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Huang H, Narayanan HV, Hoffmann A. Synergy and antagonism in the integration of BCR and CD40 signals that control B-cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.28.605521. [PMID: 39131345 PMCID: PMC11312454 DOI: 10.1101/2024.07.28.605521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
In response to infection or vaccination, a successful antibody response must enrich high-affinity antigen-reactive B-cells through positive selection, but eliminate auto-reactive B-cells through negative selection. B-cells receive signals from the B-cell receptor (BCR) which binds the antigen, and the CD40 receptor which is stimulated by neighboring T-cells that also recognize the antigen. How BCR and CD40 signaling are integrated quantitatively to jointly determine B-cell fate decision and proliferation remains unclear. To investigate this, we developed a differential-equations-based model of the BCR and CD40 signaling networks activating NFκB. Our model accurately recapitulates the NFκB dynamics of B-cells stimulated through their BCR and CD40 receptors, correctly predicting that costimulation induces more NFκB activity. However, when linking it to established cell fate decision models of cell survival and cell cycle control, it predicted potentiated population expansion that was not observed experimentally. We found that this discrepancy was due to a time-dependent functional antagonism exacerbated by BCR-induced caspase activity that can trigger apoptosis in founder cells, unless NFκB-induced survival gene expression protects B-cells in time. Guided by model predictions, sequential co-stimulation experiments revealed how the temporal dynamics of BCR and CD40 signaling control the fate decision between negative and positive selection of B-cell clonal expansion. Our quantitative findings highlight a complex non-monotonic integration of BCR and CD40 signals that is controlled by a balance between NFκB and cell-death pathways, and suggest a mechanism for regulating the stringency of B-cell selection during an antibody response.
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Affiliation(s)
- Helen Huang
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics (MIMG)
- Institute for Quantitative and Computational Biosciences (QCBio)
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, USA
| | - Haripriya Vaidehi Narayanan
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics (MIMG)
- Institute for Quantitative and Computational Biosciences (QCBio)
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics (MIMG)
- Institute for Quantitative and Computational Biosciences (QCBio)
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2
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Vaidehi Narayanan H, Xiang MY, Chen Y, Huang H, Roy S, Makkar H, Hoffmann A, Roy K. Direct observation correlates NFκB cRel in B cells with activating and terminating their proliferative program. Proc Natl Acad Sci U S A 2024; 121:e2309686121. [PMID: 39024115 PMCID: PMC11287273 DOI: 10.1073/pnas.2309686121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 05/28/2024] [Indexed: 07/20/2024] Open
Abstract
Antibody responses require the proliferative expansion of B cells controlled by affinity-dependent signals. Yet, proliferative bursts are heterogeneous, varying between 0 and 8 divisions in response to the same stimulus. NFκB cRel is activated in response to immune stimulation in B cells and is genetically required for proliferation. Here, we asked whether proliferative heterogeneity is controlled by natural variations in cRel abundance. We developed a fluorescent reporter mTFP1-cRel for the direct observation of cRel in live proliferating B cells. We found that cRel is heterogeneously distributed among naïve B cells, which are enriched for high expressors in a heavy-tailed distribution. We found that high cRel expressors show faster activation of the proliferative program, but do not sustain it well, with population expansion decaying earlier. With a mathematical model of the molecular network, we showed that cRel heterogeneity arises from balancing positive feedback by autoregulation and negative feedback by its inhibitor IκBε, confirmed by mouse knockouts. Using live-cell fluorescence microscopy, we showed that increased cRel primes B cells for early proliferation via higher basal expression of the cell cycle driver cMyc. However, peak cMyc induction amplitude is constrained by incoherent feedforward regulation, decoding the fold change of cRel activity to terminate the proliferative burst. This results in a complex nonlinear, nonmonotonic relationship between cRel expression and the extent of proliferation. These findings emphasize the importance of direct observational studies to complement gene knockout results and to learn about quantitative relationships between biological processes and their key regulators in the context of natural variations.
