1
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Tataru C, Martin A, Dunlap K, Peras M, Chrisman BS, Rutherford E, Deitzler GE, Phillips A, Yin X, Sabino K, Hannibal RL, Hartono W, Lin M, Raack E, Wu Y, DeSantis TZ, Iwai S, Wall DP, David MM. Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder. ISME Commun 2021; 1:80. [PMID: 37938270 PMCID: PMC9723651 DOI: 10.1038/s43705-021-00080-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/24/2021] [Accepted: 11/18/2021] [Indexed: 05/01/2023]
Abstract
Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder influenced by both genetic and environmental factors. Recently, gut dysbiosis has emerged as a powerful contributor to ASD symptoms. In this study, we recruited over 100 age-matched sibling pairs (between 2 and 8 years old) where one had an Autism ASD diagnosis and the other was developing typically (TD) (432 samples total). We collected stool samples over four weeks, tracked over 100 lifestyle and dietary variables, and surveyed behavior measures related to ASD symptoms. We identified 117 amplicon sequencing variants (ASVs) that were significantly different in abundance between sibling pairs across all three timepoints, 11 of which were supported by at least two contrast methods. We additionally identified dietary and lifestyle variables that differ significantly between cohorts, and further linked those variables to the ASVs they statistically relate to. Overall, dietary and lifestyle features were explanatory of ASD phenotype using logistic regression, however, global compositional microbiome features were not. Leveraging our longitudinal behavior questionnaires, we additionally identified 11 ASVs associated with changes in reported anxiety over time within and across all individuals. Lastly, we find that overall microbiome composition (beta-diversity) is associated with specific ASD-related behavioral characteristics.
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Affiliation(s)
- Christine Tataru
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.
| | - Austin Martin
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | - Kaitlyn Dunlap
- Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | - Brianna S Chrisman
- Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Grace E Deitzler
- Department of Microbiology, Oregon State University, Corvallis, OR, USA
| | | | | | | | | | | | | | | | | | | | | | - Dennis P Wall
- Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Maude M David
- Department of Microbiology, Oregon State University, Corvallis, OR, USA.
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA.
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2
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Zhang ET, Hannibal RL, Badillo Rivera KM, Song JHT, McGowan K, Zhu X, Meinhardt G, Knöfler M, Pollheimer J, Urban AE, Folkins AK, Lyell DJ, Baker JC. PRG2 and AQPEP are misexpressed in fetal membranes in placenta previa and percreta†. Biol Reprod 2021; 105:244-257. [PMID: 33982062 DOI: 10.1093/biolre/ioab068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/03/2021] [Accepted: 04/07/2021] [Indexed: 11/13/2022] Open
Abstract
The obstetrical conditions placenta accreta spectrum (PAS) and placenta previa are a significant source of pregnancy-associated morbidity and mortality, yet the specific molecular and cellular underpinnings of these conditions are not known. In this study, we identified misregulated gene expression patterns in tissues from placenta previa and percreta (the most extreme form of PAS) compared with control cases. By comparing this gene set with existing placental single-cell and bulk RNA-Seq datasets, we show that the upregulated genes predominantly mark extravillous trophoblasts. We performed immunofluorescence on several candidate molecules and found that PRG2 and AQPEP protein levels are upregulated in both the fetal membranes and the placental disk in both conditions. While this increased AQPEP expression remains restricted to trophoblasts, PRG2 is mislocalized and is found throughout the fetal membranes. Using a larger patient cohort with a diverse set of gestationally aged-matched controls, we validated PRG2 as a marker for both previa and PAS and AQPEP as a marker for only previa in the fetal membranes. Our findings suggest that the extraembryonic tissues surrounding the conceptus, including both the fetal membranes and the placental disk, harbor a signature of previa and PAS that is characteristic of EVTs and that may reflect increased trophoblast invasiveness.
