1
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Chen C, Lee S, Zyner KG, Fernando M, Nemeruck V, Wong E, Marshall LL, Wark JR, Aryamanesh N, Tam PPL, Graham ME, Gonzalez-Cordero A, Yang P. Trans-omic profiling uncovers molecular controls of early human cerebral organoid formation. Cell Rep 2024; 43:114219. [PMID: 38748874 DOI: 10.1016/j.celrep.2024.114219] [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: 01/03/2024] [Revised: 04/01/2024] [Accepted: 04/25/2024] [Indexed: 06/01/2024] Open
Abstract
Defining the molecular networks orchestrating human brain formation is crucial for understanding neurodevelopment and neurological disorders. Challenges in acquiring early brain tissue have incentivized the use of three-dimensional human pluripotent stem cell (hPSC)-derived neural organoids to recapitulate neurodevelopment. To elucidate the molecular programs that drive this highly dynamic process, here, we generate a comprehensive trans-omic map of the phosphoproteome, proteome, and transcriptome of the exit of pluripotency and neural differentiation toward human cerebral organoids (hCOs). These data reveal key phospho-signaling events and their convergence on transcriptional factors to regulate hCO formation. Comparative analysis with developing human and mouse embryos demonstrates the fidelity of our hCOs in modeling embryonic brain development. Finally, we demonstrate that biochemical modulation of AKT signaling can control hCO differentiation. Together, our data provide a comprehensive resource to study molecular controls in human embryonic brain development and provide a guide for the future development of hCO differentiation protocols.
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Affiliation(s)
- Carissa Chen
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Scott Lee
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Katherine G Zyner
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Milan Fernando
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Victoria Nemeruck
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Emilie Wong
- Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Lee L Marshall
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Jesse R Wark
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia
| | - Nader Aryamanesh
- Bioinformatics Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick P L Tam
- Embryology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark E Graham
- Synapse Proteomics, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Anai Gonzalez-Cordero
- Stem Cell and Organoid Facility, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; Stem Cell Medicine Group, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia.
| | - Pengyi Yang
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Westmead, NSW 2145, Australia; School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, NSW 2006, Australia; Charles Perkins Centre, School of Mathematics and Statistics, University of Sydney, Sydney, NSW 2006, Australia.
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2
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Kim D, Tran A, Kim HJ, Lin Y, Yang JYH, Yang P. Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data. NPJ Syst Biol Appl 2023; 9:51. [PMID: 37857632 PMCID: PMC10587078 DOI: 10.1038/s41540-023-00312-6] [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: 08/14/2023] [Accepted: 10/02/2023] [Indexed: 10/21/2023] Open
Abstract
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and their regulators. Deciphering these networks plays a critical role in understanding the underlying regulatory crosstalk that drives many cellular processes and diseases. Recent advances in sequencing technology have led to the development of state-of-the-art GRN inference methods that exploit matched single-cell multi-omic data. By employing diverse mathematical and statistical methodologies, these methods aim to reconstruct more comprehensive and precise gene regulatory networks. In this review, we give a brief overview on the statistical and methodological foundations commonly used in GRN inference methods. We then compare and contrast the latest state-of-the-art GRN inference methods for single-cell matched multi-omics data, and discuss their assumptions, limitations and opportunities. Finally, we discuss the challenges and future directions that hold promise for further advancements in this rapidly developing field.
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Affiliation(s)
- Daniel Kim
- School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, Australia
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia
| | - Andy Tran
- School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Hani Jieun Kim
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia
| | - Yingxin Lin
- School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, Australia
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia
| | - Jean Yee Hwa Yang
- School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia.
| | - Pengyi Yang
- School of Mathematics and Statistics, University of Sydney, Camperdown, NSW, Australia.
- Computational Systems Biology Unit, Children's Medical Research Institute, University of Sydney, Camperdown, NSW, Australia.
- Sydney Precision Data Science Centre, University of Sydney, Camperdown, NSW, Australia.
