1
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Wang J, Zhou X, Han T, Zhang H. Epigenetic signatures of trophoblast lineage and their biological functions. Cells Dev 2024; 179:203934. [PMID: 38942294 DOI: 10.1016/j.cdev.2024.203934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
Trophoblasts play a crucial role in embryo implantation and in interacting with the maternal uterus. The trophoblast lineage develops into a substantial part of the placenta, a temporary extra-embryonic organ, capable of undergoing distinctive epigenetic events during development. The critical role of trophoblast-specific epigenetic signatures in regulating placental development has become known, significantly advancing our understanding of trophoblast identity and lineage development. Scientific efforts are revealing how trophoblast-specific epigenetic signatures mediate stage-specific gene regulatory programming during the development of the trophoblast lineage. These epigenetic signatures have a significant impact on blastocyst formation, placental development, as well as the growth and survival of embryos and fetuses. In evolution, DNA hypomethylation in the trophoblast lineage is conserved, and there is a significant disparity in the control of epigenetic dynamics and the landscape of genomic imprinting. Scientists have used murine and human multipotent trophoblast cells as in vitro models to recapitulate the essential epigenetic processes of placental development. Here, we review the epigenetic signatures of the trophoblast lineage and their biological functions to enhance our understanding of placental evolution, development, and function.
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Affiliation(s)
- Jianqi Wang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaobo Zhou
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Reproductive Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Tingli Han
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China; The Center for Reproductive Medicine, Obstetrics and Gynecology Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Hua Zhang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China.
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2
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Ma H, Qu J, Pang Z, Luo J, Yan M, Xu W, Zhuang H, Liu L, Qu Q. Super-enhancer omics in stem cell. Mol Cancer 2024; 23:153. [PMID: 39090713 PMCID: PMC11293198 DOI: 10.1186/s12943-024-02066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
The hallmarks of stem cells, such as proliferation, self-renewal, development, differentiation, and regeneration, are critical to maintain stem cell identity which is sustained by genetic and epigenetic factors. Super-enhancers (SEs), which consist of clusters of active enhancers, play a central role in maintaining stemness hallmarks by specifically transcriptional model. The SE-navigated transcriptional complex, including SEs, non-coding RNAs, master transcriptional factors, Mediators and other co-activators, forms phase-separated condensates, which offers a toggle for directing diverse stem cell fate. With the burgeoning technologies of multiple-omics applied to examine different aspects of SE, we firstly raise the concept of "super-enhancer omics", inextricably linking to Pan-omics. In the review, we discuss the spatiotemporal organization and concepts of SEs, and describe links between SE-navigated transcriptional complex and stem cell features, such as stem cell identity, self-renewal, pluripotency, differentiation and development. We also elucidate the mechanism of stemness and oncogenic SEs modulating cancer stem cells via genomic and epigenetic alterations hijack in cancer stem cell. Additionally, we discuss the potential of targeting components of the SE complex using small molecule compounds, genome editing, and antisense oligonucleotides to treat SE-associated organ dysfunction and diseases, including cancer. This review also provides insights into the future of stem cell research through the paradigm of SEs.
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Affiliation(s)
- Hongying Ma
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
- Hunan key laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha, 410219, China
| | - Zicheng Pang
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Jian Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Min Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Weixin Xu
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Haihui Zhuang
- Department of Pharmacy, the Second Xiangya Hospital, Institute of Clinical Pharmacy, Central South University, Changsha, 410011, People's Republic of China
| | - Linxin Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, No.87 Xiangya Road, Changsha, 410008, People's Republic of China.
- Institute for Rational and Safe Medication Practices, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China.
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.
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3
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Varberg KM, Moreno-Irusta A, Novoa A, Musser B, Varberg JM, Goering JP, Saadi I, Iqbal K, Okae H, Arima T, Williams J, Pisarska MD, Soares MJ. Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2022.12.07.22283218. [PMID: 39108523 PMCID: PMC11302605 DOI: 10.1101/2022.12.07.22283218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Human trophoblast stem (TS) cells are an informative in vitro model for the generation and testing of biologically meaningful hypotheses. The goal of this project was to derive patient-specific TS cell lines from clinically available chorionic villus sampling biopsies. Cell outgrowths were captured from human chorionic villus tissue specimens cultured in modified human TS cell medium. Cell colonies emerged early during the culture and cell lines were established and passaged for several generations. Karyotypes of the newly established chorionic villus-derived trophoblast stem (TS CV ) cell lines were determined and compared to initial genetic diagnoses from freshly isolated chorionic villi. Phenotypes of TSCV cells in the stem state and following differentiation were compared to cytotrophoblast-derived TS (TS CT ) cells. TSCV and TSCT cells uniformly exhibited similarities in the stem state and following differentiation into syncytiotrophoblast and extravillous trophoblast cells. Chorionic villus tissue specimens provide a valuable source for TS cell derivation. They expand the genetic diversity of available TS cells and are associated with defined clinical outcomes. TSCV cell lines provide a new set of experimental tools for investigating trophoblast cell lineage development.
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Affiliation(s)
- Kaela M. Varberg
- 1nstitute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Ayelen Moreno-Irusta
- 1nstitute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Allynson Novoa
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Brynne Musser
- 1nstitute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | | | - Jeremy P. Goering
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Irfan Saadi
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Khursheed Iqbal
- 1nstitute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
| | - Hiroaki Okae
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - John Williams
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA
- David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Margareta D. Pisarska
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA
- David Geffen School of Medicine, University of California, Los Angeles, CA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Michael J. Soares
- 1nstitute for Reproductive and Developmental Sciences, Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160
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4
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Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024; 31:1072-1090.e8. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
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Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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5
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Gao R, Yang G, Wang M, Xiao J, Yi S, Huang Y, Guo Z, Kang Y, Fu Q, Wang M, Xu B, Shen S, Zhu Q, Liu M, Wang L, Cui X, Yi S, Kou X, Zhao Y, Gu L, Wang H, Gao S, Jiang C, Chen J. Defining a TFAP2C-centered transcription factor network during murine peri-implantation. Dev Cell 2024; 59:1146-1158.e6. [PMID: 38574734 DOI: 10.1016/j.devcel.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 12/07/2023] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
Transcription factors (TFs) play important roles in early embryonic development, but factors regulating TF action, relationships in signaling cascade, genome-wide localizations, and impacts on cell fate transitions during this process have not been clearly elucidated. In this study, we used uliCUT&RUN-seq to delineate a TFAP2C-centered regulatory network, showing that it involves promoter-enhancer interactions and regulates TEAD4 and KLF5 function to mediate cell polarization. Notably, we found that maternal retinoic acid metabolism regulates TFAP2C expression and function by inducing the active demethylation of SINEs, indicating that the RARG-TFAP2C-TEAD4/KLF5 axis connects the maternal-to-zygotic transition to polarization. Moreover, we found that both genomic imprinting and SNP-transferred genetic information can influence TF positioning to regulate parental gene expressions in a sophisticated manner. In summary, we propose a ternary model of TF regulation in murine embryonic development with TFAP2C as the core element and metabolic, epigenetic, and genetic information as nodes connecting the pathways.
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Affiliation(s)
- Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Guang Yang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Jing Xiao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanxin Huang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yunzhe Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianzheng Fu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Ben Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shijun Shen
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Qianshu Zhu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Meng Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liping Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanshan Yi
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Liang Gu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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6
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Yu H, Zhao J, Shen Y, Qiao L, Liu Y, Xie G, Chang S, Ge T, Li N, Chen M, Li H, Zhang J, Wang X. The dynamic landscape of enhancer-derived RNA during mouse early embryo development. Cell Rep 2024; 43:114077. [PMID: 38592974 DOI: 10.1016/j.celrep.2024.114077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/10/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024] Open
Abstract
Enhancer-derived RNAs (eRNAs) play critical roles in diverse biological processes by facilitating their target gene expression. However, the abundance and function of eRNAs in early embryos are not clear. Here, we present a comprehensive eRNA atlas by systematically integrating publicly available datasets of mouse early embryos. We characterize the transcriptional and regulatory network of eRNAs and show that different embryo developmental stages have distinct eRNA expression and regulatory profiles. Paternal eRNAs are activated asymmetrically during zygotic genome activation (ZGA). Moreover, we identify an eRNA, MZGAe1, which plays an important function in regulating mouse ZGA and early embryo development. MZGAe1 knockdown leads to a developmental block from 2-cell embryo to blastocyst. We create an online data portal, M2ED2, to query and visualize eRNA expression and regulation. Our study thus provides a systematic landscape of eRNA and reveals the important role of eRNAs in regulating mouse early embryo development.
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Affiliation(s)
- Hua Yu
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China; School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China; Institute of Life Sciences, Nanchang University, Nanchang 330031, China.
| | - Jing Zhao
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Yuxuan Shen
- Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lu Qiao
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Yuheng Liu
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Guanglei Xie
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Shuhui Chang
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Tingying Ge
- School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Nan Li
- HPC Center, Westlake University, Hangzhou 310024, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55904, USA
| | - Jin Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; Center of Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Xi Wang
- Westlake Genomics and Bioinformatics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China; Westlake Institute for Advanced Study, Hangzhou 310024, China.
