta. Deregulation of chromosome 19 microRNA cluster (C19MC) miRNAs expression leads to impaired cell differentiation, abnormal trophoblast invasion and pathological angiogenesis, which can lead to the development of pre-eclampsia. Information was obtained through a review of articles available in PubMed Medline. Articles on the role of the C19MC miRNA in the development of pre-eclampsia published in 2009-2022 were analyzed. This review article summarizes the current data on the role of the C19MC miRNA in the development of pre-eclampsia. They indicate a significant increase in the expression of most C19MC miRNAs in placental tissue and a high level of circulating fractions in serum and plasma, both in the first and/or third trimester in women with PE. Only for miR-525-5p, low levels of plasma expression were noted in the first trimester, and in the placenta in the third trimester. The search for molecular factors indicating the development of pre-eclampsia before the onset of clinical symptoms seems to be a promising diagnostic route. Identifying women at risk of developing pre-eclampsia at the pre-symptomatic stage would avoid serious complications in both mothers and fetuses. We believe that miRNAs belonging to cluster C19MC could be promising biomarkers of pre-eclampsia development.
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Affiliation(s)
- Ilona Jaszczuk
- Department of Cancer Genetics with Cytogenetic Laboratory, Medical University of Lublin, Radziwillowska Street 11, 20-080 Lublin, Poland
| | - Izabela Winkler
- Second Department of Gynecological Oncology, St. John’s Center of Oncology of the Lublin Region, Jaczewski Street 7, 20-090 Lublin, Poland
- Correspondence:
| | - Dorota Koczkodaj
- Department of Cancer Genetics with Cytogenetic Laboratory, Medical University of Lublin, Radziwillowska Street 11, 20-080 Lublin, Poland
| | - Maciej Skrzypczak
- Second Department of Gynecology, Lublin Medical University, Jaczewski Street 8, 20-954 Lublin, Poland
| | - Agata Filip
- Department of Cancer Genetics with Cytogenetic Laboratory, Medical University of Lublin, Radziwillowska Street 11, 20-080 Lublin, Poland
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13
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Coordinated regulation of microRNA genes in C19MC by SETDB1. Biochem Biophys Res Commun 2022; 637:17-22. [DOI: 10.1016/j.bbrc.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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14
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Partial Disturbance of Microprocessor Function in Human Stem Cells Carrying a Heterozygous Mutation in the DGCR8 Gene. Genes (Basel) 2022; 13:genes13111925. [DOI: 10.3390/genes13111925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 11/04/2022] Open
Abstract
Maturation of microRNAs (miRNAs) begins by the “Microprocessor” complex, containing the Drosha endonuclease and its partner protein, "DiGeorge Syndrome Critical Region 8" (DGCR8). Although the main function of the two proteins is to coordinate the first step of precursor miRNAs formation, several studies revealed their miRNA-independent functions in other RNA-related pathways (e.g., in snoRNA decay) or, for the DGCR8, the role in tissue development. To investigate the specific roles of DGCR8 in various cellular pathways, we previously established a human embryonic stem-cell (hESC) line carrying a monoallelic DGCR8 mutation by using the CRISPR-Cas9 system. In this study, we genetically characterized single-cell originated progenies of the cell line and showed that DGCR8 heterozygous mutation results in only a modest effect on the mRNA level but a significant decrease at the protein level. Self-renewal and trilineage differentiation capacity of these hESCs were not affected by the mutation. However, partial disturbance of the Microprocessor function could be revealed in pri-miRNA processing along the human chromosome 19 miRNA cluster in several clones. With all these studies, we can demonstrate that the mutant hESC line is a good model to study not only miRNA-related but also other “noncanonical” functions of the DGCR8 protein.
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15
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Kujawa M, O'Meara M, Li H, Xu L, Meda Venkata SP, Nguyen H, Minjares M, Zhang K, Wang JM. MicroRNA-466 and microRNA-200 increase endothelial permeability in hyperglycemia by targeting Claudin-5. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:259-271. [PMID: 35892090 PMCID: PMC9307898 DOI: 10.1016/j.omtn.2022.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 07/04/2022] [Indexed: 01/05/2023]
Abstract
Endothelial cell (EC) permeability is essential to vascular homeostasis in diabetes. MicroRNAs are critical gene regulators whose roles in the EC permeability have yet to be characterized. This study aims to examine the change in cell permeability induced by miR-200 and miR-466 in ECs. Human aortic ECs and dermal microvascular ECs from healthy subjects and type 2 diabetic patients were used. Our in vitro experiments unveiled higher expressions of miR-200 family members and miR-466 in diabetic ECs and in healthy ECs when exposed to high glucose. Overexpression of both miR-200 and miR-466 significantly increased EC permeability through transcriptional suppression of Claudin-5, the cell tight junction protein, by directly binding to its 3' untranslated region. In a mouse model of chronic hyperglycemia mimicking type 2 diabetes in humans (db/db mice), the delayed closure rate of a full-thickness excisional wound was partly rescued by topical application of the miR-200 inhibitor. The topical application of both miR-200 and miR-466 inhibitors exhibited improved efficacy in accelerating wound closure compared with the topical application of miR-200 inhibitor alone. Our study demonstrated the potentially effective approach of miR-200/miR-466 cocktail inhibition to restore vascular integrity and tissue repair in hyperglycemia.
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Affiliation(s)
- Marisa Kujawa
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Megan O'Meara
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Hainan Li
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Liping Xu
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Sai Pranathi Meda Venkata
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Huong Nguyen
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Morgan Minjares
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
| | - Kezhong Zhang
- Centers for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Jie-Mei Wang
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA.,Centers for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA
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16
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Bergamelli M, Martin H, Aubert Y, Mansuy JM, Marcellin M, Burlet-Schiltz O, Hurbain I, Raposo G, Izopet J, Fournier T, Benchoua A, Bénard M, Groussolles M, Cartron G, Tanguy Le Gac Y, Moinard N, D’Angelo G, Malnou CE. Human Cytomegalovirus Modifies Placental Small Extracellular Vesicle Composition to Enhance Infection of Fetal Neural Cells In Vitro. Viruses 2022; 14:v14092030. [PMID: 36146834 PMCID: PMC9501265 DOI: 10.3390/v14092030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Although placental small extracellular vesicles (sEVs) are extensively studied in the context of pregnancy, little is known about their role during viral congenital infection, especially at the beginning of pregnancy. In this study, we examined the consequences of human cytomegalovirus (hCMV) infection on sEVs production, composition, and function using an immortalized human cytotrophoblast cell line derived from first trimester placenta. By combining complementary approaches of biochemistry, electron microscopy, and quantitative proteomic analysis, we showed that hCMV infection increases the yield of sEVs produced by cytotrophoblasts and modifies their protein content towards a potential proviral phenotype. We further demonstrate that sEVs secreted by hCMV-infected cytotrophoblasts potentiate infection in naive recipient cells of fetal origin, including human neural stem cells. Importantly, these functional consequences are also observed with sEVs prepared from an ex vivo model of infected histocultures from early placenta. Based on these findings, we propose that placental sEVs could be important actors favoring viral dissemination to the fetal brain during hCMV congenital infection.
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Affiliation(s)
- Mathilde Bergamelli
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
| | - Hélène Martin
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
| | - Yann Aubert
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
| | - Jean-Michel Mansuy
- CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | - Marlène Marcellin
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure nationale de protéomique, ProFI, FR 2048, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Infrastructure nationale de protéomique, ProFI, FR 2048, Toulouse, France
| | - Ilse Hurbain
- Institut Curie, CNRS UMR144, Structure et Compartiments Membranaires, Université Paris Sciences et Lettres, Paris, France
- Institut Curie, CNRS UMR144, Plateforme d’imagerie cellulaire et tissulaire (PICT-IBiSA), Université Paris Sciences et Lettres, Paris, France
| | - Graça Raposo
- Institut Curie, CNRS UMR144, Structure et Compartiments Membranaires, Université Paris Sciences et Lettres, Paris, France
- Institut Curie, CNRS UMR144, Plateforme d’imagerie cellulaire et tissulaire (PICT-IBiSA), Université Paris Sciences et Lettres, Paris, France
| | - Jacques Izopet
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
- CHU Toulouse, Hôpital Purpan, Laboratoire de Virologie, Toulouse, France
| | | | - Alexandra Benchoua
- Neuroplasticity and Therapeutics, CECS, I-STEM, AFM- Téléthon, Corbeil-Essonnes, France
| | - Mélinda Bénard
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
- CHU Toulouse, Hôpital des Enfants, Service de Néonatalogie, Toulouse, France
| | - Marion Groussolles
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
- CHU Toulouse, Hôpital Paule de Viguier, Service de Diagnostic Prénatal, Toulouse, France
- Equipe SPHERE Epidémiologie et Analyses en Santé Publique: Risques, Maladies chroniques et handicaps, Université de Toulouse, INSERM UMR1027, UPS, Toulouse, France
| | - Géraldine Cartron
- CHU Toulouse, Hôpital Paule de Viguier, Service de Gynécologie Obstétrique, Toulouse, France
| | - Yann Tanguy Le Gac
- CHU Toulouse, Hôpital Paule de Viguier, Service de Gynécologie Obstétrique, Toulouse, France
| | - Nathalie Moinard
- Développement Embryonnaire, Fertilité, Environnement (DEFE), INSERM UMR 1203, Université de Toulouse et Université de Montpellier, France
- CECOS, Service médecine de la reproduction, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France
| | - Gisela D’Angelo
- Institut Curie, CNRS UMR144, Structure et Compartiments Membranaires, Université Paris Sciences et Lettres, Paris, France
| | - Cécile E. Malnou
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France
- Correspondence:
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17
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Martin H, Barthelemy J, Chin Y, Bergamelli M, Moinard N, Cartron G, Tanguy Le Gac Y, Malnou CE, Simonin Y. Usutu Virus Infects Human Placental Explants and Induces Congenital Defects in Mice. Viruses 2022; 14:v14081619. [PMID: 35893684 PMCID: PMC9330037 DOI: 10.3390/v14081619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Usutu virus (USUV) is a neurotropic mosquito-borne flavivirus that has dispersed quickly in Europe these past years. This arbovirus mainly follows an enzootic cycle involving mosquitoes and birds, but can also infect other mammals, causing notably sporadic cases in humans. Although it is mainly asymptomatic or responsible for mild clinical symptoms, USUV has been associated with neurological disorders, such as encephalitis and meningoencephalitis, highlighting the potential health threat of this virus. Among the different transmission routes described for other flaviviruses, the capacity for some of them to be transmitted vertically has been demonstrated, notably for Zika virus or West Nile virus, which are closely related to USUV. To evaluate the ability of USUV to replicate in the placenta and gain access to the fetus, we combined the use of several trophoblast model cell lines, ex vivo human placental explant cultures from first and third trimester of pregnancy, and in vivo USUV-infected pregnant mice. Our data demonstrate that human placental cells and tissues are permissive to USUV replication, and suggest that viral transmission can occur in mice during gestation. Hence, our observations suggest that USUV could be efficiently transmitted by the vertical route.
