1
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Liu Y, Zhang SY, Kleijn IT, Stumpf MPH. Approximate Bayesian computation for inferring Waddington landscapes from single-cell data. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231697. [PMID: 39076359 PMCID: PMC11285904 DOI: 10.1098/rsos.231697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 05/01/2024] [Indexed: 07/31/2024]
Abstract
Single-cell technologies allow us to gain insights into cellular processes at unprecedented resolution. In stem cell and developmental biology snapshot data allow us to characterize how the transcriptional states of cells change between successive cell types. Here, we show how approximate Bayesian computation (ABC) can be employed to calibrate mathematical models against single-cell data. In our simulation study, we demonstrate the pivotal role of the adequate choice of distance measures appropriate for single-cell data. We show that for good distance measures, notably optimal transport with the Sinkhorn divergence, we can infer parameters for mathematical models from simulated single-cell data. We show that the ABC posteriors can be used (i) to characterize parameter sensitivity and identify dependencies between different parameters and (ii) to construct representations of the Waddington or epigenetic landscape, which forms a popular and interpretable representation of the developmental dynamics. In summary, these results pave the way for fitting mechanistic models of stem cell differentiation to single-cell data.
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Affiliation(s)
- Yujing Liu
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | - Stephen Y. Zhang
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
| | | | - Michael P. H. Stumpf
- School of Mathematics and Statistics, University of Melbourne, Melbourne, Australia
- School of BioScience, University of Melbourne, Melbourne, Australia
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2
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Croydon-Veleslavov IA, Stumpf MPH. Repeated Decision Stumping Distils Simple Rules from Single-Cell Data. J Comput Biol 2024; 31:21-40. [PMID: 38170180 DOI: 10.1089/cmb.2021.0613] [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] [Indexed: 01/05/2024] Open
Abstract
Single-cell data afford unprecedented insights into molecular processes. But the complexity and size of these data sets have proved challenging and given rise to a large armory of statistical and machine learning approaches. The majority of approaches focuses on either describing features of these data, or making predictions and classifying unlabeled samples. In this study, we introduce repeated decision stumping (ReDX) as a method to distill simple models from single-cell data. We develop decision trees of depth one-hence "stumps"-to identify in an inductive manner, gene products involved in driving cell fate transitions, and in applications to published data we are able to discover the key players involved in these processes in an unbiased manner without prior knowledge. Our algorithm is deliberately targeting the simplest possible candidate hypotheses that can be extracted from complex high-dimensional data. There are three reasons for this: (1) the predictions become straightforwardly testable hypotheses; (2) the identified candidates form the basis for further mechanistic model development, for example, for engineering and synthetic biology interventions; and (3) this approach complements existing descriptive modeling approaches and frameworks. The approach is computationally efficient, has remarkable predictive power, including in simulation studies where the ground truth is known, and yields robust and statistically stable predictors; the same set of candidates is generated by applying the algorithm to different subsamples of experimental data.
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Affiliation(s)
- Ivan A Croydon-Veleslavov
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
| | - Michael P H Stumpf
- Department of Life Sciences, Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, London, United Kingdom
- School of BioSciences, University of Melbourne, Parkville, Australia
- School of Mathematics and Statistics, University of Melbourne, Parkville, Australia
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3
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Kholodenko BN, Kolch W, Rukhlenko OS. Reversing pathological cell states: the road less travelled can extend the therapeutic horizon. Trends Cell Biol 2023; 33:913-923. [PMID: 37263821 PMCID: PMC10593090 DOI: 10.1016/j.tcb.2023.04.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 06/03/2023]
Abstract
Acquisition of omics data advances at a formidable pace. Yet, our ability to utilize these data to control cell phenotypes and design interventions that reverse pathological states lags behind. Here, we posit that cell states are determined by core networks that control cell-wide networks. To steer cell fate decisions, core networks connecting genotype to phenotype must be reconstructed and understood. A recent method, cell state transition assessment and regulation (cSTAR), applies perturbation biology to quantify causal connections and mechanistically models how core networks influence cell phenotypes. cSTAR models are akin to digital cell twins enabling us to purposefully convert pathological states back to physiologically normal states. While this capability has a range of applications, here we discuss reverting oncogenic transformation.
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Affiliation(s)
- Boris N Kholodenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland; Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA.
