1
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Chen M, Wang R. Computational analysis of synergism in small networks with different logic. J Biol Phys 2023; 49:1-27. [PMID: 36580168 PMCID: PMC9958226 DOI: 10.1007/s10867-022-09620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
Cell fate decision processes are regulated by networks which contain different molecules and interactions. Different network topologies may exhibit synergistic or antagonistic effects on cellular functions. Here, we analyze six most common small networks with regulatory logic AND or OR, trying to clarify the relationship between network topologies and synergism (or antagonism) related to cell fate decisions. We systematically examine the contribution of both network topologies and regulatory logic to the cell fate synergism by bifurcation and combinatorial perturbation analysis. Initially, under a single set of parameters, the synergism of three types of networks with AND and OR logic is compared. Furthermore, to consider whether these results depend on the choices of parameter values, statistics on the synergism of five hundred parameter sets is performed. It is shown that the results are not sensitive to parameter variations, indicating that the synergy or antagonism mainly depends on the network topologies rather than the choices of parameter values. The results indicate that the topology with "Dual Inhibition" shows good synergism, while the topology with "Dual Promotion" or "Hybrid" shows antagonism. The results presented here may help us to design synergistic networks based on network structure and regulation combinations, which has promising implications for cell fate decisions and drug combinations.
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Affiliation(s)
- Menghan Chen
- Department of Mathematics, Shanghai University, Shanghai, 200444, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, 200444, China.
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2
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Cason C, Lord T. RNA Interference as a Method of Gene Knockdown in Cultured Spermatogonia. Methods Mol Biol 2023; 2656:161-177. [PMID: 37249871 DOI: 10.1007/978-1-0716-3139-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Maintenance and self-renewal of the spermatogonial stem cell (SSC) population in the testis are dictated by the expression of a unique suite of genes. In manipulating gene expression through loss-of-function approaches, we can identify important regulatory mechanisms that dictate spermatogonial fate decisions. One such approach is RNA interference (RNAi), which uses natural cellular responses to small interfering RNAs to decrease levels of a targeted transcript. RNAi is performed in primary cultures of undifferentiated spermatogonia, and can be paired with techniques such as spermatogonial transplantation to assess the functional consequences of downregulated expression of the target gene on stem cell maintenance. This approach provides an alternative or complementary strategy to the generation of knockout mouse lines / cell lines. Here, we describe the methodology of RNAi in undifferentiated spermatogonia, and outline its inherent advantages and disadvantages over other technologies in the study of gene regulation in these cells.
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Affiliation(s)
- Connor Cason
- Priority Research Centre for Reproductive Science, Discipline of Biological Sciences, The University of Newcastle, Callaghan, NSW, Australia
- Infertility and Reproduction Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Tessa Lord
- Priority Research Centre for Reproductive Science, Discipline of Biological Sciences, The University of Newcastle, Callaghan, NSW, Australia.
- Infertility and Reproduction Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia.