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Affiliation(s)
- Elisa T Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Roberta L Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Janet H T Song
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Kelly McGowan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Xiaowei Zhu
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Gudrun Meinhardt
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Martin Knöfler
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Jürgen Pollheimer
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Alexander E Urban
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Ann K Folkins
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Deirdre J Lyell
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
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3
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Vondra S, Kunihs V, Eberhart T, Eigner K, Bauer R, Haslinger P, Haider S, Windsperger K, Klambauer G, Schütz B, Mikula M, Zhu X, Urban AE, Hannibal RL, Baker J, Knöfler M, Stangl H, Pollheimer J, Röhrl C. Metabolism of cholesterol and progesterone is differentially regulated in primary trophoblastic subtypes and might be disturbed in recurrent miscarriages. J Lipid Res 2019; 60:1922-1934. [PMID: 31530576 PMCID: PMC6824492 DOI: 10.1194/jlr.p093427] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 08/12/2019] [Indexed: 02/06/2023] Open
Abstract
During pregnancy, extravillous trophoblasts (EVTs) invade the maternal decidua and remodel the local vasculature to establish blood supply for the growing fetus. Compromised EVT function has been linked to aberrant pregnancy associated with maternal and fetal morbidity and mortality. However, metabolic features of this invasive trophoblast subtype are largely unknown. Using primary human trophoblasts isolated from first trimester placental tissues, we show that cellular cholesterol homeostasis is differentially regulated in EVTs compared with villous cytotrophoblasts. Utilizing RNA-sequencing, gene set-enrichment analysis, and functional validation, we provide evidence that EVTs display increased levels of free and esterified cholesterol. Accordingly, EVTs are characterized by increased expression of the HDL-receptor, scavenger receptor class B type I, and reduced expression of the LXR and its target genes. We further reveal that EVTs express elevated levels of hydroxy-delta-5-steroid dehydrogenase 3 beta- and steroid delta-isomerase 1 (HSD3B1) (a rate-limiting enzyme in progesterone synthesis) and are capable of secreting progesterone. Increasing cholesterol export by LXR activation reduced progesterone secretion in an ABCA1-dependent manner. Importantly, HSD3B1 expression was decreased in EVTs of idiopathic recurrent spontaneous abortions, pointing toward compromised progesterone metabolism in EVTs of early miscarriages. Here, we provide insights into the regulation of cholesterol and progesterone metabolism in trophoblastic subtypes and its putative relevance in human miscarriage.
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Affiliation(s)
- Sigrid Vondra
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Victoria Kunihs
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Tanja Eberhart
- Departments of Medical Chemistry Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Karin Eigner
- Departments of Medical Chemistry Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Raimund Bauer
- Departments of Medical Chemistry Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Peter Haslinger
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Sandra Haider
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Karin Windsperger
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Günter Klambauer
- Institute of Machine Learning,Johannes Kepler University Linz, Linz, Austria
| | - Birgit Schütz
- Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Mario Mikula
- Medical Genetics, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Xiaowei Zhu
- Departments of PsychiatryStanford University School of Medicine, Stanford, CA,Genetics,Stanford University School of Medicine, Stanford, CA
| | - Alexander E. Urban
- Departments of PsychiatryStanford University School of Medicine, Stanford, CA,Genetics,Stanford University School of Medicine, Stanford, CA
| | | | - Julie Baker
- Genetics,Stanford University School of Medicine, Stanford, CA
| | - Martin Knöfler
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Herbert Stangl
- Departments of Medical Chemistry Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Jürgen Pollheimer
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria,To whom correspondence should be addressed. e-mail: (C.R.); (J.P.)
| | - Clemens Röhrl
- Departments of Medical Chemistry Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria,University of Applied Sciences Upper Austria, Wels, Austria,To whom correspondence should be addressed. e-mail: (C.R.); (J.P.)
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4
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Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. Genome amplification and cellular senescence are hallmarks of human placenta development. PLoS Genet 2018; 14:e1007698. [PMID: 30312291 PMCID: PMC6200260 DOI: 10.1371/journal.pgen.1007698] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 10/24/2018] [Accepted: 09/17/2018] [Indexed: 12/16/2022] Open
Abstract
Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM.