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Affiliation(s)
- Haripriya Vaidehi Narayanan
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Mark Y. Xiang
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Yijia Chen
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Helen Huang
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Sukanya Roy
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
| | - Himani Makkar
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles, CA90095
- Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA90095
| | - Koushik Roy
- Division of Microbiology and Immunology, Department of Pathology, University of Utah, Salt Lake City, UT84112
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Norris R, Jones J, Mancini E, Chevassut T, Simoes FA, Pepper C, Pepper A, Mitchell S. Patient-specific computational models predict prognosis in B cell lymphoma by quantifying pro-proliferative and anti-apoptotic signatures from genetic sequencing data. Blood Cancer J 2024; 14:105. [PMID: 38965209 PMCID: PMC11224250 DOI: 10.1038/s41408-024-01090-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Genetic heterogeneity and co-occurring driver mutations impact clinical outcomes in blood cancers, but predicting the emergent effect of co-occurring mutations that impact multiple complex and interacting signalling networks is challenging. Here, we used mathematical models to predict the impact of co-occurring mutations on cellular signalling and cell fates in diffuse large B cell lymphoma and multiple myeloma. Simulations predicted adverse impact on clinical prognosis when combinations of mutations induced both anti-apoptotic (AA) and pro-proliferative (PP) signalling. We integrated patient-specific mutational profiles into personalised lymphoma models, and identified patients characterised by simultaneous upregulation of anti-apoptotic and pro-proliferative (AAPP) signalling in all genomic and cell-of-origin classifications (8-25% of patients). In a discovery cohort and two validation cohorts, patients with upregulation of neither, one (AA or PP), or both (AAPP) signalling states had good, intermediate and poor prognosis respectively. Combining AAPP signalling with genetic or clinical prognostic predictors reliably stratified patients into striking prognostic categories. AAPP patients in poor prognosis genetic clusters had 7.8 months median overall survival, while patients lacking both features had 90% overall survival at 120 months in a validation cohort. Personalised computational models enable identification of novel risk-stratified patient subgroups, providing a valuable tool for future risk-adapted clinical trials.
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Affiliation(s)
- Richard Norris
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - John Jones
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Erika Mancini
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Timothy Chevassut
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Fabio A Simoes
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Chris Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Andrea Pepper
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK
| | - Simon Mitchell
- Department of Clinical and Experimental Medicine, Brighton and Sussex Medical School, Brighton, UK.
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Stephan S, Galland S, Labbani Narsis O, Shoji K, Vachenc S, Gerart S, Nicolle C. Agent-based approaches for biological modeling in oncology: A literature review. Artif Intell Med 2024; 152:102884. [PMID: 38703466 DOI: 10.1016/j.artmed.2024.102884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/06/2024]
Abstract
CONTEXT Computational modeling involves the use of computer simulations and models to study and understand real-world phenomena. Its application is particularly relevant in the study of potential interactions between biological elements. It is a promising approach to understand complex biological processes and predict their behavior under various conditions. METHODOLOGY This paper is a review of the recent literature on computational modeling of biological systems. Our study focuses on the field of oncology and the use of artificial intelligence (AI) and, in particular, agent-based modeling (ABM), between 2010 and May 2023. RESULTS Most of the articles studied focus on improving the diagnosis and understanding the behaviors of biological entities, with metaheuristic algorithms being the models most used. Several challenges are highlighted regarding increasing and structuring knowledge about biological systems, developing holistic models that capture multiple scales and levels of organization, reproducing emergent behaviors of biological systems, validating models with experimental data, improving computational performance of models and algorithms, and ensuring privacy and personal data protection are discussed.
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Affiliation(s)
- Simon Stephan
- UTBM, CIAD UMR 7533, Belfort, F-90010, France; Université de Bourgogne, CIAD UMR 7533, Dijon, F-21000, France.
| | | | | | - Kenji Shoji
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
| | - Sébastien Vachenc
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
| | - Stéphane Gerart
- Oncodesign Precision Medicine (OPM), 18 Rue Jean Mazen, Dijon, F-21000, France
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Roy K, Chakraborty M, Kumar A, Manna AK, Roy NS. The NFκB signaling system in the generation of B-cell subsets: from germinal center B cells to memory B cells and plasma cells. Front Immunol 2023; 14:1185597. [PMID: 38169968 PMCID: PMC10758606 DOI: 10.3389/fimmu.2023.1185597] [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] [Received: 03/13/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Memory B cells and antibody-secreting cells are the two prime effector B cell populations that drive infection- and vaccine-induced long-term antibody-mediated immunity. The antibody-mediated immunity mostly relies on the formation of specialized structures within secondary lymphoid organs, called germinal centers (GCs), that facilitate the interactions between B cells, T cells, and antigen-presenting cells. Antigen-activated B cells may proliferate and differentiate into GC-independent plasmablasts and memory B cells or differentiate into GC B cells. The GC B cells undergo proliferation coupled to somatic hypermutation of their immunoglobulin genes for antibody affinity maturation. Subsequently, affinity mature GC B cells differentiate into GC-dependent plasma cells and memory B cells. Here, we review how the NFκB signaling system controls B cell proliferation and the generation of GC B cells, plasmablasts/plasma cells, and memory B cells. We also identify and discuss some important unanswered questions in this connection.