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3
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Zhang G, Liu Z, Deng J, Liu L, Li Y, Weng S, Guo C, Zhou Z, Zhang L, Wang X, Liu G, Guo J, Bai J, Wang Y, Du Y, Li TS, Tang J, Zhang J. Smooth muscle cell fate decisions decipher a high-resolution heterogeneity within atherosclerosis molecular subtypes. J Transl Med 2022; 20:568. [PMID: 36474294 PMCID: PMC9724432 DOI: 10.1186/s12967-022-03795-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mounting evidence has revealed the dynamic variations in the cellular status and phenotype of the smooth muscle cell (SMC) are vital for shaping the atherosclerotic plaque microenvironment and ultimately mapping onto heterogeneous clinical outcomes in coronary artery disease. Currently, the underlying clinical significance of SMC evolutions remains unexplored in atherosclerosis. METHODS The dissociated cells from diseased segments within the right coronary artery of four cardiac transplant recipients and 1070 bulk samples with atherosclerosis from six bulk cohorts were retrieved. Following the SMC fate trajectory reconstruction, the MOVICS algorithm integrating the nearest template prediction was used to develop a stable and robust molecular classification. Subsequently, multi-dimensional potential biological implications, molecular features, and cell landscape heterogeneity among distinct clusters were decoded. RESULTS We proposed an SMC cell fate decision signature (SCFDS)-based atherosclerosis stratification system and identified three SCFDS subtypes (C1-C3) with distinguishing features: (i) C1 (DNA-damage repair type), elevated base excision repair (BER), DNA replication, as well as oxidative phosphorylation status. (ii) C2 (immune-activated type), stronger immune activation, hyper-inflammatory state, the complex as well as varied lesion microenvironment, advanced stage, the most severe degree of coronary stenosis severity. (iii) C3 (stromal-rich type), abundant fibrous content, stronger ECM metabolism, immune-suppressed microenvironment. CONCLUSIONS This study uncovered atherosclerosis complex cellular heterogeneity and a differentiated hierarchy of cell populations underlying SMC. The novel high-resolution stratification system could improve clinical outcomes and facilitate individualized management.
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Affiliation(s)
- Ge Zhang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Zaoqu Liu
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Jinhai Deng
- grid.13097.3c0000 0001 2322 6764Richard Dimbleby Laboratory of Cancer Research, School of Cancer & Pharmaceutical Sciences, King’s College London, London, UK
| | - Long Liu
- grid.412633.10000 0004 1799 0733Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Yu Li
- grid.260463.50000 0001 2182 8825Medical College, Nanchang University, Nanchang, 330006 Jiangxi China
| | - Siyuan Weng
- grid.412633.10000 0004 1799 0733Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Chunguang Guo
- grid.412633.10000 0004 1799 0733Department of Endovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Zhaokai Zhou
- grid.412633.10000 0004 1799 0733Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Li Zhang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Xiaofang Wang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Gangqiong Liu
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Jiacheng Guo
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Jing Bai
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Yunzhe Wang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Youyou Du
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Tao-Sheng Li
- grid.174567.60000 0000 8902 2273Department of Stem Cell Biology, Atomic Bomb Diseases Institute, Nagasaki University, Nagasaki, 852-8523 Japan
| | - Junnan Tang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
| | - Jinying Zhang
- grid.412633.10000 0004 1799 0733Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, No. 1 Eastern Jianshe Road, Zhengzhou, 450052 Henan China ,Henan Province Key Laboratory of Cardiac Injury and Repair, Zhengzhou, 450052 Henan China ,Henan Province Clinical Research Center for Cardiovascular Diseases, Zhengzhou, 450052 Henan China
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4
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Stutt N, Song M, Wilson MD, Scott IC. Cardiac specification during gastrulation - The Yellow Brick Road leading to Tinman. Semin Cell Dev Biol 2021; 127:46-58. [PMID: 34865988 DOI: 10.1016/j.semcdb.2021.11.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/05/2021] [Accepted: 11/11/2021] [Indexed: 02/07/2023]
Abstract
The question of how the heart develops, and the genetic networks governing this process have become intense areas of research over the past several decades. This research is propelled by classical developmental studies and potential clinical applications to understand and treat congenital conditions in which cardiac development is disrupted. Discovery of the tinman gene in Drosophila, and examination of its vertebrate homolog Nkx2.5, along with other core cardiac transcription factors has revealed how cardiac progenitor differentiation and maturation drives heart development. Careful observation of cardiac morphogenesis along with lineage tracing approaches indicated that cardiac progenitors can be divided into two broad classes of cells, namely the first and second heart fields, that contribute to the heart in two distinct waves of differentiation. Ample evidence suggests that the fate of individual cardiac progenitors is restricted to distinct cardiac structures quite early in development, well before the expression of canonical cardiac progenitor markers like Nkx2.5. Here we review the initial specification of cardiac progenitors, discuss evidence for the early patterning of cardiac progenitors during gastrulation, and consider how early gene expression programs and epigenetic patterns can direct their development. A complete understanding of when and how the developmental potential of cardiac progenitors is determined, and their potential plasticity, is of great interest developmentally and also has important implications for both the study of congenital heart disease and therapeutic approaches based on cardiac stem cell programming.