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Affiliation(s)
- Hélène Martin
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France; (H.M.); (Y.C.); (M.B.)
| | - Jonathan Barthelemy
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Montpellier, France;
| | - Yamileth Chin
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France; (H.M.); (Y.C.); (M.B.)
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Ciudad de Panamá, Panamá
| | - Mathilde Bergamelli
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France; (H.M.); (Y.C.); (M.B.)
| | - Nathalie Moinard
- Développement Embryonnaire, Fertilité, Environnement (DEFE), INSERM UMR 1203, Université de Toulouse et Université de Montpellier, France;
- CECOS, Groupe d’Activité de Médecine de la Reproduction, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France
| | - Géraldine Cartron
- CHU Toulouse, Hôpital Paule de Viguier, Service de Gynécologie Obstétrique, Toulouse, France; (G.C.); (Y.T.L.G.)
| | - Yann Tanguy Le Gac
- CHU Toulouse, Hôpital Paule de Viguier, Service de Gynécologie Obstétrique, Toulouse, France; (G.C.); (Y.T.L.G.)
| | - Cécile E. Malnou
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), Université de Toulouse, INSERM, CNRS, UPS, Toulouse, France; (H.M.); (Y.C.); (M.B.)
- Correspondence: (C.E.M.); (Y.S.)
| | - Yannick Simonin
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, Montpellier, France;
- Correspondence: (C.E.M.); (Y.S.)
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18
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Rojas-Pirela M, Andrade-Alviárez D, Medina L, Castillo C, Liempi A, Guerrero-Muñoz J, Ortega Y, Maya JD, Rojas V, Quiñones W, Michels PA, Kemmerling U. MicroRNAs: master regulators in host-parasitic protist interactions. Open Biol 2022; 12:210395. [PMID: 35702995 PMCID: PMC9198802 DOI: 10.1098/rsob.210395] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs present in a wide diversity of organisms. MiRNAs regulate gene expression at a post-transcriptional level through their interaction with the 3' untranslated regions of target mRNAs, inducing translational inhibition or mRNA destabilization and degradation. Thus, miRNAs regulate key biological processes, such as cell death, signal transduction, development, cellular proliferation and differentiation. The dysregulation of miRNAs biogenesis and function is related to the pathogenesis of diseases, including parasite infection. Moreover, during host-parasite interactions, parasites and host miRNAs determine the probability of infection and progression of the disease. The present review is focused on the possible role of miRNAs in the pathogenesis of diseases of clinical interest caused by parasitic protists. In addition, the potential role of miRNAs as targets for the design of drugs and diagnostic and prognostic markers of parasitic diseases is also discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Lisvaneth Medina
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Christian Castillo
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Núcleo de Investigación Aplicada en Ciencias Veterinarias y Agronómicas, Facultad de Medicina Veterinaria y Agronomía, Universidad de Las Américas, Chile
| | - Ana Liempi
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Jesús Guerrero-Muñoz
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Yessica Ortega
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile,Facultad de Farmacia y Bioanálisis, Universidad de Los Andes, Mérida, Venezuela
| | - Juan Diego Maya
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
| | - Verónica Rojas
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Paul A. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago de Chile 8380453, Chile
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19
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Žarković M, Hufsky F, Markert UR, Marz M. The Role of Non-Coding RNAs in the Human Placenta. Cells 2022; 11:cells11091588. [PMID: 35563893 PMCID: PMC9104507 DOI: 10.3390/cells11091588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play a central and regulatory role in almost all cells, organs, and species, which has been broadly recognized since the human ENCODE project and several other genome projects. Nevertheless, a small fraction of ncRNAs have been identified, and in the placenta they have been investigated very marginally. To date, most examples of ncRNAs which have been identified to be specific for fetal tissues, including placenta, are members of the group of microRNAs (miRNAs). Due to their quantity, it can be expected that the fairly larger group of other ncRNAs exerts far stronger effects than miRNAs. The syncytiotrophoblast of fetal origin forms the interface between fetus and mother, and releases permanently extracellular vesicles (EVs) into the maternal circulation which contain fetal proteins and RNA, including ncRNA, for communication with neighboring and distant maternal cells. Disorders of ncRNA in placental tissue, especially in trophoblast cells, and in EVs seem to be involved in pregnancy disorders, potentially as a cause or consequence. This review summarizes the current knowledge on placental ncRNA, their transport in EVs, and their involvement and pregnancy pathologies, as well as their potential for novel diagnostic tools.
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Affiliation(s)
- Milena Žarković
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Franziska Hufsky
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - Udo R. Markert
- Placenta Lab, Department of Obstetrics, University Hospital Jena, Am Klinikum 1, 07747 Jena, Germany;
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany; (M.Ž.); (F.H.)
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
- FLI Leibniz Institute for Age Research, Beutenbergstraße 11, 07745 Jena, Germany
- Aging Research Center (ARC), 07745 Jena, Germany
- Correspondence:
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20
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Kaneko-Ishino T, Ishino F. The Evolutionary Advantage in Mammals of the Complementary Monoallelic Expression Mechanism of Genomic Imprinting and Its Emergence From a Defense Against the Insertion Into the Host Genome. Front Genet 2022; 13:832983. [PMID: 35309133 PMCID: PMC8928582 DOI: 10.3389/fgene.2022.832983] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
In viviparous mammals, genomic imprinting regulates parent-of-origin-specific monoallelic expression of paternally and maternally expressed imprinted genes (PEGs and MEGs) in a region-specific manner. It plays an essential role in mammalian development: aberrant imprinting regulation causes a variety of developmental defects, including fetal, neonatal, and postnatal lethality as well as growth abnormalities. Mechanistically, PEGs and MEGs are reciprocally regulated by DNA methylation of germ-line differentially methylated regions (gDMRs), thereby exhibiting eliciting complementary expression from parental genomes. The fact that most gDMR sequences are derived from insertion events provides strong support for the claim that genomic imprinting emerged as a host defense mechanism against the insertion in the genome. Recent studies on the molecular mechanisms concerning how the DNA methylation marks on the gDMRs are established in gametes and maintained in the pre- and postimplantation periods have further revealed the close relationship between genomic imprinting and invading DNA, such as retroviruses and LTR retrotransposons. In the presence of gDMRs, the monoallelic expression of PEGs and MEGs confers an apparent advantage by the functional compensation that takes place between the two parental genomes. Thus, it is likely that genomic imprinting is a consequence of an evolutionary trade-off for improved survival. In addition, novel genes were introduced into the mammalian genome via this same surprising and complex process as imprinted genes, such as the genes acquired from retroviruses as well as those that were duplicated by retropositioning. Importantly, these genes play essential/important roles in the current eutherian developmental system, such as that in the placenta and/or brain. Thus, genomic imprinting has played a critically important role in the evolutionary emergence of mammals, not only by providing a means to escape from the adverse effects of invading DNA with sequences corresponding to the gDMRs, but also by the acquisition of novel functions in development, growth and behavior via the mechanism of complementary monoallelic expression.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- School of Medicine, Tokai University, Isehara, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
| | - Fumitoshi Ishino
- Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- *Correspondence: Tomoko Kaneko-Ishino, ; Fumitoshi Ishino,
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21
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Suzuki K, Igata H, Abe M, Yamamoto Y. Multiple cancer type classification by small RNA expression profiles with plasma samples from multiple facilities. Cancer Sci 2022; 113:2144-2166. [PMID: 35218669 PMCID: PMC9207371 DOI: 10.1111/cas.15309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/03/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022] Open
Abstract
Liquid biopsy is expected to be a promising cancer screening method because of its low invasiveness and the possibility of detecting multiple types in a single test. In the last decade, many studies on cancer detection using small RNAs in blood have been reported. To put small RNA tests into practical use as a multiple cancer type screening test, it is necessary to develop a method that can be applied to multiple facilities. We collected samples of eight cancer types and healthy controls from 20 facilities to evaluate the performance of cancer type classification. A total of 2,475 cancer samples and 496 healthy control samples were collected using a standardized protocol. After obtaining a small RNA expression profile, we constructed a classification model and evaluated its performance. First, we investigated the classification performance using samples from five single facilities. Each model showed areas under the receiver curve (AUC) ranging from 0.67 to 0.89. Second, we performed principal component analysis (PCA) to examine the characteristics of the facilities. The degree of hemolysis and the data acquisition period affected the expression profiles. Finally, we constructed the classification model by reducing the influence of these factors, and its performance had an AUC of 0.76. The results reveal that small RNA can be used for the classification of cancer types in samples from a single facility. However, interfacility biases will affect the classification of samples from multiple facilities. These findings will provide important insights to improve the performance of multiple cancer type classifications using small RNA expression profiles acquired from multiple facilities.