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland; Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
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4
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Knudsen TE, Hamilton WB, Proks M, Lykkegaard M, Linneberg-Agerholm M, Nielsen AV, Perera M, Malzard LL, Trusina A, Brickman JM. A bipartite function of ESRRB can integrate signaling over time to balance self-renewal and differentiation. Cell Syst 2023; 14:788-805.e8. [PMID: 37633265 DOI: 10.1016/j.cels.2023.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 03/22/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Cooperative DNA binding of transcription factors (TFs) integrates the cellular context to support cell specification during development. Naive mouse embryonic stem cells are derived from early development and can sustain their pluripotent identity indefinitely. Here, we ask whether TFs associated with pluripotency evolved to directly support this state or if the state emerges from their combinatorial action. NANOG and ESRRB are key pluripotency factors that co-bind DNA. We find that when both factors are expressed, ESRRB supports pluripotency. However, when NANOG is absent, ESRRB supports a bistable culture of cells with an embryo-like primitive endoderm identity ancillary to pluripotency. The stoichiometry between NANOG and ESRRB allows quantitative titration of this differentiation, and in silico modeling of bipartite ESRRB activity suggests it safeguards plasticity in differentiation. Thus, the concerted activity of cooperative TFs can transform their effect to sustain intermediate cell identities and allow ex vivo expansion of immortal stem cells. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Teresa E Knudsen
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - William B Hamilton
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Martin Proks
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Maria Lykkegaard
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Madeleine Linneberg-Agerholm
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Marta Perera
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | | | - Ala Trusina
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joshua M Brickman
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
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5
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Jiménez S, Schreiber V, Mercier R, Gradwohl G, Molina N. Characterization of cell-fate decision landscapes by estimating transcription factor dynamics. CELL REPORTS METHODS 2023; 3:100512. [PMID: 37533652 PMCID: PMC10391345 DOI: 10.1016/j.crmeth.2023.100512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023]
Abstract
Time-specific modulation of gene expression during differentiation by transcription factors promotes cell diversity. However, estimating their dynamic regulatory activity at the single-cell level and in a high-throughput manner remains challenging. We present FateCompass, an integrative approach that utilizes single-cell transcriptomics data to identify lineage-specific transcription factors throughout differentiation. By combining a probabilistic framework with RNA velocities or differentiation potential, we estimate transition probabilities, while a linear model of gene regulation is employed to compute transcription factor activities. Considering dynamic changes and correlations of expression and activities, FateCompass identifies lineage-specific regulators. Our validation using in silico data and application to pancreatic endocrine cell differentiation datasets highlight both known and potentially novel lineage-specific regulators. Notably, we uncovered undescribed transcription factors of an enterochromaffin-like population during in vitro differentiation toward ß-like cells. FateCompass provides a valuable framework for hypothesis generation, advancing our understanding of the gene regulatory networks driving cell-fate decisions.
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Affiliation(s)
- Sara Jiménez
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Valérie Schreiber
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Reuben Mercier
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Gérard Gradwohl
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
| | - Nacho Molina
- Université de Strasbourg, Strasbourg, France
- CNRS, UMR 7104, 67400 Illkirch, France
- INSERM, UMR-S 1258, 67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67400 Illkirch, France
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6
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Shlyakhtina Y, Bloechl B, Portal MM. BdLT-Seq as a barcode decay-based method to unravel lineage-linked transcriptome plasticity. Nat Commun 2023; 14:1085. [PMID: 36841849 PMCID: PMC9968323 DOI: 10.1038/s41467-023-36744-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 02/14/2023] [Indexed: 02/26/2023] Open
Abstract
Cell plasticity is a core biological process underlying a myriad of molecular and cellular events taking place throughout organismal development and evolution. It has been postulated that cellular systems thrive to balance the organization of meta-stable states underlying this phenomenon, thereby maintaining a degree of populational homeostasis compatible with an ever-changing environment and, thus, life. Notably, albeit circumstantial evidence has been gathered in favour of the latter conceptual framework, a direct observation of meta-state dynamics and the biological consequences of such a process in generating non-genetic clonal diversity and divergent phenotypic output remains largely unexplored. To fill this void, here we develop a lineage-tracing technology termed Barcode decay Lineage Tracing-Seq. BdLT-Seq is based on episome-encoded molecular identifiers that, supported by the dynamic decay of the tracing information upon cell division, ascribe directionality to a cell lineage tree whilst directly coupling non-genetic molecular features to phenotypes in comparable genomic landscapes. We show that cell transcriptome states are both inherited, and dynamically reshaped following constrained rules encoded within the cell lineage in basal growth conditions, upon oncogene activation and throughout the process of reversible resistance to therapeutic cues thus adjusting phenotypic output leading to intra-clonal non-genetic diversity.
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Affiliation(s)
- Yelyzaveta Shlyakhtina
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK
| | - Bianca Bloechl
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK
| | - Maximiliano M Portal
- Cell Plasticity & Epigenetics Lab, Cancer Research UK - Manchester Institute, The University of Manchester, SK10 4TG, Manchester, UK.
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7
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Mohammadi-Shemirani P, Sood T, Paré G. From 'Omics to Multi-omics Technologies: the Discovery of Novel Causal Mediators. Curr Atheroscler Rep 2023; 25:55-65. [PMID: 36595202 PMCID: PMC9807989 DOI: 10.1007/s11883-022-01078-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/31/2022] [Indexed: 01/04/2023]
Abstract
PURPOSE OF REVIEW 'Omics studies provide a comprehensive characterisation of a biological entity, such as the genome, epigenome, transcriptome, proteome, metabolome, or microbiome. This review covers the unique properties of these types of 'omics and their roles as causal mediators in cardiovascular disease. Moreover, applications and challenges of integrating multiple types of 'omics data to increase predictive power, improve causal inference, and elucidate biological mechanisms are discussed. RECENT FINDINGS Multi-omics approaches are growing in adoption as they provide orthogonal evidence and overcome the limitations of individual types of 'omics data. Studies with multiple types of 'omics data have improved the diagnosis and prediction of disease states and afforded a deeper understanding of underlying pathophysiological mechanisms, beyond any single type of 'omics data. For instance, disease-associated loci in the genome can be supplemented with other 'omics to prioritise causal genes and understand the function of non-coding variants. Alternatively, techniques, such as Mendelian randomisation, can leverage genetics to provide evidence supporting a causal role for disease-associated molecules, and elucidate their role in disease pathogenesis. As technologies improve, costs for 'omics studies will continue to fall and datasets will become increasingly accessible to researchers. The intrinsically unbiased nature of 'omics data is well-suited to exploratory analyses that discover causal mediators of disease, and multi-omics is an emerging discipline that leverages the strengths of each type of 'omics data to provide insights greater than the sum of its parts.