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Affiliation(s)
- Philipp Velicky
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Gudrun Meinhardt
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Kerstin Plessl
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Sigrid Vondra
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Tamara Weiss
- Children's Cancer Research Institute, St. Anna Children´s Hospital, Vienna, Austria
| | - Peter Haslinger
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Thomas Lendl
- Biooptics Facility of Institute of Molecular Pathology, Institute of Molecular Biotechnology and Gregor Mendel Institute, Vienna, Austria
| | - Karin Aumayr
- Biooptics Facility of Institute of Molecular Pathology, Institute of Molecular Biotechnology and Gregor Mendel Institute, Vienna, Austria
| | - Mario Mairhofer
- Department of Gynecological Endocrinology and Reproductive Medicine, Medical University of Vienna, Vienna, Austria
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, United States of America
| | - Birgit Schütz
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Roberta L. Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert Lindau
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Beatrix Weil
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Jan Ernerudh
- Department of Clinical Immunology and Transfusion Medicine, and Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Jürgen Neesen
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Mario Mikula
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Clemens Röhrl
- Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Alexander E. Urban
- Department of Psychiatry and Behavioral Sciences, Department of Genetics, Stanford University School of Medicine, Tasha and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, California, United States of America
| | - Julie Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Martin Knöfler
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
| | - Jürgen Pollheimer
- Department of Obstetrics and Gynaecology, Reproductive Biology Unit, Medical University of Vienna, Vienna, Austria
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5
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Hannibal RL, Cardoso-Moreira M, Chetty SP, Lau J, Qi Z, Gonzalez-Maldonado E, Cherry AM, Yu J, Norton ME, Baker JC. Investigating human placentation and pregnancy using first trimester chorionic villi. Placenta 2018; 65:65-75. [PMID: 29908643 DOI: 10.1016/j.placenta.2018.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/11/2018] [Accepted: 03/19/2018] [Indexed: 12/17/2022]
Abstract
Chorionic villus sampling (CVS), routinely used for prenatal diagnosis of cytogenetic disorders, also possesses great potential for the study of placentation. To better understand villus biology, human placentation, and how these relate to pregnancy outcomes, we examined the morphology and transcriptomes of villi obtained via CVS from 10 to 14 weeks of pregnancy and correlated these with pregnancy attributes and clinical outcomes. First, we established a morphological scoring system based on three main villus features: branching, budding and vascularization. We then tested whether morphology scores were predictive of pregnancy attributes and clinical outcomes. Finally, we used RNA sequencing to assess the transcriptional basis of villus morphology and tested the hypothesis that gene expression may predict pregnancy outcomes. We demonstrate that villus morphology varies tremendously between patients, irrespective of gestational age, and that transcriptional differences are highly predictive of villus morphology. We show that pre-eclampsia markers are associated with villi with low morphology scores. Additionally, we identify SVEP1 as a possible biomarker for defining gestational age. Overall, chorionic villi in the first trimester remain one of the few means to correlate placental function with pregnancy outcome and these samples are a valuable and increasingly rare resource.
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Affiliation(s)
- Roberta L Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States
| | | | - Shilpa P Chetty
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal Fetal Medicine, University of California, San Francisco, CA, United States
| | - Joanne Lau
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Stanford University School of Medicine, Stanford, CA, United States
| | - Zhongxia Qi
- Department of Laboratory Medicine, University of California, San Francisco, CA, United States
| | - Eduardo Gonzalez-Maldonado
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, United States
| | - Athena M Cherry
- Department of Pathology and Pediatrics, Stanford University School of Medicine, Stanford, CA, United States
| | - Jingwei Yu
- Department of Laboratory Medicine, University of California, San Francisco, CA, United States
| | - Mary E Norton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Maternal Fetal Medicine, University of California, San Francisco, CA, United States
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, United States.
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6
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Albrecht C, Baker JC, Blundell C, Chavez SL, Carbone L, Chamley L, Hannibal RL, Illsley N, Kurre P, Laurent LC, McKenzie C, Morales-Prieto D, Pantham P, Paquette A, Powell K, Price N, Rao BM, Sadovsky Y, Salomon C, Tuteja G, Wilson S, O'Tierney-Ginn PF. IFPA meeting 2016 workshop report I: Genomic communication, bioinformatics, trophoblast biology and transport systems. Placenta 2017; 60 Suppl 1:S5-S9. [PMID: 28108031 DOI: 10.1016/j.placenta.2017.01.103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 11/17/2022]
Abstract
Workshops are an important part of the IFPA annual meeting as they allow for discussion of specialized topics. At IFPA meeting 2016 there were twelve themed workshops, four of which are summarized in this report. These workshops covered innovative technologies applied to new and traditional areas of placental research: 1) genomic communication; 2) bioinformatics; 3) trophoblast biology and pathology; 4) placental transport systems.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Peter Kurre
- Oregon Health and Science University, Oregon, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - P F O'Tierney-Ginn
- Center for Reproductive Health, MetroHealth Medical Center, Case Western Reserve University, Cleveland, OH, USA.
