1
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Zhang J, Griffin J, Roy K, Hoffmann A, Zangle TA. Tracking of lineage mass via quantitative phase imaging and confinement in low refractive index microwells. LAB ON A CHIP 2024. [PMID: 39190401 DOI: 10.1039/d4lc00389f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Measurements of cell lineages are central to a variety of fundamental biological questions, ranging from developmental to cancer biology. However, accurate lineage tracing requires nearly perfect cell tracking, which can be challenging due to cell motion during imaging. Here we demonstrate the integration of microfabrication, imaging, and image processing approaches to demonstrate a platform for cell lineage tracing. We use quantitative phase imaging (QPI), a label-free imaging approach that quantifies cell mass. This gives an additional parameter, cell mass, that can be used to improve tracking accuracy. We confine lineages within microwells fabricated to reduce cell adhesion to sidewalls made of a low refractive index polymer. This also allows the microwells themselves to serve as references for QPI, enabling measurement of cell mass even in confluent microwells. We demonstrate application of this approach to immortalized adherent and nonadherent cell lines as well as stimulated primary B cells cultured ex vivo. Overall, our approach enables lineage tracking, or measurement of lineage mass, in a platform that can be customized to varied cell types.
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Affiliation(s)
- Jingzhou Zhang
- Department of Chemical Engineering, University of Utah, USA.
| | - Justin Griffin
- Department of Chemical Engineering, University of Utah, USA.
| | - Koushik Roy
- Division of Microbiology and Immunology, Department of Pathology, School of Medicine, University of Utah, USA
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, and Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Thomas A Zangle
- Department of Chemical Engineering, University of Utah, USA.
- Huntsman Cancer Institute, University of Utah, USA
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2
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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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3
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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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4
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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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5
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Mu DP, Scharer CD, Kaminski NE, Zhang Q. A multiscale spatial modeling framework for the germinal center response. Front Immunol 2024; 15:1377303. [PMID: 38881901 PMCID: PMC11179717 DOI: 10.3389/fimmu.2024.1377303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymphoid organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events, including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanistic and applied research questions on the adaptive humoral immune response in the future.
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Affiliation(s)
- Derek P. Mu
- Montgomery Blair High School, Silver Spring, MD, United States
| | - Christopher D. Scharer
- Department of Microbiology and Immunology, School of Medicine, Emory University, Atlanta, GA, United States
| | - Norbert E. Kaminski
- Department of Pharmacology & Toxicology, Institute for Integrative Toxicology, Center for Research on Ingredient Safety, Michigan State University, East Lansing, MI, United States
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, United States
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6
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Jiang F, Hu SY, Tian W, Wang NN, Yang N, Dong SS, Song HM, Zhang DJ, Gao HW, Wang C, Wu H, He CY, Zhu DL, Chen XF, Guo Y, Yang Z, Yang TL. A landscape of gene expression regulation for synovium in arthritis. Nat Commun 2024; 15:1409. [PMID: 38360850 PMCID: PMC10869817 DOI: 10.1038/s41467-024-45652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
The synovium is an important component of any synovial joint and is the major target tissue of inflammatory arthritis. However, the multi-omics landscape of synovium required for functional inference is absent from large-scale resources. Here we integrate genomics with transcriptomics and chromatin accessibility features of human synovium in up to 245 arthritic patients, to characterize the landscape of genetic regulation on gene expression and the regulatory mechanisms mediating arthritic diseases predisposition. We identify 4765 independent primary and 616 secondary cis-expression quantitative trait loci (cis-eQTLs) in the synovium and find that the eQTLs with multiple independent signals have stronger effects and heritability than single independent eQTLs. Integration of genome-wide association studies (GWASs) and eQTLs identifies 84 arthritis related genes, revealing 38 novel genes which have not been reported by previous studies using eQTL data from the GTEx project or immune cells. We further develop a method called eQTac to identify variants that could affect gene expression by affecting chromatin accessibility and identify 1517 regions with potential regulatory function of chromatin accessibility. Altogether, our study provides a comprehensive synovium multi-omics resource for arthritic diseases and gains new insights into the regulation of gene expression.
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Affiliation(s)
- Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China
| | - Wen Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Ning Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Miao Song
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Da-Jin Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hui-Wu Gao
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chen Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Hao Wu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Chang-Yi He
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710054, P.R. China.
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, P.R. China.