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Affiliation(s)
- Pedrum Mohammadi-Shemirani
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
| | - Tushar Sood
- Temerty Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Guillaume Paré
- Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Thrombosis and Atherosclerosis Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, Hamilton, ON Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- Department of Pathology and Molecular Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON Canada
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8
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Bahrami-Nejad Z, Zhang ZB, Tholen S, Sharma S, Rabiee A, Zhao ML, Kraemer FB, Teruel MN. Early enforcement of cell identity by a functional component of the terminally differentiated state. PLoS Biol 2022; 20:e3001900. [PMID: 36469503 PMCID: PMC9721491 DOI: 10.1371/journal.pbio.3001900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
How progenitor cells can attain a distinct differentiated cell identity is a challenging problem given the fluctuating signaling environment in which cells exist and that critical transcription factors are often not unique to a differentiation process. Here, we test the hypothesis that a unique differentiated cell identity can result from a core component of the differentiated state doubling up as a signaling protein that also drives differentiation. Using live single-cell imaging in the adipocyte differentiation system, we show that progenitor fat cells (preadipocytes) can only commit to terminally differentiate after up-regulating FABP4, a lipid buffer that is highly enriched in mature adipocytes. Upon induction of adipogenesis in mouse preadipocyte cells, we show that after a long delay, cells first abruptly start to engage a positive feedback between CEBPA and PPARG before then engaging, after a second delay, a positive feedback between FABP4 and PPARG. These sequential positive feedbacks both need to engage in order to drive PPARG levels past the threshold for irreversible differentiation. In the last step before commitment, PPARG transcriptionally increases FABP4 expression while fatty acid-loaded FABP4 increases PPARG activity. Together, our study suggests a control principle for robust cell identity whereby a core component of the differentiated state also promotes differentiation from its own progenitor state.
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Affiliation(s)
- Zahra Bahrami-Nejad
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Zhi-Bo Zhang
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
| | - Stefan Tholen
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Sanjeev Sharma
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
| | - Atefeh Rabiee
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Physiology and Pharmacology, Thomas J. Long School of Pharmacy and Health Sciences, University of the Pacific, Stockton, California, United States of America
| | - Michael L. Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Fredric B. Kraemer
- Department of Medicine/Division of Endocrinology, Stanford University, Stanford, California, United States of America
- VA Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Mary N. Teruel
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
- Department of Biochemistry and the Drukier Institute for Children’s Health, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
- Department of Bioengineering, Stanford University School of Medicine, Stanford, California, United States of America
- Weill Center for Metabolic Health, Division of Endocrinology, Diabetes & Metabolism, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medical College of Cornell University, New York, New York, United States of America
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9
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Toh K, Saunders D, Verd B, Steventon B. Zebrafish neuromesodermal progenitors undergo a critical state transition in vivo. iScience 2022; 25:105216. [PMID: 36274939 PMCID: PMC9579027 DOI: 10.1016/j.isci.2022.105216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/05/2022] [Accepted: 09/22/2022] [Indexed: 11/30/2022] Open
Abstract
The transition state model of cell differentiation proposes that a transient window of gene expression stochasticity precedes entry into a differentiated state. Here, we assess this theoretical model in zebrafish neuromesodermal progenitors (NMps) in vivo during late somitogenesis stages. We observed an increase in gene expression variability at the 24 somite stage (24ss) before their differentiation into spinal cord and paraxial mesoderm. Analysis of a published 18ss scRNA-seq dataset showed that the NMp population is noisier than its derivatives. By building in silico composite gene expression maps from image data, we assigned an 'NM index' to in silico NMps based on the expression of neural and mesodermal markers and demonstrated that cell population heterogeneity peaked at 24ss. Further examination revealed cells with gene expression profiles incongruent with their prospective fate. Taken together, our work supports the transition state model within an endogenous cell fate decision making event.
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Affiliation(s)
- Kane Toh
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
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10
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Rukhlenko OS, Halasz M, Rauch N, Zhernovkov V, Prince T, Wynne K, Maher S, Kashdan E, MacLeod K, Carragher NO, Kolch W, Kholodenko BN. Control of cell state transitions. Nature 2022; 609:975-985. [PMID: 36104561 PMCID: PMC9644236 DOI: 10.1038/s41586-022-05194-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/04/2022] [Indexed: 11/09/2022]
Abstract
Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment and regulation (cSTAR), an approach for mapping cell states, modelling transitions between them and predicting targeted interventions to convert cell fate decisions. cSTAR uses omics data as input, classifies cell states, and develops a workflow that transforms the input data into mechanistic models that identify a core signalling network, which controls cell fate transitions by influencing whole-cell networks. By integrating signalling and phenotypic data, cSTAR models how cells manoeuvre in Waddington's landscape1 and make decisions about which cell fate to adopt. Notably, cSTAR devises interventions to control the movement of cells in Waddington's landscape. Testing cSTAR in a cellular model of differentiation and proliferation shows a high correlation between quantitative predictions and experimental data. Applying cSTAR to different types of perturbation and omics datasets, including single-cell data, demonstrates its flexibility and scalability and provides new biological insights. The ability of cSTAR to identify targeted perturbations that interconvert cell fates will enable designer approaches for manipulating cellular development pathways and mechanistically underpinned therapeutic interventions.
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Affiliation(s)
- Oleksii S Rukhlenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Melinda Halasz
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nora Rauch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Vadim Zhernovkov
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Thomas Prince
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kieran Wynne
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Stephanie Maher
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Eugene Kashdan
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
| | - Kenneth MacLeod
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, UK
| | - Walter Kolch
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Boris N Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
- Department of Pharmacology, Yale University School of Medicine, New Haven, USA.