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7
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Hannibal RL, Chuong EB, Rivera-Mulia JC, Gilbert DM, Valouev A, Baker JC. Copy number variation is a fundamental aspect of the placental genome. PLoS Genet 2014; 10:e1004290. [PMID: 24785991 PMCID: PMC4006706 DOI: 10.1371/journal.pgen.1004290] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
Discovery of lineage-specific somatic copy number variation (CNV) in mammals has led to debate over whether CNVs are mutations that propagate disease or whether they are a normal, and even essential, aspect of cell biology. We show that 1,000N polyploid trophoblast giant cells (TGCs) of the mouse placenta contain 47 regions, totaling 138 Megabases, where genomic copies are underrepresented (UR). UR domains originate from a subset of late-replicating heterochromatic regions containing gene deserts and genes involved in cell adhesion and neurogenesis. While lineage-specific CNVs have been identified in mammalian cells, classically in the immune system where V(D)J recombination occurs, we demonstrate that CNVs form during gestation in the placenta by an underreplication mechanism, not by recombination nor deletion. Our results reveal that large scale CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during embryogenesis and are propagated by a mechanism of underreplication. Generally, every mammalian cell has the same complement of each part of its genome. However, copy number variation (CNV) can occur, where, compared to the rest of its genome, a cell has either more or less of a specific genomic region. It is unknown whether CNVs cause disease, or whether they are a normal aspect of cell biology. We investigated CNVs in polyploid trophoblast giant cells (TGCs) of the mouse placenta, which have up to 1,000 copies of the genome in each cell. We found that there are 47 regions with decreased copy number in TGCs, which we call underrepresented (UR) domains. These domains are marked in the TGC progenitor cells and we suggest that they gradually form during gestation due to slow replication versus fast replication of the rest of the genome. While UR domains contain cell adhesion and neuronal genes, they also contain significantly fewer genes than other genomic regions. Our results demonstrate that CNVs are a normal feature of the mammalian placental genome, which are regulated systematically during pregnancy.
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Affiliation(s)
- Roberta L. Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Edward B. Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Juan Carlos Rivera-Mulia
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Tallahassee Florida, United States of America
| | - Anton Valouev
- Division of Bioinformatics, Department of Preventive Medicine, University of Southern California Keck School of Medicine, Los Angeles, California, United States of America
| | - Julie C. Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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8
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Abstract
Animals have been described as segmented for more than 2,000 years, yet a precise definition of segmentation remains elusive. Here we give the history of the definition of segmentation, followed by a discussion on current controversies in defining a segment. While there is a general consensus that segmentation involves the repetition of units along the anterior-posterior (a-p) axis, long-running debates exist over whether a segment can be composed of only one tissue layer, whether the most anterior region of the arthropod head is considered segmented, and whether and how the vertebrate head is segmented. Additionally, we discuss whether a segment can be composed of a single cell in a column of cells, or a single row of cells within a grid of cells. We suggest that ‘segmentation’ be used in its more general sense, the repetition of units with a-p polarity along the a-p axis, to prevent artificial classification of animals. We further suggest that this general definition be combined with an exact description of what is being studied, as well as a clearly stated hypothesis concerning the specific nature of the potential homology of structures. These suggestions should facilitate dialogue among scientists who study vastly differing segmental structures.
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Affiliation(s)
| | - Nipam H Patel
- Departments of Molecular and Cell Biology and Integrative Biology, University of California, 519A LSA #3200, Berkeley, CA 94720-3200, USA.
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9
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Chuong EB, Hannibal RL, Green SL, Baker JC. Evolutionary perspectives into placental biology and disease. Appl Transl Genom 2013; 2:64-69. [PMID: 27896057 PMCID: PMC5121266 DOI: 10.1016/j.atg.2013.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 07/27/2013] [Indexed: 12/29/2022]
Abstract
In all mammals including humans, development takes place within the protective environment of the maternal womb. Throughout gestation, nutrients and waste products are continuously exchanged between mother and fetus through the placenta. Despite the clear importance of the placenta to successful pregnancy and the health of both mother and offspring, relatively little is understood about the biology of the placenta and its role in pregnancy-related diseases. Given that pre- and peri-natal diseases involving the placenta affect millions of women and their newborns worldwide, there is an urgent need to understand placenta biology and development. Here, we suggest that the placenta is an organ under unique selective pressures that have driven its rapid diversification throughout mammalian evolution. The high divergence of the placenta complicates the use of non-human animal models and necessitates an evolutionary perspective when studying its biology and role in disease. We suggest that diversifying evolution of the placenta is primarily driven by intraspecies evolutionary conflict between mother and fetus, and that many pregnancy diseases are a consequence of this evolutionary force. Understanding how maternal-fetal conflict shapes both basic placental and reproductive biology - in all species - will provide key insights into diseases of pregnancy.