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7
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Mu DP, Scharer CD, Kaminski NE, Zhang Q. A Multiscale Spatial Modeling Framework for the Germinal Center Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577491. [PMID: 38501122 PMCID: PMC10945589 DOI: 10.1101/2024.01.26.577491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The germinal center response or reaction (GCR) is a hallmark event of adaptive humoral immunity. Unfolding in the B cell follicles of the secondary lymph organs, a GC culminates in the production of high-affinity antibody-secreting plasma cells along with memory B cells. By interacting with follicular dendritic cells (FDC) and T follicular helper (Tfh) cells, GC B cells exhibit complex spatiotemporal dynamics. Driving the B cell dynamics are the intracellular signal transduction and gene regulatory network that responds to cell surface signaling molecules, cytokines, and chemokines. As our knowledge of the GC continues to expand in depth and in scope, mathematical modeling has become an important tool to help disentangle the intricacy of the GCR and inform novel mechanistic and clinical insights. While the GC has been modeled at different granularities, a multiscale spatial simulation framework - integrating molecular, cellular, and tissue-level responses - is still rare. Here, we report our recent progress toward this end with a hybrid stochastic GC framework developed on the Cellular Potts Model-based CompuCell3D platform. Tellurium is used to simulate the B cell intracellular molecular network comprising NF-κB, FOXO1, MYC, AP4, CXCR4, and BLIMP1 that responds to B cell receptor (BCR) and CD40-mediated signaling. The molecular outputs of the network drive the spatiotemporal behaviors of B cells, including cyclic migration between the dark zone (DZ) and light zone (LZ) via chemotaxis; clonal proliferative bursts, somatic hypermutation, and DNA damage-induced apoptosis in the DZ; and positive selection, apoptosis via a death timer, and emergence of plasma cells in the LZ. Our simulations are able to recapitulate key molecular, cellular, and morphological GC events including B cell population growth, affinity maturation, and clonal dominance. This novel modeling framework provides an open-source, customizable, and multiscale virtual GC simulation platform that enables qualitative and quantitative in silico investigations of a range of mechanic and applied research questions in future.
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8
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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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9
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Konrath F, Willenbrock M, Busse D, Scheidereit C, Wolf J. A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1. iScience 2023; 26:107917. [PMID: 37817938 PMCID: PMC10561052 DOI: 10.1016/j.isci.2023.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/01/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
The activation of IKK/NF-κB by genotoxic stress is a crucial process in the DNA damage response. Due to the anti-apoptotic impact of NF-κB, it can affect cell-fate decisions upon DNA damage and therefore interfere with tumor therapy-induced cell death. Here, we developed a dynamical model describing IKK/NF-κB signaling that faithfully reproduces quantitative time course data and enables a detailed analysis of pathway regulation. The approach elucidates a pathway topology with two hubs, where the first integrates signals from two DNA damage sensors and the second forms a coherent feedforward loop. The analyses reveal a critical role of the sensor protein PARP-1 in the pathway regulation. Introducing a method for calculating the impact of changes in individual components on pathway activity in a time-resolved manner, we show how irradiation dose influences pathway activation. Our results give a mechanistic understanding relevant for the interpretation of experimental and clinical studies.
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Affiliation(s)
- Fabian Konrath
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michael Willenbrock
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dorothea Busse
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Claus Scheidereit
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Mathematics and Computer Science, Free University Berlin, Germany
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10
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Brownlie RJ, Kennedy R, Wilson EB, Milanovic M, Taylor CF, Wang D, Davies JR, Owston H, Adams EJ, Stephenson S, Caeser R, Gewurz BE, Giannoudis PV, Scuoppo C, McGonagle D, Hodson DJ, Tooze RM, Doody GM, Cook G, Westhead DR, Klein U. Cytokine receptor IL27RA is an NF-κB-responsive gene involved in CD38 upregulation in multiple myeloma. Blood Adv 2023; 7:3874-3890. [PMID: 36867577 PMCID: PMC10405202 DOI: 10.1182/bloodadvances.2022009044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/27/2023] [Indexed: 03/04/2023] Open
Abstract
Multiple myeloma (MM) shows constitutive activation of canonical and noncanonical nuclear factor κB (NF-κB) signaling via genetic mutations or tumor microenvironment (TME) stimulations. A subset of MM cell lines showed dependency for cell growth and survival on the canonical NF-κB transcription factor RELA alone, suggesting a critical role for a RELA-mediated biological program in MM pathogenesis. Here, we determined the RELA-dependent transcriptional program in MM cell lines and found the expression of the cell surface molecules interleukin-27 receptor-α (IL-27Rα) and the adhesion molecule JAM2 to be responsive to RELA at the messenger RNA and protein levels. IL-27Rα and JAM2 were expressed on primary MM cells at higher levels than on healthy long-lived plasma cells (PCs) in the bone marrow. IL-27 activated STAT1, and to a lesser extent STAT3, in MM cell lines and in PCs generated from memory B cells in an IL-21-dependent in vitro PC differentiation assay. Concomitant activity of IL-21 and IL-27 enhanced differentiation into PCs and increased the cell-surface expression of the known STAT target gene CD38. In accordance, a subset of MM cell lines and primary MM cells cultured with IL-27 upregulated CD38 cell-surface expression, a finding with potential implications for enhancing the efficacy of CD38-directed monoclonal antibody therapies by increasing CD38 expression on tumor cells. The elevated expression of IL-27Rα and JAM2 on MM cells compared with that on healthy PCs may be exploited for the development of targeted therapeutic strategies that modulate the interaction of MM cells with the TME.