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Affiliation(s)
- Koushik Roy
- Division of Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Mainak Chakraborty
- Division of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Ashok Kumar
- Division of Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT, United States
| | - Asit Kumar Manna
- Division of Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, Salt Lake City, UT, United States
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Neeladri Sekhar Roy
- Department of Biochemistry, School of Medicine, Emory University, Atlanta, GA, United States
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Jayawant E, Pack A, Clark H, Kennedy E, Ghodke A, Jones J, Pepper C, Pepper A, Mitchell S. NF-κB fingerprinting reveals heterogeneous NF-κB composition in diffuse large B-cell lymphoma. Front Oncol 2023; 13:1181660. [PMID: 37333821 PMCID: PMC10272839 DOI: 10.3389/fonc.2023.1181660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/23/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction Improving treatments for Diffuse Large B-Cell Lymphoma (DLBCL) is challenged by the vast heterogeneity of the disease. Nuclear factor-κB (NF-κB) is frequently aberrantly activated in DLBCL. Transcriptionally active NF-κB is a dimer containing either RelA, RelB or cRel, but the variability in the composition of NF-κB between and within DLBCL cell populations is not known. Results Here we describe a new flow cytometry-based analysis technique termed "NF-κB fingerprinting" and demonstrate its applicability to DLBCL cell lines, DLBCL core-needle biopsy samples, and healthy donor blood samples. We find each of these cell populations has a unique NF-κB fingerprint and that widely used cell-of-origin classifications are inadequate to capture NF-κB heterogeneity in DLBCL. Computational modeling predicts that RelA is a key determinant of response to microenvironmental stimuli, and we experimentally identify substantial variability in RelA between and within ABC-DLBCL cell lines. We find that when we incorporate NF-κB fingerprints and mutational information into computational models we can predict how heterogeneous DLBCL cell populations respond to microenvironmental stimuli, and we validate these predictions experimentally. Discussion Our results show that the composition of NF-κB is highly heterogeneous in DLBCL and predictive of how DLBCL cells will respond to microenvironmental stimuli. We find that commonly occurring mutations in the NF-κB signaling pathway reduce DLBCL's response to microenvironmental stimuli. NF-κB fingerprinting is a widely applicable analysis technique to quantify NF-κB heterogeneity in B cell malignancies that reveals functionally significant differences in NF-κB composition within and between cell populations.
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Mitchell S, Tsui R, Tan ZC, Pack A, Hoffmann A. The NF-κB multidimer system model: A knowledge base to explore diverse biological contexts. Sci Signal 2023; 16:eabo2838. [PMID: 36917644 PMCID: PMC10195159 DOI: 10.1126/scisignal.abo2838] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/22/2023] [Indexed: 03/16/2023]
Abstract
The nuclear factor κB (NF-κB) system is critical for various biological functions in numerous cell types, including the inflammatory response, cell proliferation, survival, differentiation, and pathogenic responses. Each cell type is characterized by a subset of 15 NF-κB dimers whose activity is regulated in a stimulus-responsive manner. Numerous studies have produced different mathematical models that account for cell type-specific NF-κB activities. However, whereas the concentrations or abundances of NF-κB subunits may differ between cell types, the biochemical interactions that constitute the NF-κB signaling system do not. Here, we synthesized a consensus mathematical model of the NF-κB multidimer system, which could account for the cell type-specific repertoires of NF-κB dimers and their cell type-specific activation and cross-talk. Our review demonstrates that these distinct cell type-specific properties of NF-κB signaling can be explained largely as emergent effects of the cell type-specific expression of NF-κB monomers. The consensus systems model represents a knowledge base that may be used to gain insights into the control and function of NF-κB in diverse physiological and pathological scenarios and that describes a path for generating similar regulatory knowledge bases for other pleiotropic signaling systems.
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Affiliation(s)
- Simon Mitchell
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
- Brighton and Sussex Medical School, Department of Clinical and Experimental Medicine, University of Sussex, Falmer, East Sussex, BN1 9PX, UK
| | - Rachel Tsui
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Zhixin Cyrillus Tan
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
| | - Arran Pack
- Brighton and Sussex Medical School, Department of Clinical and Experimental Medicine, University of Sussex, Falmer, East Sussex, BN1 9PX, UK
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, UCLA, Los Angeles, CA 90095, USA
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Vaidehi Narayanan H, Hoffmann A. From Antibody Repertoires to Cell-Cell Interactions to Molecular Networks: Bridging Scales in the Germinal Center. Front Immunol 2022; 13:898078. [PMID: 35603162 PMCID: PMC9114758 DOI: 10.3389/fimmu.2022.898078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 01/02/2023] Open
Abstract
Antibody-mediated adaptive immunity must provide effective long-term protection with minimal adverse effects, against rapidly mutating pathogens, in a human population with diverse ages, genetics, and immune histories. In order to grasp and leverage the complexities of the antibody response, we advocate for a mechanistic understanding of the multiscale germinal center (GC) reaction - the process by which precursor B-cells evolve high-affinity antigen-specific antibodies, forming an effector repertoire of plasma and memory cells for decades-long protection. The regulatory dynamics of B-cells within the GC are complex, and unfold across multiple interacting spatial and temporal scales. At the organism scale, over weeks to years, the antibody sequence repertoire formed by various B-cell clonal lineages modulates antibody quantity and quality over time. At the tissue and cellular scale, over hours to weeks, B-cells undergo selection via spatially distributed interactions with local stroma, antigen, and helper T-cells. At the molecular scale, over seconds to days, intracellular signaling, transcriptional, and epigenetic networks modulate B-cell fates and shape their clonal lineages. We summarize our current understanding within each of these scales, and identify missing links in connecting them. We suggest that quantitative multi-scale mathematical models of B-cell and GC reaction dynamics provide predictive frameworks that can apply basic immunological knowledge to practical challenges such as rational vaccine design.
