1
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Kim HS, Kim YI, Cho JY. ARID3C Acts as a Regulator of Monocyte-to-Macrophage Differentiation Interacting with NPM1. J Proteome Res 2024. [PMID: 38231884 DOI: 10.1021/acs.jproteome.3c00509] [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: 01/19/2024]
Abstract
ARID3C is a protein located on human chromosome 9 and expressed at low levels in various organs, yet its biological function has not been elucidated. In this study, we investigated both the cellular localization and function of ARID3C. Employing a combination of LC-MS/MS and deep learning techniques, we identified NPM1 as a binding partner for ARID3C's nuclear shuttling. ARID3C was found to predominantly localize with the nucleus, where it functioned as a transcription factor for genes STAT3, STAT1, and JUNB, thereby facilitating monocyte-to-macrophage differentiation. The precise binding sites between ARID3C and NPM1 were predicted by AlphaFold2. Mutating this binding site prevented ARID3C from interacting with NPM1, resulting in its retention in the cytoplasm instead of translocation to the nucleus. Consequently, ARID3C lost its ability to bind to the promoters of target genes, leading to a loss of monocyte-to-macrophage differentiation. Collectively, our findings indicate that ARID3C forms a complex with NPM1 to translocate to the nucleus, acting as a transcription factor that promotes the expression of the genes involved in monocyte-to-macrophage differentiation.
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Affiliation(s)
- Hui-Su Kim
- Department of Biochemistry, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Comparative Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-In Kim
- Department of Biochemistry, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Comparative Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, College of Veterinary Medicine, Research Institute for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading Education and Research Center, Seoul National University, Seoul 08826, Republic of Korea
- Comparative Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
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2
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Davenport KM, O'Neil EV, Ortega MS, Patterson A, Kelleher AM, Warren WC, Spencer TE. Single-cell insights into development of the bovine placenta†. Biol Reprod 2024; 110:169-184. [PMID: 37707543 DOI: 10.1093/biolre/ioad123] [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: 07/14/2023] [Revised: 08/23/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023] Open
Abstract
A central determinant of pregnancy success is proper development of the conceptus (embryo/fetus and associated extraembryonic membranes including the placenta). Although the gross morphology and histology of the bovine placenta have been well studied, the cellular and molecular mechanisms regulating placenta development and trophoblast differentiation and function remain essentially undefined. Here, single-cell transcriptome (scRNA-seq) analysis was performed on the day 17 bovine conceptus and chorion of day 24, 30, and 50 conceptuses (n = 3-4 samples per day) using the 10X Genomics platform. Bioinformatic analyses identified cell types and their ontogeny including trophoblast, mesenchyme, and immune cells. Loss of interferon tau-expressing trophoblast uninucleate cells occurred between days 17 and 30, whereas binucleate cells, identified based on expression of placental lactogen (CSH2) and specific pregnancy-associated glycoprotein genes (PAGs), first appeared on day 24. Several different types of uninucleate cells were present in day 24, 30, and 50 samples, but only one (day 24) or two types of binucleate cells (days 30 and 50). Cell trajectory analyses provided a conceptual framework for uninucleate cell development and binucleate cell differentiation, and bioinformatic analyses identified candidate transcription factors governing differentiation and function of the trophoblasts. The digital atlas of cell types in the developing bovine conceptus reported here serves as a resource to discover key genes and biological pathways regulating its development during the critical periods of implantation and placentation.
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Affiliation(s)
| | - Eleanore V O'Neil
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - M Sofia Ortega
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Amanda Patterson
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Department of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, MO, USA
| | - Andrew M Kelleher
- Department of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, USA
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
- Department of Obstetrics, Gynecology, and Women's Health, University of Missouri, Columbia, MO, USA
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3
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Pham TXA, Panda A, Kagawa H, To SK, Ertekin C, Georgolopoulos G, van Knippenberg SSFA, Allsop RN, Bruneau A, Chui JSH, Vanheer L, Janiszewski A, Chappell J, Oberhuemer M, Tchinda RS, Talon I, Khodeer S, Rossant J, Lluis F, David L, Rivron N, Balaton BP, Pasque V. Modeling human extraembryonic mesoderm cells using naive pluripotent stem cells. Cell Stem Cell 2022; 29:1346-1365.e10. [PMID: 36055191 PMCID: PMC9438972 DOI: 10.1016/j.stem.2022.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 06/08/2022] [Accepted: 08/05/2022] [Indexed: 12/31/2022]
Abstract
A hallmark of primate postimplantation embryogenesis is the specification of extraembryonic mesoderm (EXM) before gastrulation, in contrast to rodents where this tissue is formed only after gastrulation. Here, we discover that naive human pluripotent stem cells (hPSCs) are competent to differentiate into EXM cells (EXMCs). EXMCs are specified by inhibition of Nodal signaling and GSK3B, are maintained by mTOR and BMP4 signaling activity, and their transcriptome and epigenome closely resemble that of human and monkey embryo EXM. EXMCs are mesenchymal, can arise from an epiblast intermediate, and are capable of self-renewal. Thus, EXMCs arising via primate-specific specification between implantation and gastrulation can be modeled in vitro. We also find that most of the rare off-target cells within human blastoids formed by triple inhibition (Kagawa et al., 2021) correspond to EXMCs. Our study impacts our ability to model and study the molecular mechanisms of early human embryogenesis and related defects.