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7
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Lavaud M, Tesfaye R, Lassous L, Brounais B, Baud'huin M, Verrecchia F, Lamoureux F, Georges S, Ory B. Super-enhancers: drivers of cells' identities and cells' debacles. Epigenomics 2024; 16:681-700. [PMID: 38587919 PMCID: PMC11160454 DOI: 10.2217/epi-2023-0409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/18/2024] [Indexed: 04/10/2024] Open
Abstract
Precise spatiotemporal regulations of gene expression are essential for determining cells' fates and functions. Enhancers are cis-acting DNA elements that act as periodic transcriptional thrusters and their activities are cell type specific. Clusters of enhancers, called super-enhancers, are more densely occupied by transcriptional activators than enhancers, driving stronger expression of their target genes, which have prominent roles in establishing and maintaining cellular identities. Here we review the current knowledge on the composition and structure of super-enhancers to understand how they robustly stimulate the expression of cellular identity genes. We also review their involvement in the development of various cell types and both noncancerous and cancerous disorders, implying the therapeutic interest of targeting them to fight against various diseases.
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Affiliation(s)
- Mélanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Robel Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Léa Lassous
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Bénédicte Brounais
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University & Angers University, Medical School, Nantes, 44035, France
- Cancéropôle Grand-Ouest, Réseau Épigénétique, Medical School, Nantes, 44035, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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8
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Lee BK, Salamah J, Cheeran E, Adu-Gyamfi EA. Dynamic and distinct histone modifications facilitate human trophoblast lineage differentiation. Sci Rep 2024; 14:4505. [PMID: 38402275 PMCID: PMC10894295 DOI: 10.1038/s41598-024-55189-0] [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: 12/08/2023] [Accepted: 02/21/2024] [Indexed: 02/26/2024] Open
Abstract
The placenta serves as an essential organ for fetal growth throughout pregnancy. Histone modification is a crucial regulatory mechanism involved in numerous biological processes and development. Nevertheless, there remains a significant gap in our understanding regarding the epigenetic regulations that influence trophoblast lineage differentiation, a fundamental aspect of placental development. Here, through comprehensive mapping of H3K4me3, H3K27me3, H3K9me3, and H3K27ac loci during the differentiation of trophoblast stem cells (TSCs) into syncytiotrophoblasts (STs) and extravillous trophoblasts (EVTs), we reveal dynamic reconfiguration in H3K4me3 and H3K27ac patterns that establish an epigenetic landscape conducive to proper trophoblast lineage differentiation. We observe that broad H3K4me3 domains are associated with trophoblast lineage-specific gene expression. Unlike embryonic stem cells, TSCs lack robust bivalent domains. Notably, the repression of ST- and EVT-active genes in TSCs is primarily attributed to the weak H3K4me3 signal rather than bivalent domains. We also unveil the inactivation of TSC enhancers precedes the activation of ST enhancers during ST formation. Our results provide a comprehensive global map of diverse histone modifications, elucidating the dynamic histone modifications during trophoblast lineage differentiation.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA.
| | - Joudi Salamah
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Elisha Cheeran
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
| | - Enoch Appiah Adu-Gyamfi
- Department of Biomedical Sciences, Cancer Research Center, University at Albany, State University of New York, Rensselaer, NY, 12144, USA
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9
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Choi TY, Jeon H, Jeong S, Kim EJ, Kim J, Jeong YH, Kang B, Choi M, Koo JW. Distinct prefrontal projection activity and transcriptional state conversely orchestrate social competition and hierarchy. Neuron 2024; 112:611-627.e8. [PMID: 38086372 DOI: 10.1016/j.neuron.2023.11.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 09/20/2023] [Accepted: 11/13/2023] [Indexed: 02/24/2024]
Abstract
Social animals compete for limited resources, resulting in a social hierarchy. Although different neuronal subpopulations in the medial prefrontal cortex (mPFC), which has been mechanistically implicated in social dominance behavior, encode distinct social competition behaviors, their identities and associated molecular underpinnings have not yet been identified. In this study, we found that mPFC neurons projecting to the nucleus accumbens (mPFC-NAc) encode social winning behavior, whereas mPFC neurons projecting to the ventral tegmental area (mPFC-VTA) encode social losing behavior. High-throughput single-cell transcriptomic analysis and projection-specific genetic manipulation revealed that the expression level of POU domain, class 3, transcription factor 1 (Pou3f1) in mPFC-VTA neurons controls social hierarchy. Optogenetic activation of mPFC-VTA neurons increases Pou3f1 expression and lowers social rank. Together, these data demonstrate that discrete activity and gene expression in separate mPFC projections oppositely orchestrate social competition and hierarchy.
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Affiliation(s)
- Tae-Yong Choi
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Hyoungseok Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sejin Jeong
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Republic of Korea
| | - Eum Ji Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Jeongseop Kim
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea
| | - Yun Ha Jeong
- Neurodegenerative Disease Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Byungsoo Kang
- Sysoft R&D Center, Daegu 41065, Republic of Korea; Neurovascular Unit Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea
| | - Murim Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
| | - Ja Wook Koo
- Emotion, Cognition and Behavior Research Group, Korea Brain Research Institute, Daegu 41062, Republic of Korea; Department of Brain Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 41988, Republic of Korea.
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10
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Dou C, Wu L, Zhang J, He H, Xu T, Yu Z, Su P, Zhang X, Wang J, Miao YL, Zhou J. The transcriptional activator Klf5 recruits p300-mediated H3K27ac for maintaining trophoblast stem cell pluripotency. J Mol Cell Biol 2024; 15:mjad045. [PMID: 37533201 PMCID: PMC10768793 DOI: 10.1093/jmcb/mjad045] [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: 10/02/2022] [Revised: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 08/04/2023] Open
Abstract
The effective proliferation and differentiation of trophoblast stem cells (TSCs) is indispensable for the development of the placenta, which is the key to maintaining normal fetal growth during pregnancy. Kruppel-like factor 5 (Klf5) is implicated in the activation of pluripotency gene expression in embryonic stem cells (ESCs), yet its function in TSCs is poorly understood. Here, we showed that Klf5 knockdown resulted in the downregulation of core TSC-specific genes, consequently causing rapid differentiation of TSCs. Consistently, Klf5-depleted embryos lost the ability to establish TSCs in vitro. At the molecular level, Klf5 preferentially occupied the proximal promoter regions and maintained an open chromatin architecture of key TSC-specific genes. Deprivation of Klf5 impaired the enrichment of p300, a major histone acetyl transferase of H3 lysine 27 acetylation (H3K27ac), and further reduced the occupancy of H3K27ac at promoter regions, leading to decreased transcriptional activity of TSC pluripotency genes. Thus, our findings highlight a novel mechanism of Klf5 in regulating the self-renewal and differentiation of TSCs and provide a reference for understanding placental development and improving pregnancy rates.
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Affiliation(s)
- Chengli Dou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Hainan He
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Tian Xu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Zhisheng Yu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Peng Su
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
| | - Junling Wang
- Department of Reproductive Medicine, Huangshi Central Hospital, Affiliated Hospital of Hubei Polytechnic, Edong Healthcare Group, Huangshi 435000, China
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jilong Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction (Huazhong Agricultural University), Ministry of Education, Wuhan 430070, China
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11
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat Struct Mol Biol 2024; 31:125-140. [PMID: 38053013 PMCID: PMC10897904 DOI: 10.1038/s41594-023-01130-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/18/2023] [Indexed: 12/07/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- 3D Chromatin Conformation and RNA Genomics Laboratory, Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ly-Sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, USA.
- Department of Medicine, New York University Langone Health, New York, NY, USA.
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA.
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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12
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Lin Q, Cao J, Yu J, Zhu Y, Shen Y, Wang S, Wang Y, Liu Z, Chang Y. YAP-mediated trophoblast dysfunction: the common pathway underlying pregnancy complications. Cell Commun Signal 2023; 21:353. [PMID: 38098027 PMCID: PMC10722737 DOI: 10.1186/s12964-023-01371-2] [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: 07/30/2023] [Accepted: 10/29/2023] [Indexed: 12/17/2023] Open
Abstract
Yes-associated protein (YAP) is a pivotal regulator in cellular proliferation, survival, differentiation, and migration, with significant roles in embryonic development, tissue repair, and tumorigenesis. At the maternal-fetal interface, emerging evidence underscores the importance of precisely regulated YAP activity in ensuring successful pregnancy initiation and progression. However, despite the established association between YAP dysregulation and adverse pregnancy outcomes, insights into the impact of aberrant YAP levels in fetal-derived, particularly trophoblast cells, and the ensuing dysfunction at the maternal-fetal interface remain limited. This review comprehensively examines YAP expression and its regulatory mechanisms in trophoblast cells throughout pregnancy. We emphasize its integral role in placental development and maternal-fetal interactions and delve into the correlations between YAP dysregulation and pregnancy complications. A nuanced understanding of YAP's functions during pregnancy could illuminate intricate molecular mechanisms and pave the way for innovative prevention and treatment strategies for pregnancy complications. Video Abstract.
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Affiliation(s)
- Qimei Lin
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Maternity Hospital, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, 300100, China
| | - Jiasong Cao
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Maternity Hospital, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, 300100, China
| | - Jing Yu
- School of Clinical Medicine, Tianjin Medical University, Tianjin, 300070, China
| | - Yu Zhu
- School of Clinical Medicine, Tianjin Medical University, Tianjin, 300070, China
| | - Yongmei Shen
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Maternity Hospital, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, 300100, China
| | - Shuqi Wang
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Maternity Hospital, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, 300100, China
| | - Yixin Wang
- School of Medicine, Nankai University, Tianjin, 300071, China
| | - Zhen Liu
- Academy of Clinical Medicine, Medical College, Tianjin University, Tianjin, 300072, China
| | - Ying Chang
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Maternity Hospital, Tianjin Central Hospital of Obstetrics and Gynecology, Tianjin, 300100, China.
- Academy of Clinical Medicine, Medical College, Tianjin University, Tianjin, 300072, China.