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Affiliation(s)
- Edward B Chuong
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roberta L Hannibal
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sherril L Green
- Department of Comparative Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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10
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Hannibal RL, Price AL, Patel NH. The functional relationship between ectodermal and mesodermal segmentation in the crustacean, Parhyale hawaiensis. Dev Biol 2012; 361:427-38. [DOI: 10.1016/j.ydbio.2011.09.033] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 09/27/2011] [Accepted: 09/27/2011] [Indexed: 11/27/2022]
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11
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Vargas-Vila MA, Hannibal RL, Parchem RJ, Liu PZ, Patel NH. A prominent requirement for single-minded and the ventral midline in patterning the dorsoventral axis of the crustacean Parhyale hawaiensis. Development 2010; 137:3469-76. [PMID: 20843860 DOI: 10.1242/dev.055160] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In bilaterians, establishing the correct spatial positioning of structures along the dorsoventral (DV) axis is essential for proper embryonic development. Insects such as Drosophila rely on the Dorsal activity gradient and Bone morphogenetic protein (BMP) signaling to establish cell fates along the DV axis, leading to the distinction between tissues such as mesoderm, neurogenic ectoderm and dorsal ectoderm in the developing embryo. Subsequently, the ventral midline plays a more restricted role in DV patterning by establishing differential cell fates in adjacent regions of the neurogenic ectoderm. In this study, we examine the function of the ventral midline and the midline-associated gene single-minded (Ph-sim) in the amphipod crustacean Parhyale hawaiensis. Remarkably, we found that Ph-sim and the ventral midline play a central role in establishing proper fates along the entire DV axis in this animal; laser ablation of midline cells causes a failure to form neurogenic ectoderm and Ph-sim RNAi results in severely dorsalized embryos lacking both neurogenic ectoderm and the appendage-bearing lateral ectoderm. Furthermore, we hypothesize that this role of midline cells was present in the last common ancestor of crustaceans and insects. We predict that the transition to a Dorsal-dependent DV patterning system in the phylogenetically derived insect lineage leading to Drosophila has led to a more restricted role of the ventral midline in patterning the DV axis of these insects.
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Affiliation(s)
- Mario A Vargas-Vila
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3200, USA
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Abstract
The great diversity of arthropod body plans, together with our detailed understanding of fruit fly development, makes arthropods a premier taxon for examining the evolutionary diversification of developmental patterns and hence the diversity of extant life. Crustaceans, in particular, show a remarkable range of morphologies and provide a useful outgroup to the insects. The amphipod crustacean Parhyale hawaiensis is becoming established as a model organism for developmental studies within the arthropods. This protocol describes the dissection and fixation of P. hawaiensis embryos. Embryonic tissue fixed in the following manner is suitable for in situ hybridization experiments to study mRNA expression or for immunocytochemistry to study protein localization.
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Affiliation(s)
- E Jay Rehm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3140, USA
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Abstract
The great diversity of arthropod body plans, together with our detailed understanding of fruit fly development, makes arthropods a premier taxon for examining the evolutionary diversification of developmental patterns and hence the diversity of extant life. Crustaceans, in particular, show a remarkable range of morphologies and provide a useful outgroup to the insects. The amphipod crustacean Parhyale hawaiensis is becoming established as a model organism for developmental studies within the arthropods. This protocol provides a simplified protocol for antibody staining of P. hawaiensis embryos. The method also works well for other arthropods and phyla. Fixed embryos are rehydrated, washed, blocked with normal goat serum, and incubated overnight with primary antibody. Embryos are then washed and incubated with a peroxidase-conjugated secondary antibody that binds to the primary antibody. A subsequent histochemical reaction produces a black stain in those cells where antibodies have localized.
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Affiliation(s)
- E Jay Rehm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3140, USA
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Price AL, Modrell MS, Hannibal RL, Patel NH. Mesoderm and ectoderm lineages in the crustacean Parhyale hawaiensis display intra-germ layer compensation. Dev Biol 2009; 341:256-66. [PMID: 20005872 DOI: 10.1016/j.ydbio.2009.12.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 12/04/2009] [Accepted: 12/04/2009] [Indexed: 11/25/2022]
Abstract
In Parhyale hawaiensis, the first three divisions are holoblastic and asymmetric, resulting in an embryo comprised of eight cells-four macromeres and four micromeres. Lineage studies performed at this stage demonstrate that the progeny of each cell contribute to specific portions of different germ layers. However, it is not known if this lineage pattern means a given blastomere is committed to its specific fate, indicative of mosaic development, or if regulation can occur between blastomere progeny so that the loss of a blastomere could be compensated for during development. Furthermore, if compensation occurs, what would be the source of such replacement? To investigate these possibilities, we performed ablation experiments at the eight-cell stage. We find that loss of blastomeres results in compensation. To determine the compensation pattern, we combined ablation and cell lineage tracing to reveal that progeny of mesoderm and ectoderm producing blastomeres display intra-germ layer compensation. Furthermore, by ablating lineages later in development, we identify a key interval between gastrulation and germband elongation after which compensation no longer occurs. Our results suggest that Parhyale possesses a mechanism to assess the status of mesoderm and ectoderm formation and alter development to replace the missing portions of these lineages.