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Affiliation(s)
- Nathan Stutt
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Mengyi Song
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Michael D Wilson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada
| | - Ian C Scott
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S1A8, Canada.
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5
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Alvarez Fallas ME, Pedraza-Arevalo S, Cujba AM, Manea T, Lambert C, Morrugares R, Sancho R. Stem/progenitor cells in normal physiology and disease of the pancreas. Mol Cell Endocrinol 2021; 538:111459. [PMID: 34543699 PMCID: PMC8573583 DOI: 10.1016/j.mce.2021.111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 03/19/2021] [Accepted: 09/13/2021] [Indexed: 02/08/2023]
Abstract
Though embryonic pancreas progenitors are well characterised, the existence of stem/progenitor cells in the postnatal mammalian pancreas has been long debated, mainly due to contradicting results on regeneration after injury or disease in mice. Despite these controversies, sequencing advancements combined with lineage tracing and organoid technologies indicate that homeostatic and trigger-induced regenerative responses in mice could occur. The presence of putative progenitor cells in the adult pancreas has been proposed during homeostasis and upon different stress challenges such as inflammation, tissue damage and oncogenic stress. More recently, single cell transcriptomics has revealed a remarkable heterogeneity in all pancreas cell types, with some cells showing the signature of potential progenitors. In this review we provide an overview on embryonic and putative adult pancreas progenitors in homeostasis and disease, with special emphasis on in vitro culture systems and scRNA-seq technology as tools to address the progenitor nature of different pancreatic cells.
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Affiliation(s)
- Mario Enrique Alvarez Fallas
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Sergio Pedraza-Arevalo
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Ana-Maria Cujba
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Teodora Manea
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Christopher Lambert
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Rosario Morrugares
- Instituto Maimonides de Investigacion Biomedica de Cordoba (IMIBIC), Cordoba, Spain; Departamento de Biologia Celular, Fisiologia e Inmunologia, Universidad de Cordoba, Cordoba, Spain; Hospital Universitario Reina Sofia, Cordoba, Spain
| | - Rocio Sancho
- Centre for Stem Cells and Regenerative Medicine, Faculty of Life Sciences & Medicine, King's College London, London, UK; Department of Medicine III, University Hospital Carl Gustav Carus, Dresden, Germany.
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6
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Abstract
Asymmetric cell division (ACD) is an evolutionarily conserved mechanism used by prokaryotes and eukaryotes alike to control cell fate and generate cell diversity. A detailed mechanistic understanding of ACD is therefore necessary to understand cell fate decisions in health and disease. ACD can be manifested in the biased segregation of macromolecules, the differential partitioning of cell organelles, or differences in sibling cell size or shape. These events are usually preceded by and influenced by symmetry breaking events and cell polarization. In this Review, we focus predominantly on cell intrinsic mechanisms and their contribution to cell polarization, ACD and binary cell fate decisions. We discuss examples of polarized systems and detail how polarization is established and, whenever possible, how it contributes to ACD. Established and emerging model organisms will be considered alike, illuminating both well-documented and underexplored forms of polarization and ACD.