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Affiliation(s)
- Rebecca J. Brownlie
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Ruth Kennedy
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Erica B. Wilson
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Maja Milanovic
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Claire F. Taylor
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Dapeng Wang
- Leeds Omics, University of Leeds, Leeds, United Kingdom
| | - John R. Davies
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Heather Owston
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, United Kingdom
- National Institute for Health Research, Leeds Biomedical Research Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Emma J. Adams
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Sophie Stephenson
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Rebecca Caeser
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | | | - Peter V. Giannoudis
- Leeds Orthopaedic & Trauma Sciences, Leeds General Infirmary, and Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, United Kingdom
| | - Claudio Scuoppo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY
| | - Dennis McGonagle
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, United Kingdom
- National Institute for Health Research, Leeds Biomedical Research Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Daniel J. Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Reuben M. Tooze
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Gina M. Doody
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
| | - Gordon Cook
- CRUK Clinical Trials Unit, Leeds Institute of Clinical Trial Research, University of Leeds, Leeds, United Kingdom
| | - David R. Westhead
- Bioinformatics Group, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ulf Klein
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s Hospital, University of Leeds, Leeds, United Kingdom
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11
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Lam JH, Baumgarth N. Toll-like receptor mediated inflammation directs B cells towards protective antiviral extrafollicular responses. Nat Commun 2023; 14:3979. [PMID: 37407556 DOI: 10.1038/s41467-023-39734-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/27/2023] [Indexed: 07/07/2023] Open
Abstract
Extrafollicular plasmablast responses (EFRs) are considered to generate antibodies of low affinity that offer little protection from infections. Paradoxically, high avidity antigen-B cell receptor engagement is thought to be the main driver of B cell differentiation, whether in EFRs or slower-developing germinal centers (GCs). Here we show that influenza infection rapidly induces EFRs, generating protective antibodies via Toll-like receptor (TLR)-mediated mechanisms that are both B cell intrinsic and extrinsic. B cell-intrinsic TLR signals support antigen-stimulated B cell survival, clonal expansion, and the differentiation of B cells via induction of IRF4, the master regulator of B cell differentiation, through activation of NF-kB c-Rel. Provision of sustained TLR4 stimulation after immunization shifts the fate of virus-specific B cells towards EFRs instead of GCs, prompting rapid antibody production and improving their protective capacity over antigen/alum administration alone. Thus, inflammatory signals act as B cell fate-determinants for the rapid generation of protective antiviral extrafollicular responses.
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Affiliation(s)
- Jonathan H Lam
- Graduate Group in Immunology, University of California Davis, Davis, USA
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, USA
- Dept. Pathology, Microbiology and Immunology, University of California Davis, Davis, USA
| | - Nicole Baumgarth
- Graduate Group in Immunology, University of California Davis, Davis, USA.
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, USA.
- Dept. Pathology, Microbiology and Immunology, University of California Davis, Davis, USA.
- W. Harry Feinstone Dept Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, E4135, Baltimore, MD, 21205, USA.
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12
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Cloete I, Smith VM, Jackson RA, Pepper A, Pepper C, Vogler M, Dyer MJS, Mitchell S. Computational modeling of DLBCL predicts response to BH3-mimetics. NPJ Syst Biol Appl 2023; 9:23. [PMID: 37280330 PMCID: PMC10244332 DOI: 10.1038/s41540-023-00286-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/26/2023] [Indexed: 06/08/2023] Open
Abstract
In healthy cells, pro- and anti-apoptotic BCL2 family and BH3-only proteins are expressed in a delicate equilibrium. In contrast, this homeostasis is frequently perturbed in cancer cells due to the overexpression of anti-apoptotic BCL2 family proteins. Variability in the expression and sequestration of these proteins in Diffuse Large B cell Lymphoma (DLBCL) likely contributes to variability in response to BH3-mimetics. Successful deployment of BH3-mimetics in DLBCL requires reliable predictions of which lymphoma cells will respond. Here we show that a computational systems biology approach enables accurate prediction of the sensitivity of DLBCL cells to BH3-mimetics. We found that fractional killing of DLBCL, can be explained by cell-to-cell variability in the molecular abundances of signaling proteins. Importantly, by combining protein interaction data with a knowledge of genetic lesions in DLBCL cells, our in silico models accurately predict in vitro response to BH3-mimetics. Furthermore, through virtual DLBCL cells we predict synergistic combinations of BH3-mimetics, which we then experimentally validated. These results show that computational systems biology models of apoptotic signaling, when constrained by experimental data, can facilitate the rational assignment of efficacious targeted inhibitors in B cell malignancies, paving the way for development of more personalized approaches to treatment.
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Affiliation(s)
- Ielyaas Cloete
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Victoria M Smith
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research center, University of Leicester, Leicester, UK
| | - Ross A Jackson
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research center, University of Leicester, Leicester, UK
| | - Andrea Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Chris Pepper
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Meike Vogler
- Institute for Experimental Cancer Research in Pediatrics, Goethe-University, Frankfurt, Germany
| | - Martin J S Dyer
- Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- The Ernest and Helen Scott Haematological Research Institute, Leicester Cancer Research center, University of Leicester, Leicester, UK
| | - Simon Mitchell
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK.