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Affiliation(s)
- Thi Xuan Ai Pham
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Amitesh Panda
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Harunobu Kagawa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - San Kit To
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Cankat Ertekin
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Grigorios Georgolopoulos
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Sam S F A van Knippenberg
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Ryan Nicolaas Allsop
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Alexandre Bruneau
- Nantes Université, CHU Nantes, Inserm, CR2TI, UMR 1064, F-44000, Nantes, France
| | - Jonathan Sai-Hong Chui
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Lotte Vanheer
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Adrian Janiszewski
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Joel Chappell
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Michael Oberhuemer
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Raissa Songwa Tchinda
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Irene Talon
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Sherif Khodeer
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Janet Rossant
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5V 0B1, Canada
| | - Frederic Lluis
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium
| | - Laurent David
- Nantes Université, CHU Nantes, Inserm, CR2TI, UMR 1064, F-44000, Nantes, France; Nantes Université, CHU Nantes, Inserm, CNRS, BioCore, F-44000 Nantes, France
| | - Nicolas Rivron
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Bradley Philip Balaton
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium.
| | - Vincent Pasque
- Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven Institute for Single-cell Omics (LISCO), KU Leuven-University of Leuven, 3000 Leuven, Belgium.
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4
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Chakraborty P, Chatterjee S, Chatterjee I, Mitra I, Kalapahar S, Sharma S, Chattopadhyay R, Haldar R, Chaudhury K, Chakravarty B. Attenuation of placental pyruvate kinase M2 promotes oxidative imbalance and enhances inflammatory- apoptosis cross talk in rats with hyperhomocysteinemia associated pregnancy loss.. [DOI: 10.21203/rs.3.rs-1997950/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
Abstract
Abstract
10-15% of clinically recognized pregnancies end in miscarriage. Hyperhomocysteinemia in pregnant women has been associated with deep venous thrombosis, recurrent miscarriage, preeclampsia to name a few. Impaired placental function due to overt oxidative stress is one of the key mechanisms in development of pregnancy loss. Paucity of pathway–based microarray approach in embryonic–endometrial communication warrants elucidation of distinct profile of miRNAs in hyperhomocysteinemia-associated pregnancy loss (HAPL). Hyperhomocysteinemia was induced at a dose of 100mg/kg body-weight/day for D1-D18 of pregnancy. Placental histology by haematoxylin-eosin staining documented thrombus with reduced area of spongiotropoblasts in chorionic plate vessel. Placental mRNA was subjected to microarray analysis followed by pathway-analysis using Ingenuity Pathway Analysis (IPA). Genes involved in reproductive physiology, inflammatory pathways, immune responses, homocysteine metabolism, glucose metabolism, and oxidative stress were differentially expressed in HAPL. 21 pathways documented by IPA, were skewed to 10 by recursive feature elimination highlighting possible deregulation/s. Expression/s was re-confirmed by quantitative real- time PCR (qRT-PCR), western blot and flow cytometric analysis (FACS). Nine priori molecules (PKM2, AKT, PI3K, NF-κB, COX-2, sflt-1, HIF-1α, bax, caspase 9) were specifically modulated in HAPL as demonstrated by protein and mRNA expression. A parallel increase in insulin signaling (PI3K+,AKT+), inflammation (COX2+,NF-κB+), hypoxia (sflt-1+,HIF-1α+), apoptosis (bax+,caspase9+) with concomitant decrease in pyruvate kinase M2 in hyperhomocysteinemic placental cells by FACS with CD56, a marker for pregnancy loss was documented. The findings provide evidence that an oxidative stress-mediated placental damage perhaps represents the pathogenesis of HAPL, which may explore pathway-based therapeutic options for recurrent miscarriage.10–15% of clinically recognized pregnancies end in miscarriage. Hyperhomocysteinemia in pregnant women has been associated with deep venous thrombosis, recurrent miscarriage, preeclampsia to name a few. Impaired placental function due to overt oxidative stress is one of the key mechanisms in development of pregnancy loss. Paucity of pathway–based microarray approach in embryonic–endometrial communication warrants elucidation of distinct profile of miRNAs in hyperhomocysteinemia-associated pregnancy loss (HAPL). Hyperhomocysteinemia was induced at a dose of 100mg/kg body-weight/day for D1-D18 of pregnancy. Placental histology by haematoxylin-eosin staining documented thrombus with reduced area of spongiotropoblasts in chorionic plate vessel. Placental mRNA was subjected to microarray analysis followed by pathway-analysis using Ingenuity Pathway Analysis (IPA). Genes involved in reproductive physiology, inflammatory pathways, immune responses, homocysteine metabolism, glucose metabolism, and oxidative stress were differentially expressed in HAPL. 21 pathways documented by IPA, were skewed to 10 by recursive feature elimination highlighting possible deregulation/s. Expression/s was re-confirmed by quantitative real- time PCR (qRT-PCR), western blot and flow cytometric analysis (FACS). Nine priori molecules (PKM2, AKT, PI3K, NF-κB, COX-2, sflt-1, HIF-1α, bax, caspase 9) were specifically modulated in HAPL as demonstrated by protein and mRNA expression. A parallel increase in insulin signaling (PI3K+,AKT+), inflammation (COX2+,NF-κB+), hypoxia (sflt-1+,HIF-1α+), apoptosis (bax+,caspase9+) with concomitant decrease in pyruvate kinase M2 in hyperhomocysteinemic placental cells by FACS with CD56, a marker for pregnancy loss was documented. The findings provide evidence that an oxidative stress-mediated placental damage perhaps represents the pathogenesis of HAPL, which may explore pathway-based therapeutic options for recurrent miscarriage.