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Affiliation(s)
- Bharath Sunchu
- Department of Biology, University of Washington, Life Science Building, Seattle, WA 98195, USA
| | - Clemens Cabernard
- Department of Biology, University of Washington, Life Science Building, Seattle, WA 98195, USA
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7
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Abstract
Background Time series single-cell RNA sequencing (scRNA-seq) data are emerging. However, the analysis of time series scRNA-seq data could be compromised by 1) distortion created by assorted sources of data collection and generation across time samples and 2) inheritance of cell-to-cell variations by stochastic dynamic patterns of gene expression. This calls for the development of an algorithm able to visualize time series scRNA-seq data in order to reveal latent structures and uncover dynamic transition processes. Results In this study, we propose an algorithm, termed time series elastic embedding (TSEE), by incorporating experimental temporal information into the elastic embedding (EE) method, in order to visualize time series scRNA-seq data. TSEE extends the EE algorithm by penalizing the proximal placement of latent points that correspond to data points otherwise separated by experimental time intervals. TSEE is herein used to visualize time series scRNA-seq datasets of embryonic developmental processed in human and zebrafish. We demonstrate that TSEE outperforms existing methods (e.g. PCA, tSNE and EE) in preserving local and global structures as well as enhancing the temporal resolution of samples. Meanwhile, TSEE reveals the dynamic oscillation patterns of gene expression waves during zebrafish embryogenesis. Conclusions TSEE can efficiently visualize time series scRNA-seq data by diluting the distortions of assorted sources of data variation across time stages and achieve the temporal resolution enhancement by preserving temporal order and structure. TSEE uncovers the subtle dynamic structures of gene expression patterns, facilitating further downstream dynamic modeling and analysis of gene expression processes. The computational framework of TSEE is generalizable by allowing the incorporation of other sources of information.
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Affiliation(s)
- Shaokun An
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Ma
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Lin Wan
- Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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8
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Stefanovic S, Zaffran S. Mechanisms of retinoic acid signaling during cardiogenesis. Mech Dev 2016; 143:9-19. [PMID: 28007475 DOI: 10.1016/j.mod.2016.12.002] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 11/29/2016] [Accepted: 12/12/2016] [Indexed: 10/20/2022]
Abstract
Substantial experimental and epidemiological data have highlighted the interplay between nutritional and genetic factors in the development of congenital heart defects. Retinoic acid (RA), a derivative of vitamin A, plays a key role during vertebrate development including the formation of the heart. Retinoids bind to RA and retinoid X receptors (RARs and RXRs) which then regulate tissue-specific genes. Here, we will focus on the roles of RA signaling and receptors in gene regulation during cardiogenesis, and the consequence of deregulated retinoid signaling on heart formation and congenital heart defects.
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9
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Rao J, Greber B. Concise Review: Signaling Control of Early Fate Decisions Around the Human Pluripotent Stem Cell State. Stem Cells 2016; 35:277-283. [PMID: 27758015 DOI: 10.1002/stem.2527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/22/2016] [Accepted: 10/04/2016] [Indexed: 01/23/2023]
Abstract
Human embryonic stem cells (hESCs) present a fascinating and powerful system for generating specialized cell types of the human body. Culture and directed differentiation of these cells however requires an understanding of the pluripotent ground state and of how cell lineage decisions in this system are made. In this review, we highlight both these aspects in light of recent findings and technical progress. Hence, advances in culturing the human preimplantation embryo beyond the implantation barrier and in analyzing it at the single-cell level shed new light on the hESC tissue of origin. We argue that these findings have important implications for our view of hESC identity and we critically discuss recent efforts in converting these cells to a more primitive state. With an emphasis on the roles played by major signaling pathways, we furthermore attempt to infer key principles underlying cell fate control in hESCs from recently published work. This integrated model combines defined signaling pathway manipulation with the regulation of core hESC genes, to aid in controlling cell lineage allocation in a rational manner. Stem Cells 2017;35:277-283.