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13
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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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14
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Rivera CE, Zhou Y, Chupp DP, Yan H, Fisher AD, Simon R, Zan H, Xu Z, Casali P. Intrinsic B cell TLR-BCR linked coengagement induces class-switched, hypermutated, neutralizing antibody responses in absence of T cells. SCIENCE ADVANCES 2023; 9:eade8928. [PMID: 37115935 PMCID: PMC10146914 DOI: 10.1126/sciadv.ade8928] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Maturation of antibody responses entails somatic hypermutation (SHM), class-switch DNA recombination (CSR), plasma cell differentiation, and generation of memory B cells, and it is thought to require T cell help. We showed that B cell Toll-like receptor 4 (TLR4)-B cell receptor (BCR) (receptor for antigen) coengagement by 4-hydroxy-3-nitrophenyl acetyl (NP)-lipopolysaccharide (LPS) (Escherichia coli lipid A polysaccharide O-antigen) or TLR5-BCR coengagement by Salmonella flagellin induces mature antibody responses to NP and flagellin in Tcrβ-/-Tcrδ-/- and NSG/B mice. TLR-BCR coengagement required linkage of TLR and BCR ligands, "linked coengagement." This induced B cell CSR/SHM, germinal center-like differentiation, clonal expansion, intraconal diversification, plasma cell differentiation, and an anamnestic antibody response. In Tcrβ-/-Tcrδ-/- mice, linked coengagement of TLR4-BCR by LPS or TLR5-BCR by flagellin induced protective antibodies against E. coli or Salmonella Typhimurium. Our findings unveiled a critical role of B cell TLRs in inducing neutralizing antibody responses, including those to microbial pathogens, without T cell help.
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Affiliation(s)
- Carlos E. Rivera
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Yulai Zhou
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Daniel P. Chupp
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Hui Yan
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Amanda D. Fisher
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Raphael Simon
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Hong Zan
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Zhenming Xu
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology & Molecular Genetics, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
- Department of Medicine, University of Texas Long School of Medicine, UT Health Science Center, San Antonio, TX 78229, USA
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15
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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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16
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Pasqualucci L, Klein U. NF-κB Mutations in Germinal Center B-Cell Lymphomas: Relation to NF-κB Function in Normal B Cells. Biomedicines 2022; 10:biomedicines10102450. [PMID: 36289712 PMCID: PMC9599362 DOI: 10.3390/biomedicines10102450] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Most B cell lymphomas arise from the oncogenic transformation of B cells that have undergone the germinal center (GC) reaction of the T cell-dependent immune response, where high-affinity memory B cells and plasma cells are generated. The high proliferation of GC B cells coupled with occasional errors in the DNA-modifying processes of somatic hypermutation and class switch recombination put the cell at a risk to obtain transforming genetic aberrations, which may activate proto-oncogenes or inactivate tumour suppressor genes. Several subtypes of GC lymphomas harbor genetic mutations leading to constitutive, aberrant activation of the nuclear factor-κB (NF-κB) signaling pathway. In normal B cells, NF-κB has crucial biological roles in development and physiology. GC lymphomas highjack these activities to promote tumour-cell growth and survival. It has become increasingly clear that the separate canonical and non-canonical routes of the NF-κB pathway and the five downstream NF-κB transcription factors have distinct functions in the successive stages of GC B-cell development. These findings may have direct implications for understanding how aberrant NF-κB activation promotes the genesis of various GC lymphomas corresponding to the developmentally distinct GC B-cell subsets. The knowledge arising from these studies may be explored for the development of precision medicine approaches aimed at more effective treatments of the corresponding tumours with specific NF-κB inhibitors, thus reducing systemic toxicity. We here provide an overview on the patterns of genetic NF-κB mutations encountered in the various GC lymphomas and discuss the consequences of aberrant NF-κB activation in those malignancies as related to the biology of NF-κB in their putative normal cellular counterparts.
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Affiliation(s)
- Laura Pasqualucci
- Institute for Cancer Genetics, Department of Pathology & Cell Biology, The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
- Correspondence: (L.P.); (U.K.)
| | - Ulf Klein
- Division of Haematology & Immunology, Leeds Institute of Medical Research at St. James’s, University of Leeds, Leeds LS9 7TF, UK
- Correspondence: (L.P.); (U.K.)