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Affiliation(s)
- Alivia L Price
- University of California-Berkeley, Departments of Molecular and Cell Biology, Integrative Biology, Center for Integrative Genomics, and HHMI, 3060 VLSB # 3140, Berkeley, CA 94720-3140, USA
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Hannibal RL, Patel NH. The role of cyclical Ph-Snail1 expression during stem cell migration. Dev Biol 2009. [DOI: 10.1016/j.ydbio.2009.05.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Gilder AL, Hannibal RL, Patel NH. Comparative analysis of regulatory elements associated with snail in Parhyale hawaiensis and Drosophila melanogaster. Dev Biol 2009. [DOI: 10.1016/j.ydbio.2009.05.292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rehm EJ, Hannibal RL, Chaw RC, Vargas-Vila MA, Patel NH. Injection of Parhyale hawaiensis blastomeres with fluorescently labeled tracers. Cold Spring Harb Protoc 2009; 2009:pdb.prot5128. [PMID: 20147023 DOI: 10.1101/pdb.prot5128] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The great diversity of arthropod body plans, together with our detailed understanding of fruit fly development, makes arthropods a premier taxon for examining the evolutionary diversification of developmental patterns and hence the diversity of extant life. Crustaceans, in particular, show a remarkable range of morphologies and provide a useful outgroup to the insects. The amphipod crustacean Parhyale hawaiensis is becoming established as a model organism for developmental studies within the arthropods. This protocol describes the injection of P. hawaiensis blastomeres with fluorescently labeled tracers for the purpose of cell-lineage analysis. The total (holoblastic) cleavages that characterize early embryogenesis in P. hawaiensis generate an eight-cell embryo with a stereotypical arrangement of blastomeres, each of which already possesses an invariant cell fate. Fluorochrome-conjugated dextran solutions, mRNAs encoding fluorescent proteins, and biotin-dextran have all proven to be useful lineage markers. The relative merits of various tracers are considered.
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Affiliation(s)
- E Jay Rehm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3140, USA
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Rehm EJ, Hannibal RL, Chaw RC, Vargas-Vila MA, Patel NH. The crustacean Parhyale hawaiensis: a new model for arthropod development. Cold Spring Harb Protoc 2009; 2009:pdb.emo114. [PMID: 20147009 DOI: 10.1101/pdb.emo114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The great diversity of arthropod body plans, together with our detailed understanding of fruit fly development, makes arthropods a premier taxon for examining the evolutionary diversification of developmental patterns and hence the diversity of extant life. Crustaceans, in particular, show a remarkable range of morphologies and provide a useful outgroup to the insects. The amphipod crustacean Parhyale hawaiensis is becoming established as a model organism for developmental studies within the arthropods. In addition to its phylogenetically strategic position, P. hawaiensis has proven to be highly amenable to experimental manipulation, is straightforward to rear in the laboratory, and has large numbers of embryos that are available year-round. A detailed staging system has been developed to characterize P. hawaiensis embryogenesis. Robust protocols exist for the collection and fixation of all embryonic stages, in situ hybridization to study mRNA localization, and immunohistochemistry to study protein localization. Microinjection of blastomeres enables detailed cell-lineage analyses, transient and transgenic introduction of recombinant genetic material, and targeted knockdowns of gene function using either RNA interference (RNAi) or morpholino methods. Directed genome sequencing will generate important data for comparative studies aimed at understanding cis-regulatory evolution. Bacterial artificial chromosome (BAC) clones containing genes of interest to the developmental and evolutionary biology communities are being targeted for sequencing. An expressed sequence tag (EST) database will facilitate discovery of additional developmental genes and should broaden our understanding of the genetic controls of body patterning. A reference genome from the related amphipod crustacean Jassa slatteryi will shortly be available.
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Affiliation(s)
- E Jay Rehm
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3140, USA
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