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11
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Ham L, Coomer M, Stumpf M. The chemical Langevin equation for biochemical systems in dynamic environments. J Chem Phys 2022; 157:094105. [DOI: 10.1063/5.0095840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Modelling and simulation of complex biochemical reaction networks form cornerstones of modern biophysics. Many of the approaches developed so far capture temporal fluctuations due to the inherent stochasticity of the biophysical processes, referred to as intrinsic noise. Stochastic fluctuations, however, predominantly stem from the interplay of the network with many other - and mostly unknown - fluctuating processes, as well as with various random signals arising from the extracellular world; these sources contribute extrinsic noise. Here we provide a computational simulation method to probe the stochastic dynamics of biochemical systems subject to both intrinsic and extrinsic noise. We develop an extrinsic chemical Langevin equation-a physically motivated extension of the chemical Langevin equation- to model intrinsically noisy reaction networks embedded in a stochastically fluctuating environment. The extrinsic CLE is a continuous approximation to the Chemical Master Equation (CME) with time-varying propensities. In our approach, noise is incorporated at the level of the CME, and can account for the full dynamics of the exogenous noise process, irrespective of timescales and their mismatches. We show that our method accurately captures the first two moments of the stationary probability density when compared with exact stochastic simulation methods, while reducing the computational runtime by several orders of magnitude. Our approach provides a method that is practical, computationally efficient and physically accurate to study systems that are simultaneously subject to a variety of noise sources.
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Affiliation(s)
- Lucy Ham
- The University of Melbourne, University of Melbourne, Australia
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12
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Sáez M, Briscoe J, Rand DA. Dynamical landscapes of cell fate decisions. Interface Focus 2022; 12:20220002. [PMID: 35860004 PMCID: PMC9184965 DOI: 10.1098/rsfs.2022.0002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The generation of cellular diversity during development involves differentiating cells transitioning between discrete cell states. In the 1940s, the developmental biologist Conrad Waddington introduced a landscape metaphor to describe this process. The developmental path of a cell was pictured as a ball rolling through a terrain of branching valleys with cell fate decisions represented by the branch points at which the ball decides between one of two available valleys. Here we discuss progress in constructing quantitative dynamical models inspired by this view of cellular differentiation. We describe a framework based on catastrophe theory and dynamical systems methods that provides the foundations for quantitative geometric models of cellular differentiation. These models can be fit to experimental data and used to make quantitative predictions about cellular differentiation. The theory indicates that cell fate decisions can be described by a small number of decision structures, such that there are only two distinct ways in which cells make a binary choice between one of two fates. We discuss the biological relevance of these mechanisms and suggest the approach is broadly applicable for the quantitative analysis of differentiation dynamics and for determining principles of developmental decisions.
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Affiliation(s)
- M. Sáez
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- IQS, Universitat Ramon Llull, Via Augusta 390, Barcelona 08017, Spain
| | - J. Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - D. A. Rand
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK
- Zeeman Institute for Systems Biology and Infectious Epidemiology Research, University of Warwick, Coventry CV4 7AL, UK
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13
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Cho H, Kuo YH, Rockne RC. Comparison of cell state models derived from single-cell RNA sequencing data: graph versus multi-dimensional space. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:8505-8536. [PMID: 35801475 PMCID: PMC9308174 DOI: 10.3934/mbe.2022395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-cell sequencing technologies have revolutionized molecular and cellular biology and stimulated the development of computational tools to analyze the data generated from these technology platforms. However, despite the recent explosion of computational analysis tools, relatively few mathematical models have been developed to utilize these data. Here we compare and contrast two cell state geometries for building mathematical models of cell state-transitions with single-cell RNA-sequencing data with hematopoeisis as a model system; (i) by using partial differential equations on a graph representing intermediate cell states between known cell types, and (ii) by using the equations on a multi-dimensional continuous cell state-space. As an application of our approach, we demonstrate how the calibrated models may be used to mathematically perturb normal hematopoeisis to simulate, predict, and study the emergence of novel cell states during the pathogenesis of acute myeloid leukemia. We particularly focus on comparing the strength and weakness of the graph model and multi-dimensional model.
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Affiliation(s)
- Heyrim Cho
- Department of Mathematics, University of California Riverside, Riverside, CA, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, USA
| | - Ya-Huei Kuo
- Department of Hematologic Malignancies Translational Science, City of Hope, Duarte, CA, USA
| | - Russell C. Rockne
- Department of Computational and Quantitative Medicine, Division of Mathematical Oncology, City of Hope, Duarte, CA, USA
- Interdisciplinary Center for Quantitative Modeling in Biology, University of California Riverside, Riverside, CA, USA
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14
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Li C, Dong J, Li J, Zhu W, Wang P, Yao Y, Wei C, Han H. Deciphering landscape dynamics of cell fate decision via a Lyapunov method. Comput Biol Chem 2022; 98:107689. [DOI: 10.1016/j.compbiolchem.2022.107689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/15/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
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15
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Wang W, Poe D, Yang Y, Hyatt T, Xing J. Epithelial-to-mesenchymal transition proceeds through directional destabilization of multidimensional attractor. eLife 2022; 11:74866. [PMID: 35188459 PMCID: PMC8920502 DOI: 10.7554/elife.74866] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 02/06/2022] [Indexed: 11/13/2022] Open
Abstract