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17
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King JK, Tran TM, Paing MH, Yin Y, Jaiswal AK, Tso CH, Roy K, Casero D, Rao DS. Regulation of T-independent B-cell responses by microRNA-146a. Front Immunol 2022; 13:984302. [PMID: 36172375 PMCID: PMC9511149 DOI: 10.3389/fimmu.2022.984302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
The microRNA, miR-146a, is a negative feedback regulator of the central immune transcription factor, nuclear factor kappa B (NFkB). MiR-146a plays important roles in the immune system, and miR-146a deficient mice show a complex phenotype with features of chronic inflammation and autoimmune disease. In this study, we examined the role of miR-146a in extrafollicular B-cell responses, finding that miR-146a suppresses cellular responses in vivo and in vitro. Gene expression profiling revealed that miR-146a-deficient B-cells showed upregulation of interferon pathway genes, including Traf6, a known miR-146a target. We next interrogated the role of TRAF6 in these B-cell responses, finding that TRAF6 is required for proliferation by genetic and pharmacologic inhibition. Together, our findings demonstrate a novel role for miR-146a and TRAF6 in the extrafollicular B-cell responses, which have recently been tied to autoimmune disease pathogenesis. Our work highlights the pathogenetic role of miR-146a and the potential of pharmacologic inhibition of TRAF6 in autoimmune diseases in which miR-146a is deregulated.
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Affiliation(s)
- Jennifer K. King
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - Tiffany M. Tran
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - May H. Paing
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - Yuxin Yin
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - Amit K. Jaiswal
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - Ching-Hsuan Tso
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
| | - Koushik Roy
- Department of Pathology, University of Utah Salt Lake City, UT, United States
| | - David Casero
- F Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Dinesh S. Rao
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, CA, United States
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18
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SoRelle ED, Dai J, Reinoso-Vizcaino NM, Barry AP, Chan C, Luftig MA. Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection. Cell Rep 2022; 40:111286. [PMID: 36044865 PMCID: PMC9879279 DOI: 10.1016/j.celrep.2022.111286] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/07/2022] [Accepted: 08/08/2022] [Indexed: 01/28/2023] Open
Abstract
Epstein-Barr virus infection of B lymphocytes elicits diverse host responses via well-adapted transcriptional control dynamics. Consequently, this host-pathogen interaction provides a powerful system to explore fundamental processes leading to consensus fate decisions. Here, we use single-cell transcriptomics to construct a genome-wide multistate model of B cell fates upon EBV infection. Additional single-cell data from human tonsils reveal correspondence of model states to analogous in vivo phenotypes within secondary lymphoid tissue, including an EBV+ analog of multipotent activated precursors that can yield early memory B cells. These resources yield exquisitely detailed perspectives of the transforming cellular landscape during an oncogenic viral infection that simulates antigen-induced B cell activation and differentiation. Thus, they support investigations of state-specific EBV-host dynamics, effector B cell fates, and lymphomagenesis. To demonstrate this potential, we identify EBV infection dynamics in FCRL4+/TBX21+ atypical memory B cells that are pathogenically associated with numerous immune disorders.
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Affiliation(s)
- Elliott D. SoRelle
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710,Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710,Corresponding Authors: Elliott D. SoRelle () & Micah A. Luftig ()
| | - Joanne Dai
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710,Current address: Amgen Inc., 1120 Veterans Blvd, South San Francisco, CA 94080
| | - Nicolás M. Reinoso-Vizcaino
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710
| | - Ashley P. Barry
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC 27710
| | - Micah A. Luftig
- Department of Molecular Genetics and Microbiology, Duke Center for Virology, Duke University School of Medicine, Durham, NC 27710,Corresponding Authors: Elliott D. SoRelle () & Micah A. Luftig ()
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19
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Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers. PLoS Genet 2022; 18:e1010235. [PMID: 35648786 PMCID: PMC9191726 DOI: 10.1371/journal.pgen.1010235] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 06/13/2022] [Accepted: 05/03/2022] [Indexed: 11/19/2022] Open
Abstract
The transcription factor NF-κB, which plays an important role in cell fate determination, is involved in the activation of super-enhancers (SEs). However, the biological functions of the NF-κB SEs in gene control are not fully elucidated. We investigated the characteristics of NF-κB-mediated SE activity using fluorescence imaging of RelA, single-cell transcriptome and chromatin accessibility analyses in anti-IgM-stimulated B cells. The formation of cell stimulation-induced nuclear RelA foci was abolished in the presence of hexanediol, suggesting an underlying process of liquid-liquid phase separation. The gained SEs induced a switch-like expression and enhanced cell-to-cell variability in transcriptional response. These properties were correlated with the number of gained cis-regulatory interactions, while switch-like gene induction was associated with the number of NF-κB binding sites in SE. Our study suggests that NF-κB SEs have an important role in the transcriptional regulation of B cells possibly through liquid condensate formation consisting of macromolecular interactions. NF-κB produces an all-or-none activation response upon the activation of B cell receptors. These dynamics modulate the amplitude and frequency of target mRNA induction in cell populations. In this research, we performed single-cell assessment of chromatin accessibility and RNA expression, coupled with fluorescence imaging to characterize the nuclear dynamics of NF-κB proteins in B cell upon receptor stimulation. We found that upon cellular activation, NF-κB-mediated long-range activation of enhancers cooperatively evoked RNA production. In addition, predicted DNA contacts brought by open chromatin led to the high heterogeneity of RNA levels in cell populations. Stimuli-dependent NF-κB foci formation was further inhibited by 1,6-hexanediol (liquid-liquid phase separation inhibitor) and JQ1 (coactivator protein BRD4 inhibitor). We thus propose that nuclear NF-κB plays an important role in the transcriptional regulation of B cell development possibly through the formation of liquid condensates.