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Affiliation(s)
- Jyoti Rao
- Max Planck Institute for Molecular Biomedicine, Human Stem Cell Pluripotency Group, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
| | - Boris Greber
- Max Planck Institute for Molecular Biomedicine, Human Stem Cell Pluripotency Group, Münster, Germany.,Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany
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10
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Liu Y, Li S, Liu Z, Wang R. Bifurcation-based approach reveals synergism and optimal combinatorial perturbation. J Biol Phys 2016; 42:399-414. [PMID: 27079194 DOI: 10.1007/s10867-016-9414-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 03/02/2016] [Indexed: 12/28/2022] Open
Abstract
Cells accomplish the process of fate decisions and form terminal lineages through a series of binary choices in which cells switch stable states from one branch to another as the interacting strengths of regulatory factors continuously vary. Various combinatorial effects may occur because almost all regulatory processes are managed in a combinatorial fashion. Combinatorial regulation is crucial for cell fate decisions because it may effectively integrate many different signaling pathways to meet the higher regulation demand during cell development. However, whether the contribution of combinatorial regulation to the state transition is better than that of a single one and if so, what the optimal combination strategy is, seem to be significant issue from the point of view of both biology and mathematics. Using the approaches of combinatorial perturbations and bifurcation analysis, we provide a general framework for the quantitative analysis of synergism in molecular networks. Different from the known methods, the bifurcation-based approach depends only on stable state responses to stimuli because the state transition induced by combinatorial perturbations occurs between stable states. More importantly, an optimal combinatorial perturbation strategy can be determined by investigating the relationship between the bifurcation curve of a synergistic perturbation pair and the level set of a specific objective function. The approach is applied to two models, i.e., a theoretical multistable decision model and a biologically realistic CREB model, to show its validity, although the approach holds for a general class of biological systems.
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Affiliation(s)
- Yanwei Liu
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Shanshan Li
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Zengrong Liu
- Department of Mathematics, Shanghai University, Shanghai, China
| | - Ruiqi Wang
- Department of Mathematics, Shanghai University, Shanghai, China.
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11
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Wingert S, Thalheimer FB, Haetscher N, Rehage M, Schroeder T, Rieger MA. DNA-damage response gene GADD45A induces differentiation in hematopoietic stem cells without inhibiting cell cycle or survival. Stem Cells 2016; 34:699-710. [PMID: 26731607 PMCID: PMC4832267 DOI: 10.1002/stem.2282] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 10/07/2015] [Accepted: 10/25/2015] [Indexed: 01/26/2023]
Abstract
Hematopoietic stem cells (HSCs) maintain blood cell production life-long by their unique abilities of self-renewal and differentiation into all blood cell lineages. Growth arrest and DNA-damage-inducible 45 alpha (GADD45A) is induced by genotoxic stress in HSCs. GADD45A has been implicated in cell cycle control, cell death and senescence, as well as in DNA-damage repair. In general, GADD45A provides cellular stability by either arresting the cell cycle progression until DNA damage is repaired or, in cases of fatal damage, by inducing apoptosis. However, the function of GADD45A in hematopoiesis remains controversial. We revealed the changes in murine HSC fate control orchestrated by the expression of GADD45A at single cell resolution. In contrast to other cellular systems, GADD45A expression did not cause a cell cycle arrest or an alteration in the decision between cell survival and apoptosis in HSCs. Strikingly, GADD45A strongly induced and accelerated the differentiation program in HSCs. Continuous tracking of individual HSCs and their progeny via time-lapse microscopy elucidated that once GADD45A was expressed, HSCs differentiate into committed progenitors within 29 hours. GADD45A-expressing HSCs failed to long-term reconstitute the blood of recipients by inducing multilineage differentiation in vivo. Importantly, γ-irradiation of HSCs induced their differentiation by upregulating endogenous GADD45A. The differentiation induction by GADD45A was transmitted by activating p38 Mitogen-activated protein kinase (MAPK) signaling and allowed the generation of megakaryocytic-erythroid, myeloid, and lymphoid lineages. These data indicate that genotoxic stress-induced GADD45A expression in HSCs prevents their fatal transformation by directing them into differentiation and thereby clearing them from the system.