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Affiliation(s)
- Kuno Suzuki
- Healthcare Business Department, PFDeNA, Inc, Tokyo, Japan
| | | | | | - Yusuke Yamamoto
- Laboratory of Integrative Oncology, National Cancer Center Research Institute, Tokyo, Japan
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22
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Preeclampsia, Natural History, Genes, and miRNAs Associated with the Syndrome. J Pregnancy 2022; 2022:3851225. [PMID: 35198246 PMCID: PMC8860533 DOI: 10.1155/2022/3851225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/19/2022] [Indexed: 12/13/2022] Open
Abstract
Preeclampsia (PE) is a hypertensive disease that affects pregnant women after 20 weeks of gestation. This disease is associated with an important risk of maternal and fetal mortality. PE is described as a placental pathology because, after delivery, most women recover normal arterial pressure. Poor invasion of the spiral arteries is a phenomenon well described in PE; this leads to a hypoxic uterine bed and imbalance of antiangiogenic and proangiogenic factors in the uteroplacental region, which in turn triggers the disease phenotype. The causes of the pathology are unclear; nevertheless, numerous approaches, including next-generation sequencing, association, and case control and miRNA studies, have shed light on the genetic/molecular basis of PE. These studies help us better understand the disease to advance new treatment strategies.
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23
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Légaré C, Clément AA, Desgagné V, Thibeault K, White F, Guay SP, Arsenault BJ, Scott MS, Jacques PÉ, Perron P, Guérin R, Hivert MF, Bouchard L. Human plasma pregnancy-associated miRNAs and their temporal variation within the first trimester of pregnancy. Reprod Biol Endocrinol 2022; 20:14. [PMID: 35031065 PMCID: PMC8759232 DOI: 10.1186/s12958-021-00883-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/20/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND During pregnancy, maternal metabolism undergoes substantial changes to support the developing fetus. Such changes are finely regulated by different mechanisms carried out by effectors such as microRNAs (miRNAs). These small non-coding RNAs regulate numerous biological functions, mostly through post-transcriptional repression of gene expression. miRNAs are also secreted in circulation by numerous organs, such as the placenta. However, the complete plasmatic microtranscriptome of pregnant women has still not been fully described, although some miRNA clusters from the chromosome 14 (C14MC) and the chromosome 19 (C19MC and miR-371-3 cluster) have been proposed as being specific to pregnancy. Our aims were thus to describe the plasma microtranscriptome during the first trimester of pregnancy, by assessing the differences with non-pregnant women, and how it varies between the 4th and the 16th week of pregnancy. METHODS Plasmatic miRNAs from 436 pregnant (gestational week 4 to 16) and 15 non-pregnant women were quantified using Illumina HiSeq next-generation sequencing platform. Differentially abundant miRNAs were identified using DESeq2 package (FDR q-value ≤ 0.05) and their targeted biological pathways were assessed with DIANA-miRpath. RESULTS A total of 2101 miRNAs were detected, of which 191 were differentially abundant (fold change < 0.05 or > 2, FDR q-value ≤ 0.05) between pregnant and non-pregnant women. Of these, 100 miRNAs were less and 91 miRNAs were more abundant in pregnant women. Additionally, the abundance of 57 miRNAs varied according to gestational age at first trimester, of which 47 were positively and 10 were negatively associated with advancing gestational age. miRNAs from the C19MC were positively associated with both pregnancy and gestational age variation during the first trimester. Biological pathway analysis revealed that these 191 (pregnancy-specific) and 57 (gestational age markers) miRNAs targeted genes involved in fatty acid metabolism, ECM-receptor interaction and TGF-beta signaling pathways. CONCLUSION We have identified circulating miRNAs specific to pregnancy and/or that varied with gestational age in first trimester. These miRNAs target biological pathways involved in lipid metabolism as well as placenta and embryo development, suggesting a contribution to the maternal metabolic adaptation to pregnancy and fetal growth.
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Affiliation(s)
- Cécilia Légaré
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Andrée-Anne Clément
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Véronique Desgagné
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada
| | - Kathrine Thibeault
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Frédérique White
- Department of Biology, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Simon-Pierre Guay
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Centre, Montreal, QC, Canada
| | - Benoit J Arsenault
- Centre de Recherche de L'Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Québec, QC, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Pierre-Étienne Jacques
- Department of Biology, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada
- Department of Medicine, FMHS, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Renée Guérin
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, USA
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences (FMHS), Université de Sherbrooke, Sherbrooke, QC, Canada.
- Clinical Department of Laboratory Medicine, Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay-Lac-St-Jean - Hôpital Universitaire de Chicoutimi, Pavillon des Augustines, 305 rue St-Vallier, Saguenay, QC, G7H 5H6, Canada.
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CR-CHUS), Sherbrooke, QC, Canada.
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24
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Diniz WJ, Reynolds LP, Ward AK, Borowicz PP, Sedivec KK, McCarthy KL, Kassetas CJ, Baumgaertner F, Kirsch JD, Dorsam ST, Neville TL, Forcherio JC, Scott RR, Caton JS, Dahlen CR. Untangling the placentome gene network of beef heifers in early gestation. Genomics 2022; 114:110274. [DOI: 10.1016/j.ygeno.2022.110274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 11/04/2022]
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25
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Fudono A, Imai C, Takimoto H, Tarui I, Aoyama T, Yago S, Okamitsu M, Muramatsu M, Sato N, Miyasaka N. Trimester-specific associations between extracellular vesicle microRNAs and fetal growth. J Matern Fetal Neonatal Med 2021; 35:8728-8734. [PMID: 34779347 DOI: 10.1080/14767058.2021.2000598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Placenta-derived extracellular vesicles and their cargoes, especially microRNAs (EV-miRNAs), may contribute to fetal and placental development. During pregnancy, the levels of several maternal blood EV-miRNAs, including miRNAs of placental origin, vary among individuals and change throughout gestation. However, the effects of these miRNAs on fetal growth and trimester-specificity have not been fully elucidated. The purpose of this study is to test the hypothesis that the serum levels of two extracellular vesicles (EV)-miRNAs (miR-127-3p and miR-26b-5p), which may be involved in fetoplacental regulation, would be significantly associated with fetal growth in a trimester-specific manner. MATERIALS AND METHODS This is a single-center birth cohort of maternal serum samples obtained at both the second and third trimesters. To minimize the influence of confounding factors, the analysis was limited to singleton vaginal deliveries, resulting in 27 participants being included in this study. EV RNAs were isolated using a membrane affinity method, and the relative expression levels of miR-127-3p and miR-26b-5p were measured using the RT-qPCR method with miR-484 as control. The associations between the two EV-miRNAs and fetal and placental growth were evaluated using a linear regression model and compared between the two trimesters. RESULTS EV-miR-127-3p levels tended to correlate inversely with the z-scores of birth weight for gestational age (BWGA) and placental weight for gestational age (PWGA) in the second trimester, but not in the third trimester. EV-miR-26b-5p levels were positively associated with birth weight in the second trimester, but this association was weakened in the third trimester. CONCLUSION Our results suggest a trimester-specific association of circulating miRNA levels with fetal and placental growth. The precise roles of EV-miR-127-3p and EV-miR-26b-5p in fetal and placental development warrant further investigation.
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Affiliation(s)
- Ayako Fudono
- Comprehensive Reproductive Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chihiro Imai
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidemi Takimoto
- Department of Nutritional Epidemiology and Shokuiku, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Iori Tarui
- Department of Nutritional Epidemiology and Shokuiku, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Tomoko Aoyama
- Department of Nutritional Epidemiology and Shokuiku, National Institutes of Biomedical Innovation, Health and Nutrition, Tokyo, Japan
| | - Satoshi Yago
- Child and Family Nursing, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Motoko Okamitsu
- Child and Family Nursing, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaaki Muramatsu
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Noriko Sato
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Naoyuki Miyasaka
- Comprehensive Reproductive Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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26
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Munjas J, Sopić M, Stefanović A, Košir R, Ninić A, Joksić I, Antonić T, Spasojević-Kalimanovska V, Prosenc Zmrzljak U. Non-Coding RNAs in Preeclampsia-Molecular Mechanisms and Diagnostic Potential. Int J Mol Sci 2021; 22:10652. [PMID: 34638993 PMCID: PMC8508896 DOI: 10.3390/ijms221910652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/26/2021] [Indexed: 02/07/2023] Open
Abstract
Preeclampsia (PE) is a leading cause of maternal and neonatal morbidity and mortality worldwide. Defects in trophoblast invasion, differentiation of extravillous trophoblasts and spiral artery remodeling are key factors in PE development. Currently there are no predictive biomarkers clinically available for PE. Recent technological advancements empowered transcriptome exploration and led to the discovery of numerous non-coding RNA species of which microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the most investigated. They are implicated in the regulation of numerous cellular functions, and as such are being extensively explored as potential biomarkers for various diseases. Altered expression of numerous lncRNAs and miRNAs in placenta has been related to pathophysiological processes that occur in preeclampsia. In the following text we offer summary of the latest knowledge of the molecular mechanism by which lnRNAs and miRNAs (focusing on the chromosome 19 miRNA cluster (C19MC)) contribute to pathophysiology of PE development and their potential utility as biomarkers of PE, with special focus on sample selection and techniques for the quantification of lncRNAs and miRNAs in maternal circulation.
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Affiliation(s)
- Jelena Munjas
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
| | - Miron Sopić
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
| | - Aleksandra Stefanović
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
| | - Rok Košir
- BIA Separations CRO, Labena Ltd., Street Verovškova 64, 1000 Ljubljana, Slovenia;
| | - Ana Ninić
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
| | - Ivana Joksić
- Genetic Laboratory Department, Obstetrics and Gynaecology Clinic “Narodni Front”, Street Kraljice Natalije 62, 11000 Belgrade, Serbia;
| | - Tamara Antonić
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
| | - Vesna Spasojević-Kalimanovska
- Department of Medical Biochemistry, Faculty of Pharmacy, University of Belgrade, Street Vojvode Stepe 450, 11000 Belgrade, Serbia; (J.M.); (M.S.); (A.S.); (A.N.); (T.A.); (V.S.-K.)