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Affiliation(s)
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, United States
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9
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Bioimaging approaches for quantification of individual cell behavior during cell fate decisions. Biochem Soc Trans 2022; 50:513-527. [PMID: 35166330 DOI: 10.1042/bst20210534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Tracking individual cells has allowed a new understanding of cellular behavior in human health and disease by adding a dynamic component to the already complex heterogeneity of single cells. Technically, despite countless advances, numerous experimental variables can affect data collection and interpretation and need to be considered. In this review, we discuss the main technical aspects and biological findings in the analysis of the behavior of individual cells. We discuss the most relevant contributions provided by these approaches in clinically relevant human conditions like embryo development, stem cells biology, inflammation, cancer and microbiology, along with the cellular mechanisms and molecular pathways underlying these conditions. We also discuss the key technical aspects to be considered when planning and performing experiments involving the analysis of individual cells over long periods. Despite the challenges in automatic detection, features extraction and long-term tracking that need to be tackled, the potential impact of single-cell bioimaging is enormous in understanding the pathogenesis and development of new therapies in human pathophysiology.
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Cheon H, Kan A, Prevedello G, Oostindie SC, Dovedi SJ, Hawkins ED, Marchingo JM, Heinzel S, Duffy KR, Hodgkin PD. Cyton2: A Model of Immune Cell Population Dynamics That Includes Familial Instructional Inheritance. FRONTIERS IN BIOINFORMATICS 2021; 1:723337. [PMID: 36303793 PMCID: PMC9581048 DOI: 10.3389/fbinf.2021.723337] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Lymphocytes are the central actors in adaptive immune responses. When challenged with antigen, a small number of B and T cells have a cognate receptor capable of recognising and responding to the insult. These cells proliferate, building an exponentially growing, differentiating clone army to fight off the threat, before ceasing to divide and dying over a period of weeks, leaving in their wake memory cells that are primed to rapidly respond to any repeated infection. Due to the non-linearity of lymphocyte population dynamics, mathematical models are needed to interrogate data from experimental studies. Due to lack of evidence to the contrary and appealing to arguments based on Occam's Razor, in these models newly born progeny are typically assumed to behave independently of their predecessors. Recent experimental studies, however, challenge that assumption, making clear that there is substantial inheritance of timed fate changes from each cell by its offspring, calling for a revision to the existing mathematical modelling paradigms used for information extraction. By assessing long-term live-cell imaging of stimulated murine B and T cells in vitro, we distilled the key phenomena of these within-family inheritances and used them to develop a new mathematical model, Cyton2, that encapsulates them. We establish the model's consistency with these newly observed fine-grained features. Two natural concerns for any model that includes familial correlations would be that it is overparameterised or computationally inefficient in data fitting, but neither is the case for Cyton2. We demonstrate Cyton2's utility by challenging it with high-throughput flow cytometry data, which confirms the robustness of its parameter estimation as well as its ability to extract biological meaning from complex mixed stimulation experiments. Cyton2, therefore, offers an alternate mathematical model, one that is, more aligned to experimental observation, for drawing inferences on lymphocyte population dynamics.
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Affiliation(s)
- HoChan Cheon
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Andrey Kan
- Immunology Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | | | - Simone C. Oostindie
- Immunology Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | | | - Edwin D. Hawkins
- Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
- Division of Inflammation, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Julia M. Marchingo
- Cell Signalling and Immunology Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Susanne Heinzel
- Immunology Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Ken R. Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Philip D. Hodgkin
- Immunology Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
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11
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Jangid A, Selvarajan S, Ramaswamy R. A stochastic model of homeostasis: The roles of noise and nuclear positioning in deciding cell fate. iScience 2021; 24:103199. [PMID: 34703995 PMCID: PMC8524154 DOI: 10.1016/j.isci.2021.103199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/21/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022] Open
Abstract
We study a population-based cellular model that starts from a single stem cell that divides stochastically to give rise to either daughter stem cells or differentiated daughter cells. There are three main components in the model: nucleus position, the underlying gene-regulatory network, and stochastic segregation of transcription factors in the daughter cells. The proportion of self-renewal and differentiated cell lines as a function of the nucleus position which in turn decides the plane of cleavage is studied. Both nuclear position and noise play an important role in determining the stem cell genealogies. We have observed both long and short genealogies in model simulation, and these compare well with experimental results from neuroblast and B-cell division. Symmetric divisions are observed in apical nuclei, while asymmetric division occurs when the nucleus is toward the base. In this model, the number of clones decreases over time, although the average clone size increases.