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13
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Abstract
Enhancers are cis-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,CONTACT Amandine Barral Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania. 3400 Civic Blvd, Philadelphia, Pennsylvania19104, USA
| | - Jérôme Déjardin
- Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, Montpellier, France,Jérôme Déjardin Biology of repetitive sequences, Institute of Human Genetics CNRS-Université de Montpellier UMR 9002, 141 rue de la Cardonille, Montpellier34000, France
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14
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Gao Z, Guo J, Gou B, Gu Z, Jia T, Ma S, Jiang L, Liu W, Zhou L, Gu Q. Microcarriers promote the through interface movement of mouse trophoblast stem cells by regulating stiffness. Bioact Mater 2023; 28:196-205. [PMID: 37250864 PMCID: PMC10220236 DOI: 10.1016/j.bioactmat.2023.05.007] [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] [Received: 01/19/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023] Open
Abstract
Mechanical force is crucial in the whole process of embryonic development. However, the role of trophoblast mechanics during embryo implantation has rarely been studied. In this study, we constructed a model to explore the effect of stiffness changes in mouse trophoblast stem cells (mTSCs) on implantation: microcarrier was prepared by sodium alginate using a droplet microfluidics system, and mTSCs were attached to the microcarrier surface with laminin modifications, called T(micro). Compared with the spheroid, formed by the self-assembly of mTSCs (T(sph)), we could regulate the stiffness of the microcarrier, making the Young's modulus of mTSCs (367.70 ± 79.81 Pa) similar to that of the blastocyst trophoblast ectoderm (432.49 ± 151.90 Pa). Moreover, T(micro) contributes to improve the adhesion rate, expansion area and invasion depth of mTSCs. Further, T(micro) was highly expressed in tissue migration-related genes due to the activation of the Rho-associated coiled-coil containing protein kinase (ROCK) pathway at relatively similar modulus of trophoblast. Overall, our study explores the embryo implantation process with a new perspective, and provides theoretical support for understanding the effect of mechanics on embryo implantation.
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Affiliation(s)
- Zili Gao
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jia Guo
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Bo Gou
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Zhen Gu
- Department of Chemistry and Biological Engineering, University of Science and Technology, Beijing, 100083, PR China
| | - Tan Jia
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Sinan Ma
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- School of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Liyuan Jiang
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- School of Life Sciences, Northeast Agricultural University, Harbin, 150030, PR China
| | - Wenli Liu
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
| | - Lixun Zhou
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
| | - Qi Gu
- State Key Laboratory of Membrane Biology, The State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, PR China
- University of Chinese Academy of Sciences, Beijing, 100049, PR China
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15
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Chen Y, Pan Y, Gao H, Yi Y, Qin S, Ma F, Zhou X, Guan M. Mechanistic insights into super-enhancer-driven genes as prognostic signatures in patients with glioblastoma. J Cancer Res Clin Oncol 2023; 149:12315-12332. [PMID: 37432454 DOI: 10.1007/s00432-023-05121-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/04/2023] [Indexed: 07/12/2023]
Abstract
BACKGROUND Glioblastoma (GBM) is one of the most common malignant brain tumors in adults and is characterized by high aggressiveness and rapid progression, poor treatment, high recurrence rate, and poor prognosis. Although super-enhancer (SE)-driven genes haven been recognized as prognostic markers for several cancers, whether it can be served as effective prognostic markers for patients with GBM has not been evaluated. METHODS We first combined histone modification data with transcriptome data to identify SE-driven genes associated with prognosis in patients with GBM. Second, we developed a SE-driven differentially expressed genes (SEDEGs) risk score prognostic model by univariate Cox analysis, KM survival analysis, multivariate Cox analysis and least absolute shrinkage and selection operator (LASSO) regression. Its reliability in predicting was verified by two external data sets. Third, through mutation analysis, immune infiltration, we explored the molecular mechanisms of prognostic genes. Next, Genomics of Drug Sensitivity in Cancer (GDSC) and the Connectivity Map (cMap) database were employed to assess different sensitivities to chemotherapeutic agents and small-molecule drug candidates between high- and low-risk patients. Finally, SEanalysis database was chosen to identify SE-driven transcription factors (TFs) regulating prognostic markers which will reveal a potential SE-driven transcriptional regulatory network. RESULTS First, we developed a 11-gene risk score prognostic model (NCF2, MTHFS, DUSP6, G6PC3, HOXB2, EN2, DLEU1, LBH, ZEB1-AS1, LINC01265, and AGAP2-AS1) selected from 1,154 SEDEGs, which is not only an independent prognostic factor for patients, but also can effectively predict the survival rate of patients. The model can effectively predict 1-, 2- and 3-year survival of patients and was validated in external Chinese Glioma Genome Atlas (CGGA) and Gene Expression Omnibus (GEO) datasets. Second, the risk score was positively correlated with the infiltration of regulatory T cell, CD4 memory activated T cell, activated NK cell, neutrophil, resting mast cell, M0 macrophage, and memory B cell. Third, we found that high-risk patients showed higher sensitivity than low-risk patients to both 27 chemotherapeutic agents and 4 small-molecule drug candidates which might benefit further precision therapy for GBM patients. Finally, 13 potential SE-driven TFs imply how SE regulates GBM patient's prognosis. CONCLUSION The SEDEG risk model not only helps to elucidate the impact of SEs on the course of GBM, but also provides a bright future for prognosis determination and choice of treatment for GBM patients.
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Affiliation(s)
- Youran Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yi Pan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Hanyu Gao
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Yunmeng Yi
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Shijie Qin
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Fei Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China
| | - Xue Zhou
- School of Chemistry and Biological Engineering, Nanjing Normal University Taizhou College, Taizhou, 225300, China.
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, Jiangsu, China.
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16
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Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape. Nat Commun 2023; 14:4826. [PMID: 37563143 PMCID: PMC10415281 DOI: 10.1038/s41467-023-40424-5] [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: 05/24/2022] [Accepted: 07/27/2023] [Indexed: 08/12/2023] Open
Abstract
The extravillous trophoblast cell lineage is a key feature of placentation and successful pregnancy. Knowledge of transcriptional regulation driving extravillous trophoblast cell development is limited. Here, we map the transcriptome and epigenome landscape as well as chromatin interactions of human trophoblast stem cells and their transition into extravillous trophoblast cells. We show that integrating chromatin accessibility, long-range chromatin interactions, transcriptomic, and transcription factor binding motif enrichment enables identification of transcription factors and regulatory mechanisms critical for extravillous trophoblast cell development. We elucidate functional roles for TFAP2C, SNAI1, and EPAS1 in the regulation of extravillous trophoblast cell development. EPAS1 is identified as an upstream regulator of key extravillous trophoblast cell transcription factors, including ASCL2 and SNAI1 and together with its target genes, is linked to pregnancy loss and birth weight. Collectively, we reveal activation of a dynamic regulatory network and provide a framework for understanding extravillous trophoblast cell specification in trophoblast cell lineage development and human placentation.
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Affiliation(s)
- Kaela M Varberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
| | - Esteban M Dominguez
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Boryana Koseva
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Joseph M Varberg
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Ross P McNally
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Ayelen Moreno-Irusta
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Emily R Wesley
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Warren A Cheung
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Carl Schwendinger-Schreck
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Craig Smail
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
- Department of Trophoblast Research, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Michael Lydic
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Kristin Holoch
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Courtney Marsh
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Michael J Soares
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
| | - Elin Grundberg
- Institute for Reproductive and Developmental Sciences, University of Kansas Medical Center, Kansas City, Kansas, 66160, USA.
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, Kansas City, MO, 64108, USA.