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20
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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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21
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Erikson E, Ádori M, Khoenkhoen S, Zhang J, Rorbach J, Castro Dopico X, Karlsson Hedestam GB. Impaired plasma cell differentiation associates with increased oxidative metabolism in IκBNS-deficient B cells. Cell Immunol 2022; 375:104516. [DOI: 10.1016/j.cellimm.2022.104516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/03/2022]
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22
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Smulski CR, Zhang L, Burek M, Teixidó Rubio A, Briem JS, Sica MP, Sevdali E, Vigolo M, Willen L, Odermatt P, Istanbullu D, Herr S, Cavallari M, Hess H, Rizzi M, Eibel H, Schneider P. Ligand-independent oligomerization of TACI is controlled by the transmembrane domain and regulates proliferation of activated B cells. Cell Rep 2022; 38:110583. [PMID: 35354034 DOI: 10.1016/j.celrep.2022.110583] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
In mature B cells, TACI controls class-switch recombination and differentiation into plasma cells during T cell-independent antibody responses. TACI binds the ligands BAFF and APRIL. Approximately 10% of patients with common variable immunodeficiency (CVID) carry TACI mutations, of which A181E and C172Y are in the transmembrane domain. Residues A181 and C172 are located on distinct sides of the transmembrane helix, which is predicted by molecular modeling to spontaneously assemble into trimers and dimers. In human B cells, these mutations impair ligand-dependent (C172Y) and -independent (A181E) TACI multimerization and signaling, as well as TACI-enhanced proliferation and/or IgA production. Genetic inactivation of TACI in primary human B cells impaired survival of CpG-activated cells in the absence of ligand. These results identify the transmembrane region of TACI as an active interface for TACI multimerization in signal transduction, in particular for ligand-independent signals. These functions are perturbed by CVID-associated mutations.
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Affiliation(s)
- Cristian R Smulski
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland; Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany; Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida E- Bustillo 9500, R8402AGP Río Negro, San Carlos de Bariloche, Argentina.
| | - Luyao Zhang
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Malte Burek
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Ariadna Teixidó Rubio
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Jana-Susann Briem
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Mauricio P Sica
- Medical Physics Department, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida E- Bustillo 9500, R8402AGP Río Negro, San Carlos de Bariloche, Argentina; Instituto de Energía y Desarrollo Sustentable, Centro Atómico Bariloche, Comisión Nacional de Energía Atómica (CNEA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida E- Bustillo 9500, R8402AGP Río Negro, San Carlos de Bariloche, Argentina
| | - Eirini Sevdali
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Michele Vigolo
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Laure Willen
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland
| | - Patricia Odermatt
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Duygu Istanbullu
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Stephanie Herr
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Marco Cavallari
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, 79104 Freiburg, Germany
| | | | - Marta Rizzi
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Hermann Eibel
- Faculty of Medicine and Medical Center, University of Freiburg, Department of Rheumatology and Center for Chronic Immunodeficiency, Breisacherstr. 115, 79106 Freiburg, Germany
| | - Pascal Schneider
- Department of Biochemistry, University of Lausanne, Ch. des Boveresses 155, 1066 Epalinges, Switzerland.
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23
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CD40 signaling-mediated delay in terminal differentiation of B cells enables alternate fate choices during early divisions. Mol Immunol 2022; 144:1-15. [PMID: 35149319 DOI: 10.1016/j.molimm.2022.01.012] [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: 09/08/2021] [Revised: 01/17/2022] [Accepted: 01/23/2022] [Indexed: 11/20/2022]
Abstract
Memory B cells and differentiated plasma cells combine to confer sustained humoral immunity. Nonetheless, we are yet to understand how B cells decide between these fates. Although pan-T cell help augments plasma cell differentiation, signaling via CD40 alone is considered to be inhibitory. Here, we examine the capacity of CD40 signaling to interfere with lipopolysaccharide-induced differentiation. Whereas lipopolysaccharide stimulation yielded only short-lived plasmablasts, co-stimulation of CD40 enhanced activation, proliferation, survival, and isotype-switching, leading to alternate fate choices such as germinal center and memory B cells during early divisions. Contrary to the notion that CD40 signaling simply arrests differentiation, the survivors, at later time points, developed into long-lived mature plasma cells, after progressively losing their ability to get restimulated. Counterintuitively, as constitutive lipopolysaccharide stimulation itself hampered differentiation, we identified that the proliferation potential of cells acted alongside CD40 signaling. Accordingly, we propose a bi-layered regulation of differentiation - CD40 signaling and proliferation potential of cells independently inhibit the commitment to and maturation of differentiation, respectively. Elucidating such cell fate decision mechanisms will aid in better vaccine design and disease management.