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Affiliation(s)
| | - Sujan Chatterjee
- Molecular Biology and Tissue Culture Laboratory, Post Graduate Department of Zoology, Vidyasagar College, Kolkata- 700006
| | | | - Imon Mitra
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, India
| | | | | | | | - Rajen Haldar
- Department of Physiology, UCSTA, University of Calcutta
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, India
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5
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Plianchaisuk A, Kusama K, Kato K, Sriswasdi S, Tamura K, Iwasaki W. Origination of LTR retroelement-derived NYNRIN coincides with therian placental emergence. Mol Biol Evol 2022; 39:6661932. [PMID: 35959649 PMCID: PMC9447858 DOI: 10.1093/molbev/msac176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The emergence of the placenta is a revolutionary event in the evolution of therian mammals, to which some LTR retroelement–derived genes, such as PEG10, RTL1, and syncytin, are known to contribute. However, therian genomes contain many more LTR retroelement–derived genes that may also have contributed to placental evolution. We conducted large-scale evolutionary genomic and transcriptomic analyses to comprehensively search for LTR retroelement–derived genes whose origination coincided with therian placental emergence and that became consistently expressed in therian placentae. We identified NYNRIN as another Ty3/Gypsy LTR retroelement–derived gene likely to contribute to placental emergence in the therian stem lineage. NYNRIN knockdown inhibited the invasion of HTR8/SVneo invasive-type trophoblasts, whereas the knockdown of its nonretroelement-derived homolog KHNYN did not. Functional enrichment analyses suggested that NYNRIN modulates trophoblast invasion by regulating epithelial-mesenchymal transition and extracellular matrix remodeling and that the ubiquitin-proteasome system is responsible for the functional differences between NYNRIN and KHNYN. These findings extend our knowledge of the roles of LTR retroelement–derived genes in the evolution of therian mammals.
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Affiliation(s)
- Arnon Plianchaisuk
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Kazuya Kusama
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Kiyoko Kato
- Department of Obstetrics and Gynecology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Sira Sriswasdi
- Center of Excellence in Computational Molecular Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University, Pathum Wan, Bangkok, 10330, Thailand
| | - Kazuhiro Tamura
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Wataru Iwasaki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, 277-0882, Japan.,Institute for Quantitative Biosciences, The University of Tokyo. Bunkyo-ku, Tokyo 113-0032, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
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6
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Dong C, Fu S, Karvas RM, Chew B, Fischer LA, Xing X, Harrison JK, Popli P, Kommagani R, Wang T, Zhang B, Theunissen TW. A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. Nat Commun 2022; 13:2548. [PMID: 35538076 PMCID: PMC9090837 DOI: 10.1038/s41467-022-30207-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/21/2022] [Indexed: 12/26/2022] Open
Abstract
The recent derivation of human trophoblast stem cells (hTSCs) provides a scalable in vitro model system of human placental development, but the molecular regulators of hTSC identity have not been systematically explored thus far. Here, we utilize a genome-wide CRISPR-Cas9 knockout screen to comprehensively identify essential and growth-restricting genes in hTSCs. By cross-referencing our data to those from similar genetic screens performed in other cell types, as well as gene expression data from early human embryos, we define hTSC-specific and -enriched regulators. These include both well-established and previously uncharacterized trophoblast regulators, such as ARID3A, GATA2, and TEAD1 (essential), and GCM1, PTPN14, and TET2 (growth-restricting). Integrated analysis of chromatin accessibility, gene expression, and genome-wide location data reveals that the transcription factor TEAD1 regulates the expression of many trophoblast regulators in hTSCs. In the absence of TEAD1, hTSCs fail to complete faithful differentiation into extravillous trophoblast (EVT) cells and instead show a bias towards syncytiotrophoblast (STB) differentiation, thus indicating that this transcription factor safeguards the bipotent lineage potential of hTSCs. Overall, our study provides a valuable resource for dissecting the molecular regulation of human placental development and diseases.
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Affiliation(s)
- Chen Dong
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shuhua Fu
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Rowan M Karvas
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Brian Chew
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Laura A Fischer
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xiaoyun Xing
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jessica K Harrison
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Pooja Popli
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ramakrishna Kommagani
- Department of Obstetrics and Gynecology, Center for Reproductive Health Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Genetics, Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Bo Zhang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Thorold W Theunissen
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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7
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Solmonson A, Faubert B, Gu W, Rao A, Cowdin MA, Menendez-Montes I, Kelekar S, Rogers TJ, Pan C, Guevara G, Tarangelo A, Zacharias LG, Martin-Sandoval MS, Do D, Pachnis P, Dumesnil D, Mathews TP, Tasdogan A, Pham A, Cai L, Zhao Z, Ni M, Cleaver O, Sadek HA, Morrison SJ, DeBerardinis RJ. Compartmentalized metabolism supports midgestation mammalian development. Nature 2022; 604:349-353. [PMID: 35388219 PMCID: PMC9007737 DOI: 10.1038/s41586-022-04557-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
Abstract
Mammalian embryogenesis requires rapid growth and proper metabolic regulation1. Midgestation features increasing oxygen and nutrient availability concomitant with fetal organ development2,3. Understanding how metabolism supports development requires approaches to observe metabolism directly in model organisms in utero. Here we used isotope tracing and metabolomics to identify evolving metabolic programmes in the placenta and embryo during midgestation in mice. These tissues differ metabolically throughout midgestation, but we pinpointed gestational days (GD) 10.5-11.5 as a transition period for both placenta and embryo. Isotope tracing revealed differences in carbohydrate metabolism between the tissues and rapid glucose-dependent purine synthesis, especially in the embryo. Glucose's contribution to the tricarboxylic acid (TCA) cycle rises throughout midgestation in the embryo but not in the placenta. By GD12.5, compartmentalized metabolic programmes are apparent within the embryo, including different nutrient contributions to the TCA cycle in different organs. To contextualize developmental anomalies associated with Mendelian metabolic defects, we analysed mice deficient in LIPT1, the enzyme that activates 2-ketoacid dehydrogenases related to the TCA cycle4,5. LIPT1 deficiency suppresses TCA cycle metabolism during the GD10.5-GD11.5 transition, perturbs brain, heart and erythrocyte development and leads to embryonic demise by GD11.5. These data document individualized metabolic programmes in developing organs in utero.