How a cell changes from one stable phenotype to another one is a fundamental problem in developmental and cell biology. Mathematically, a stable phenotype corresponds to a stable attractor in a generally multi-dimensional state space, which needs to be destabilized so the cell relaxes to a new attractor. Two basic mechanisms for destabilizing a stable fixed point, pitchfork and saddle-node bifurcations, have been extensively studied theoretically; however, direct experimental investigation at the single-cell level remains scarce. Here, we performed live cell imaging studies and analyses in the framework of dynamical systems theories on epithelial-to-mesenchymal transition (EMT). While some mechanistic details remain controversial, EMT is a cell phenotypic transition (CPT) process central to development and pathology. Through time-lapse imaging we recorded single cell trajectories of human A549/Vim-RFP cells undergoing EMT induced by different concentrations of exogenous TGF-β in a multi-dimensional cell feature space. The trajectories clustered into two distinct groups, indicating that the transition dynamics proceeds through parallel paths. We then reconstructed the reaction coordinates and the corresponding quasi-potentials from the trajectories. The potentials revealed a plausible mechanism for the emergence of the two paths where the original stable epithelial attractor collides with two saddle points sequentially with increased TGF-β concentration, and relaxes to a new one. Functionally, the directional saddle-node bifurcation ensures a CPT proceeds towards a specific cell type, as a mechanistic realization of the canalization idea proposed by Waddington. Cells with the same genetic code can take on many different formss, or phenotypes, which have distinct roles and appearances. Sometimes cells switch from one phenotype to another as part of healthy growth or during disease. One such change is the epithelial-to-mesenchymal transition (EMT), which is involved in fetal development, wound healing and the spread of cancer cells. During EMT, closely connected epithelial cells detach from one another and change into mesenchymal cells that are able to migrate. Cells undergo a number of changes during this transition; however, the path they take to reach their new form is not entirely clear. For instance, do all cells follow the same route, or are there multiple ways that cells can shift from one state to the next? To address this question, Wang et al. studied individual lung cancer cells that had been treated with a protein that drives EMT. The cells were then imaged at regular intervals over the course of two to three days to see how they changed in response to different concentrations of protein. Using a mathematical analysis designed to study chemical reactions, Wang et al. showed that the cells transform into the mesenchymal phenotype through two main routes. This result suggests that attempts to prevent EMT, in cancer treatment for instance, would require blocking both paths taken by the cells. This information could be useful for biomedical researchers trying to regulate the EMT process. The quantitative approach of this study could also help physicists and mathematicians study other types of transition that occur in biology.
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Affiliation(s)
- Weikang Wang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Dante Poe
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Yaxuan Yang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
| | - Thomas Hyatt
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, United States
| | - Jianhua Xing
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, United States
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16
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Abstract
Network inference is a notoriously challenging problem. Inferred networks are associated with high uncertainty and likely riddled with false positive and false negative interactions. Especially for biological networks we do not have good ways of judging the performance of inference methods against real networks, and instead we often rely solely on the performance against simulated data. Gaining confidence in networks inferred from real data nevertheless thus requires establishing reliable validation methods. Here, we argue that the expectation of mixing patterns in biological networks such as gene regulatory networks offers a reasonable starting point: interactions are more likely to occur between nodes with similar biological functions. We can quantify this behaviour using the assortativity coefficient, and here we show that the resulting heuristic, functional assortativity, offers a reliable and informative route for comparing different inference algorithms.
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17
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Murugan R, Kreiman G. Multiple transcription auto regulatory loops can act as robust oscillators and decision-making motifs. Comput Struct Biotechnol J 2022; 20:5115-5135. [PMID: 36187915 PMCID: PMC9493064 DOI: 10.1016/j.csbj.2022.08.065] [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: 04/18/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
We have shown that: Negative transcription auto regulation can speed up the response time at the cost of reduced steady state protein levels. Under strong binding conditions, one can increase the steady state protein level by increasing the gene copy number without a compromise on the response time. Multiple negative transcription autoregulatory motifs can be tuned for both the response time as well as steady state protein levels by varying the gene copy number. Multiple negative autoregulatory loops can act as robust genetic oscillators. Dual feedback motifs constructed with multiple negative and positive autoregulatory loop components can act as robust oscillators and bistable decision making units within the transcription factor networks.
Response time decides how fast a gene can react against an external signal at the transcription level in a signalling cascade. The steady state protein levels of the responding genes decide the coupling between two consecutive members of a signalling cascade. A negative autoregulatory loop (NARL) present in a transcription factor network can speed up the response time of the regulated gene at the cost of reduced steady state protein level. We present here a multi NARL motif which can be tuned for both the steady state protein level as well as response time in the required direction. Remarkably, there exists an optimum Hill coefficient nopt≅4 at which the response time of the NARL motif is at minimum. When the Hill coefficient is n < nopt, then under strong binding conditions, one can raise the steady state protein level by increasing the gene copy number with almost no change in the response time of the multi NARL motif. Using detailed computational analysis, we show that the coupled multi NARL and positive auto regulatory loop (PARL) motifs can act as an oscillator as well as decision making component which are robust against extrinsic fluctuations in the control parameters. We further demonstrate that the period of oscillation of the coupled multi NARL-PARL dual feedback oscillator can also be fine-tuned by the gene copy number apart from the inducer concentration. We finally demonstrate robustness of bistable dual feedback decision making motifs with multi autoregulatory loop component.
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Affiliation(s)
- Rajamanickam Murugan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, India
| | - Gabriel Kreiman
- Children’s Hospital Boston, Harvard Medical School, Boston, USA
- Corresponding author at: Children’s Hospital Boston, Harvard Medical School, Boston, USA.
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18
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Rocca A, Kholodenko BN. Can Systems Biology Advance Clinical Precision Oncology? Cancers (Basel) 2021; 13:6312. [PMID: 34944932 PMCID: PMC8699328 DOI: 10.3390/cancers13246312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Precision oncology is perceived as a way forward to treat individual cancer patients. However, knowing particular cancer mutations is not enough for optimal therapeutic treatment, because cancer genotype-phenotype relationships are nonlinear and dynamic. Systems biology studies the biological processes at the systems' level, using an array of techniques, ranging from statistical methods to network reconstruction and analysis, to mathematical modeling. Its goal is to reconstruct the complex and often counterintuitive dynamic behavior of biological systems and quantitatively predict their responses to environmental perturbations. In this paper, we review the impact of systems biology on precision oncology. We show examples of how the analysis of signal transduction networks allows to dissect resistance to targeted therapies and inform the choice of combinations of targeted drugs based on tumor molecular alterations. Patient-specific biomarkers based on dynamical models of signaling networks can have a greater prognostic value than conventional biomarkers. These examples support systems biology models as valuable tools to advance clinical and translational oncological research.