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17
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. Core conserved transcriptional regulatory networks define the invasive trophoblast cell lineage. Development 2023; 150:dev201826. [PMID: 37417811 PMCID: PMC10445752 DOI: 10.1242/dev.201826] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
The invasive trophoblast cell lineages in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model for studying hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus ATAC-seq data from gestation day 15.5 and 19.5 rat uterine-placental interface tissues, and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial and smooth muscle cells, and compared invasive trophoblast chromatin accessibility with extravillous trophoblast cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Center for Perinatal Research, Children's Mercy Research Institute, Children's Mercy, Kansas City, MO 64108, USA
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011, USA
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18
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549714. [PMID: 37577543 PMCID: PMC10422694 DOI: 10.1101/2023.07.19.549714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE). Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements via which transcriptional regulators enact these fates remain understudied. To address this gap, we have characterized, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observed extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although there are distinct groups of genes that are irresponsive to topological changes. In each lineage, a high degree of connectivity or "hubness" positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages, compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a novel predictive model for transcriptional regulation (3D-HiChAT), which outperformed models that use only 1D promoter or proximal variables in predicting levels and cell-type specificity of gene expression. Using 3D-HiChAT, we performed genome-wide in silico perturbations to nominate candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments we validated several novel enhancers that control expression of one or more genes in their respective lineages. Our study comprehensively identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
- 3D Chromatin Conformation and RNA genomics laboratory, Instituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy (current affiliation)
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, 10065, New York, USA
| | - Christopher M. Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Ly-sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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19
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Yu W, Xie Z, Li J, Lin J, Su Z, Che Y, Ye F, Zhang Z, Xu P, Zeng Y, Xu X, Li Z, Feng P, Mi R, Wu Y, Shen H. Super enhancers targeting ZBTB16 in osteogenesis protect against osteoporosis. Bone Res 2023; 11:30. [PMID: 37280207 DOI: 10.1038/s41413-023-00267-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 03/20/2023] [Accepted: 04/18/2023] [Indexed: 06/08/2023] Open
Abstract
As the major cell precursors in osteogenesis, mesenchymal stem cells (MSCs) are indispensable for bone homeostasis and development. However, the primary mechanisms regulating osteogenic differentiation are controversial. Composed of multiple constituent enhancers, super enhancers (SEs) are powerful cis-regulatory elements that identify genes that ensure sequential differentiation. The present study demonstrated that SEs were indispensable for MSC osteogenesis and involved in osteoporosis development. Through integrated analysis, we identified the most common SE-targeted and osteoporosis-related osteogenic gene, ZBTB16. ZBTB16, positively regulated by SEs, promoted MSC osteogenesis but was expressed at lower levels in osteoporosis. Mechanistically, SEs recruited bromodomain containing 4 (BRD4) at the site of ZBTB16, which then bound to RNA polymerase II-associated protein 2 (RPAP2) that transported RNA polymerase II (POL II) into the nucleus. The subsequent synergistic regulation of POL II carboxyterminal domain (CTD) phosphorylation by BRD4 and RPAP2 initiated ZBTB16 transcriptional elongation, which facilitated MSC osteogenesis via the key osteogenic transcription factor SP7. Bone-targeting ZBTB16 overexpression had a therapeutic effect on the decreased bone density and remodeling capacity of Brd4fl/fl Prx1-cre mice and osteoporosis (OP) models. Therefore, our study shows that SEs orchestrate the osteogenesis of MSCs by targeting ZBTB16 expression, which provides an attractive focus and therapeutic target for osteoporosis. Without SEs located on osteogenic genes, BRD4 is not able to bind to osteogenic identity genes due to its closed structure before osteogenesis. During osteogenesis, histones on osteogenic identity genes are acetylated, and OB-gain SEs appear, enabling the binding of BRD4 to the osteogenic identity gene ZBTB16. RPAP2 transports RNA Pol II from the cytoplasm to the nucleus and guides Pol II to target ZBTB16 via recognition of the navigator BRD4 on SEs. After the binding of the RPAP2-Pol II complex to BRD4 on SEs, RPAP2 dephosphorylates Ser5 at the Pol II CTD to terminate the transcriptional pause, and BRD4 phosphorylates Ser2 at the Pol II CTD to initiate transcriptional elongation, which synergistically drives efficient transcription of ZBTB16, ensuring proper osteogenesis. Dysregulation of SE-mediated ZBTB16 expression leads to osteoporosis, and bone-targeting ZBTB16 overexpression is efficient in accelerating bone repair and treating osteoporosis.
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Affiliation(s)
- Wenhui Yu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Zhongyu Xie
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
- Shenzhen Key Laboratory of Ankylosing Spondylitis, Shenzhen, 518003, PR China
| | - Jinteng Li
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Jiajie Lin
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Zepeng Su
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Yunshu Che
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Feng Ye
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, PR China
| | - Zhaoqiang Zhang
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Peitao Xu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Yipeng Zeng
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Xiaojun Xu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Zhikun Li
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Pei Feng
- Center for Biotherapy, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Rujia Mi
- Center for Biotherapy, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China
| | - Yanfeng Wu
- Shenzhen Key Laboratory of Ankylosing Spondylitis, Shenzhen, 518003, PR China.
- Center for Biotherapy, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China.
| | - Huiyong Shen
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518003, PR China.
- Shenzhen Key Laboratory of Ankylosing Spondylitis, Shenzhen, 518003, PR China.
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20
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Tesfaye RA, Lavaud M, Charrier C, Brounais-Le Royer B, Cartron PF, Verrecchia F, Baud'huin M, Lamoureux F, Georges S, Ory B. Tracking Targets of Dynamic Super-Enhancers in Vitro to Better Characterize Osteoclastogenesis and to Evaluate the Effect of Diuron on the Maturation of Human Bone Cells. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:67007. [PMID: 37307168 DOI: 10.1289/ehp11690] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUND Osteoclasts are major actors in the maintenance of bone homeostasis. The full functional maturation of osteoclasts from monocyte lineage cells is essential for the degradation of old/damaged bone matrix. Diuron is one of the most frequently encountered herbicides, particularly in water sources. However, despite a reported delayed ossification in vivo, its impact on bone cells remains largely unknown. OBJECTIVES The objectives of this study were to first better characterize osteoclastogenesis by identifying genes that drive the differentiation of CD14+ monocyte progenitors into osteoclasts and to evaluate the toxicity of diuron on osteoblastic and osteoclastic differentiation in vitro. METHODS We performed chromatin immunoprecipitation (ChIP) against H3K27ac followed by ChIP-sequencing (ChIP-Seq) and RNA-sequencing (RNA-Seq) at different stages of differentiation of CD14+ monocytes into active osteoclasts. Differentially activated super-enhancers and their potential target genes were identified. Then to evaluate the toxicity of diuron on osteoblasts and osteoclasts, we performed RNA-Seq and functional tests during in vitro osteoblastic and osteoclastic differentiation by exposing cells to different concentrations of diuron. RESULTS The combinatorial study of the epigenetic and transcriptional remodeling taking place during differentiation has revealed a very dynamic epigenetic profile that supports the expression of genes vital for osteoclast differentiation and function. In total, we identified 122 genes induced by dynamic super-enhancers at late days. Our data suggest that high concentration of diuron (50μM) affects viability of mesenchymal stem cells (MSCs) in vitro associated with a decrease of bone mineralization. At a lower concentration (1μM), an inhibitory effect was observed in vitro on the number of osteoclasts derived from CD14+ monocytes without affecting cell viability. Among the diuron-affected genes, our analysis suggests a significant enrichment of genes targeted by pro-differentiation super-enhancers, with an odds ratio of 5.12 (ρ=2.59×10-5). DISCUSSION Exposure to high concentrations of diuron decreased the viability of MSCs and could therefore affect osteoblastic differentiation and bone mineralization. This pesticide also disrupted osteoclasts maturation by impairing the expression of cell-identity determining genes. Indeed, at sublethal concentrations, differences in the expression of these key genes were mild during the course of in vitro osteoclast differentiation. Taken together our results suggest that high exposure levels of diuron could have an effect on bone homeostasis. https://doi.org/10.1289/EHP11690.
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Affiliation(s)
- Robel A Tesfaye
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Melanie Lavaud
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Céline Charrier
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | | | - Pierre-François Cartron
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- LaBCT, Institut de Cancérologie de l'Ouest, Saint Herblain, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
| | - Franck Verrecchia
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Marc Baud'huin
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - François Lamoureux
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Steven Georges
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
| | - Benjamin Ory
- CRCI2NA, INSERM UMR 1307, CNRS UMR 6075, Nantes University and Angers University, Nantes, France
- Cancéropole Grand-Ouest, réseau Epigénétique, Nantes, France
- EpiSAVMEN, Epigenetic consortium Pays de la Loire, France
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21
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Lackner A, Müller M, Gamperl M, Stoeva D, Langmann O, Papuchova H, Roitinger E, Dürnberger G, Imre R, Mechtler K, Latos PA. The Fgf/Erf/NCoR1/2 repressive axis controls trophoblast cell fate. Nat Commun 2023; 14:2559. [PMID: 37137875 DOI: 10.1038/s41467-023-38101-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/15/2023] [Indexed: 05/05/2023] Open
Abstract
Placental development relies on coordinated cell fate decisions governed by signalling inputs. However, little is known about how signalling cues are transformed into repressive mechanisms triggering lineage-specific transcriptional signatures. Here, we demonstrate that upon inhibition of the Fgf/Erk pathway in mouse trophoblast stem cells (TSCs), the Ets2 repressor factor (Erf) interacts with the Nuclear Receptor Co-Repressor Complex 1 and 2 (NCoR1/2) and recruits it to key trophoblast genes. Genetic ablation of Erf or Tbl1x (a component of the NCoR1/2 complex) abrogates the Erf/NCoR1/2 interaction. This leads to mis-expression of Erf/NCoR1/2 target genes, resulting in a TSC differentiation defect. Mechanistically, Erf regulates expression of these genes by recruiting the NCoR1/2 complex and decommissioning their H3K27ac-dependent enhancers. Our findings uncover how the Fgf/Erf/NCoR1/2 repressive axis governs cell fate and placental development, providing a paradigm for Fgf-mediated transcriptional control.
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Affiliation(s)
- Andreas Lackner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Michael Müller
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Magdalena Gamperl
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Delyana Stoeva
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Olivia Langmann
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | - Henrieta Papuchova
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria
| | | | | | - Richard Imre
- Institute of Molecular Pathology, A-1030, Vienna, Austria
| | - Karl Mechtler
- Institute of Molecular Pathology, A-1030, Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090, Vienna, Austria.
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22
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Kravchuk EV, Ashniev GA, Gladkova MG, Orlov AV, Vasileva AV, Boldyreva AV, Burenin AG, Skirda AM, Nikitin PI, Orlova NN. Experimental Validation and Prediction of Super-Enhancers: Advances and Challenges. Cells 2023; 12:cells12081191. [PMID: 37190100 DOI: 10.3390/cells12081191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Super-enhancers (SEs) are cis-regulatory elements of the human genome that have been widely discussed since the discovery and origin of the term. Super-enhancers have been shown to be strongly associated with the expression of genes crucial for cell differentiation, cell stability maintenance, and tumorigenesis. Our goal was to systematize research studies dedicated to the investigation of structure and functions of super-enhancers as well as to define further perspectives of the field in various applications, such as drug development and clinical use. We overviewed the fundamental studies which provided experimental data on various pathologies and their associations with particular super-enhancers. The analysis of mainstream approaches for SE search and prediction allowed us to accumulate existing data and propose directions for further algorithmic improvements of SEs' reliability levels and efficiency. Thus, here we provide the description of the most robust algorithms such as ROSE, imPROSE, and DEEPSEN and suggest their further use for various research and development tasks. The most promising research direction, which is based on topic and number of published studies, are cancer-associated super-enhancers and prospective SE-targeted therapy strategies, most of which are discussed in this review.