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Affiliation(s)
- Ashley Solmonson
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Brandon Faubert
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Section of Hematology and Oncology, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Wen Gu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Aparna Rao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Mitzy A Cowdin
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ivan Menendez-Montes
- Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sherwin Kelekar
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas J Rogers
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Chunxiao Pan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gerardo Guevara
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Amy Tarangelo
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lauren G Zacharias
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Misty S Martin-Sandoval
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Duyen Do
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Panayotis Pachnis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dennis Dumesnil
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas P Mathews
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Alpaslan Tasdogan
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Department of Dermatology, University Hospital Essen and German Cancer Consortium, Partner Site Essen, Essen, Germany
| | - An Pham
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ling Cai
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiyu Zhao
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ondine Cleaver
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hesham A Sadek
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Division of Cardiology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean J Morrison
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA. .,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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8
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Sobhani NC, Mernoff R, Abraha M, Okorie CN, Marquez-Magana L, Gaw SL, Robinson JF. Integrated analysis of transcriptomic datasets to identify placental biomarkers of spontaneous preterm birth. Placenta 2022; 122:66-73. [DOI: 10.1016/j.placenta.2022.03.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/06/2022] [Accepted: 03/22/2022] [Indexed: 11/28/2022]
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9
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Lasorsa VA, Montella A, Cantalupo S, Tirelli M, de Torres C, Aveic S, Tonini GP, Iolascon A, Capasso M. Somatic mutations enriched in cis-regulatory elements affect genes involved in embryonic development and immune system response in neuroblastoma. Cancer Res 2022; 82:1193-1207. [PMID: 35101866 DOI: 10.1158/0008-5472.can-20-3788] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 11/04/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022]
Abstract
Noncoding cis-regulatory variants have gained interest as cancer drivers, yet progress in understanding their significance is hindered by the numerous challenges and limitations of variant prioritization. To overcome these limitations, we focused on active cis-regulatory elements (aCRE) in order to design a customized panel for the deep sequencing of 56 neuroblastoma tumor and normal DNA sample pairs. In order to search for driver mutations, aCREs were defined by reanalysis of H3K27ac ChiP-seq peaks in 25 neuroblastoma cell lines. These regulatory genomic regions were tested for an excess of somatic mutations and assessed for statistical significance using a global approach that accounted for chromatin accessibility and replication timing. Additional validation was provided by whole genome sequence analysis of 151 neuroblastomas. Analysis of Hi-C data determined the presence of candidate target genes interacting with mutated regions. An excess of somatic mutations in aCREs of diverse genes were identified, including IPO7, HAND2, and ARID3A. CRISPR-Cas9 editing was utilized to assess the functional consequences of mutations in the IPO7 aCRE. Patients with noncoding mutations in aCREs showed inferior overall and event-free survival independent of age at diagnosis, stage, risk stratification, and MYCN status. Expression of aCRE-interacting genes correlated strongly with negative prognostic markers and low survival rates. Moreover, a convergence between the biological functions of aCRE target genes and transcription factors with mutated binding motifs was associated with embryonic development and immune system response. Overall, this strategy enabled the identification of somatic mutations in regulatory elements that collectively promote neuroblastoma tumorigenesis.
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Affiliation(s)
- Vito Alessandro Lasorsa
- Department of Molecular Medicine and Medical Biotechnology, Università degli Studi di Napoli Federico II
| | - Annalaura Montella
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II di Napoli, CEINGE Biotecnologie Avanzate
| | | | | | - Carmen de Torres
- Developmental Tumor Biology Laboratory and Department of Oncology, Hospital Sant Joan de Déu Barcelona
| | - Sanja Aveic
- Neuroblastoma Laboratory, Fondazione Istituto di Ricerca Pediatrica Citta della Speranza
| | | | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II
| | - Mario Capasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II
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10
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ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat Commun 2020; 11:4267. [PMID: 32848148 PMCID: PMC7449963 DOI: 10.1038/s41467-020-18035-1] [Citation(s) in RCA: 237] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
While footprinting analysis of ATAC-seq data can theoretically enable investigation of transcription factor (TF) binding, the lack of a computational tool able to conduct different levels of footprinting analysis has so-far hindered the widespread application of this method. Here we present TOBIAS, a comprehensive, accurate, and fast footprinting framework enabling genome-wide investigation of TF binding dynamics for hundreds of TFs simultaneously. We validate TOBIAS using paired ATAC-seq and ChIP-seq data, and find that TOBIAS outperforms existing methods for bias correction and footprinting. As a proof-of-concept, we illustrate how TOBIAS can unveil complex TF dynamics during zygotic genome activation in both humans and mice, and propose how zygotic Dux activates cascades of TFs, binds to repeat elements and induces expression of novel genetic elements.