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Affiliation(s)
- Amit Jangid
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suriya Selvarajan
- Department of Theoretical Physics, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ram Ramaswamy
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
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12
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Martin EW, Pacholewska A, Patel H, Dashora H, Sung MH. Integrative analysis suggests cell type-specific decoding of NF-κB dynamics. Sci Signal 2020; 13:13/620/eaax7195. [PMID: 32098801 DOI: 10.1126/scisignal.aax7195] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The complex signaling dynamics of transcription factors can encode both qualitative and quantitative information about the extracellular environment, which increases the information transfer capacity and potentially supports accurate cellular decision-making. An important question is how these signaling dynamics patterns are translated into functionally appropriate gene regulation programs. To address this question for transcription factors of the nuclear factor κB (NF-κB) family, we profiled the single-cell dynamics of two major NF-κB subunits, RelA and c-Rel, induced by a panel of pathogen-derived stimuli in immune and nonimmune cellular contexts. Diverse NF-κB-activating ligands produced different patterns of RelA and c-Rel signaling dynamic features, such as variations in duration or time-integrated activity. Analysis of nascent transcripts delineated putative direct targets of NF-κB as compared to genes controlled by other transcriptional and posttranscriptional mechanisms and showed that the transcription of more than half of the induced genes was tightly linked to specific dynamic features of NF-κB signaling. Fibroblast and macrophage cell lines shared a cluster of such "NF-κB dynamics-decoding" genes, as well as cell type-specific decoding genes. Dissecting the subunit specificity of dynamics-decoding genes suggested that target genes were most often linked to both RelA and c-Rel or to RelA alone. Thus, our analysis reveals the cell type-specific interpretation of pathogenic information through the signaling dynamics of NF-κB.
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Affiliation(s)
- Erik W Martin
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Alicja Pacholewska
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Heta Patel
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Himanshu Dashora
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Myong-Hee Sung
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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13
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Mitchell S. What Will B Will B: Identifying Molecular Determinants of Diverse B-Cell Fate Decisions Through Systems Biology. Front Cell Dev Biol 2020; 8:616592. [PMID: 33511125 PMCID: PMC7835399 DOI: 10.3389/fcell.2020.616592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/02/2020] [Indexed: 12/25/2022] Open
Abstract
B-cells are the poster child for cellular diversity and heterogeneity. The diverse repertoire of B lymphocytes, each expressing unique antigen receptors, provides broad protection against pathogens. However, B-cell diversity goes beyond unique antigen receptors. Side-stepping B-cell receptor (BCR) diversity through BCR-independent stimuli or engineered organisms with monoclonal BCRs still results in seemingly identical B-cells reaching a wide variety of fates in response to the same challenge. Identifying to what extent the molecular state of a B-cell determines its fate is key to gaining a predictive understanding of B-cells and consequently the ability to control them with targeted therapies. Signals received by B-cells through transmembrane receptors converge on intracellular molecular signaling networks, which control whether each B-cell divides, dies, or differentiates into a number of antibody-secreting distinct B-cell subtypes. The signaling networks that interpret these signals are well known to be susceptible to molecular variability and noise, providing a potential source of diversity in cell fate decisions. Iterative mathematical modeling and experimental studies have provided quantitative insight into how B-cells achieve distinct fates in response to pathogenic stimuli. Here, we review how systems biology modeling of B-cells, and the molecular signaling networks controlling their fates, is revealing the key determinants of cell-to-cell variability in B-cell destiny.
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Roy K, Mitchell S, Liu Y, Ohta S, Lin YS, Metzig MO, Nutt SL, Hoffmann A. A Regulatory Circuit Controlling the Dynamics of NFκB cRel Transitions B Cells from Proliferation to Plasma Cell Differentiation. Immunity 2019; 50:616-628.e6. [PMID: 30850343 DOI: 10.1016/j.immuni.2019.02.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 11/20/2018] [Accepted: 02/06/2019] [Indexed: 01/05/2023]
Abstract
Humoral immunity depends on efficient activation of B cells and their subsequent differentiation into antibody-secreting cells (ASCs). The transcription factor NFκB cRel is critical for B cell proliferation, but incorporating its known regulatory interactions into a mathematical model of the ASC differentiation circuit prevented ASC generation in simulations. Indeed, experimental ectopic cRel expression blocked ASC differentiation by inhibiting the transcription factor Blimp1, and in wild-type (WT) cells cRel was dynamically repressed during ASC differentiation by Blimp1 binding the Rel locus. Including this bi-stable circuit of mutual cRel-Blimp1 antagonism into a multi-scale model revealed that dynamic repression of cRel controls the switch from B cell proliferation to ASC generation phases and hence the respective cell population dynamics. Our studies provide a mechanistic explanation of how dysregulation of this bi-stable circuit might result in pathologic B cell population phenotypes and thus offer new avenues for diagnostic stratification and treatment.