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Affiliation(s)
- Ekaterina V Kravchuk
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
| | - German A Ashniev
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, Leninskiye Gory, MSU, 1-12, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Marina G Gladkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, GSP-1, Leninskiye Gory, MSU, 1-73, 119234 Moscow, Russia
| | - Alexey V Orlov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anastasiia V Vasileva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Anna V Boldyreva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Alexandr G Burenin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Artemiy M Skirda
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Petr I Nikitin
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
| | - Natalia N Orlova
- Prokhorov General Physics Institute of the Russian Academy of Sciences, 38 Vavilov St., 119991 Moscow, Russia
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23
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Vu HTH, Scott RL, Iqbal K, Soares MJ, Tuteja G. CORE CONSERVED TRANSCRIPTIONAL REGULATORY NETWORKS DEFINE THE INVASIVE TROPHOBLAST CELL LINEAGE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.30.534962. [PMID: 37066272 PMCID: PMC10103937 DOI: 10.1101/2023.03.30.534962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The invasive trophoblast cell lineage in rat and human share crucial responsibilities in establishing the uterine-placental interface of the hemochorial placenta. These observations have led to the rat becoming an especially useful animal model to study hemochorial placentation. However, our understanding of similarities or differences between regulatory mechanisms governing rat and human invasive trophoblast cell populations is limited. In this study, we generated single-nucleus (sn) ATAC-seq data from gestation day (gd) 15.5 and 19.5 rat uterine-placental interface tissues and integrated the data with single-cell RNA-seq data generated at the same stages. We determined the chromatin accessibility profiles of invasive trophoblast, natural killer, macrophage, endothelial, and smooth muscle cells, and compared invasive trophoblast chromatin accessibility to extravillous trophoblast (EVT) cell accessibility. In comparing chromatin accessibility profiles between species, we found similarities in patterns of gene regulation and groups of motifs enriched in accessible regions. Finally, we identified a conserved gene regulatory network in invasive trophoblast cells. Our data, findings and analysis will facilitate future studies investigating regulatory mechanisms essential for the invasive trophoblast cell lineage.
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Affiliation(s)
- Ha T. H. Vu
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
| | - Regan L. Scott
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Khursheed Iqbal
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
| | - Michael J. Soares
- Institute for Reproductive and Developmental Sciences and Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, 66160
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS, 66160
- Center for Perinatal Research, Children’s Mercy Research Institute, Children’s Mercy, Kansas City, MO, 64108
| | - Geetu Tuteja
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011
- Bioinformatics and Computational Biology Interdepartmental Graduate Program, Iowa State University, Ames, IA 50011
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24
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Takezawa Y, Iwai M, Fujiki Y, Yokomizo R, Kishigami H, Miyado M, Kawano N, Yamada M, Shindo M, Suzuki M, Sato B, Katano D, Kamijo S, Hamatani T, Tanaka M, Umezawa A, Kang W, Miyado K. Embryonic β-Catenin Is Required for Priming of the Uterus to Implantation. J Transl Med 2023; 103:100026. [PMID: 36925206 DOI: 10.1016/j.labinv.2022.100026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 10/04/2022] [Accepted: 11/03/2022] [Indexed: 01/11/2023] Open
Abstract
Repeated implantation failure is a major cause of infertility among healthy women. Uterine β-catenin (CTNNB1) plays a critical role in implantation. However, the role of embryonic CTNNB1 during implantation remains unclear. We addressed this topic by analyzing mice carrying Ctnnb1-deficient (Ctnnb1Δ/Δ) embryos. Ctnnb1Δ/Δ embryos were produced by intercrossing mice bearing Ctnnb1-deficient eggs and sperms. We found that Ctnnb1Δ/Δ embryos developed to the blastocyst stage; thereafter, they were resorbed, leaving empty decidual capsules. Moreover, leukemia inhibitory factor, a uterine factor essential for implantation, was undetectable in Ctnnb1Δ/Δ blastocysts. Furthermore, CDX2, a transcription factor that determines the fate of trophectoderm cells, was not observed in Ctnnb1Δ/Δ blastocysts. Intrauterine injection with uterine fluids (from control mice) and recombinant mouse leukemia inhibitory factor proteins rescued the uterine response to Ctnnb1Δ/Δ blastocysts. These results suggest that embryonic CTNNB1 is required for the secretion of blastocyst-derived factor(s) that open the implantation window, indicating that the uterine response to implantation can be induced using supplemental materials. Therefore, our results may contribute to the discovery of a similar mechanism in humans, leading to a better understanding of the pathogenesis of repeated implantation failure.
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Affiliation(s)
- Youki Takezawa
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Iwai
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Yukiko Fujiki
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Ryo Yokomizo
- Department of Obstetrics and Gynecology, The Jikei University School of Medicine, Tokyo, Japan
| | - Harue Kishigami
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Mami Miyado
- Department of Food and Nutrition, Beppu University, Oita, Japan; Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Natsuko Kawano
- Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
| | - Mitsutoshi Yamada
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Miyuki Shindo
- Division of Laboratory Animal Resources, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Miki Suzuki
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Ban Sato
- Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
| | - Daiki Katano
- Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
| | - Shintaro Kamijo
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Toshio Hamatani
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Mamoru Tanaka
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Akihiro Umezawa
- National Research Institute for Child Health and Development, Tokyo, Japan
| | - Woojin Kang
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
| | - Kenji Miyado
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo, Japan.
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25
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Li H, Sun J, Dong Y, Huang Y, Wu L, Xi C, Su Z, Xiao Y, Zhang C, Liang Y, Li Y, Lin Z, Shen L, Zuo Y, Abudureheman A, Yin J, Wang H, Kong X, Le R, Gao S, Zhang Y. Remodeling of H3K9me3 during the pluripotent to totipotent-like state transition. Stem Cell Reports 2023; 18:449-462. [PMID: 36638787 PMCID: PMC9968986 DOI: 10.1016/j.stemcr.2022.12.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
Multiple chromatin modifiers associated with H3K9me3 play important roles in the transition from embryonic stem cells to 2-cell (2C)-like cells. However, it remains elusive how H3K9me3 is remodeled and its association with totipotency. Here, we integrated transcriptome and H3K9me3 profiles to conduct a detailed comparison of 2C embryos and 2C-like cells. Globally, H3K9me3 is highly preserved and H3K9me3 dynamics within the gene locus is not associated with gene expression change during 2C-like transition. Promoter-deposited H3K9me3 plays non-repressive roles in the activation of genes during 2C-like transition. In contrast, transposable elements, residing in the nearby regions of up-regulated genes, undergo extensive elimination of H3K9me3 and are tended to be induced in 2C-like transitions. Furthermore, a large fraction of trophoblast stem cell-specific enhancers undergo loss of H3K9me3 exclusively in MERVL+/Zscan4+ cells. Our study therefore reveals the unique H3K9me3 profiles of 2C-like cells, facilitating the further exploration of totipotency.
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Affiliation(s)
- Hu Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Sciences and Technology, Xinxiang Medical University, Xinxiang, Henan Province 453003, China
| | - Jiatong Sun
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yu Dong
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixin Huang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Li Wu
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chenxiang Xi
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongqu Su
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yihan Xiao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Chuyu Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yuwei Liang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yujun Li
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhiyi Lin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Lu Shen
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yixing Zuo
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Abuduwaili Abudureheman
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiangyin Kong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Rongrong Le
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
| | - Yanping Zhang
- Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China.
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26
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Yu Y, Mu C, Xu Y, Li Y, Ren S, Kong S, Deng W, Wang Y, Wang H, Lu J. Adgrg1 is a new transcriptional target of Hand1 during trophoblast giant cell differentiation. J Reprod Immunol 2022; 154:103753. [PMID: 36228547 DOI: 10.1016/j.jri.2022.103753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 12/14/2022]
Abstract
The placenta, forming the maternal-fetal interface, is essential for the survival and development of the fetus. It has been shown that the basic helix-loop-helix (bHLH) transcription factor Hand1 plays an important role in trophoblast giant cells (TGCs) differentiation during placental development in mice. However, the underlying molecular mechanism remains elusive. We hereby report that Adgrg1 (GPR56), a G protein coupled receptor, was a new transcriptional target of Hand1. Hand1 activated the expression of Adgrg1 by binding to its promoter region during TGCs differentiation. Double in situ hybridization revealed co-expression of Hand1 and Adgrg1 in Prl2c2+ TGCs located in the junctional zone of the placenta. Knockdown of Adgrg1 not only led to increased Prl2c2 expression, but also the improvement of cell migration and invasion during TGC differentiation. Moreover, the ligand of Adgrg1, Tgm2, was expressed in Prl2c2+ TGCs located in the placental junctional zone and Tgm2 Knockdown increased cell migration and invasion, suggesting Tgm2 is a potential ligand involved in the functions of Adgrg1 during TGC differentiation in the manners of autocrine. Collectively, these results demonstrate that Adgrg1 is a new transcriptional target of Hand1, affecting Prl2c2 expression as well as cell migration and invasion during TGCs differentiation. As a transmembrane receptor, Adgrg1 perhaps could act as a potential therapeutic target for placental-associated diseases caused by abnormal trophoblast migration and invasion, providing new insights for the preventions and therapies of placenta-related diseases.