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11
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The Role of LIN28- let-7-ARID3B Pathway in Placental Development. Int J Mol Sci 2020; 21:ijms21103637. [PMID: 32455665 PMCID: PMC7279312 DOI: 10.3390/ijms21103637] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Placental disorders are a major cause of pregnancy loss in humans, and 40–60% of embryos are lost between fertilization and birth. Successful embryo implantation and placental development requires rapid proliferation, invasion, and migration of trophoblast cells. In recent years, microRNAs (miRNAs) have emerged as key regulators of molecular pathways involved in trophoblast function. A miRNA binds its target mRNA in the 3ʹ-untranslated region (3ʹ-UTR), causing its degradation or translational repression. Lethal-7 (let-7) miRNAs induce cell differentiation and reduce cell proliferation by targeting proliferation-associated genes. The oncoprotein LIN28 represses the biogenesis of mature let-7 miRNAs. Proliferating cells have high LIN28 and low let-7 miRNAs, whereas differentiating cells have low LIN28 and high let-7 miRNAs. In placenta, low LIN28 and high let-7 miRNAs can lead to reduced proliferation of trophoblast cells, resulting in abnormal placental development. In trophoblast cells, let-7 miRNAs reduce the expression of proliferation factors either directly by binding their mRNA in 3ʹ-UTR or indirectly by targeting the AT-rich interaction domain (ARID)3B complex, a transcription-activating complex comprised of ARID3A, ARID3B, and histone demethylase 4C (KDM4C). In this review, we discuss regulation of trophoblast function by miRNAs, focusing on the role of LIN28-let-7-ARID3B pathway in placental development.
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12
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Trophectoderm-Specific Knockdown of LIN28 Decreases Expression of Genes Necessary for Cell Proliferation and Reduces Elongation of Sheep Conceptus. Int J Mol Sci 2020; 21:ijms21072549. [PMID: 32268593 PMCID: PMC7177537 DOI: 10.3390/ijms21072549] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023] Open
Abstract
LIN28 inhibits let-7 miRNA maturation which prevents cell differentiation and promotes proliferation. We hypothesized that the LIN28-let-7 axis regulates proliferation-associated genes in sheep trophectoderm in vivo. Day 9-hatched sheep blastocysts were incubated with lentiviral particles to deliver shRNA targeting LIN28 specifically to trophectoderm cells. At day 16, conceptus elongation was significantly reduced in LIN28A and LIN28B knockdowns. Let-7 miRNAs were significantly increased and IGF2BP1-3, HMGA1, ARID3B, and c-MYC were decreased in trophectoderm from knockdown conceptuses. Ovine trophoblast (OTR) cells derived from day 16 trophectoderm are a useful tool for in vitro experiments. Surprisingly, LIN28 was significantly reduced and let-7 miRNAs increased after only a few passages of OTR cells, suggesting these passaged cells represent a more differentiated phenotype. To create an OTR cell line more similar to day 16 trophectoderm we overexpressed LIN28A and LIN28B, which significantly decreased let-7 miRNAs and increased IGF2BP1-3, HMGA1, ARID3B, and c-MYC compared to control. This is the first study showing the role of the LIN28-let-7 axis in trophoblast proliferation and conceptus elongation in vivo. These results suggest that reduced LIN28 during early placental development can lead to reduced trophoblast proliferation and sheep conceptus elongation at a critical period for successful establishment of pregnancy.
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13
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ARID3A and ARID3B induce stem promoting pathways in ovarian cancer cells. Gene 2020; 738:144458. [PMID: 32061921 DOI: 10.1016/j.gene.2020.144458] [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] [Received: 08/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/14/2022]
Abstract
ARID3A and ARID3B are paralogs from the AT-Rich interactive Domain (ARID) family. ARID3A and ARID3B associate to regulate genes in B-cells and cancer. We were the first to demonstrate that ARID3B regulates stem cell genes and promotes the cancer stem cell phenotype. Importantly, different knockout phenotypes in mice and distinct patterns of expression in adult animals suggests that ARID3A and ARID3B may have unique functions. In addition, high levels of ARID3B but not ARID3A induce cell death. Our goal was to express ARID3A, ARID3B, or both genes at a moderate level (as can be observed in cancer) and then identify ARID3 regulated genes. We transduced ovarian cancer cells with ARID3A-GFP, ARID3B-RFP, or both. RNA-sequencing was conducted. ARID3A and ARID3B regulated nearly identical sets of genes. Few genes (<5%) were uniquely regulated by ARID3A or ARID3B. ARID3A/B induced genes involved in cancer and stem cell processes including: Twist, MYCN, MMP2, GLI2, TIMP3, and WNT5B. We found that ARID3A and ARID3B also induced expression of each other, providing evidence of the cooperativity. While ARID3A and ARID3B likely have unique functions in distinct contexts, they are largely capable of regulating the same stem cell genes in cancer cells. This study provides a comprehensive list of genes and pathways regulated by ARID3A and ARID3B in ovarian cancer cells.
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14
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Yao C, Zhang W, Shuai L. The first cell fate decision in pre-implantation mouse embryos. CELL REGENERATION 2019; 8:51-57. [PMID: 31844518 PMCID: PMC6895705 DOI: 10.1016/j.cr.2019.10.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 10/27/2022]
Abstract
Fertilization happens when sperm and oocytes meet, which is a complicated process involving many important types of biological activation. Beginning in the 2-cell stage, an important event referred to as zygotic genome activation (ZGA) occurs, which governs the subsequent development of the embryo. In ZGA, multiple epigenetic modifications are involved and critical for pre-implantation development. These changes occur after ZGA, resulting in blastomeres segregate into two different lineages. Some blastomeres develop into the inner cell mass (ICM), and others develop into the trophectoderm (TE), which is considered the first cell fate decision. How this process is initiated and the exact molecular mechanisms involved are fascinating questions that remain to be answered. In this review, we introduce some possible developmental models of the first cell fate decision and discuss the signalling pathways and transcriptional networks regulating this process.