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Affiliation(s)
- Koushik Roy
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Simon Mitchell
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Liu
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sho Ohta
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yu-Sheng Lin
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Marie Oliver Metzig
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Stephen L Nutt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3050, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3010, Australia
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proc Natl Acad Sci U S A 2018; 115:E11061-E11070. [PMID: 30401736 DOI: 10.1073/pnas.1809609115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
MicroRNA (miRNA)-124 is expressed in neurons, where it represses genes inhibitory for neuronal differentiation, including the RNA binding protein PTBP1. PTBP1 maintains nonneuronal splicing patterns of mRNAs that switch to neuronal isoforms upon neuronal differentiation. We find that primary (pri)-miR-124-1 is expressed in mouse embryonic stem cells where mature miR-124 is absent. PTBP1 binds to this precursor RNA upstream of the miRNA stem-loop to inhibit mature miR-124 expression in vivo and DROSHA cleavage of pri-miR-124-1 in vitro. This function for PTBP1 in repressing miR-124 biogenesis defines an additional regulatory loop in the already intricate interplay between these two molecules. Applying mathematical modeling to examine the dynamics of this regulation, we find that the pool of pri-miR-124 whose maturation is blocked by PTBP1 creates a robust and self-reinforcing transition in gene expression as PTBP1 is depleted during early neuronal differentiation. While interlocking regulatory loops are often found between miRNAs and transcriptional regulators, our results indicate that miRNA targeting of posttranscriptional regulators also reinforces developmental decisions. Notably, induction of neuronal differentiation observed upon PTBP1 knockdown likely results from direct derepression of miR-124, in addition to indirect effects previously described.
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Mitchell S, Roy K, Zangle TA, Hoffmann A. Nongenetic origins of cell-to-cell variability in B lymphocyte proliferation. Proc Natl Acad Sci U S A 2018; 115:E2888-E2897. [PMID: 29514960 PMCID: PMC5866559 DOI: 10.1073/pnas.1715639115] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Rapid antibody production in response to invading pathogens requires the dramatic expansion of pathogen-derived antigen-specific B lymphocyte populations. Whether B cell population dynamics are based on stochastic competition between competing cell fates, as in the development of competence by the bacterium Bacillus subtilis, or on deterministic cell fate decisions that execute a predictable program, as during the development of the worm Caenorhabditis elegans, remains unclear. Here, we developed long-term live-cell microscopy of B cell population expansion and multiscale mechanistic computational modeling to characterize the role of molecular noise in determining phenotype heterogeneity. We show that the cell lineage trees underlying B cell population dynamics are mediated by a largely predictable decision-making process where the heterogeneity of cell proliferation and death decisions at any given timepoint largely derives from nongenetic heterogeneity in the founder cells. This means that contrary to previous models, only a minority of genetically identical founder cells contribute the majority to the population response. We computationally predict and experimentally confirm nongenetic molecular determinants that are predictive of founder cells' proliferative capacity. While founder cell heterogeneity may arise from different exposure histories, we show that it may also be due to the gradual accumulation of small amounts of intrinsic noise during the lineage differentiation process of hematopoietic stem cells to mature B cells. Our finding of the largely deterministic nature of B lymphocyte responses may provide opportunities for diagnostic and therapeutic development.
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Affiliation(s)
- Simon Mitchell
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Koushik Roy
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Thomas A Zangle
- Department Chemical Engineering and Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, CA 90095;
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
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Sarabipour S, Mac Gabhann F. Computational Systems Biochemistry: Beyond the Static Interactome. Biochemistry 2018; 57:9-10. [PMID: 29220167 DOI: 10.1021/acs.biochem.7b01133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Sarvenaz Sarabipour
- Institute for Computational Medicine, Department of Biomedical Engineering, and Institute for NanoBio Technology, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Feilim Mac Gabhann
- Institute for Computational Medicine, Department of Biomedical Engineering, and Institute for NanoBio Technology, Johns Hopkins University , Baltimore, Maryland 21218, United States
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Mitchell S, Hoffmann A. Identifying Noise Sources governing cell-to-cell variability. ACTA ACUST UNITED AC 2017; 8:39-45. [PMID: 29623300 DOI: 10.1016/j.coisb.2017.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Phenotypic differences often occur even in clonal cell populations. Many potential sources of such variation have been identified, from biophysical rate variance intrinsic to all chemical processes to asymmetric division of molecular components extrinsic to any particular signaling pathway. Identifying the sources of phenotypic variation and quantifying their contributions to cell fate variation is not possible without accurate single cell data. By combining such data with mathematical models of potential noise sources it is possible to characterize the impact of varying levels of each noise source and identify which sources of variation best explain the experimental observations. The mathematical framework of information theory provides metrics of the impact of noise on the reliability of a cell to sense its environment. While the presence of noise in a single cellular system reduces the reliability of signal transduction its impact on a population of varied single cells remains unclear.