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Affiliation(s)
- Yongqin Yu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Change Mu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yingchun Xu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yuanyuan Li
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shengnan Ren
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yinan Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China.
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27
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PIM3-AMPK-HDAC4/5 axis restricts MuERVL-marked 2-cell-like state in embryonic stem cells. Stem Cell Reports 2022; 17:2256-2271. [PMID: 36150380 PMCID: PMC9561635 DOI: 10.1016/j.stemcr.2022.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/24/2022] Open
Abstract
A minority of embryonic stem cells (ESCs) marked by endogenous retrovirus MuERVL are totipotent 2-cell-like cells. However, the majority of ESCs repress MuERVL. Currently, it is still unclear regarding the signaling pathway(s) repressing the MuERVL-associated 2-cell-like state of ESCs. Here, we identify the PIM3-downstream signaling axis as a key route to repress MuERVL and 2-cell-like state. Downregulation, deletion, or inhibition of PIM3 activated MuERVL, 2-cell genes, and trophectodermal genes in ESCs. By screening PIM3-regulated pathways, we discovered AMPK as its key target. The loss of Pim3 caused an increase in AMPK phosphorylation, which phosphorylated HDAC4/5 and triggered their transfer out of the nucleus in Pim3−/− ESCs. The reduction of nuclear HDAC4/5 caused increased H3K9ac and reduced H3K9me1/2 enrichment on MuERVL, thus activating MuERVL and 2-cell-like state. In summary, our study uncovers a novel axis by which PIM3 suppresses 2-cell marker MuERVL and totipotent state in ESCs. PIM3 signaling pathway represses MuERVL and 2-cell-like state Pim3 loss promotes AMPK phosphorylation, which activates MuERVL Phosphorylated AMPK mediates HDAC4/5 export from the nucleus HDAC4/5 repress MuERVL through modulating H3K9ac and H3K9me1/2
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28
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Stefanucci L, Frontini M. Non-coding genetic variation in regulatory elements determines thrombosis and hemostasis phenotypes. J Thromb Haemost 2022; 20:1759-1765. [PMID: 35514262 PMCID: PMC9540108 DOI: 10.1111/jth.15754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 11/26/2022]
Abstract
Since the early inception of genome-wide association studies (GWAS), it became clear that, in all diseases or traits studied, most genetic variants are likely to exert their effect on gene expression mainly by altering the function of regulatory elements. At the same time, the regulation of the gene expression field broadened its boundaries, from the univocal relationship between regulatory elements and genes to include genome organization, long-range DNA interactions, and epigenetics. Next-generation sequencing has introduced genome-wide approaches that have greatly improved our understanding of the general principles of gene expression. However, elucidating how these apply in every single genomic locus still requires painstaking experimental work, in which several independent lines of evidence are required, and often this is helped by rare genetic variants in individuals with rare diseases. This review will focus on the non-coding features of the genome involved in transcriptional regulation, that when altered, leads to known cases of inherited (familial) thrombotic and hemostatic phenotypes, emphasizing the role of enhancers and super-enhancers.
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Affiliation(s)
- Luca Stefanucci
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
| | - Mattia Frontini
- Department of HaematologyUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- National Health Service (NHS) Blood and TransplantCambridge Biomedical CampusCambridgeUK
- British Heart Foundation, Cambridge Centre for Research ExcellenceUniversity of Cambridge, Cambridge Biomedical CampusCambridgeUK
- Institute of Biomedical & Clinical Science, College of Medicine and HealthUniversity of Exeter Medical SchoolExeterUK
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29
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Comparative parallel multi-omics analysis during the induction of pluripotent and trophectoderm states. Nat Commun 2022; 13:3475. [PMID: 35715410 PMCID: PMC9205865 DOI: 10.1038/s41467-022-31131-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/31/2022] [Indexed: 11/09/2022] Open
Abstract
Following fertilization, it is only at the 32-64-cell stage when a clear segregation between cells of the inner cell mass and trophectoderm is observed, suggesting a 'T'-shaped model of specification. Here, we examine whether the acquisition of these two states in vitro, by nuclear reprogramming, share similar dynamics/trajectories. Using a comparative parallel multi-omics analysis (i.e., bulk RNA-seq, scRNA-seq, ATAC-seq, ChIP-seq, RRBS and CNVs) on cells undergoing reprogramming to pluripotency and TSC state we show that each reprogramming system exhibits specific trajectories from the onset of the process, suggesting 'V'-shaped model. We describe in detail the various trajectories toward the two states and illuminate reprogramming stage-specific markers, blockers, facilitators and TSC subpopulations. Finally, we show that while the acquisition of the TSC state involves the silencing of embryonic programs by DNA methylation, during the acquisition of pluripotency these regions are initially defined but retain inactive by the elimination of H3K27ac.
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30
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Transcription factor networks in trophoblast development. Cell Mol Life Sci 2022; 79:337. [PMID: 35657505 PMCID: PMC9166831 DOI: 10.1007/s00018-022-04363-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022]
Abstract
The placenta sustains embryonic development and is critical for a successful pregnancy outcome. It provides the site of exchange between the mother and the embryo, has immunological functions and is a vital endocrine organ. To perform these diverse roles, the placenta comprises highly specialized trophoblast cell types, including syncytiotrophoblast and extravillous trophoblast. The coordinated actions of transcription factors (TFs) regulate their emergence during development, subsequent specialization, and identity. These TFs integrate diverse signaling cues, form TF networks, associate with chromatin remodeling and modifying factors, and collectively determine the cell type-specific characteristics. Here, we summarize the general properties of TFs, provide an overview of TFs involved in the development and function of the human trophoblast, and address similarities and differences to their murine orthologs. In addition, we discuss how the recent establishment of human in vitro models combined with -omics approaches propel our knowledge and transform the human trophoblast field.
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31
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LncRNA NEAT1 controls the lineage fates of BMSCs during skeletal aging by impairing mitochondrial function and pluripotency maintenance. Cell Death Differ 2022; 29:351-365. [PMID: 34497381 PMCID: PMC8816946 DOI: 10.1038/s41418-021-00858-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
Aged bone marrow mesenchymal stem cells (BMSCs) exhibit aberrant self-renewal and lineage specification, which contribute to imbalanced bone-fat and progressive bone loss. In addition to known master regulators of lineage commitment, it is crucial to identify pivotal switches governing the specific differentiation fate of aged BMSCs. Here, we profiled differences in epigenetic regulation between adipogenesis and osteogenesis and identified super-enhancer associated lncRNA nuclear-enriched abundant transcript 1 (NEAT1) as a key bone-fat switch in aged BMSCs. We validated that NEAT1 with high enhancer activity was transcriptionally activated by ATF2 and directed aged BMSCs to a greater propensity to differentiate toward adipocytes than osteoblasts by mediating mitochondrial function. Furthermore, we confirmed NEAT1 as a protein-binding scaffold in which phosphorylation modification of SOX2 Ser249/250 by CDK2 impaired SOX2/OCT4 complex stability and dysregulated downstream transcription networks of pluripotency maintenance. In addition, by sponging miR-27b-3p, NEAT1 upregulated BNIP3L, BMP2K, and PPARG expression to shape mitochondrial function and osteogenic/adipogenic differentiation commitment, respectively. In extracellular communication, NEAT1 promoted CSF1 secretion from aged BMSCs and then strengthened osteoclastic differentiation by extracellular vesicle delivery. Notably, Neat1 small interfering RNA delivery induced increased bone mass in aged mice and decreased fat accumulation in the bone marrow. These findings suggest that NEAT1 regulates the lineage fates of BMSCs by orchestrating mitochondrial function and pluripotency maintenance, and might be a potential therapeutic target for skeletal aging.
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No Need to Stick Together to Be Connected: Multiple Types of Enhancers' Networking. Cancers (Basel) 2021; 13:cancers13205201. [PMID: 34680347 PMCID: PMC8533737 DOI: 10.3390/cancers13205201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Simple Summary Transcription regulation programs require the functional interaction of distal and proximal regulatory regions, interacting by specific 3D chromatin configurations. Enhancers are cis-acting regulatory elements able to promote gene expression regardless their orientation and distance from the transcription starting site. Their systematic mapping by genome-wide chromatin profiling and chromosome conformation analysis, combined with the development of gene-editing approaches to modulate their function, revealed that many enhancers work together to fine-tune the expression of their target genes. This review aim to describe the functions of different types of enhancers and the modalities of enhancers’ interaction, focusing on their role in the regulation of complex biological processes like cancer development. Abstract The control of gene expression at a transcriptional level requires a widespread landscape of regulatory elements. Central to these regulatory circuits are enhancers (ENHs), which are defined as cis-acting DNA elements able to increase the transcription of a target gene in a distance- and orientation-independent manner. ENHs are not independent functional elements but work in a complex and dynamic cooperative network, constituting the building blocks of multimodular domains of gene expression regulation. The information from each of these elements converges on the target promoter, contributing to improving the precision and sharpness of gene modulation. ENHs’ interplay varies in its nature and extent, ranging from an additive to redundant effect depending on contexts. Moving from super-enhancers that drive the high expression levels of identity genes, to shadow-enhancers, whose redundant functions contribute to buffering the variation in gene expression, this review aims to describe the different modalities of ENHs’ interaction and their role in the regulation of complex biological processes like cancer development.