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Affiliation(s)
- Andrea Rocca
- Hygiene and Public Health, Local Health Unit of Romagna, 47121 Forlì, Italy
| | - Boris N. Kholodenko
- Systems Biology Ireland, School of Medicine, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
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19
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Zhang S, Afanassiev A, Greenstreet L, Matsumoto T, Schiebinger G. Optimal transport analysis reveals trajectories in steady-state systems. PLoS Comput Biol 2021; 17:e1009466. [PMID: 34860824 PMCID: PMC8691649 DOI: 10.1371/journal.pcbi.1009466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 12/21/2021] [Accepted: 09/20/2021] [Indexed: 01/25/2023] Open
Abstract
Understanding how cells change their identity and behaviour in living systems is an important question in many fields of biology. The problem of inferring cell trajectories from single-cell measurements has been a major topic in the single-cell analysis community, with different methods developed for equilibrium and non-equilibrium systems (e.g. haematopoeisis vs. embryonic development). We show that optimal transport analysis, a technique originally designed for analysing time-courses, may also be applied to infer cellular trajectories from a single snapshot of a population in equilibrium. Therefore, optimal transport provides a unified approach to inferring trajectories that is applicable to both stationary and non-stationary systems. Our method, StationaryOT, is mathematically motivated in a natural way from the hypothesis of a Waddington's epigenetic landscape. We implement StationaryOT as a software package and demonstrate its efficacy in applications to simulated data as well as single-cell data from Arabidopsis thaliana root development.
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Affiliation(s)
- Stephen Zhang
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Anton Afanassiev
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Laura Greenstreet
- Department of Mathematics, University of British Columbia, Vancouver, Canada
| | - Tetsuya Matsumoto
- Department of Mathematics, University of British Columbia, Vancouver, Canada
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20
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Noise distorts the epigenetic landscape and shapes cell-fate decisions. Cell Syst 2021; 13:83-102.e6. [PMID: 34626539 DOI: 10.1016/j.cels.2021.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 06/21/2021] [Accepted: 09/02/2021] [Indexed: 12/24/2022]
Abstract
The Waddington epigenetic landscape has become an iconic representation of the cellular differentiation process. Recent single-cell transcriptomic data provide new opportunities for quantifying this originally conceptual tool, offering insight into the gene regulatory networks underlying cellular development. While many methods for constructing the landscape have been proposed, by far the most commonly employed approach is based on computing the landscape as the negative logarithm of the steady-state probability distribution. Here, we use simple models to highlight the complexities and limitations that arise when reconstructing the potential landscape in the presence of stochastic fluctuations. We consider how the landscape changes in accordance with different stochastic systems and show that it is the subtle interplay between the deterministic and stochastic components of the system that ultimately shapes the landscape. We further discuss how the presence of noise has important implications for the identifiability of the regulatory dynamics from experimental data. A record of this paper's transparent peer review process is included in the supplemental information.
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21
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Zhou P, Wang S, Li T, Nie Q. Dissecting transition cells from single-cell transcriptome data through multiscale stochastic dynamics. Nat Commun 2021; 12:5609. [PMID: 34556644 PMCID: PMC8460805 DOI: 10.1038/s41467-021-25548-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/11/2021] [Indexed: 11/25/2022] Open
Abstract
Advances in single-cell technologies allow scrutinizing of heterogeneous cell states, however, detecting cell-state transitions from snap-shot single-cell transcriptome data remains challenging. To investigate cells with transient properties or mixed identities, we present MuTrans, a method based on multiscale reduction technique to identify the underlying stochastic dynamics that prescribes cell-fate transitions. By iteratively unifying transition dynamics across multiple scales, MuTrans constructs the cell-fate dynamical manifold that depicts progression of cell-state transitions, and distinguishes stable and transition cells. In addition, MuTrans quantifies the likelihood of all possible transition trajectories between cell states using coarse-grained transition path theory. Downstream analysis identifies distinct genes that mark the transient states or drive the transitions. The method is consistent with the well-established Langevin equation and transition rate theory. Applying MuTrans to datasets collected from five different single-cell experimental platforms, we show its capability and scalability to robustly unravel complex cell fate dynamics induced by transition cells in systems such as tumor EMT, iPSC differentiation and blood cell differentiation. Overall, our method bridges data-driven and model-based approaches on cell-fate transitions at single-cell resolution.
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Affiliation(s)
- Peijie Zhou
- LMAM and School of Mathematical Sciences, Peking University, Beijing, China
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Shuxiong Wang
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA
| | - Tiejun Li
- LMAM and School of Mathematical Sciences, Peking University, Beijing, China.
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, Irvine, CA, USA.
- Department of Cell and Developmental Biology, University of California, Irvine, CA, USA.
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22
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Winkley KM, Reeves WM, Veeman MT. Single-cell analysis of cell fate bifurcation in the chordate Ciona. BMC Biol 2021; 19:180. [PMID: 34465302 PMCID: PMC8408944 DOI: 10.1186/s12915-021-01122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. RESULTS AND CONCLUSIONS We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a "broad-hourglass" model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.
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Affiliation(s)
- Konner M Winkley
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Wendy M Reeves
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA
| | - Michael T Veeman
- Division of Biology, Kansas State University, Manhattan, KS, 66506, USA.