- Charles Perkins Centre, University of Sydney, Camperdown, NSW, Australia.
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3
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Masamsetti VP, Tam PP. Rat epiblast-derived stem cells recapitulate the attributes of pre-gastrulation epiblast. CELL REPORTS METHODS 2023; 3:100575. [PMID: 37671029 PMCID: PMC10475837 DOI: 10.1016/j.crmeth.2023.100575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Iwatsuki and colleagues have generated self-renewing pluripotent stem cells from the pre-gastrulation epiblast of the rat embryo and from other cellular sources: rat embryonic stem cells (rESCs) and epiblast-like cells derived from the rESCs. These rat epiblast-derived stem cells (rEpiSCs) display germ-line competence that is characteristic of mouse formative stem cells and early signature of specification of germ layer lineages typical of primed state mouse epiblast stem cells.
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Affiliation(s)
- V. Pragathi Masamsetti
- Embryology Research Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- The University of Sydney, Faculty of Medicine and Health, School of Medical Sciences, NSW 2006, Australia
| | - Patrick P.L. Tam
- Embryology Research Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW 2145, Australia
- The University of Sydney, Faculty of Medicine and Health, School of Medical Sciences, NSW 2006, Australia
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4
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Ruan Y, Wang J, Yu M, Wang F, Wang J, Xu Y, Liu L, Cheng Y, Yang R, Zhang C, Yang Y, Wang J, Wu W, Huang Y, Tian Y, Chen G, Zhang J, Jian R. A multi-omics integrative analysis based on CRISPR screens re-defines the pluripotency regulatory network in ESCs. Commun Biol 2023; 6:410. [PMID: 37059858 PMCID: PMC10104827 DOI: 10.1038/s42003-023-04700-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/13/2023] [Indexed: 04/16/2023] Open
Abstract
A comprehensive and precise definition of the pluripotency gene regulatory network (PGRN) is crucial for clarifying the regulatory mechanisms in embryonic stem cells (ESCs). Here, after a CRISPR/Cas9-based functional genomics screen and integrative analysis with other functional genomes, transcriptomes, proteomes and epigenome data, an expanded pluripotency-associated gene set is obtained, and a new PGRN with nine sub-classes is constructed. By integrating the DNA binding, epigenetic modification, chromatin conformation, and RNA expression profiles, the PGRN is resolved to six functionally independent transcriptional modules (CORE, MYC, PAF, PRC, PCGF and TBX). Spatiotemporal transcriptomics reveal activated CORE/MYC/PAF module activity and repressed PRC/PCGF/TBX module activity in both mouse ESCs (mESCs) and pluripotent cells of early embryos. Moreover, this module activity pattern is found to be shared by human ESCs (hESCs) and cancers. Thus, our results provide novel insights into elucidating the molecular basis of ESC pluripotency.
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Affiliation(s)
- Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Meng Yu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China
| | - Fengsheng Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China
| | - Jiangjun Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Cell Biology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Ran Yang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
- Department of Pathophysiology, College of High Altitude Military Medicine, Army Medical University, Chongqing, 400038, China
| | - Chen Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - JiaLi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yi Huang
- Biomedical Analysis Center, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Guangxing Chen
- Department of Joint Surgery, The First Affiliated Hospital, Army Medical University, Chongqing, 400038, China.