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27
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Bergamelli M, Martin H, Bénard M, Ausseil J, Mansuy JM, Hurbain I, Mouysset M, Groussolles M, Cartron G, Tanguy le Gac Y, Moinard N, Suberbielle E, Izopet J, Tscherning C, Raposo G, Gonzalez-Dunia D, D'Angelo G, Malnou CE. Human Cytomegalovirus Infection Changes the Pattern of Surface Markers of Small Extracellular Vesicles Isolated From First Trimester Placental Long-Term Histocultures. Front Cell Dev Biol 2021; 9:689122. [PMID: 34568315 PMCID: PMC8461063 DOI: 10.3389/fcell.2021.689122] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/28/2021] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicles (EVs) have increasingly been recognized as key players in a wide variety of physiological and pathological contexts, including during pregnancy. Notably, EVs appear both as possible biomarkers and as mediators involved in the communication of the placenta with the maternal and fetal sides. A better understanding of the physiological and pathological roles of EVs strongly depends on the development of adequate and reliable study models, specifically at the beginning of pregnancy where many adverse pregnancy outcomes have their origin. In this study, we describe the isolation of small EVs from a histoculture model of first trimester placental explants in normal conditions as well as upon infection by human cytomegalovirus. Using bead-based multiplex cytometry and electron microscopy combined with biochemical approaches, we characterized these small EVs and defined their associated markers and ultrastructure. We observed that infection led to changes in the expression level of several surface markers, without affecting the secretion and integrity of small EVs. Our findings lay the foundation for studying the functional role of EVs during early pregnancy, along with the identification of new predictive biomarkers for the severity and outcome of this congenital infection, which are still sorely lacking.
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Affiliation(s)
- Mathilde Bergamelli
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Hélène Martin
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Mélinda Bénard
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France.,Service de Néonatalogie, CHU Toulouse, Hôpital des Enfants, Toulouse, France
| | - Jérôme Ausseil
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France.,Laboratoire de Biochimie, CHU Toulouse, Hôpital Rangueil, Toulouse, France
| | - Jean-Michel Mansuy
- Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, Toulouse, France
| | - Ilse Hurbain
- CNRS UMR 144, Structure et Compartiments Membranaires, Institut Curie, Université Paris Sciences et Lettres, Paris, France.,CNRS UMR 144, Plateforme d'Imagerie Cellulaire et Tissulaire (PICT-IBiSA), Institut Curie, Université Paris Sciences et Lettres, Paris, France
| | - Maïlys Mouysset
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Marion Groussolles
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France.,Service de Diagnostic Prénatal, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France.,INSERM UMR 1027, UPS, Equipe SPHERE Epidémiologie et Analyses en Santé Publique: Risques, Maladies Chroniques et Handicaps, Université de Toulouse, Toulouse, France
| | - Géraldine Cartron
- Service de Gynécologie Obstétrique, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France
| | - Yann Tanguy le Gac
- Service de Gynécologie Obstétrique, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France
| | - Nathalie Moinard
- Développement Embryonnaire, Fertilité, Environnement (DEFE), INSERM UMR 1203, Université de Toulouse et Université de Montpellier, Montpellier, France.,CECOS, Groupe d'Activité de Médecine de la Reproduction, CHU Toulouse, Hôpital Paule de Viguier, Toulouse, France
| | - Elsa Suberbielle
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Jacques Izopet
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France.,Laboratoire de Virologie, CHU Toulouse, Hôpital Purpan, Toulouse, France
| | - Charlotte Tscherning
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Graça Raposo
- CNRS UMR 144, Structure et Compartiments Membranaires, Institut Curie, Université Paris Sciences et Lettres, Paris, France.,CNRS UMR 144, Plateforme d'Imagerie Cellulaire et Tissulaire (PICT-IBiSA), Institut Curie, Université Paris Sciences et Lettres, Paris, France
| | - Daniel Gonzalez-Dunia
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Gisela D'Angelo
- CNRS UMR 144, Structure et Compartiments Membranaires, Institut Curie, Université Paris Sciences et Lettres, Paris, France
| | - Cécile E Malnou
- Institut Toulousain des Maladies Infectieuses et Inflammatoires (Infinity), INSERM, CNRS, UPS, Université de Toulouse, Toulouse, France
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28
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Huttener R, Thorrez L, Veld TI, Potter B, Baele G, Granvik M, Van Lommel L, Schuit F. Regional effect on the molecular clock rate of protein evolution in Eutherian and Metatherian genomes. BMC Ecol Evol 2021; 21:153. [PMID: 34348656 PMCID: PMC8336415 DOI: 10.1186/s12862-021-01882-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Different types of proteins diverge at vastly different rates. Moreover, the same type of protein has been observed to evolve with different rates in different phylogenetic lineages. In the present study we measured the rates of protein evolution in Eutheria (placental mammals) and Metatheria (marsupials) on a genome-wide basis and we propose that the gene position in the genome landscape has an important influence on the rate of protein divergence. RESULTS We analyzed a protein-encoding gene set (n = 15,727) common to 16 mammals (12 Eutheria and 4 Metatheria). Using sliding windows that averaged regional effects of protein divergence we constructed landscapes in which strong and lineage-specific regional effects were seen on the molecular clock rate of protein divergence. Within each lineage, the relatively high rates were preferentially found in subtelomeric chromosomal regions. Such regions were observed to contain important and well-studied loci for fetal growth, uterine function and the generation of diversity in the adaptive repertoire of immunoglobulins. CONCLUSIONS A genome landscape approach visualizes lineage-specific regional differences between Eutherian and Metatherian rates of protein evolution. This phenomenon of chromosomal position is a new element that explains at least part of the lineage-specific effects and differences between proteins on the molecular clock rates.
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Affiliation(s)
- Raf Huttener
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Lieven Thorrez
- Tissue Engineering Laboratory, Department of Development and Regeneration, KU Leuven, Kortrijk, Belgium
| | - Thomas In't Veld
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Barney Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Mikaela Granvik
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Leentje Van Lommel
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium
| | - Frans Schuit
- Gene Expression Unit, Dept. of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, O&N1, Bus 901, 3000, Leuven, Belgium.
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Exploring chromatin structural roles of non-coding RNAs at imprinted domains. Biochem Soc Trans 2021; 49:1867-1879. [PMID: 34338292 PMCID: PMC8421051 DOI: 10.1042/bst20210758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 12/11/2022]
Abstract
Different classes of non-coding RNA (ncRNA) influence the organization of chromatin. Imprinted gene domains constitute a paradigm for exploring functional long ncRNAs (lncRNAs). Almost all express an lncRNA in a parent-of-origin dependent manner. The mono-allelic expression of these lncRNAs represses close by and distant protein-coding genes, through diverse mechanisms. Some control genes on other chromosomes as well. Interestingly, several imprinted chromosomal domains show a developmentally regulated, chromatin-based mechanism of imprinting with apparent similarities to X-chromosome inactivation. At these domains, the mono-allelic lncRNAs show a relatively stable, focal accumulation in cis. This facilitates the recruitment of Polycomb repressive complexes, lysine methyltranferases and other nuclear proteins — in part through direct RNA–protein interactions. Recent chromosome conformation capture and microscopy studies indicate that the focal aggregation of lncRNA and interacting proteins could play an architectural role as well, and correlates with close positioning of target genes. Higher-order chromatin structure is strongly influenced by CTCF/cohesin complexes, whose allelic association patterns and actions may be influenced by lncRNAs as well. Here, we review the gene-repressive roles of imprinted non-coding RNAs, particularly of lncRNAs, and discuss emerging links with chromatin architecture.
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Strawn M, Samal A, Sarker MB, Dhakal P, Behura SK. Relevance of microRNAs to the regulation of the brain-placental axis in mice. Placenta 2021; 112:123-131. [PMID: 34332202 DOI: 10.1016/j.placenta.2021.07.293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/13/2022]
Abstract
INTRODUCTION The development of fetal brain is intricately dependent upon placental functions. Recently, we showed that the placenta and fetal brain express genes in a coordinated manner in mice. But, how the brain-placental axis is regulated at the molecular level remains poorly understood. The microRNAs (miRNAs) play diverse roles in pregnancy including regulation of placenta function as well as brain development. Thus, we hypothesized that specific miRNAs are expressed in the placenta and fetal brain to coordinate gene regulation in the brain-placental axis. METHODS To test this hypothesis, we performed deep sequencing of small RNAs in mouse placenta and fetal brain of both sexes. RESULTS The findings study show that miRNAs are potent regulators of gene expression in the placenta and fetal brain. Our data provides evidence that fetal sex influences the regulation of miRNAs between the placenta and fetal brain. Functional annotation of known target genes of the differentially expressed miRNAs show that they are significantly enriched with specific signaling and transporter pathways. DISCUSSION Together, the results of this study suggest that placental miRNAs are potent regulators of fetal brain development in mice.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Ananya Samal
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | | | - Pramod Dhakal
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
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Profiling the small non-coding RNA transcriptome of the human placenta. Sci Data 2021; 8:166. [PMID: 34215751 PMCID: PMC8253835 DOI: 10.1038/s41597-021-00948-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
Proper functioning of the human placenta is critical for maternal and fetal health. While microRNAs (miRNAs) are known to impact placental gene expression, the effects of other small non-coding RNAs (sncRNAs) on the placental transcriptome are not well-established, and are emerging topics in the study of environmental influence on fetal development and reproductive health. Here, we assembled a cohort of 30 placental chorionic villi samples of varying gestational ages (M ± SD = 23.7 ± 11.3 weeks) to delineate the human placental sncRNA transcriptome through small RNA sequence analysis. We observed expression of 1544 sncRNAs, which include 48 miRNAs previously unannotated in humans. Additionally, 18,003 miRNA variants (isomiRs) were identified from the 654 observed miRNA species. This characterization of the term and pre-term placental sncRNA transcriptomes provides data fundamental to future investigations of their regulatory functions in the human placenta, and the baseline expression pattern needed for identifying changes in response to environmental factors, or under disease conditions.