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Affiliation(s)
- Simon Mitchell
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
| | - Alexander Hoffmann
- Institute for Quantitative and Computational Biosciences and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA 90095
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El Cheikh R, Bernard S, El Khatib N. A multiscale modelling approach for the regulation of the cell cycle by the circadian clock. J Theor Biol 2017; 426:117-125. [PMID: 28551367 DOI: 10.1016/j.jtbi.2017.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 05/16/2017] [Accepted: 05/17/2017] [Indexed: 12/20/2022]
Abstract
We present a multiscale mathematical model for the regulation of the cell cycle by the circadian clock. Biologically, the model describes the proliferation of a population of heterogeneous cells connected to each other. The model consists of a high dimensional transport equation structured by molecular contents of the cell cycle-circadian clock coupled oscillator. We propose a computational method for resolution adapted from the concept of particle methods. We study the impact of molecular dynamics on cell proliferation and show an example where discordance of division rhythms between population and single cell levels is observed. This highlights the importance of multiscale modeling where such results cannot be inferred from considering solely one biological level.
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Affiliation(s)
- Raouf El Cheikh
- Aix Marseille Univ, Inserm S_911 CRO2, SMARTc Pharmacokinetics Unit, 27 Bd Jean Moulin, Marseille, France
| | - Samuel Bernard
- CNRS UMR 5208, Institut Camille Jordan, Université Lyon1, 43 blvd. du 11 novembre 1918, F-69622 Villeurbanne cedex, France
| | - Nader El Khatib
- Lebanese American University, Department of Computer Science and Mathematics, Byblos, P.O. Box 36, Byblos, Lebanon.
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Magi S, Iwamoto K, Okada-Hatakeyama M. Current status of mathematical modeling of cancer – From the viewpoint of cancer hallmarks. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.coisb.2017.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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21
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Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Wuchter P, Ho AD, Timmer J, Schilling M, Höfer T, Klingmüller U. Protein abundance of AKT and ERK pathway components governs cell type-specific regulation of proliferation. Mol Syst Biol 2017; 13:904. [PMID: 28123004 PMCID: PMC5293153 DOI: 10.15252/msb.20167258] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Signaling through the AKT and ERK pathways controls cell proliferation. However, the integrated regulation of this multistep process, involving signal processing, cell growth and cell cycle progression, is poorly understood. Here, we study different hematopoietic cell types, in which AKT and ERK signaling is triggered by erythropoietin (Epo). Although these cell types share the molecular network topology for pro‐proliferative Epo signaling, they exhibit distinct proliferative responses. Iterating quantitative experiments and mathematical modeling, we identify two molecular sources for cell type‐specific proliferation. First, cell type‐specific protein abundance patterns cause differential signal flow along the AKT and ERK pathways. Second, downstream regulators of both pathways have differential effects on proliferation, suggesting that protein synthesis is rate‐limiting for faster cycling cells while slower cell cycles are controlled at the G1‐S progression. The integrated mathematical model of Epo‐driven proliferation explains cell type‐specific effects of targeted AKT and ERK inhibitors and faithfully predicts, based on the protein abundance, anti‐proliferative effects of inhibitors in primary human erythroid progenitor cells. Our findings suggest that the effectiveness of targeted cancer therapy might become predictable from protein abundance.
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Affiliation(s)
- Lorenz Adlung
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sandip Kar
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,BioQuant Center, University of Heidelberg, Heidelberg, Germany.,Department of Chemistry, Indian Institute of Technology, Mumbai, India
| | - Marie-Christine Wagner
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bin She
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sajib Chakraborty
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jie Bao
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany
| | - Susen Lattermann
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melanie Boerries
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hauke Busch
- Systems Biology of the Cellular Microenvironment Group, IMMZ, ALU, Freiburg, Germany.,German Cancer Consortium (DKTK), Freiburg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Wuchter
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany.,Institute for Transfusion Medicine and Immunology, University of Heidelberg, Mannheim, Germany
| | - Anthony D Ho
- Department of Medicine V, University of Heidelberg, Heidelberg, Germany
| | - Jens Timmer
- Center for Biological Signaling Studies (BIOSS), Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Marcel Schilling
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany .,BioQuant Center, University of Heidelberg, Heidelberg, Germany
| | - Ursula Klingmüller
- Division of Systems Biology of Signal Transduction, German Cancer Research Center (DKFZ), Heidelberg, Germany .,Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
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Mitchell S, Vargas J, Hoffmann A. Signaling via the NFκB system. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:227-41. [PMID: 26990581 DOI: 10.1002/wsbm.1331] [Citation(s) in RCA: 658] [Impact Index Per Article: 82.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 01/12/2016] [Accepted: 01/12/2016] [Indexed: 12/25/2022]
Abstract