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
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5
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Xiao D, Chen C, Yang P. Computational systems approach towards phosphoproteomics and their downstream regulation. Proteomics 2023; 23:e2200068. [PMID: 35580145 DOI: 10.1002/pmic.202200068] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/26/2022] [Accepted: 05/03/2022] [Indexed: 11/07/2022]
Abstract
Protein phosphorylation plays an essential role in modulating cell signalling and its downstream transcriptional and translational regulations. Until recently, protein phosphorylation has been studied mostly using low-throughput biochemical assays. The advancement of mass spectrometry (MS)-based phosphoproteomics transformed the field by enabling measurement of proteome-wide phosphorylation events, where tens of thousands of phosphosites are routinely identified and quantified in an experiment. This has brought a significant challenge in analysing large-scale phosphoproteomic data, making computational methods and systems approaches integral parts of phosphoproteomics. Previous works have primarily focused on reviewing the experimental techniques in MS-based phosphoproteomics, yet a systematic survey of the computational landscape in this field is still missing. Here, we review computational methods and tools, and systems approaches that have been developed for phosphoproteomics data analysis. We categorise them into four aspects including data processing, functional analysis, phosphoproteome annotation and their integration with other omics, and in each aspect, we discuss the key methods and example studies. Lastly, we highlight some of the potential research directions on which future work would make a significant contribution to this fast-growing field. We hope this review provides a useful snapshot of the field of computational systems phosphoproteomics and stimulates new research that drives future development.
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Affiliation(s)
- Di Xiao
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Carissa Chen
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Pengyi Yang
- Computational Systems Biology Group, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia.,School of Mathematics and Statistics, The University of Sydney, Sydney, New South Wales, Australia
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6
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Integrative analysis reveals histone demethylase LSD1 promotes RNA polymerase II pausing. iScience 2022; 25:105049. [PMID: 36124234 PMCID: PMC9482124 DOI: 10.1016/j.isci.2022.105049] [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: 03/18/2022] [Revised: 07/18/2022] [Accepted: 08/26/2022] [Indexed: 11/21/2022] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is well-known for its role in decommissioning enhancers during mouse embryonic stem cell (ESC) differentiation. Its role in gene promoters remains poorly understood despite its widespread presence at these sites. Here, we report that LSD1 promotes RNA polymerase II (RNAPII) pausing, a rate-limiting step in transcription regulation, in ESCs. We found the knockdown of LSD1 preferentially affects genes with higher RNAPII pausing. Next, we demonstrate that the co-localization sites of LSD1 and MYC, a factor known to regulate pause-release, are enriched for other RNAPII pausing factors. We show that LSD1 and MYC directly interact and MYC recruitment to genes co-regulated with LSD1 is dependent on LSD1 but not vice versa. The co-regulated gene set is significantly enriched for housekeeping processes and depleted of transcription factors compared to those bound by LSD1 alone. Collectively, our integrative analysis reveals a pleiotropic role of LSD1 in promoting RNAPII pausing. LSD1 promotes RNA polymerase II pausing in mouse embryonic stem cells LSD1 knockdown causes global reduction of RNAPII pausing Co-localized sites of LSD1 and MYC are enriched for RNAPII pausing and releasing factors MYC recruitment to co-regulated genes is dependent on LSD1 but not vice versa
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7
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Wang R, Amoyel M. mRNA Translation Is Dynamically Regulated to Instruct Stem Cell Fate. Front Mol Biosci 2022; 9:863885. [PMID: 35433828 PMCID: PMC9008482 DOI: 10.3389/fmolb.2022.863885] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 12/12/2022] Open
Abstract
Stem cells preserve tissue homeostasis by replacing the cells lost through damage or natural turnover. Thus, stem cells and their daughters can adopt two identities, characterized by different programs of gene expression and metabolic activity. The composition and regulation of these programs have been extensively studied, particularly by identifying transcription factor networks that define cellular identity and the epigenetic changes that underlie the progressive restriction in gene expression potential. However, there is increasing evidence that post-transcriptional mechanisms influence gene expression in stem cells and their progeny, in particular through the control of mRNA translation. Here, we review the described roles of translational regulation in controlling all aspects of stem cell biology, from the decision to enter or exit quiescence to maintaining self-renewal and promoting differentiation. We focus on mechanisms controlling global translation rates in cells, mTOR signaling, eIF2ɑ phosphorylation, and ribosome biogenesis and how they allow stem cells to rapidly change their gene expression in response to tissue needs or environmental changes. These studies emphasize that translation acts as an additional layer of control in regulating gene expression in stem cells and that understanding this regulation is critical to gaining a full understanding of the mechanisms that underlie fate decisions in stem cells.