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Andersen CL, Li R, Ye X. Mouse placental microRNA profiling upon zearalenone exposure. Biol Reprod 2021; 102:5-7. [PMID: 31504204 DOI: 10.1093/biolre/ioz176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 08/27/2019] [Accepted: 08/26/2019] [Indexed: 11/12/2022] Open
Affiliation(s)
- Christian Lee Andersen
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA.,Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
| | - Rong Li
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA.,Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
| | - Xiaoqin Ye
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA.,Interdisciplinary Toxicology Program, University of Georgia, Athens, Georgia, USA
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Zhang Y, Mustieles V, Williams PL, Wylie BJ, Souter I, Calafat AM, Demokritou M, Lee A, Vagios S, Hauser R, Messerlian C. Parental preconception exposure to phenol and phthalate mixtures and the risk of preterm birth. ENVIRONMENT INTERNATIONAL 2021; 151:106440. [PMID: 33640694 PMCID: PMC8488320 DOI: 10.1016/j.envint.2021.106440] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 05/21/2023]
Abstract
BACKGROUND Parental preconception exposure to select phenols and phthalates was previously associated with increased risk of preterm birth in single chemical analyses. However, the joint effect of phenol and phthalate mixtures on preterm birth is unknown. METHODS We included 384 female and 211 male (203 couples) participants seeking infertility treatment in the Environment and Reproductive Health (EARTH) Study who gave birth to 384 singleton infants between 2005 and 2018. Mean preconception urinary concentrations of bisphenol A (BPA), parabens, and eleven phthalate biomarkers, including di(2-ethylhexyl) phthalate (DEHP) metabolites, were examined. We used principal component analysis (PCA) with log-Poisson regression and Probit Bayesian Kernel Machine Regression (BKMR) with hierarchical variable selection to examine maternal and paternal phenol and phthalate mixtures in relation to preterm birth. Couple-based BKMR model was fit to assess couples' joint mixtures in relation to preterm birth. RESULTS PCA identified the same four factors for maternal and paternal preconception mixtures. Each unit increase in PCA scores of maternal (adjusted Risk Ratio (aRR): 1.36, 95%CI: 1.00, 1.84) and paternal (aRR: 1.47, 95%CI: 0.90, 2.42) preconception DEHP-BPA factor was positively associated with preterm birth. Maternal and paternal BKMR models consistently presented the DEHP-BPA factor with the highest group Posterior Inclusion Probability (PIP). BKMR models further showed that maternal preconception BPA and mono(2-ethyl-5-hydroxyhexyl) phthalate, and paternal preconception mono(2-ethylhexyl) phthalate were positively associated with preterm birth when the remaining mixture components were held at their median concentrations. Couple-based BKMR models showed a similar relative contribution of paternal (PIP: 61%) and maternal (PIP: 77%) preconception mixtures on preterm birth. We found a positive joint effect on preterm birth across increasing quantiles of couples' total mixture concentrations. CONCLUSION In this prospective cohort of subfertile couples, maternal BPA and DEHP, and paternal DEHP exposure before conception were positively associated with preterm birth. Both parental windows jointly contributed to the outcome. These results suggest that preterm birth may be a couple-based pregnancy outcome.
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Affiliation(s)
- Yu Zhang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Vicente Mustieles
- University of Granada, Center for Biomedical Research (CIBM), Spain; Instituto de Investigación Biosanitaria Ibs GRANADA, Spain; Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 18100, Spain
| | - Paige L Williams
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Blair J Wylie
- Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Irene Souter
- Massachusetts General Hospital Fertility Center, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, USA
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Melina Demokritou
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexandria Lee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Stylianos Vagios
- Massachusetts General Hospital Fertility Center, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, USA
| | - Russ Hauser
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carmen Messerlian
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Massachusetts General Hospital Fertility Center, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Department of Obstetrics and Gynecology, Massachusetts General Hospital, Boston, MA, USA.
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Cohn DE, Barros-Filho MC, Minatel BC, Pewarchuk ME, Marshall EA, Vucic EA, Sage AP, Telkar N, Stewart GL, Jurisica I, Reis PP, Robinson WP, Lam WL. Reactivation of Multiple Fetal miRNAs in Lung Adenocarcinoma. Cancers (Basel) 2021; 13:2686. [PMID: 34072436 PMCID: PMC8199175 DOI: 10.3390/cancers13112686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) play vital roles in the regulation of normal developmental pathways. However, cancer cells can co-opt these miRNAs, and the pathways that they regulate, to drive pro-tumourigenic phenotypes. Characterization of the miRNA transcriptomes of fetal organs is essential for identifying these oncofetal miRNAs, but it has been limited by fetal sample availability. As oncofetal miRNAs are absent from healthy adult lungs, they represent ideal targets for developing diagnostic and therapeutic strategies. We conducted small RNA sequencing of a rare collection of 25 human fetal lung (FL) samples and compared them to two independent cohorts (n = 140, n = 427), each comprised of adult non-neoplastic lung (ANL) and lung adenocarcinoma (LUAD) samples. We identified 13 oncofetal miRNAs that were expressed in FL and LUAD but not in ANL. These oncofetal miRNAs are potential biomarkers for LUAD detection (AUC = 0.963). Five of these miRNAs are derived from the imprinted C14MC miRNA cluster at the 14q32 locus, which has been associated with cancer development and abnormal fetal and placental development. Additionally, we observed the pulmonary expression of 44 previously unannotated miRNAs. The sequencing of these fetal lung samples also provides a baseline resource against which aberrant samples can be compared.
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Affiliation(s)
- David E. Cohn
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Mateus C. Barros-Filho
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- International Research Center, A.C. Camargo Cancer Center, São Paulo, SP 01525-001, Brazil
| | - Brenda C. Minatel
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Michelle E. Pewarchuk
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Erin A. Marshall
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Emily A. Vucic
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- NYU Langone Medical Center, New York, NY 10016, USA
| | - Adam P. Sage
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Nikita Telkar
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Greg L. Stewart
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
| | - Igor Jurisica
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada;
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada
| | - Patricia P. Reis
- Faculty of Medicine, São Paulo State University (UNESP), Botucatu, SP 18618-687, Brazil;
| | - Wendy P. Robinson
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Wan L. Lam
- British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada; (M.C.B.-F.); (B.C.M.); (M.E.P.); (E.A.M.); (E.A.V.); (A.P.S.); (N.T.); (G.L.S.); (W.L.L.)
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Gong S, Gaccioli F, Dopierala J, Sovio U, Cook E, Volders PJ, Martens L, Kirk PDW, Richardson S, Smith GCS, Charnock-Jones DS. The RNA landscape of the human placenta in health and disease. Nat Commun 2021; 12:2639. [PMID: 33976128 PMCID: PMC8113443 DOI: 10.1038/s41467-021-22695-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is the interface between mother and fetus and inadequate function contributes to short and long-term ill-health. The placenta is absent from most large-scale RNA-Seq datasets. We therefore analyze long and small RNAs (~101 and 20 million reads per sample respectively) from 302 human placentas, including 94 cases of preeclampsia (PE) and 56 cases of fetal growth restriction (FGR). The placental transcriptome has the seventh lowest complexity of 50 human tissues: 271 genes account for 50% of all reads. We identify multiple circular RNAs and validate 6 of these by Sanger sequencing across the back-splice junction. Using large-scale mass spectrometry datasets, we find strong evidence of peptides produced by translation of two circular RNAs. We also identify novel piRNAs which are clustered on Chr1 and Chr14. PE and FGR are associated with multiple and overlapping differences in mRNA, lincRNA and circRNA but fewer consistent differences in small RNAs. Of the three protein coding genes differentially expressed in both PE and FGR, one encodes a secreted protein FSTL3 (follistatin-like 3). Elevated serum levels of FSTL3 in pregnant women are predictive of subsequent PE and FGR. To aid visualization of our placenta transcriptome data, we develop a web application ( https://www.obgyn.cam.ac.uk/placentome/ ).
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Affiliation(s)
- Sungsam Gong
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Francesca Gaccioli
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Justyna Dopierala
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Functional Genomics, GlaxoSmithKline Limited, Stevenage, Hertfordshire, UK
| | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Pieter-Jan Volders
- Computational Omics and Systems Biology Group, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Computational Omics and Systems Biology Group, Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Paul D W Kirk
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sylvia Richardson
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, UK
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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Guo S, Huang S, Jiang X, Hu H, Han D, Moreno CS, Fairbrother GL, Hughes DA, Stoneking M, Khaitovich P. Variation of microRNA expression in the human placenta driven by population identity and sex of the newborn. BMC Genomics 2021; 22:286. [PMID: 33879051 PMCID: PMC8059241 DOI: 10.1186/s12864-021-07542-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/22/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Analysis of lymphocyte cell lines revealed substantial differences in the expression of mRNA and microRNA (miRNA) among human populations. The extent of such population-associated differences in actual human tissues remains largely unexplored. The placenta is one of the few solid human tissues that can be collected in substantial numbers in a controlled manner, enabling quantitative analysis of transient biomolecules such as RNA transcripts. Here, we analyzed microRNA (miRNA) expression in human placental samples derived from 36 individuals representing four genetically distinct human populations: African Americans, European Americans, South Asians, and East Asians. All samples were collected at the same hospital following a unified protocol, thus minimizing potential biases that might influence the results. RESULTS Sequence analysis of the miRNA fraction yielded 938 annotated and 70 novel miRNA transcripts expressed in the placenta. Of them, 82 (9%) of annotated and 11 (16%) of novel miRNAs displayed quantitative expression differences among populations, generally reflecting reported genetic and mRNA-expression-based distances. Several co-expressed miRNA clusters stood out from the rest of the population-associated differences in terms of miRNA evolutionary age, tissue-specificity, and disease-association characteristics. Among three non-environmental influenced demographic parameters, the second largest contributor to miRNA expression variation after population was the sex of the newborn, with 32 miRNAs (3% of detected) exhibiting significant expression differences depending on whether the newborn was male or female. Male-associated miRNAs were evolutionarily younger and correlated inversely with the expression of target mRNA involved in neuron-related functions. In contrast, both male and female-associated miRNAs appeared to mediate different types of hormonal responses. Demographic factors further affected reported imprinted expression of 66 placental miRNAs: the imprinting strength correlated with the mother's weight, but not height. CONCLUSIONS Our results showed that among 12 assessed demographic variables, population affiliation and fetal sex had a substantial influence on miRNA expression variation among human placental samples. The effect of newborn-sex-associated miRNA differences further led to expression inhibition of the target genes clustering in specific functional pathways. By contrast, population-driven miRNA differences might mainly represent neutral changes with minimal functional impacts.