The nuclear factor kappa B (NFκB) family of transcription factors is a key regulator of immune development, immune responses, inflammation, and cancer. The NFκB signaling system (defined by the interactions between NFκB dimers, IκB regulators, and IKK complexes) is responsive to a number of stimuli, and upon ligand-receptor engagement, distinct cellular outcomes, appropriate to the specific signal received, are set into motion. After almost three decades of study, many signaling mechanisms are well understood, rendering them amenable to mathematical modeling, which can reveal deeper insights about the regulatory design principles. While other reviews have focused on upstream, receptor proximal signaling (Hayden MS, Ghosh S. Signaling to NF-κB. Genes Dev 2004, 18:2195-2224; Verstrepen L, Bekaert T, Chau TL, Tavernier J, Chariot A, Beyaert R. TLR-4, IL-1R and TNF-R signaling to NF-κB: variations on a common theme. Cell Mol Life Sci 2008, 65:2964-2978), and advances through computational modeling (Basak S, Behar M, Hoffmann A. Lessons from mathematically modeling the NF-κB pathway. Immunol Rev 2012, 246:221-238; Williams R, Timmis J, Qwarnstrom E. Computational models of the NF-KB signalling pathway. Computation 2014, 2:131), in this review we aim to summarize the current understanding of the NFκB signaling system itself, the molecular mechanisms, and systems properties that are key to its diverse biological functions, and we discuss remaining questions in the field. WIREs Syst Biol Med 2016, 8:227-241. doi: 10.1002/wsbm.1331 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Simon Mitchell
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jesse Vargas
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Alexander Hoffmann
- Department of Microbiology, Immunology, and Molecular Genetics, and Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, Los Angeles, CA, USA
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Hross S, Hasenauer J. Analysis of CFSE time-series data using division-, age- and label-structured population models. Bioinformatics 2016; 32:2321-9. [PMID: 27153577 DOI: 10.1093/bioinformatics/btw131] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 03/01/2016] [Indexed: 01/12/2023] Open
Abstract
MOTIVATION In vitro and in vivo cell proliferation is often studied using the dye carboxyfluorescein succinimidyl ester (CFSE). The CFSE time-series data provide information about the proliferation history of populations of cells. While the experimental procedures are well established and widely used, the analysis of CFSE time-series data is still challenging. Many available analysis tools do not account for cell age and employ optimization methods that are inefficient (or even unreliable). RESULTS We present a new model-based analysis method for CFSE time-series data. This method uses a flexible description of proliferating cell populations, namely, a division-, age- and label-structured population model. Efficient maximum likelihood and Bayesian estimation algorithms are introduced to infer the model parameters and their uncertainties. These methods exploit the forward sensitivity equations of the underlying partial differential equation model for efficient and accurate gradient calculation, thereby improving computational efficiency and reliability compared with alternative approaches and accelerating uncertainty analysis. The performance of the method is assessed by studying a dataset for immune cell proliferation. This revealed the importance of different factors on the proliferation rates of individual cells. Among others, the predominate effect of cell age on the division rate is found, which was not revealed by available computational methods. AVAILABILITY AND IMPLEMENTATION The MATLAB source code implementing the models and algorithms is available from http://janhasenauer.github.io/ShAPE-DALSP/Contact: jan.hasenauer@helmholtz-muenchen.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sabrina Hross
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany Department of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching 85748, Germany
| | - Jan Hasenauer
- Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg 85764, Germany Department of Mathematical Modeling of Biological Systems, Center for Mathematics, Technische Universität München, Garching 85748, Germany
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B-cell survival and development controlled by the coordination of NF-κB family members RelB and cRel. Blood 2016; 127:1276-86. [PMID: 26773039 PMCID: PMC4786837 DOI: 10.1182/blood-2014-10-606988] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 12/29/2015] [Indexed: 11/20/2022] Open
Abstract
Targeted deletion of BAFF causes severe deficiency of splenic B cells. BAFF-R is commonly thought to signal to nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB)-inducing kinase dependent noncanonical NF-κB RelB. However, RelB-deficient mice have normal B-cell numbers. Recent studies showed that BAFF also signals to the canonical NF-κB pathway, and we found that both RelB and cRel are persistently activated, suggesting BAFF signaling coordinates both pathways to ensure robust B-cell development. Indeed, we report now that combined loss of these 2 NF-κB family members leads to impaired BAFF-mediated survival and development in vitro. Although single deletion of RelB and cRel was dispensable for normal B-cell development, double knockout mice displayed an early B-cell developmental blockade and decreased mature B cells. Despite disorganized splenic architecture in Relb(-/-)cRel(-/-) mice, generation of mixed-mouse chimeras established the developmental phenotype to be B-cell intrinsic. Together, our results indicate that BAFF signals coordinate both RelB and cRel activities to ensure survival during peripheral B-cell maturation.
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Abstract
Recognized public community databases for image data deposition have been lacking so far. New databases are emerging that provide a promising infrastructure for hosting and distributing high content imaging datasets. Recognized public community databases for image data deposition have been lacking so far. New databases are emerging that provide a promising infrastructure for hosting and distributing high content imaging datasets.
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