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24
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Saini A, Ghoneim HE, Lio CWJ, Collins PL, Oltz EM. Gene Regulatory Circuits in Innate and Adaptive Immune Cells. Annu Rev Immunol 2022; 40:387-411. [PMID: 35119910 DOI: 10.1146/annurev-immunol-101320-025949] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell identity and function largely rely on the programming of transcriptomes during development and differentiation. Signature gene expression programs are orchestrated by regulatory circuits consisting of cis-acting promoters and enhancers, which respond to a plethora of cues via the action of transcription factors. In turn, transcription factors direct epigenetic modifications to revise chromatin landscapes, and drive contacts between distal promoter-enhancer combinations. In immune cells, regulatory circuits for effector genes are especially complex and flexible, utilizing distinct sets of transcription factors and enhancers, depending on the cues each cell type receives during an infection, after sensing cellular damage, or upon encountering a tumor. Here, we review major players in the coordination of gene regulatory programs within innate and adaptive immune cells, as well as integrative omics approaches that can be leveraged to decipher their underlying circuitry. Expected final online publication date for the Annual Review of Immunology, Volume 40 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ankita Saini
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Chan-Wang Jerry Lio
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Patrick L Collins
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
| | - Eugene M Oltz
- Department of Microbial Infection and Immunity and Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, College of Medicine, The Ohio State University, Columbus, Ohio, USA; ,
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25
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Liu ZH, Zhang L, Jing FJ, Xiao SX, Gao Y, Bian HY, Zhao X. Genetic Polymorphisms in NLRP3 Inflammasome-Associated Genes in Patients with B-Cell Non-Hodgkin's Lymphoma. J Inflamm Res 2021; 14:5687-5697. [PMID: 34754215 PMCID: PMC8570379 DOI: 10.2147/jir.s329090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/07/2021] [Indexed: 12/28/2022] Open
Abstract
Purpose The role of NLRP3 inflammasome in the progression of many diseases has been increasingly recognized. However, the function of this molecular assembly in the development and progression of B-cell non-Hodgkin's lymphoma remains unclear. Patients and Methods In this study, we investigated the polymorphisms in the NLRP3 inflammasome associated genes in 281 patients with B-cell non-Hodgkin's lymphoma and 385 age- and gender-matched healthy controls. Results We found that IL-18 (rs1946518) and NFκB-94 ins/del (rs28362491) contributed to susceptibility to B-cell non-Hodgkin's lymphoma. Specifically, the allele "G" in IL-18 (rs1946518) and allele "ins" in NFκB-94 ins/del (rs28362491) were significantly associated with the risk of disease. The AA genotype of CARD8 (rs2043211) and the higher level of serum lactate dehydrogenase (LDH) led to statistically poorer B-cell non-Hodgkin's lymphoma survival. Less frequent genotype TT of CARD8 (rs2043211) was observed in patients with higher LDH level, clinical stages III-IV of disease, and IPI 3-5, although the relationship did not reach statistical significance. However, IPI is an independent prognostic factor for B-cell non-Hodgkin's lymphoma. Conclusion IL-18 (rs1946518) and NFκB-94 ins/del (rs28362491) gene polymorphisms appear to be the factors influencing the risk of B-cell non-Hodgkin's lymphoma. CARD8 (rs2043211) polymorphisms are important factors for the survival of patients with this disease.
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Affiliation(s)
- Zhi-He Liu
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Lin Zhang
- Laboratory of Molecular Diagnosis and Regenerative Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Fan-Jing Jing
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Shu-Xin Xiao
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Yan Gao
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Hai-Yan Bian
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
| | - Xia Zhao
- Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, 266000, Shandong, People's Republic of China
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26
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Thobe K, Konrath F, Chapuy B, Wolf J. Patient-Specific Modeling of Diffuse Large B-Cell Lymphoma. Biomedicines 2021; 9:biomedicines9111655. [PMID: 34829885 PMCID: PMC8615565 DOI: 10.3390/biomedicines9111655] [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: 09/30/2021] [Revised: 10/30/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Personalized medicine aims to tailor treatment to patients based on their individual genetic or molecular background. Especially in diseases with a large molecular heterogeneity, such as diffuse large B-cell lymphoma (DLBCL), personalized medicine has the potential to improve outcome and/or to reduce resistance towards treatment. However, integration of patient-specific information into a computational model is challenging and has not been achieved for DLBCL. Here, we developed a computational model describing signaling pathways and expression of critical germinal center markers. The model integrates the regulatory mechanism of the signaling and gene expression network and covers more than 50 components, many carrying genetic lesions common in DLBCL. Using clinical and genomic data of 164 primary DLBCL patients, we implemented mutations, structural variants and copy number alterations as perturbations in the model using the CoLoMoTo notebook. Leveraging patient-specific genotypes and simulation of the expression of marker genes in specific germinal center conditions allows us to predict the consequence of the modeled pathways for each patient. Finally, besides modeling how genetic perturbations alter physiological signaling, we also predicted for each patient model the effect of rational inhibitors, such as Ibrutinib, that are currently discussed as possible DLBCL treatments, showing patient-dependent variations in effectiveness and synergies.