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Affiliation(s)
- Song Guo
- Skolkovo Institute of Science and Technology, 121205, Moscow, Russia
| | - Shuyun Huang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Xi Jiang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Haiyang Hu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Dingding Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, CAS, 320 Yue Yang Road, Shanghai, 200031, China
| | - Carlos S Moreno
- Department of Pathology and Laboratory Medicine and Department of Biomedical Informatics, Emory University, Atlanta, GA, 30322, USA
| | - Genevieve L Fairbrother
- Obstetrics and Gynecology of Atlanta, 1100 Johnson Ferry Rd NE Suite 800, Center 2, Atlanta, GA, 30342, USA
| | - David A Hughes
- MRC Integrative Epidemiology Unit at University of Bristol, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Mark Stoneking
- Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
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Howe CG, Foley HB, Kennedy EM, Eckel SP, Chavez TA, Faham D, Grubbs BH, Al-Marayati L, Lerner D, Suglia S, Bastain TM, Marsit CJ, Breton CV. Extracellular vesicle microRNA in early versus late pregnancy with birth outcomes in the MADRES study. Epigenetics 2021; 17:269-285. [PMID: 33734019 DOI: 10.1080/15592294.2021.1899887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Circulating miRNA may contribute to the development of adverse birth outcomes. However, few studies have investigated extracellular vesicle (EV) miRNA, which play important roles in intercellular communication, or compared miRNA at multiple time points in pregnancy. In the current study, 800 miRNA were profiled for EVs from maternal plasma collected in early (median: 12.5 weeks) and late (median: 31.8 weeks) pregnancy from 156 participants in the MADRES Study, a health disparity pregnancy cohort. Associations between miRNA and birth weight, birth weight for gestational age (GA), and GA at birth were examined using covariate-adjusted robust linear regression. Differences by infant sex and maternal BMI were also investigated. Late pregnancy measures of 13 miRNA were associated with GA at birth (PFDR<0.050). Negative associations were observed for eight miRNA (miR-4454+ miR-7975, miR-4516, let-7b-5p, miR-126-3p, miR-29b-3p, miR-15a-5p, miR-15b-5p, miR-19b-3p) and positive associations for five miRNA (miR-212-3p, miR-584-5p, miR-608, miR-210-3p, miR-188-5p). Predicted target genes were enriched (PFDR<0.050) in pathways involved in organogenesis and placental development. An additional miRNA (miR-107), measured in late pregnancy, was positively associated with GA at birth in infants born to obese women (PFDR for BMI interaction = 0.011). In primary analyses, the associations between early pregnancy miRNA and birth outcomes were not statistically significant (PFDR≥0.05). However, sex-specific associations were observed for early pregnancy measures of 37 miRNA and GA at birth (PFDR for interactions<0.050). None of the miRNA were associated with fetal growth measures (PFDR≥0.050). Our findings suggest that EV miRNA in both early and late pregnancy may influence gestational duration.
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Affiliation(s)
- Caitlin G Howe
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Helen B Foley
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Elizabeth M Kennedy
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Sandrah P Eckel
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Thomas A Chavez
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Dema Faham
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Brendan H Grubbs
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, CA, USA
| | - Laila Al-Marayati
- Department of Obstetrics and Gynecology, Keck School of Medicine, Los Angeles, CA, USA.,Eisner Health, Los Angeles, CA, USA
| | | | - Shakira Suglia
- Department of Epidemiology, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Theresa M Bastain
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA.,Department of Epidemiology, Emory Rollins School of Public Health, Atlanta, GA, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine at the University of Southern California, Los Angeles, CA, USA
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Groleau M, White F, Cardenas A, Perron P, Hivert MF, Bouchard L, Jacques PÉ. Comparative epigenome-wide analysis highlights placenta-specific differentially methylated regions. Epigenomics 2021; 13:357-368. [PMID: 33661023 DOI: 10.2217/epi-2020-0271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: The placenta undergoes DNA methylation (DNAm) programming that is unique compared with all other fetal tissues. We aim to decipher some of the physiologic roles of the placenta by comparing its DNAm profile with that of another fetal tissue. Materials & methods: We performed a comparative analysis of genome-wide DNAm of 444 placentas paired with cord blood samples collected at birth. Gene ontology term analyses were conducted on the resulting differentially methylated regions. Results: Genomic regions upstream of transcription start sites showing lower DNAm in the placenta were enriched with terms related to miRNA functions and genes encoding G-protein-coupled receptors. Conclusion: These results highlight genomic regions that are differentially methylated in the placenta in contrast to fetal blood.
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Affiliation(s)
- Marika Groleau
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Frédérique White
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, 94720-7360, USA
| | - Patrice Perron
- Département de Médecine, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada.,Department of Population Medicine, Harvard Pilgrim Health Care Institute, Harvard Medical School, Boston, MA, 02115, USA.,Diabetes Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada.,Department of Biochemistry & Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada.,Department of Medical Biology, CIUSSS Saguenay-Lac-Saint-Jean, Hôpital de Chicoutimi, Saguenay, Québec, G7H 7K9, Canada
| | - Pierre-Étienne Jacques
- Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, J1K 2R1, Canada.,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
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Gottlieb A, Flor I, Nimzyk R, Burchardt L, Helmke B, Langenbuch M, Spiekermann M, Feidicker S, Bullerdiek J. The expression of miRNA encoded by C19MC and miR-371-3 strongly varies among individual placentas but does not differ between spontaneous and induced abortions. PROTOPLASMA 2021; 258:209-218. [PMID: 33034783 PMCID: PMC7782366 DOI: 10.1007/s00709-020-01548-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/24/2020] [Indexed: 06/11/2023]
Abstract
miRNAs of the largest human miRNA gene cluster at all, i.e., C19MC, are almost exclusively expressed in the placenta. Nevertheless, only little is known about the interindividual variation of their expression and even about possible influence of gestational age, conflicting data is reported as well as for miRNAs of the much smaller miR-371-3 cluster. Our present study aims at the analyses of the expression of miRNAs from both clusters at different times of pregnancy, possible differences between placenta samples obtained from spontaneous or induced abortions in the first trimester, and the possible variation of miRNA expression at different sites within same placentas. miR-371a-3p, miR-372-3p, miR-373-3p, miR-517a-3p, and miR-520c-3p were quantified in 85 samples and miR-371a-3p was quantified in maternal serum samples taken immediately before delivery. While for miRNA-517a-3p and miR-520c-3p the expression increased with increasing gestational age, the present study revealed strong interindividual differences in the expression of miR-371-3 in full-term placental tissue as well as for miRNAs of the C19MC cluster, where the levels differed to a much lesser extent than for the former microRNAs. Also, strong interindividual differences were noted between the serum samples but differences related to the site of the placenta where the sample has been taken from were excluded. For neither of the data from placental tissue, the study revealed differences between the spontaneous and induced abortion group. Thus, the differences do not in general seem to be related to first trimester abortion. It remains to be elucidated whether or not they affect other prenatal processes.
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Affiliation(s)
- Andrea Gottlieb
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany
| | - Inga Flor
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany
| | - Rolf Nimzyk
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany
| | - Lars Burchardt
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany
| | - Burkhard Helmke
- Institute for Pathology, Elbe Clinic Stade-Buxtehude, Bremervörder Strasse 111, 21682, Stade, Germany
| | - Marc Langenbuch
- Clinic of Gynecology and Obstetrics, Helios Clinic, Altenwalder Chaussee 10, 27474, Cuxhaven, Germany
| | - Meike Spiekermann
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany
| | - Susanne Feidicker
- Department of Gynecology and Obstetrics, Evang. Diakonie-Hospital, Gröpelinger Heerstrasse 406-408, 28239, Bremen, Germany
- Department of Obstetrics and Gynecology, University Hospital Frankfurt, Theodor-Stern Kai 7, 60590, Frankfurt am Main, Germany
| | - Jörn Bullerdiek
- Center of Human Genetics, University of Bremen, Leobener Strasse 2, 28359, Bremen, Germany.
- Institute for Medical Genetics, University of Rostock, University Medicine, Ernst-Heydemann-Strasse 8, 18057, Rostock, Germany.
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40
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Pan CT, Lin YS. MicroRNA retrocopies generated via L1-mediated retrotransposition in placental mammals help to reveal how their parental genes were transcribed. Sci Rep 2020; 10:20612. [PMID: 33244051 PMCID: PMC7692494 DOI: 10.1038/s41598-020-77381-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
In mammalian genomes, most retrocopies emerged via the L1 retrotransposition machinery. The hallmarks of an L1-mediated retrocopy, i.e., the intronlessness, the presence of a 3′ poly-A tail, and the TSDs at both ends, were frequently used to identify retrotransposition events. However, most previous studies only focused on protein-coding genes as their possible parental sources and thus only a few retrocopies derived from non-coding genes were reported. Remarkably, none of them was from microRNAs. Here in this study, we found several retrocopies generated from the mir-302–367 cluster gene (MIR302CHG), and identified a novel alternatively spliced exon encoding mir-302a. The other recognized microRNA retrotransposition events are primate-specific with mir-373 and mir-498 as their parental genes. The 3′ poly-A tracts of these two retrocopy groups were directly attached to the end of the microRNA precursor homologous regions, which suggests that their parental transcripts might alternatively terminate at the end of mir-373 and mir-498. All the three parental microRNAs are highly expressed in specific tissues with elevated retrotransposon activity, such as the embryonic stem cells and the placenta. This might be the reason that our first microRNA retrocopy findings were derived from these three microRNA genes.