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Hornbachner R, Lackner A, Papuchova H, Haider S, Knöfler M, Mechtler K, Latos PA. MSX2 safeguards syncytiotrophoblast fate of human trophoblast stem cells. Proc Natl Acad Sci U S A 2021; 118:e2105130118. [PMID: 34507999 PMCID: PMC8449346 DOI: 10.1073/pnas.2105130118] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2021] [Indexed: 11/18/2022] Open
Abstract
Multiple placental pathologies are associated with failures in trophoblast differentiation, yet the underlying transcriptional regulation is poorly understood. Here, we discovered msh homeobox 2 (MSX2) as a key transcriptional regulator of trophoblast identity using the human trophoblast stem cell model. Depletion of MSX2 resulted in activation of the syncytiotrophoblast transcriptional program, while forced expression of MSX2 blocked it. We demonstrated that a large proportion of the affected genes were directly bound and regulated by MSX2 and identified components of the SWItch/Sucrose nonfermentable (SWI/SNF) complex as strong MSX2 interactors and target gene cobinders. MSX2 cooperated specifically with the SWI/SNF canonical BAF (cBAF) subcomplex and cooccupied, together with H3K27ac, a number of differentiation genes. Increased H3K27ac and cBAF occupancy upon MSX2 depletion imply that MSX2 prevents premature syncytiotrophoblast differentiation. Our findings established MSX2 as a repressor of the syncytiotrophoblast lineage and demonstrated its pivotal role in cell fate decisions that govern human placental development and disease.
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Affiliation(s)
- Ruth Hornbachner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Andreas Lackner
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Henrieta Papuchova
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria
| | - Sandra Haider
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, A-1090 Vienna, Austria
| | - Martin Knöfler
- Department of Obstetrics and Gynecology, Reproductive Biology Unit, Medical University of Vienna, A-1090 Vienna, Austria
| | - Karl Mechtler
- Protein Chemistry Facility, Institute of Molecular Pathology, A-1030 Vienna, Austria
| | - Paulina A Latos
- Center for Anatomy and Cell Biology, Medical University of Vienna, A-1090 Vienna, Austria;
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Kochat V, Raman AT, Landers SM, Tang M, Schulz J, Terranova C, Landry JP, Bhalla AD, Beird HC, Wu CC, Jiang Y, Mao X, Lazcano R, Gite S, Ingram DR, Yi M, Zhang J, Keung EZ, Scally CP, Roland CL, Hunt KK, Feig BW, Futreal PA, Hwu P, Wang WL, Lazar AJ, Slopis JM, Wilson-Robles H, Wiener DJ, McCutcheon IE, Wustefeld-Janssens B, Rai K, Torres KE. Enhancer reprogramming in PRC2-deficient malignant peripheral nerve sheath tumors induces a targetable de-differentiated state. Acta Neuropathol 2021; 142:565-590. [PMID: 34283254 DOI: 10.1007/s00401-021-02341-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/09/2021] [Accepted: 06/22/2021] [Indexed: 02/03/2023]
Abstract
Malignant peripheral nerve sheath tumors (MPNSTs) are soft tissue sarcomas that frequently harbor genetic alterations in polycomb repressor complex 2 (PRC2) components-SUZ12 and EED. Here, we show that PRC2 loss confers a dedifferentiated early neural-crest phenotype which is exclusive to PRC2-mutant MPNSTs and not a feature of neurofibromas. Neural crest phenotype in PRC2 mutant MPNSTs was validated via cross-species comparative analysis using spontaneous and transgenic MPNST models. Systematic chromatin state profiling of the MPNST cells showed extensive epigenomic reprogramming or chromatin states associated with PRC2 loss and identified gains of active enhancer states/super-enhancers on early neural crest regulators in PRC2-mutant conditions around genomic loci that harbored repressed/poised states in PRC2-WT MPNST cells. Consistently, inverse correlation between H3K27me3 loss and H3K27Ac gain was noted in MPNSTs. Epigenetic editing experiments established functional roles for enhancer gains on DLX5-a key regulator of neural crest phenotype. Consistently, blockade of enhancer activity by bromodomain inhibitors specifically suppressed this neural crest phenotype and tumor burden in PRC2-mutant PDXs. Together, these findings reveal accumulation of dedifferentiated neural crest like state in PRC2-mutant MPNSTs that can be targeted by enhancer blockade.
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Affiliation(s)
- Veena Kochat
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayush T Raman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sharon M Landers
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Tang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Schulz
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher Terranova
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jace P Landry
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Angela D Bhalla
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yingda Jiang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Swati Gite
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Min Yi
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Z Keung
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christopher P Scally
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina L Roland
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kelly K Hunt
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barry W Feig
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology and Sarcoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Wei-Lien Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John M Slopis
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heather Wilson-Robles
- Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Dominique J Wiener
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Science, Texas A&M University, College Station, TX, USA
| | - Ian E McCutcheon
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Brandan Wustefeld-Janssens
- Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.,Department of Surgical Oncology, Flint Animal Cancer Center, Colorado State University, Fort Collins, CO, USA
| | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA.
| | - Keila E Torres
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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35
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Liu N, Low WY, Alinejad-Rokny H, Pederson S, Sadlon T, Barry S, Breen J. Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics Chromatin 2021; 14:41. [PMID: 34454581 PMCID: PMC8399707 DOI: 10.1186/s13072-021-00417-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/19/2021] [Indexed: 11/30/2022] Open
Abstract
Eukaryotic genomes are highly organised within the nucleus of a cell, allowing widely dispersed regulatory elements such as enhancers to interact with gene promoters through physical contacts in three-dimensional space. Recent chromosome conformation capture methodologies such as Hi-C have enabled the analysis of interacting regions of the genome providing a valuable insight into the three-dimensional organisation of the chromatin in the nucleus, including chromosome compartmentalisation and gene expression. Complicating the analysis of Hi-C data, however, is the massive amount of identified interactions, many of which do not directly drive gene function, thus hindering the identification of potentially biologically functional 3D interactions. In this review, we collate and examine the downstream analysis of Hi-C data with particular focus on methods that prioritise potentially functional interactions. We classify three groups of approaches: structural-based discovery methods, e.g. A/B compartments and topologically associated domains, detection of statistically significant chromatin interactions, and the use of epigenomic data integration to narrow down useful interaction information. Careful use of these three approaches is crucial to successfully identifying potentially functional interactions within the genome.
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Affiliation(s)
- Ning Liu
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia
| | - Hamid Alinejad-Rokny
- BioMedical Machine Learning Lab, The Graduate School of Biomedical Engineering, The University of New South Wales, NSW, 2052, Sydney, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
| | - Stephen Pederson
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
- Dame Roma Mitchell Cancer Research Laboratories (DRMCRL), Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - Simon Barry
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia
- Core Member of UNSW Data Science Hub, The University of New South Wales, 2052, Sydney, Australia
- Women's & Children's Health Network, SA, 5006, North Adelaide, Australia
| | - James Breen
- Computational & Systems Biology, Precision Medicine Theme, South Australian Health & Medical Research Institute, SA, 5000, Adelaide, Australia.
- Robinson Research Institute, University of Adelaide, SA, 5005, Adelaide, Australia.
- Adelaide Medical School, University of Adelaide, SA, 5005, Adelaide, Australia.
- South Australian Genomics Centre (SAGC), South Australian Health & Medical Research Institute (SAHMRI), SA, 5000, Adelaide, Australia.
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ELF3 activated by a superenhancer and an autoregulatory feedback loop is required for high-level HLA-C expression on extravillous trophoblasts. Proc Natl Acad Sci U S A 2021; 118:2025512118. [PMID: 33622787 PMCID: PMC7936349 DOI: 10.1073/pnas.2025512118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
HLA-C arose during evolution of pregnancy in the great apes 10 to 15 million years ago. It has a dual function on placental extravillous trophoblasts (EVTs) as it contributes to both tolerance and immunity at the maternal-fetal interface. The mode of its regulation is of considerable interest in connection with the biology of pregnancy and pregnancy abnormalities. First-trimester primary EVTs in which HLA-C is highly expressed, as well as JEG3, an EVT model cell line, were employed. Single-cell RNA-seq data and quantitative PCR identified high expression of the transcription factor ELF3 in those cells. Chromatin immunoprecipitation (ChIP)-PCR confirmed that both ELF3 and MED1 bound to the proximal HLA-C promoter region. However, binding of RFX5 to this region was absent or severely reduced, and the adjacent HLA-B locus remained closed. Expression of HLA-C was inhibited by ELF3 small interfering RNAs (siRNAs) and by wrenchnolol treatment. Wrenchnolol is a cell-permeable synthetic organic molecule that mimics ELF3 and is relatively specific for binding to ELF3's coactivator, MED23, as our data also showed in JEG3. Moreover, the ELF3 gene is regulated by a superenhancer that spans more than 5 Mb, identified by assay for transposase-accessible chromatin using sequencing (ATAC-seq), as well as by its sensitivity to (+)-JQ1 (inhibitor of BRD4). ELF3 bound to its own promoter, thus creating an autoregulatory feedback loop that establishes expression of ELF3 and HLA-C in trophoblasts. Wrenchnolol blocked binding of MED23 to ELF3, thus disrupting the positive-feedback loop that drives ELF3 expression, with down-regulation of HLA-C expression as a consequence.