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Affiliation(s)
- Chunmeng Yao
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Wenhao Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China.,State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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15
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Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells. Nat Commun 2019; 10:4749. [PMID: 31628347 PMCID: PMC6802173 DOI: 10.1038/s41467-019-12720-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/26/2019] [Indexed: 02/07/2023] Open
Abstract
Trophectoderm (TE) lineage development is pivotal for proper implantation, placentation, and healthy pregnancy. However, only a few TE-specific transcription factors (TFs) have been systematically characterized, hindering our understanding of the process. To elucidate regulatory mechanisms underlying TE development, here we map super-enhancers (SEs) in trophoblast stem cells (TSCs) as a model. We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated. Mapping targets of 27 SE-predicted TFs reveals a highly intertwined transcriptional regulatory circuitry. Intriguingly, SE-predicted TFs show 4 distinct expression patterns with dynamic alterations of their targets during TSC differentiation. Furthermore, depletion of a subset of TFs results in dysregulation of the markers for specialized cell types in placenta, suggesting a role during TE differentiation. Collectively, we characterize an expanded TE-specific regulatory network, providing a framework for understanding TE lineage development and placentation. Trophectoderm lineage development is essential for implantation, placentation, and healthy pregnancy. Here the authors map super-enhancers (SEs) in trophoblast stem cells and find both TE-specific master regulators and 150 previous uncharacterised transcription factors that are SE-associated, providing insight into trophectoderm-specific regulatory networks.
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16
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Abstract
Systemic lupus erythematosus (SLE) is a devastating and heterogeneous autoimmune disease that affects multiple organs, and for which the underlying causes are unknown. The majority of SLE patients produce autoantibodies, have increased levels of type-I inflammatory cytokines, and can develop glomerulonephritis. Recent studies indicate an unexpected but strong association between increased disease activity in SLE patients and the expression of the DNA-binding protein ARID3a (A + T rich interaction domain protein 3a) in a number of peripheral blood cell types. ARID3a expression was first associated with autoantibody production in B cells; however, more recent findings also indicate associations with expression of the inflammatory cytokine interferon alpha in SLE plasmacytoid dendritic cells and low-density neutrophils. In addition, ARID3a is expressed in hematopoietic stem cells and some adult kidney progenitor cells. SLE cells expressing enhanced ARID3a levels show differential gene expression patterns compared with homologous healthy control cells, identifying new pathways potentially regulated by ARID3a. The associations of ARID3a expression with increased disease severity in SLE, suggest that it, or its downstream targets, may provide new therapeutic targets for SLE.
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17
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Ali A, Anthony RV, Bouma GJ, Winger QA. LIN28- let-7 axis regulates genes in immortalized human trophoblast cells by targeting the ARID3B-complex. FASEB J 2019; 33:12348-12363. [PMID: 31415216 DOI: 10.1096/fj.201900718rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Abnormal placental development is one of the main etiological factors for intrauterine growth restriction (IUGR). Here, we show that LIN28A and LIN28B are significantly lower and lethal-7 (let-7) microRNAs (miRNAs) significantly higher in term human IUGR vs. normal placentas. We hypothesize that let-7 miRNAs regulate genes with known importance for human placental development [high-mobility group AT-hook 1 (HMGA1), transcriptional regulator Myc-like (c-myc), vascular endothelial growth factor A (VEGF-A), and Wnt family member 1 (WNT1)] by targeting the AT-rich interacting domain (ARID)-3B complex. ACH-3P cells with LIN28A and LIN28B knockout (DKOs) significantly increased let-7 miRNAs, leading to significantly decreased ARID3A, ARID3B, and lysine demethylase 4C (KDM4C). Similarly, Sw.71 cells overexpressing LIN28A and LIN28B (DKIs) significantly decreased let-7 miRNAs, leading to significantly increased ARID3A, ARID3B, and KDM4C. In ACH-3P cells, ARID3A, ARID3B, and KDM4C make a triprotein complex [triprotein complex comprising ARID3A, ARID3B, and KDM4C (ARID3B-complex)] that binds the promoter regions of HMGA1, c-MYC, VEGF-A, and WNT1. ARID3B knockout in ACH-3P cells disrupted the ARID3B-complex, leading to a significant decrease in HMGA1, c-MYC, VEGF-A, and WNT1. DKOs had a significant reduction, whereas DKIs had a significant increase in HMGA1, c-MYC, VEGF-A, and WNT1, potentially due to regulation by the ARID3B-complex. This is the first study showing regulation of let-7 targets in immortalized human trophoblast cells by the ARID3B-complex.-Ali, A., Anthony, R. V., Bouma, G. J., Winger, Q. A. LIN28-let-7 axis regulates genes in immortalized human trophoblast cells by targeting the ARID3B-complex.