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Affiliation(s)
- Susanne Wingert
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Frederic B Thalheimer
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Nadine Haetscher
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Maike Rehage
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - Timm Schroeder
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Michael A Rieger
- LOEWE Center for Cell and Gene Therapy and Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Frankfurt am Main, Germany.,Georg-Speyer-Haus, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Stefanovic S, Christoffels VM. GATA-dependent transcriptional and epigenetic control of cardiac lineage specification and differentiation. Cell Mol Life Sci 2015; 72:3871-81. [PMID: 26126786 DOI: 10.1007/s00018-015-1974-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 06/15/2015] [Accepted: 06/17/2015] [Indexed: 12/14/2022]
Abstract
Heart progenitor cells differentiate into various cell types including pacemaker and working cardiomyocytes. Cell-type specific gene expression is achieved by combinatorial interactions between tissue-specific transcription factors (TFs), co-factors, and chromatin remodelers and DNA binding elements in regulatory regions. Dysfunction of these transcriptional networks may result in congenital heart defects. Functional analysis of the regulatory DNA sequences has contributed substantially to the identification of the transcriptional network components and combinatorial interactions regulating the tissue-specific gene programs. GATA TFs have been identified as central players in these networks. In particular, GATA binding elements have emerged as a platform to recruit broadly active histone modification enzymes and cell-type-specific co-factors to drive cell-type-specific gene programs. Here, we discuss the role of GATA factors in cell fate decisions and differentiation in the developing heart.
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Daniel G, Schmidt-Edelkraut U, Spengler D, Hoffmann A. Imprinted Zac1 in neural stem cells. World J Stem Cells 2015; 7:300-314. [PMID: 25815116 PMCID: PMC4369488 DOI: 10.4252/wjsc.v7.i2.300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/24/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023] Open
Abstract
Neural stem cells (NSCs) and imprinted genes play an important role in brain development. On historical grounds, these two determinants have been largely studied independently of each other. Recent evidence suggests, however, that NSCs can reset select genomic imprints to prevent precocious depletion of the stem cell reservoir. Moreover, imprinted genes like the transcriptional regulator Zac1 can fine tune neuronal vs astroglial differentiation of NSCs. Zac1 binds in a sequence-specific manner to pro-neuronal and imprinted genes to confer transcriptional regulation and furthermore coregulates members of the p53-family in NSCs. At the genome scale, Zac1 is a central hub of an imprinted gene network comprising genes with an important role for NSC quiescence, proliferation and differentiation. Overall, transcriptional, epigenomic, and genomic mechanisms seem to coordinate the functional relationships of NSCs and imprinted genes from development to maturation, and possibly aging.
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Li S, Liu Y, Liu Z, Wang R. Bifurcation dynamics and determination of alternate cell fates in bipotent progenitor cells. Cogn Neurodyn 2015; 9:221-9. [PMID: 25852780 DOI: 10.1007/s11571-014-9318-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 09/29/2014] [Accepted: 11/03/2014] [Indexed: 01/29/2023] Open
Abstract
The gene regulatory networks in which two lineage-affiliated transcription factors, such as GATA1 and PU.1, inhibit each other but activate themselves so as to regulate the choice between alternative cell fates have been extensively studied. These simple networks can generate bistability and explain the transitions between the alternative cell fates. The commitment of a progenitor cell to a new fate corresponds to the occurrence of different types of bifurcations, depending on if a system is symmetrical and how perturbations affect the system. Here we take a general modeling and analyzing approach and show that the lateral inhibition with symmetry and asymmetry can lead to different bifurcation dynamics. Especially, if cell fate decision-making is initiated with asymmetry or symmetry-breaking perturbations, a progenitor cell pre-patterns itself into a polarized cell, depending on the asymmetry or symmetry-breaking perturbations. This study may help us understand the fundamental features of binary cell fate decisions more clearly and further apply to a wider range of decision-making processes.
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Affiliation(s)
- Shanshan Li
- Institute of Systems Biology, Shanghai University, Shanghai, 200444 China
| | - Yanwei Liu
- Institute of Systems Biology, Shanghai University, Shanghai, 200444 China
| | - Zengrong Liu
- Institute of Systems Biology, Shanghai University, Shanghai, 200444 China
| | - Ruiqi Wang
- Institute of Systems Biology, Shanghai University, Shanghai, 200444 China
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