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Affiliation(s)
- Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Biological Science and Technology, College of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Chiao Tung University, Hsinchu, 300, Taiwan.
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41
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Fóthi Á, Biró O, Erdei Z, Apáti Á, Orbán TI. Tissue-specific and transcription-dependent mechanisms regulate primary microRNA processing efficiency of the human chromosome 19 MicroRNA cluster. RNA Biol 2020; 18:1170-1180. [PMID: 33052778 DOI: 10.1080/15476286.2020.1836457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
One of the longest human microRNA (miRNA) clusters is located on chromosome 19 (C19MC), containing 46 miRNA genes, which were considered to be expressed simultaneously and at similar levels from a common long noncoding transcript. Investigating the two tissue types where C19MC is exclusively expressed, we could show that there is a tissue-specific and chromosomal position-dependent decrease in mature miRNA levels towards the 3' end of the cluster in embryonic stem cells but not in placenta. Although C19MC transcription level is significantly lower in stem cells, this gradual decrease is not present at the primary miRNA levels, indicating that a difference in posttranscriptional processing could explain this observation. By depleting Drosha, the nuclease component of the Microprocessor complex, we could further enhance the positional decrease in stem cells, demonstrating that a tissue-specific, local availability of the Microprocessor complex could lie behind the phenomenon. Moreover, we could describe a tissue-specific promoter being exclusively active in placenta, and the epigenetic mark analysis suggested the presence of several putative enhancer sequences in this region. Performing specific chromatin immunoprecipitation followed by quantitative real-time PCR experiments we could show a strong association of Drosha with selected enhancer regions in placenta, but not in embryonic stem cells. These enhancers could provide explanation for a more efficient co-transcriptional recruitment of the Microprocessor, and therefore a more efficient processing of pri-miRNAs throughout the cluster in placenta. Our results point towards a new model where tissue-specific, posttranscriptional 'fine-tuning' can differentiate among miRNAs that are expressed simultaneously from a common precursor.
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Affiliation(s)
- Ábel Fóthi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Biró
- Department of Obstetrics and Gynaecology, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Erdei
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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42
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Eaves L, Phookphan P, Rager J, Bangma J, Santos HP, Smeester L, O'Shea TM, Fry R. A role for microRNAs in the epigenetic control of sexually dimorphic gene expression in the human placenta. Epigenomics 2020; 12:1543-1558. [PMID: 32901510 DOI: 10.2217/epi-2020-0062] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: The contribution of miRNAs as epigenetic regulators of sexually dimorphic gene expression in the placenta is unknown. Materials & methods: 382 placentas from the extremely low gestational age newborns (ELGAN) cohort were evaluated for expression levels of 37,268 mRNAs and 2,102 miRNAs using genome-wide RNA-sequencing. Differential expression analysis was used to identify differences in the expression based on the sex of the fetus. Results: Sexually dimorphic expression was observed for 128 mRNAs and 59 miRNAs. A set of 25 miRNA master regulators was identified that likely contribute to the sexual dimorphic mRNA expression. Conclusion: These data highlight sex-dependent miRNA and mRNA patterning in the placenta and provide insight into a potential mechanism for observed sex differences in outcomes.
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Affiliation(s)
- Lauren Eaves
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Preeyaphan Phookphan
- Laboratory of Environmental Toxicology, Chulabhorn Research Institute, Laksi, Bangkok 10210, Thailand
| | - Julia Rager
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jacqueline Bangma
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hudson P Santos
- Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,School of Nursing, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lisa Smeester
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas Michael O'Shea
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rebecca Fry
- Department of Environmental Sciences & Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Institute for Environmental Health Solutions, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
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43
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Haig D, Mainieri A. The Evolution of Imprinted microRNAs and Their RNA Targets. Genes (Basel) 2020; 11:genes11091038. [PMID: 32899179 PMCID: PMC7564603 DOI: 10.3390/genes11091038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 12/19/2022] Open
Abstract
Mammalian genomes contain many imprinted microRNAs. When an imprinted miRNA targets an unimprinted mRNA their interaction may have different fitness consequences for the loci encoding the miRNA and mRNA. In one possible outcome, the mRNA sequence evolves to evade regulation by the miRNA by a simple change of target sequence. Such a response is unavailable if the targeted sequence is strongly constrained by other functions. In these cases, the mRNA evolves to accommodate regulation by the imprinted miRNA. These evolutionary dynamics are illustrated using the examples of the imprinted C19MC cluster of miRNAs in primates and C2MC cluster in mice that are paternally expressed in placentas. The 3′ UTR of PTEN, a gene with growth-related and metabolic functions, appears to be an important target of miRNAs from both clusters.
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44
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Lambo S, von Hoff K, Korshunov A, Pfister SM, Kool M. ETMR: a tumor entity in its infancy. Acta Neuropathol 2020; 140:249-266. [PMID: 32601913 PMCID: PMC7423804 DOI: 10.1007/s00401-020-02182-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 06/04/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022]
Abstract
Embryonal tumor with Multilayered Rosettes (ETMR) is a relatively rare but typically deadly type of brain tumor that occurs mostly in infants. Since the discovery of the characteristic chromosome 19 miRNA cluster (C19MC) amplification a decade ago, the methods for diagnosing this entity have improved and many new insights in the molecular landscape of ETMRs have been acquired. All ETMRs, despite their highly heterogeneous histology, are characterized by specific high expression of the RNA-binding protein LIN28A, which is, therefore, often used as a diagnostic marker for these tumors. ETMRs have few recurrent genetic aberrations, mainly affecting the miRNA pathway and including amplification of C19MC (embryonal tumor with multilayered rosettes, C19MC-altered) and mutually exclusive biallelic DICER1 mutations of which the first hit is typically inherited through the germline (embryonal tumor with multilayered rosettes, DICER1-altered). Identification of downstream pathways affected by the deregulated miRNA machinery has led to several proposed potential therapeutical vulnerabilities including targeting the WNT, SHH, or mTOR pathways, MYCN or chromosomal instability. However, despite those findings, treatment outcomes have only marginally improved, since the initial description of this tumor entity. Many patients do not survive longer than a year after diagnosis and the 5-year overall survival rate is still lower than 30%. Thus, there is an urgent need to translate the new insights in ETMR biology into more effective treatments. Here, we present an overview of clinical and molecular characteristics of ETMRs and the current progress on potential targeted therapies.
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Affiliation(s)
- Sander Lambo
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja von Hoff
- Department of Pediatric Oncology/Hematology, Charité University Medicine, Berlin, Germany
| | - Andrey Korshunov
- Department of Neuropathology, Heidelberg University Hospital, Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany.
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
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45
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Awamleh Z, Han VKM. Potential pathophysiological role of microRNA 193b-5p in human placentae from pregnancies complicated by preeclampsia and intrauterine growth restriction. Mol Biol Rep 2020; 47:6531-6544. [PMID: 32803505 DOI: 10.1007/s11033-020-05705-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/02/2020] [Indexed: 12/21/2022]
Abstract
Preeclampsia (PE) and intrauterine growth restriction (IUGR) are pregnancy complications resulting from abnormal placental development. MicroRNAs can regulate placental development and contribute to disease, by influencing gene expression. Our previous study revealed an increase in miR-193b-5p expression in placentae from patients with early-onset pregnancy complications and identified candidate gene targets for miR-193b-5p. The purpose of this study is two-fold, first to validate candidate gene targets predicted for miR-193b-5p from microRNA-RNA expression data. Second, to overexpress miR-193b-5p in a trophoblast cell line (HTR-8/SVneo) to assess impact on trophoblast cell proliferation and migration. Integration of the miRNA and RNA sequencing expression data revealed 10 candidate gene targets for miR-193b-5p across all patient groups (PE only, IUGR only, PE + IUGR). Luciferase experiments identified two gene targets for miR-193b-5p, APLN and FGF13. Real-time PCR confirmed a median 45% decrease of FGF13 expression across 3 patient groups, and 50% decrease of APLN expression in patients with PE + IUGR. Following transfection of HTR-8/SVneo cells with miR-193b-5p mimics, APLN and FGF13 mRNA expression in HTR-8/SVneo was reduced by a median percentage of 30% and 45%, respectively. Concomitantly, HTR-8/SVneo cells demonstrate 40% reduction in cell migration. APLN and FGF13 immunoreactivity was identified strongly in the cytotrophoblast cells of the human placentae. These findings suggest that miR-193b-5p may contribute to trophoblast dysfunction observed in pregnancy complications such as PE and IUGR.
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Affiliation(s)
- Zain Awamleh
- Children's Health Research Institute, 800 Commissioners Road East, London, ON, N6C 2V5, Canada.