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Affiliation(s)
- Asghar Ali
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Russell V Anthony
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Gerrit J Bouma
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Quinton A Winger
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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18
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Xu Y, Luo X, Fang Z, Zheng X, Zeng Y, Zhu C, Gu J, Tang F, Hu Y, Hu G, Jin Y, Li H. Transcription coactivator Cited1 acts as an inducer of trophoblast-like state from mouse embryonic stem cells through the activation of BMP signaling. Cell Death Dis 2018; 9:924. [PMID: 30206204 PMCID: PMC6134011 DOI: 10.1038/s41419-018-0991-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/16/2018] [Accepted: 08/01/2018] [Indexed: 12/31/2022]
Abstract
Trophoblast lineages, precursors of the placenta, are essential for post-implantation embryo survival. However, the regulatory network of trophoblast development remains incompletely understood. Here, we report that Cited1, a transcription coactivator, is a robust inducer for trophoblast-like state from mouse embryonic stem cells (ESCs). Depletion of Cited1 in ESCs compromises the trophoblast lineage specification induced by BMP signaling. In contrast, overexpression of Cited1 in ESCs induces a trophoblast-like state with elevated expression of trophoblast marker genes in vitro and generation of trophoblastic tumors in vivo. Furthermore, global transcriptome profile analysis indicates that ectopic Cited1 activates a trophoblast-like transcriptional program in ESCs. Mechanistically, Cited1 interacts with Bmpr2 and Smad4 to activate the Cited1–Bmpr2–Smad1/5/8 axis in the cytoplasm and Cited1–Smad4–p300 complexes in the nucleus, respectively. Collectively, our results show that Cited1 plays an important role in regulating trophoblast lineage specification through activating the BMP signaling pathway.
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Affiliation(s)
- Yanli Xu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Xinlong Luo
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China.,KU Leuven Department of Development and Regeneration, Stem Cell Institute Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Zhuoqing Fang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200032, Shanghai, China
| | - Xiaofeng Zheng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Yanwu Zeng
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Chaonan Zhu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Junjie Gu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Fan Tang
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Yanqin Hu
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA
| | - Ying Jin
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China. .,CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, CAS Center for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, 200032, Shanghai, China.
| | - Hui Li
- Basic Clinical Research Center, Renji Hospital, Department of Histology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Shanghai JiaoTong University School of Medicine, 225 South Chongqing Road, 200025, Shanghai, China.
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19
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Soncin F, Khater M, To C, Pizzo D, Farah O, Wakeland A, Arul Nambi Rajan K, Nelson KK, Chang CW, Moretto-Zita M, Natale DR, Laurent LC, Parast MM. Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development. Development 2018; 145:dev.156273. [PMID: 29361559 DOI: 10.1242/dev.156273] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 01/09/2018] [Indexed: 01/08/2023]
Abstract
An increasing body of evidence points to significant spatio-temporal differences in early placental development between mouse and human, but a detailed comparison of placentae in these two species is missing. We set out to compare placentae from both species across gestation, with a focus on trophoblast progenitor markers. We found that CDX2 and ELF5, but not EOMES, are expressed in early post-implantation trophoblast subpopulations in both species. Genome-wide expression profiling of mouse and human placentae revealed clusters of genes with distinct co-expression patterns across gestation. Overall, there was a closer fit between patterns observed in the placentae when the inter-species comparison was restricted to human placentae through gestational week 16 (thus, excluding full-term samples), suggesting that the developmental timeline in mouse runs parallel to the first half of human placental development. In addition, we identified VGLL1 as a human-specific marker of proliferative cytotrophoblast, where it is co-expressed with the transcription factor TEAD4. As TEAD4 is involved in trophectoderm specification in the mouse, we posit a regulatory role for VGLL1 in early events during human placental development.
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Affiliation(s)
- Francesca Soncin
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Marwa Khater
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Cuong To
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Donald Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Omar Farah
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Anna Wakeland
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Kanaga Arul Nambi Rajan
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Katharine K Nelson
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Ching-Wen Chang
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Matteo Moretto-Zita
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - David R Natale
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Louise C Laurent
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA 92093, USA .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
| | - Mana M Parast
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA .,Sanford Consortium for Regenerative Medicine, La Jolla, CA, 92037, USA
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20
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Lee BK, Uprety N, Jang YJ, Tucker SK, Rhee C, LeBlanc L, Beck S, Kim J. Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells. Stem Cell Res 2017; 26:95-102. [PMID: 29272857 PMCID: PMC5899959 DOI: 10.1016/j.scr.2017.12.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/05/2017] [Accepted: 12/10/2017] [Indexed: 11/30/2022] Open
Abstract
During early development in placental mammals, proper trophoblast lineage development is essential for implantation and placentation. Defects in this lineage can cause early pregnancy failures and other pregnancy disorders. However, transcription factors controlling trophoblast development remain poorly understood. Here, we utilize Fosl1, previously implicated in trophoblast giant cell development as a member of the AP-1 complex, to trans-differentiate embryonic stem (ES) cells to trophoblast lineage-like cells. We first show that the ectopic expression of Fosl1 is sufficient to induce trophoblast-specific gene expression programs in ES cells. Surprisingly, we find that this transcriptional reprogramming occurs independently of changes in levels of ES cell core factors during the cell fate change. This suggests that Fosl1 acts in a novel way to orchestrate the ES to trophoblast cell fate conversion compared to previously known reprogramming factors. Mapping of Fosl1 targets reveals that Fosl1 directly activates TE lineage-specific genes as a pioneer factor. Our work suggests Fosl1 may be used to reprogram ES cells into differentiated cell types in trophoblast lineage, which not only enhances our knowledge of global trophoblast gene regulation but also may provide a future therapeutic tool for generating induced trophoblast cells from patient-derived pluripotent stem cells.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Nadima Uprety
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Yu Jin Jang
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Scott K Tucker
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Catherine Rhee
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Lucy LeBlanc
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Samuel Beck
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States; Kathryn W. Davis Center for Regenerative Biology and Medicine, MDI Biological Laboratory, Salisbury Cove, ME 04672, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, United States.