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23
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Camacho-Aguilar E, Warmflash A, Rand DA. Quantifying cell transitions in C. elegans with data-fitted landscape models. PLoS Comput Biol 2021; 17:e1009034. [PMID: 34061834 PMCID: PMC8195438 DOI: 10.1371/journal.pcbi.1009034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/11/2021] [Accepted: 05/03/2021] [Indexed: 12/19/2022] Open
Abstract
Increasing interest has emerged in new mathematical approaches that simplify the study of complex differentiation processes by formalizing Waddington's landscape metaphor. However, a rational method to build these landscape models remains an open problem. Here we study vulval development in C. elegans by developing a framework based on Catastrophe Theory (CT) and approximate Bayesian computation (ABC) to build data-fitted landscape models. We first identify the candidate qualitative landscapes, and then use CT to build the simplest model consistent with the data, which we quantitatively fit using ABC. The resulting model suggests that the underlying mechanism is a quantifiable two-step decision controlled by EGF and Notch-Delta signals, where a non-vulval/vulval decision is followed by a bistable transition to the two vulval states. This new model fits a broad set of data and makes several novel predictions.
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Affiliation(s)
- Elena Camacho-Aguilar
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- Department of Biosciences, Rice University, Houston, Texas, United States of America
| | - Aryeh Warmflash
- Department of Biosciences, Rice University, Houston, Texas, United States of America
- Department of Bioengineering, Rice University, Houston, Texas, United States of America
| | - David A. Rand
- Mathematics Institute, University of Warwick, Coventry, United Kingdom
- Zeeman Institute for Systems Biology & Infectious Disease Epidemiology Research, University of Warwick, Coventry, United Kingdom
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24
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Lambert J, Lloret-Fernández C, Laplane L, Poole RJ, Jarriault S. On the origins and conceptual frameworks of natural plasticity-Lessons from single-cell models in C. elegans. Curr Top Dev Biol 2021; 144:111-159. [PMID: 33992151 DOI: 10.1016/bs.ctdb.2021.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
How flexible are cell identities? This problem has fascinated developmental biologists for several centuries and can be traced back to Abraham Trembley's pioneering manipulations of Hydra to test its regeneration abilities in the 1700s. Since the cell theory in the mid-19th century, developmental biology has been dominated by a single framework in which embryonic cells are committed to specific cell fates, progressively and irreversibly acquiring their differentiated identities. This hierarchical, unidirectional and irreversible view of cell identity has been challenged in the past decades through accumulative evidence that many cell types are more plastic than previously thought, even in intact organisms. The paradigm shift introduced by such plasticity calls into question several other key traditional concepts, such as how to define a differentiated cell or more generally cellular identity, and has brought new concepts, such as distinct cellular states. In this review, we want to contribute to this representation by attempting to clarify the conceptual and theoretical frameworks of cell plasticity and identity. In the context of these new frameworks we describe here an atlas of natural plasticity of cell identity in C. elegans, including our current understanding of the cellular and molecular mechanisms at play. The worm further provides interesting cases at the borderlines of cellular plasticity that highlight the conceptual challenges still ahead. We then discuss a set of future questions and perspectives arising from the studies of natural plasticity in the worm that are shared with other reprogramming and plasticity events across phyla.
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Affiliation(s)
- Julien Lambert
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Strasbourg, France
| | - Carla Lloret-Fernández
- Department of Cell and Developmental Biology, University College London, London, United Kingdom
| | - Lucie Laplane
- CNRS UMR 8590, University Paris I Panthéon-Sorbonne, IHPST, Paris, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, London, United Kingdom.
| | - Sophie Jarriault
- IGBMC, Development and Stem Cells Department, CNRS UMR7104, INSERM U1258, Université de Strasbourg, Strasbourg, France.
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25
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Guillemin A, Stumpf MPH. Noise and the molecular processes underlying cell fate decision-making. Phys Biol 2021; 18:011002. [PMID: 33181489 DOI: 10.1088/1478-3975/abc9d1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cell fate decision-making events involve the interplay of many molecular processes, ranging from signal transduction to genetic regulation, as well as a set of molecular and physiological feedback loops. Each aspect offers a rich field of investigation in its own right, but to understand the whole process, even in simple terms, we need to consider them together. Here we attempt to characterise this process by focussing on the roles of noise during cell fate decisions. We use a range of recent results to develop a view of the sequence of events by which a cell progresses from a pluripotent or multipotent to a differentiated state: chromatin organisation, transcription factor stoichiometry, and cellular signalling all change during this progression, and all shape cellular variability, which becomes maximal at the transition state.
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Affiliation(s)
- Anissa Guillemin
- School of BioSciences, University of Melbourne, Parkville, Australia
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26
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Sinha S, Jones BM, Traniello IM, Bukhari SA, Halfon MS, Hofmann HA, Huang S, Katz PS, Keagy J, Lynch VJ, Sokolowski MB, Stubbs LJ, Tabe-Bordbar S, Wolfner MF, Robinson GE. Behavior-related gene regulatory networks: A new level of organization in the brain. Proc Natl Acad Sci U S A 2020; 117:23270-23279. [PMID: 32661177 PMCID: PMC7519311 DOI: 10.1073/pnas.1921625117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neuronal networks are the standard heuristic model today for describing brain activity associated with animal behavior. Recent studies have revealed an extensive role for a completely distinct layer of networked activities in the brain-the gene regulatory network (GRN)-that orchestrates expression levels of hundreds to thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial as well as temporal dimensions, across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing inspiration from the rich literature on GRNs related to animal development, comparing and contrasting these two broad classes of GRNs as they relate to their respective phenotypic manifestations. Developmental GRNs also represent a third layer of network biology, playing out over a third timescale, which is believed to play a crucial mediatory role between neuronal networks and behavioral GRNs. We end with a special emphasis on social behavior, discuss whether unique GRN organization and cis-regulatory architecture underlies this special class of behavior, and review literature that suggests an affirmative answer.