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Affiliation(s)
| | - Marc Amoyel
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
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8
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Yan M, Hu J, Yuan H, Xu L, Liao G, Jiang Z, Zhu J, Pang B, Ping Y, Zhang Y, Xiao Y, Li X. Dynamic regulatory networks of T cell trajectory dissect transcriptional control of T cell state transition. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 26:1115-1129. [PMID: 34786214 PMCID: PMC8577129 DOI: 10.1016/j.omtn.2021.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022]
Abstract
T cells exhibit heterogeneous functional states, which correlate with responsiveness to immune checkpoint blockade and prognosis of tumor patients. However, the molecular regulatory mechanisms underlying the dynamic process of T cell state transition remain largely unknown. Based on single-cell transcriptome data of T cells in non-small cell lung cancer, we combined cell states and pseudo-times to propose a pipeline to construct dynamic regulatory networks for dissecting the process of T cell dysfunction. Candidate regulators at different stages were revealed in the process of tumor-infiltrating T cell dysfunction. Through comparing dynamic networks across the T cell state transition, we revealed frequent regulatory interaction rewiring and further refined critical regulators mediating each state transition. Several known regulators were identified, including TCF7, EOMES, ID2, and TOX. Notably, one of the critical regulators, TSC22D3, was frequently identified in the state transitions from the intermediate state to the pre-dysfunction and dysfunction state, exerting diverse roles in each state transition by regulatory interaction rewiring. Moreover, higher expression of TSC22D3 was associated with the clinical outcome of tumor patients. Our study embedded transcription factors (TFs) within the temporal dynamic networks, providing a comprehensive view of dynamic regulatory mechanisms controlling the process of T cell state transition.
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Affiliation(s)
- Min Yan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Huating Yuan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Liwen Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Gaoming Liao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Zedong Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Jiali Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
| | - Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin, Heilongjiang 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang 150081, China
- Key Laboratory of High Throughput Omics Big Data for Cold Region’s Major Diseases in Heilongjiang Province, Harbin, Heilongjiang 150081, China
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9
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Abdulhasan M, Ruden X, Rappolee B, Dutta S, Gurdziel K, Ruden DM, Awonuga AO, Korzeniewski SJ, Puscheck EE, Rappolee DA. Stress Decreases Host Viral Resistance and Increases Covid Susceptibility in Embryonic Stem Cells. Stem Cell Rev Rep 2021; 17:2164-2177. [PMID: 34155611 PMCID: PMC8216586 DOI: 10.1007/s12015-021-10188-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 12/13/2022]
Abstract
Stress-induced changes in viral receptor and susceptibility gene expression were measured in embryonic stem cells (ESC) and differentiated progeny. Rex1 promoter-Red Fluorescence Protein reporter ESC were tested by RNAseq after 72hr exposures to control stress hyperosmotic sorbitol under stemness culture (NS) to quantify stress-forced differentiation (SFD) transcriptomic programs. Control ESC cultured with stemness factor removal produced normal differentiation (ND). Bulk RNAseq transcriptomic analysis showed significant upregulation of two genes involved in Covid-19 cell uptake, Vimentin (VIM) and Transmembrane Serine Protease 2 (TMPRSS2). SFD increased the hepatitis A virus receptor (Havcr1) and the transplacental Herpes simplex 1 (HSV1) virus receptor (Pvrl1) compared with ESC undergoing ND. Several other coronavirus receptors, Glutamyl Aminopeptidase (ENPEP) and Dipeptidyl Peptidase 4 (DPP4) were upregulated significantly in SFD>ND. Although stressed ESC are more susceptible to infection due to increased expression of viral receptors and decreased resistance, the necessary Covid-19 receptor, angiotensin converting enzyme (ACE)2, was not expressed in our experiments. TMPRSS2, ENPEP, and DPP4 mediate Coronavirus uptake, but are also markers of extra-embryonic endoderm (XEN), which arise from ESC undergoing ND or SFD. Mouse and human ESCs differentiated to XEN increase TMPRSS2 and other Covid-19 uptake-mediating gene expression, but only some lines express ACE2. Covid-19 susceptibility appears to be genotype-specific and not ubiquitous. Of the 30 gene ontology (GO) groups for viral susceptibility, 15 underwent significant stress-forced changes. Of these, 4 GO groups mediated negative viral regulation and most genes in these increase in ND and decrease with SFD, thus suggesting that stress increases ESC viral susceptibility. Taken together, the data suggest that a control hyperosmotic stress can increase Covid-19 susceptibility and decrease viral host resistance in mouse ESC. However, this limited pilot study should be followed with studies in human ESC, tests of environmental, hormonal, and pharmaceutical stressors and direct tests for infection of stressed, cultured ESC and embryos by Covid-19.