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON, N6A 3K7, Canada.
| | - Victor K M Han
- Children's Health Research Institute, 800 Commissioners Road East, London, ON, N6C 2V5, Canada
- Department of Biochemistry, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON, N6A 3K7, Canada
- Department of Pediatrics, Schulich School of Medicine & Dentistry, The University of Western Ontario, London, ON, N6A 3K7, Canada
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46
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Addo KA, Palakodety N, Hartwell HJ, Tingare A, Fry RC. Placental microRNAs: Responders to environmental chemicals and mediators of pathophysiology of the human placenta. Toxicol Rep 2020; 7:1046-1056. [PMID: 32913718 PMCID: PMC7472806 DOI: 10.1016/j.toxrep.2020.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/02/2020] [Accepted: 08/03/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are epigenetic modifiers that play an important role in the regulation of the expression of genes across the genome. miRNAs are expressed in the placenta as well as other organs, and are involved in several biological processes including the regulation of trophoblast differentiation, migration, invasion, proliferation, apoptosis, angiogenesis and cellular metabolism. Related to their role in disease process, miRNAs have been shown to be differentially expressed between normal placentas and placentas obtained from women with pregnancy/health complications such as preeclampsia, gestational diabetes mellitus, and obesity. This dysregulation indicates that miRNAs in the placenta likely play important roles in the pathogenesis of diseases during pregnancy. Furthermore, miRNAs in the placenta are susceptible to altered expression in relation to exposure to environmental toxicants. With relevance to the placenta, the dysregulation of miRNAs in both placenta and blood has been associated with maternal exposures to several toxicants. In this review, we provide a summary of miRNAs that have been assessed in the context of human pregnancy-related diseases and in relation to exposure to environmental toxicants in the placenta. Where data are available, miRNAs are discussed in their context as biomarkers of exposure and/or disease, with comparisons made across-tissue types, and conservation across studies detailed.
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Affiliation(s)
- Kezia A. Addo
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Niharika Palakodety
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Hadley J. Hartwell
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Aishani Tingare
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Rebecca C. Fry
- Curriculum in Toxicology and Environmental Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
- Department of Environmental Sciences and Engineering, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Institute for Environmental Health Solutions, Gilling School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
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47
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van der Kwast RVCT, Parma L, van der Bent ML, van Ingen E, Baganha F, Peters HAB, Goossens EAC, Simons KH, Palmen M, de Vries MR, Quax PHA, Nossent AY. Adenosine-to-Inosine Editing of Vasoactive MicroRNAs Alters Their Targetome and Function in Ischemia. MOLECULAR THERAPY-NUCLEIC ACIDS 2020; 21:932-953. [PMID: 32814251 PMCID: PMC7452086 DOI: 10.1016/j.omtn.2020.07.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/14/2020] [Indexed: 12/17/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing in the seed sequence of microRNAs can shift the microRNAs’ targetomes and thus their function. Using public RNA-sequencing data, we identified 35 vasoactive microRNAs that are A-to-I edited. We quantified A-to-I editing of the primary (pri-)microRNAs in vascular fibroblasts and endothelial cells. Nine pri-microRNAs were indeed edited, and editing consistently increased under ischemia. We determined mature microRNA editing for the highest expressed microRNAs, i.e., miR-376a-3p, miR-376c-3p, miR-381-3p, and miR-411-5p. All four mature microRNAs were edited in their seed sequence. We show that both ADAR1 and ADAR2 (adenosine deaminase acting on RNA 1 and RNA 2) can edit pri-microRNAs in a microRNA-specific manner. MicroRNA editing also increased under ischemia in vivo in a murine hindlimb ischemia model and ex vivo in human veins. For each edited microRNA, we confirmed a shift in targetome. Expression of the edited microRNA targetomes, not the wild-type targetomes, was downregulated under ischemia in vivo. Furthermore, microRNA editing enhanced angiogenesis in vitro and ex vivo. In conclusion, we show that microRNA A-to-I editing is a widespread phenomenon, induced by ischemia. Each editing event results in a novel microRNA with a unique targetome, leading to increased angiogenesis.
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Affiliation(s)
- Reginald V C T van der Kwast
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Laura Parma
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - M Leontien van der Bent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eva van Ingen
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Fabiana Baganha
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Hendrika A B Peters
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Eveline A C Goossens
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Karin H Simons
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Meindert Palmen
- Department of Cardiothoracic Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Margreet R de Vries
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Paul H A Quax
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - A Yaël Nossent
- Department of Surgery, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria; Department of Internal Medicine II, Medical University of Vienna, 1090 Vienna, Austria.
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From animal models to patients: the role of placental microRNAs, miR-210, miR-126, and miR-148a/152 in preeclampsia. Clin Sci (Lond) 2020; 134:1001-1025. [PMID: 32337535 PMCID: PMC7239341 DOI: 10.1042/cs20200023] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/23/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
Placental microRNAs (miRNAs) regulate the placental transcriptome and play a pathological role in preeclampsia (PE), a hypertensive disorder of pregnancy. Three PE rodent model studies explored the role of placental miRNAs, miR-210, miR-126, and miR-148/152 respectively, by examining expression of the miRNAs, their inducers, and potential gene targets. This review evaluates the role of miR-210, miR-126, and miR-148/152 in PE by comparing findings from the three rodent model studies with in vitro studies, other animal models, and preeclamptic patients to provide comprehensive insight into genetic components and pathological processes in the placenta contributing to PE. The majority of studies demonstrate miR-210 is upregulated in PE in part driven by HIF-1α and NF-κBp50, stimulated by hypoxia and/or immune-mediated processes. Elevated miR-210 may contribute to PE via inhibiting anti-inflammatory Th2-cytokines. Studies report an up- and downregulation of miR-126, arguably reflecting differences in expression between cell types and its multifunctional capacity. MiR-126 may play a pro-angiogenic role by mediating the PI3K-Akt pathway. Most studies report miR-148/152 family members are upregulated in PE. Evidence suggests they may inhibit DNA methylation of genes involved in metabolic and inflammatory pathways. Given the genetic heterogeneity of PE, it is unlikely that a single placental miRNA is a suitable therapeutic target for all patients. Investigating miRNAs in PE subtypes in patients and animal models may represent a more appropriate approach going forward. Developing methods for targeting placental miRNAs and specific placental cell types remains crucial for research seeking to target placental miRNAs as a novel treatment for PE.
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Loss of H3K27me3 imprinting in the Sfmbt2 miRNA cluster causes enlargement of cloned mouse placentas. Nat Commun 2020; 11:2150. [PMID: 32358519 PMCID: PMC7195362 DOI: 10.1038/s41467-020-16044-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 04/07/2020] [Indexed: 01/31/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) in mammals is an inefficient process that is frequently associated with abnormal phenotypes, especially in placentas. Recent studies demonstrated that mouse SCNT placentas completely lack histone methylation (H3K27me3)-dependent imprinting, but how it affects placental development remains unclear. Here, we provide evidence that the loss of H3K27me3 imprinting is responsible for abnormal placental enlargement and low birth rates following SCNT, through upregulation of imprinted miRNAs. When we restore the normal paternal expression of H3K27me3-dependent imprinted genes (Sfmbt2, Gab1, and Slc38a4) in SCNT placentas by maternal knockout, the placentas remain enlarged. Intriguingly, correcting the expression of clustered miRNAs within the Sfmbt2 gene ameliorates the placental phenotype. Importantly, their target genes, which are confirmed to cause SCNT-like placental histology, recover their expression level. The birth rates increase about twofold. Thus, we identify loss of H3K27me3 imprinting as an epigenetic error that compromises embryo development following SCNT. Somatic cell nuclear transfer (SCNT) frequently results in abnormal placenta development in cloned mice. Here the authors show that loss of histone methylation (H3K27me3) imprinting in clustered Sfmbt2 miRNAs contributes to SCNT placenta defect.
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Setty BA, Jinesh GG, Arnold M, Pettersson F, Cheng CH, Cen L, Yoder SJ, Teer JK, Flores ER, Reed DR, Brohl AS. The genomic landscape of undifferentiated embryonal sarcoma of the liver is typified by C19MC structural rearrangement and overexpression combined with TP53 mutation or loss. PLoS Genet 2020; 16:e1008642. [PMID: 32310940 PMCID: PMC7192511 DOI: 10.1371/journal.pgen.1008642] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 04/30/2020] [Accepted: 01/31/2020] [Indexed: 12/30/2022] Open
Abstract
Undifferentiated embryonal sarcoma of the liver (UESL) is a rare and aggressive malignancy. Though the molecular underpinnings of this cancer have been largely unexplored, recurrent chromosomal breakpoints affecting a noncoding region on chr19q13, which includes the chromosome 19 microRNA cluster (C19MC), have been reported in several cases. We performed comprehensive molecular profiling on samples from 14 patients diagnosed with UESL. Congruent with prior reports, we identified structural variants in chr19q13 in 10 of 13 evaluable tumors. From whole transcriptome sequencing, we observed striking expressional activity of the entire C19MC region. Concordantly, in 7 of 7 samples undergoing miRNAseq, we observed hyperexpression of the miRNAs within this cluster to levels >100 fold compared to matched normal tissue or a non-C19MC amplified cancer cell line. Concurrent TP53 mutation or copy number loss was identified in all evaluable tumors with evidence of C19MC overexpression. We find that C19MC miRNAs exhibit significant negative correlation to TP53 regulatory miRNAs and K-Ras regulatory miRNAs. Using RNA-seq we identified that pathways relevant to cellular differentiation as well as mRNA translation machinery are transcriptionally enriched in UESL. In summary, utilizing a combination of next-generation sequencing and high-density arrays we identify the combination of C19MC hyperexpression via chromosomal structural event with TP53 mutation or loss as highly recurrent genomic features of UESL.
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Affiliation(s)
- Bhuvana A. Setty
- Division of Hematology/Oncology/BMT, Nationwide Children’s Hospital, Columbus, Ohio, United States of America
- Department of Pediatrics, The Ohio State University Wexner Medical Center Columbus, Ohio, United States of America
| | - Goodwin G. Jinesh
- Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center, Florida, United States of America
| | - Michael Arnold
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio, United States of America
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Fredrik Pettersson
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Chia-Ho Cheng
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Ling Cen
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Sean J. Yoder
- Molecular Genomics Core Facility, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Jamie K. Teer
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Elsa R. Flores
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Damon R. Reed
- Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center, Florida, United States of America
- Adolescent and Young Adult Program, Moffitt Cancer Center, Tampa, Florida, United States of America
- Sarcoma Department, Moffitt Cancer Center, Tampa, Florida, United States of America
| | - Andrew S. Brohl
- Chemical Biology and Molecular Medicine Program, Moffitt Cancer Center, Florida, United States of America
- Sarcoma Department, Moffitt Cancer Center, Tampa, Florida, United States of America
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