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37
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Lee BK, Kim J. Integrating High-Throughput Approaches and in vitro Human Trophoblast Models to Decipher Mechanisms Underlying Early Human Placenta Development. Front Cell Dev Biol 2021; 9:673065. [PMID: 34150768 PMCID: PMC8206641 DOI: 10.3389/fcell.2021.673065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
The placenta is a temporary but pivotal organ for human pregnancy. It consists of multiple specialized trophoblast cell types originating from the trophectoderm of the blastocyst stage of the embryo. While impaired trophoblast differentiation results in pregnancy disorders affecting both mother and fetus, the molecular mechanisms underlying early human placenta development have been poorly understood, partially due to the limited access to developing human placentas and the lack of suitable human in vitro trophoblast models. Recent success in establishing human trophoblast stem cells and other human in vitro trophoblast models with their differentiation protocols into more specialized cell types, such as syncytiotrophoblast and extravillous trophoblast, has provided a tremendous opportunity to understand early human placenta development. Unfortunately, while high-throughput research methods and omics tools have addressed numerous molecular-level questions in various research fields, these tools have not been widely applied to the above-mentioned human trophoblast models. This review aims to provide an overview of various omics approaches that can be utilized in the study of human in vitro placenta models by exemplifying some important lessons obtained from omics studies of mouse model systems and introducing recently available human in vitro trophoblast model systems. We also highlight some key unknown questions that might be addressed by such techniques. Integrating high-throughput omics approaches and human in vitro model systems will facilitate our understanding of molecular-level regulatory mechanisms underlying early human placenta development as well as placenta-associated complications.
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Affiliation(s)
- Bum-Kyu Lee
- Department of Biomedical Sciences, Cancer Research Center, University at Albany-State University of New York, Rensselaer, NY, United States
| | - Jonghwan Kim
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, United States
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38
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Chromatin Regulation in Development: Current Understanding and Approaches. Stem Cells Int 2021; 2021:8817581. [PMID: 33603792 PMCID: PMC7872760 DOI: 10.1155/2021/8817581] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/29/2020] [Accepted: 01/21/2021] [Indexed: 11/24/2022] Open
Abstract
The regulation of mammalian stem cell fate during differentiation is complex and can be delineated across many levels. At the chromatin level, the replacement of histone variants by chromatin-modifying proteins, enrichment of specific active and repressive histone modifications, long-range gene interactions, and topological changes all play crucial roles in the determination of cell fate. These processes control regulatory elements of critical transcriptional factors, thereby establishing the networks unique to different cell fates and initiate waves of distinctive transcription events. Due to the technical challenges posed by previous methods, it was difficult to decipher the mechanism of cell fate determination at early embryogenesis through chromatin regulation. Recently, single-cell approaches have revolutionised the field of developmental biology, allowing unprecedented insights into chromatin structure and interactions in early lineage segregation events during differentiation. Here, we review the recent technological advancements and how they have furthered our understanding of chromatin regulation during early differentiation events.
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39
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Zhang J, Yue W, Zhou Y, Liao M, Chen X, Hua J. Super enhancers-Functional cores under the 3D genome. Cell Prolif 2021; 54:e12970. [PMID: 33336467 PMCID: PMC7848964 DOI: 10.1111/cpr.12970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/28/2020] [Accepted: 12/07/2020] [Indexed: 12/13/2022] Open
Abstract
Complex biochemical reactions take place in the nucleus all the time. Transcription machines must follow the rules. The chromatin state, especially the three-dimensional structure of the genome, plays an important role in gene regulation and expression. The super enhancers are important for defining cell identity in mammalian developmental processes and human diseases. It has been shown that the major components of transcriptional activation complexes are recruited by super enhancer to form phase-separated condensates. We summarize the current knowledge about super enhancer in the 3D genome. Furthermore, a new related transcriptional regulation model from super enhancer is outlined to explain its role in the mammalian cell progress.
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Affiliation(s)
- Juqing Zhang
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Wei Yue
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
| | - Yaqi Zhou
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Mingzhi Liao
- College of Life ScienceNorthwest A&F UniversityYanglingChina
| | - Xingqi Chen
- Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Jinlian Hua
- College of Veterinary MedicineShaanxi Centre of Stem Cells Engineering & TechnologyNorthwest A&F UniversityYanglingChina
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40
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Ostrop J, Zwiggelaar RT, Terndrup Pedersen M, Gerbe F, Bösl K, Lindholm HT, Díez-Sánchez A, Parmar N, Radetzki S, von Kries JP, Jay P, Jensen KB, Arrowsmith C, Oudhoff MJ. A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. Front Cell Dev Biol 2021; 8:618552. [PMID: 33575256 PMCID: PMC7872100 DOI: 10.3389/fcell.2020.618552] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Intestinal organoids are an excellent model to study epithelial biology. Yet, the selection of analytical tools to accurately quantify heterogeneous organoid cultures remains limited. Here, we developed a semi-automated organoid screening method, which we applied to a library of highly specific chemical probes to identify epigenetic regulators of intestinal epithelial biology. The role of epigenetic modifiers in adult stem cell systems, such as the intestinal epithelium, is still undefined. Based on this resource dataset, we identified several targets that affected epithelial cell differentiation, including HDACs, EP300/CREBBP, LSD1, and type I PRMTs, which were verified by complementary methods. For example, we show that inhibiting type I PRMTs, which leads enhanced epithelial differentiation, blocks the growth of adenoma but not normal organoid cultures. Thus, epigenetic probes are powerful tools to study intestinal epithelial biology and may have therapeutic potential.
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Affiliation(s)
- Jenny Ostrop
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosalie T. Zwiggelaar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marianne Terndrup Pedersen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - François Gerbe
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Korbinian Bösl
- Department of Bioinformatics, Computational Biological Unit, University of Bergen, Bergen, Norway
| | - Håvard T. Lindholm
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Alberto Díez-Sánchez
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Naveen Parmar
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Silke Radetzki
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Jens Peter von Kries
- Screening Unit, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Philippe Jay
- Cancer Biology Department, Institute of Functional Genomics, University of Montpellier, Montpellier, France
| | - Kim B. Jensen
- BRIC - Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Menno J. Oudhoff
- Centre of Molecular Inflammation Research (CEMIR), Department of Clinical and Molecular Medicine (IKOM), NTNU - Norwegian University of Science and Technology, Trondheim, Norway
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Liu X, Shen S, Zhu L, Su R, Zheng J, Ruan X, Shao L, Wang D, Yang C, Liu Y. SRSF10 inhibits biogenesis of circ-ATXN1 to regulate glioma angiogenesis via miR-526b-3p/MMP2 pathway. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:121. [PMID: 32600379 PMCID: PMC7325155 DOI: 10.1186/s13046-020-01625-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/18/2020] [Indexed: 12/13/2022]
Abstract
Background Angiogenesis plays an important role in the progress of glioma. RNA-binding proteins (RBPs) and circular RNAs (circRNAs), dysregulated in various tumors, have been verified to mediate diverse biological behaviors including angiogenesis. Methods Quantitative real-time PCR (qRT-PCR) and western blot were performed to detect the expression of SRSF10, circ-ATXN1, miR-526b-3p, and MMP2/VEGFA. The potential function of SRSF10/circ-ATXN1/miR-526b-3p axis in glioma-associated endothelial cells (GECs) angiogenesis was further studied. Results SRSF10 and circ-ATXN1 were significantly upregulated in GECs compared with astrocyte-associated endothelial cells (AECs). Knockdown of SRSF10 or circ-ATXN1 significantly inhibited cell viability, migration and tube formation of GECs where knockdown of SRSF10 exerted its function by inhibiting the formation of circ-ATXN1. Moreover, the combined knockdown of SRSF10 and circ-ATXN1 significantly enhanced the inhibitory effects on cell viability, migration and tube formation of GECs, compared with knockdown of SRSF10 and circ-ATXN1, respectively. MiR-526b-3p was downregulated in GECs. Circ-ATXN1 functionally targeted miR-526b-3p in an RNA-induced silencing complex. Up-regulation of miR-526b-3p inhibited cell viability, migration and tube formation of GECs. Furthermore, miR-526b-3p affected the angiogenesis of GECs via negatively regulating the expression of MMP2/VEGFA. Conclusion SRSF10/circ-ATXN1/miR-526b-3p axis played a crucial role in regulating the angiogenesis of GECs. The above findings provided new targets for anti-angiogenic therapy in glioma.
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Affiliation(s)
- Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, 110004, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
| | - Shuyuan Shen
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, 110122, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, China
| | - Lu Zhu
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, 110122, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, China
| | - Rui Su
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, 110122, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, 110004, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
| | - Xuelei Ruan
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, 110122, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, China
| | - Lianqi Shao
- Department of Neurobiology, School of life Sciences, China Medical University, Shenyang, 110122, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University, Shenyang, 110122, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University, Shenyang, 110122, China
| | - Di Wang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, 110004, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
| | - Chunqing Yang
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, 110004, China.,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China. .,Liaoning Clinical Medical Research Center in Nervous System Disease, Shenyang, 110004, China. .,Key Laboratory of Neuro-Oncology in Liaoning Province, Shenyang, 110004, China.
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Dubois-Chevalier J, Dubois V, Staels B, Lefebvre P, Eeckhoute J. Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes. Epigenomics 2020; 12:715-723. [PMID: 32396464 DOI: 10.2217/epi-2019-0290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Super-enhancers (SE) have become a popular concept and are widely used as a feature defining key identity genes. Here, we provide perspectives on the use of SE to define and identify cell/tissue-identity genes. By mining SE and their associated genes using murine functional genomics data, we highlight and discuss current limitations and open questions regarding both the sensitivity and specificity of identity genes/transcription factors predicted by SE. In this context, we point to cell/tissue-specific promoters as an important additional level of information, which we propose to combine with SE when aiming to define potential identity genes.
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Affiliation(s)
- Julie Dubois-Chevalier
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Vanessa Dubois
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Bart Staels
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Philippe Lefebvre
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
| | - Jérôme Eeckhoute
- University of Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, Lille F-59000 Lille, France
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