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Affiliation(s)
- Mohammed Abdulhasan
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.,Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA
| | - Ximena Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | | | - Sudipta Dutta
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.,Reproductive Endocrinology and Cell Signaling LaboratoryDepartment of Integrative BiosciencesCollege of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Katherine Gurdziel
- Genome Sciences Center, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Douglas M Ruden
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.,Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Awoniyi O Awonuga
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA
| | - Steve J Korzeniewski
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA
| | - Elizabeth E Puscheck
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA.,Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA.,Invia Fertility Clinics, Hoffman Estates, Illinois, 60169, USA
| | - Daniel A Rappolee
- Department of Ob/Gyn, Reproductive Endocrinology and Infertility, CS Mott Center for Human Growth and Development, WayneState UniversitySchoolofMedicine, Detroit, Michigan, 48201, USA. .,Reproductive Stress 3M Inc, Grosse Pointe Farms, MI, 48236, USA. .,Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, 48202, USA. .,Program for Reproductive Sciences and Department of Physiology, Wayne State University School of Medicine, Detroit, MI, 48201, USA. .,Department of Biology, University of Windsor, Windsor, ON, N9B 3P4, Canada. .,CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, 275 East Hancock, Detroit, MI, 48201, USA.
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10
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Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR. An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. Front Cell Dev Biol 2021; 9:630067. [PMID: 33816475 PMCID: PMC8017264 DOI: 10.3389/fcell.2021.630067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/17/2021] [Indexed: 01/02/2023] Open
Abstract
Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodeling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory “dimensions” coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors, plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb module.
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Affiliation(s)
- Ana Sevilla
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Departament de Biología Cellular, Fisiología i Immunología, Facultat de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Dimitri Papatsenko
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Amin R Mazloom
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Huilei Xu
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ana Vasileva
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Richard D Unwin
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom.,Centre for Advanced Discovery and Experimental Therapeutics, Central Manchester University Hospitals NHS Foundation Trust, Institute of Human Development, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Gary LeRoy
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Edward Y Chen
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Francine E Garrett-Bakelman
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Dung-Fang Lee
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benjamin Trinite
- Institut de Recerca de La Sida, IrsiCaixa AIDS Research Institute, Germans Trias I Pujol Research Institute, Hospital Universitari Germans Trias I Pujol, Catalonia, Spain
| | - Ryan L Webb
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zichen Wang
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jie Su
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Julian Gingold
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ari Melnick
- Department of Medicine, Division of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, United States
| | - Benjamin A Garcia
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States
| | - Anthony D Whetton
- Stem Cell and Leukaemia Proteomics Laboratory, School of Cancer and Enabling Sciences, Faculty of Medical and Human Sciences, University of Manchester, Manchester, United Kingdom.,Academic Health Science Centre, Wolfson Molecular Imaging Centre, Manchester, United Kingdom
| | - Ben D MacArthur
- The Centre for Human Development, Stem Cells and Regeneration, Institute of Developmental Sciences, University of Southampton, Southampton, United Kingdom
| | - Avi Ma'ayan
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ihor R Lemischka
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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