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Affiliation(s)
- Saurabh Sinha
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL 61801;
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Beryl M Jones
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544
| | - Ian M Traniello
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Neuroscience Program, University of Illinois, Urbana-Champaign, IL 61801
| | - Syed A Bukhari
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Informatics Program, University of Illinois, Urbana-Champaign, IL 61820
| | - Marc S Halfon
- Department of Biochemistry, University at Buffalo-State University of New York, Buffalo, NY 14203
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712
| | - Sui Huang
- Institute for Systems Biology, Seattle, WA 98109
| | - Paul S Katz
- Department of Biology, University of Massachusetts, Amherst, MA 01003
| | - Jason Keagy
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Vincent J Lynch
- Department of Biological Sciences, University at Buffalo-State University of New York, Buffalo, NY 14260
| | - Marla B Sokolowski
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Program in Child and Brain Development, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada
| | - Lisa J Stubbs
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801
- Department of Cell and Developmental Biology, University of Illinois, Urbana-Champaign, IL 61801
| | - Shayan Tabe-Bordbar
- Department of Computer Science, University of Illinois, Urbana-Champaign, IL 61801
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14850
| | - Gene E Robinson
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL 61801;
- Neuroscience Program, University of Illinois, Urbana-Champaign, IL 61801
- Department of Entomology, University of Illinois, Urbana-Champaign, IL 61801
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27
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A system-level mechanistic explanation for asymmetric stem cell fates: Arabidopsis thaliana root niche as a study system. Sci Rep 2020; 10:3525. [PMID: 32103059 PMCID: PMC7044435 DOI: 10.1038/s41598-020-60251-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 11/09/2022] Open
Abstract
Asymmetric divisions maintain long-term stem cell populations while producing new cells that proliferate and then differentiate. Recent reports in animal systems show that divisions of stem cells can be uncoupled from their progeny differentiation, and the outcome of a division could be influenced by microenvironmental signals. But the underlying system-level mechanisms, and whether this dynamics also occur in plant stem cell niches (SCN), remain elusive. This article presents a cell fate regulatory network model that contributes to understanding such mechanism and identify critical cues for cell fate transitions in the root SCN. Novel computational and experimental results show that the transcriptional regulator SHR is critical for the most frequent asymmetric division previously described for quiescent centre stem cells. A multi-scale model of the root tip that simulated each cell's intracellular regulatory network, and the dynamics of SHR intercellular transport as a cell-cell coupling mechanism, was developed. It revealed that quiescent centre cell divisions produce two identical cells, that may acquire different fates depending on the feedback between SHR's availability and the state of the regulatory network. Novel experimental data presented here validates our model, which in turn, constitutes the first proposed systemic mechanism for uncoupled SCN cell division and differentiation.
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Kang X, Li C. Landscape inferred from gene expression data governs pluripotency in embryonic stem cells. Comput Struct Biotechnol J 2020; 18:366-374. [PMID: 32128066 PMCID: PMC7044515 DOI: 10.1016/j.csbj.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/21/2022] Open
Abstract
Embryonic stem cells (ESCs) can differentiate into diverse cell types and have the ability of self-renewal. Therefore, the study of cell fate decisions on embryonic stem cells has far-reaching significance for regenerative medicine and other biomedical fields. Mathematical models have been used to study emryonic stem cell differentiation. However, the underlying mechanisms of cell differentiation and lineage reprogramming remain to be elucidated. Especially, how to integrate the computational models with quantitative experimental data is still challenging. In this work, we developed a data-constrained modelling approach, and established a model of mouse embryonic stem cells. We used the truncated moment equations (TME) method to quantify the potential landscape of the ESC network. We identified two attractors on the landscape, which represent the embryonic stem cell (ESC) state and differentiated cell (DC) state, respectively, and quantified high dimensional biological paths for differentiation and reprogramming process. Through identifying the optimal combinations of gene targets based on a landscape control strategy, we offered some predictions about the key regulatory factors that govern the differentiation and reprogramming in ESCs.
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Affiliation(s)
- Xin Kang
- School of Mathematical Sciences, Fudan University, Shanghai, China.,Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China
| | - Chunhe Li
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, China.,Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
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Roesch E, Stumpf MPH. Parameter inference in dynamical systems with co-dimension 1 bifurcations. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190747. [PMID: 31824698 PMCID: PMC6837231 DOI: 10.1098/rsos.190747] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 09/20/2019] [Indexed: 05/03/2023]
Abstract
Dynamical systems with intricate behaviour are all-pervasive in biology. Many of the most interesting biological processes indicate the presence of bifurcations, i.e. phenomena where a small change in a system parameter causes qualitatively different behaviour. Bifurcation theory has become a rich field of research in its own right and evaluating the bifurcation behaviour of a given dynamical system can be challenging. An even greater challenge, however, is to learn the bifurcation structure of dynamical systems from data, where the precise model structure is not known. Here, we study one aspects of this problem: the practical implications that the presence of bifurcations has on our ability to infer model parameters and initial conditions from empirical data; we focus on the canonical co-dimension 1 bifurcations and provide a comprehensive analysis of how dynamics, and our ability to infer kinetic parameters are linked. The picture thus emerging is surprisingly nuanced and suggests that identification of the qualitative dynamics-the bifurcation diagram-should precede any attempt at inferring kinetic parameters.
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