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21
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Rhee C, Lee BK, Beck S, LeBlanc L, Tucker HO, Kim J. Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells. Nucleic Acids Res 2017; 45:10103-10114. [PMID: 28973471 PMCID: PMC5737334 DOI: 10.1093/nar/gkx692] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 08/02/2017] [Indexed: 11/16/2022] Open
Abstract
Direct reprogramming can be achieved by forced expression of master transcription factors. Yet how such factors mediate repression of initial cell-type-specific genes while activating target cell-type-specific genes is unclear. Through embryonic stem (ES) to trophoblast stem (TS)-like cell reprogramming by introducing individual TS cell-specific ‘CAG’ factors (Cdx2, Arid3a and Gata3), we interrogate their chromosomal target occupancies, modulation of global transcription and chromatin accessibility at the initial stage of reprogramming. From the studies, we uncover a sequential, two-step mechanism of cellular reprogramming in which repression of pre-existing ES cell-associated gene expression program is followed by activation of TS cell-specific genes by CAG factors. Therefore, we reveal that CAG factors function as both decommission and pioneer factors during ES to TS-like cell fate conversion.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bum-Kyu Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Samuel Beck
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Lucy LeBlanc
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
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22
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Rhee C, Kim J, Tucker HO. Transcriptional Regulation of the First Cell Fate Decision. JOURNAL OF DEVELOPMENTAL BIOLOGY & REGENERATIVE MEDICINE 2017; 1:102. [PMID: 29658952 PMCID: PMC5897107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding how the first cell fate decision has chosen is a fascinating biological question that was received consider attention over the last decade. Numerous transcription factors are required, and many have been shown to have essential roles in this process. Here we reexamine the function that transcription factors play primarily in the mouse-the model system most thoroughly examined in this process. We address how the first embryonic lineage is established and maintained, with a particular emphasis on subsequent trophectoderm development and the role of the recently established Arid3a transcription factor in this process. In addition, we review relevant aspects of embryonic stem cell reprogramming into trophoblast stem cells -the equivalent of the epiblast (inner cell mass) and the establishment of induced trophoblast stem cells-the in vitro equivalent of the trophectoderm.
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Affiliation(s)
- Catherine Rhee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge MA 02138, USA
| | - Jonghwan Kim
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Haley O. Tucker
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA
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23
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Khedgikar V, Abbruzzese G, Mathavan K, Szydlo H, Cousin H, Alfandari D. Dual control of pcdh8l/PCNS expression and function in Xenopus laevis neural crest cells by adam13/33 via the transcription factors tfap2α and arid3a. eLife 2017; 6:26898. [PMID: 28829038 PMCID: PMC5601995 DOI: 10.7554/elife.26898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/21/2017] [Indexed: 01/11/2023] Open
Abstract
Adam13/33 is a cell surface metalloprotease critical for cranial neural crest (CNC) cell migration. It can cleave multiple substrates including itself, fibronectin, ephrinB, cadherin-11, pcdh8 and pcdh8l (this work). Cleavage of cadherin-11 produces an extracellular fragment that promotes CNC migration. In addition, the adam13 cytoplasmic domain is cleaved by gamma secretase, translocates into the nucleus and regulates multiple genes. Here, we show that adam13 interacts with the arid3a/dril1/Bright transcription factor. This interaction promotes a proteolytic cleavage of arid3a and its translocation to the nucleus where it regulates another transcription factor: tfap2α. Tfap2α in turn activates multiple genes including the protocadherin pcdh8l (PCNS). The proteolytic activity of adam13 is critical for the release of arid3a from the plasma membrane while the cytoplasmic domain appears critical for the cleavage of arid3a. In addition to this transcriptional control of pcdh8l, adam13 cleaves pcdh8l generating an extracellular fragment that also regulates cell migration.
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Affiliation(s)
- Vikram Khedgikar
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Genevieve Abbruzzese
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Ketan Mathavan
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States.,Molecular and Cellular Biology graduate program, University of Massachusetts, Amherst, United States
| | - Hannah Szydlo
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Helene Cousin
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States
| | - Dominique Alfandari
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, United States.,Molecular and Cellular Biology graduate program, University of Massachusetts, Amherst, United States
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24
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Popowski M, Lee BK, Rhee C, Iyer VR, Tucker HO. Arid3a regulates mesoderm differentiation in mouse embryonic stem cells. JOURNAL OF STEM CELL THERAPY AND TRANSPLANTATION 2017; 1:52-62. [PMID: 31080945 PMCID: PMC6510499 DOI: 10.29328/journal.jsctt.1001005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Research into regulation of the differentiation of stem cells is critical to understanding early developmental decisions and later development growth. The transcription factor ARID3A previously was shown to be critical for trophectoderm and hematopoetic development. Expression of ARID3A increases during embryonic differentiation, but the underlying reason remained unclear. Here we show that Arid3a null embryonic stem (ES) cells maintain an undifferentiated gene expression pattern and form teratomas in immune-compromised mice. However, Arid3a null ES cells differentiated in vitro into embryoid bodies (EBs) significantly faster than control ES cells, and the majority forming large cystic embryoid EBs. Analysis of gene expression during this transition indicated that Arid3a nulls differentiated spontaneously into mesoderm and neuroectoderm lineages. While young ARID3A-deficient mice showed no gross tissue morphology, proliferative and structural abnormalities were observed in the kidneys of older null mice. Together these data suggest that ARID3A is not only required hematopoiesis, but is critical for early mesoderm differentiation.
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Affiliation(s)
- Melissa Popowski
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Bum-kyu Lee
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Cathy Rhee
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vishwanath R Iyer
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Haley O Tucker
- Department of Molecular Biosciences, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
- Address for Correspondence: Haley O Tucker, Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA.
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