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Affiliation(s)
- Kirsten Thobe
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
| | - Fabian Konrath
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
| | - Björn Chapuy
- Department of Hematology and Medical Oncology, University of Göttingen, 37075 Göttingen, Germany;
- Department of Hematology, Oncology and Cancer Immunology, Berlin Medical Center Charité, 12203 Berlin, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrück Center for Molecular Medicine, 13125 Berlin-Buch, Germany; (K.T.); (F.K.)
- Department of Mathematics and Computer Science, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
- Correspondence:
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27
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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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28
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Lévy R, Langlais D, Béziat V, Rapaport F, Rao G, Lazarov T, Bourgey M, Zhou YJ, Briand C, Moriya K, Ailal F, Avery DT, Markle J, Lim AI, Ogishi M, Yang R, Pelham S, Emam M, Migaud M, Deswarte C, Habib T, Saraiva LR, Moussa EA, Guennoun A, Boisson B, Belkaya S, Martinez-Barricarte R, Rosain J, Belkadi A, Breton S, Payne K, Benhsaien I, Plebani A, Lougaris V, Di Santo JP, Neven B, Abel L, Ma CS, Bousfiha AA, Marr N, Bustamante J, Liu K, Gros P, Geissmann F, Tangye SG, Casanova JL, Puel A. Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to multiple infectious agents. J Clin Invest 2021; 131:150143. [PMID: 34623332 DOI: 10.1172/jci150143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/08/2021] [Indexed: 12/26/2022] Open
Abstract
We studied a child with severe viral, bacterial, fungal, and parasitic diseases, who was homozygous for a loss-of-function mutation of REL, encoding c-Rel, which is selectively expressed in lymphoid and myeloid cells. The patient had low frequencies of NK, effector memory cells reexpressing CD45RA (Temra) CD8+ T cells, memory CD4+ T cells, including Th1 and Th1*, Tregs, and memory B cells, whereas the counts and proportions of other leukocyte subsets were normal. Functional deficits of myeloid cells included the abolition of IL-12 and IL-23 production by conventional DC1s (cDC1s) and monocytes, but not cDC2s. c-Rel was also required for induction of CD86 expression on, and thus antigen-presenting cell function of, cDCs. Functional deficits of lymphoid cells included reduced IL-2 production by naive T cells, correlating with low proliferation and survival rates and poor production of Th1, Th2, and Th17 cytokines by memory CD4+ T cells. In naive CD4+ T cells, c-Rel is dispensable for early IL2 induction but contributes to later phases of IL2 expression. The patient's naive B cells displayed impaired MYC and BCL2L1 induction, compromising B cell survival and proliferation and preventing their differentiation into Ig-secreting plasmablasts. Inherited c-Rel deficiency disrupts the development and function of multiple myeloid and lymphoid cells, compromising innate and adaptive immunity to multiple infectious agents.
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Affiliation(s)
- Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | | | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Geetha Rao
- Garvan Institute, Darlinghurst, New South Wales 2010, Australia
| | - Tomi Lazarov
- Memorial Sloan Kettering Institute, New York, New York, USA
| | | | - Yu J Zhou
- Columbia University, New York, New York, USA
| | - Coralie Briand
- Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Kunihiko Moriya
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | | | | | - Janet Markle
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | | | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Rui Yang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Simon Pelham
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Mehdi Emam
- McGill University, Montreal, Quebec, Canada
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | | | | | | | | | - Bertrand Boisson
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Serkan Belkaya
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Ruben Martinez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France
| | - Sylvain Breton
- Pediatric Radiology, Necker Hospital for Sick Children, Paris, France
| | - Kathryn Payne
- Garvan Institute, Darlinghurst, New South Wales 2010, Australia
| | | | - Alessandro Plebani
- University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | - Vassilios Lougaris
- University of Brescia and ASST-Spedali Civili of Brescia, Brescia, Italy
| | | | - Bénédicte Neven
- University of Paris, Imagine Institute, Paris, France.,Pediatric Immunology, Hematology and Rheumatology Unit, Necker Hospital for Sick Children, AP-HP, Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
| | - Cindy S Ma
- Garvan Institute, Darlinghurst, New South Wales 2010, Australia
| | | | - Nico Marr
- Sidra Medicine, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA.,Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, Paris, France
| | - Kang Liu
- Columbia University, New York, New York, USA
| | | | | | - Stuart G Tangye
- Garvan Institute, Darlinghurst, New South Wales 2010, Australia
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA.,Howard Hughes Medical Institute (HHMI), New York, New York, USA
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Paris, France.,University of Paris, Imagine Institute, Paris, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, New York, USA
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29
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Keim D, Gollner K, Gollner U, Jérôme V, Freitag R. Generation of Recombinant Primary Human B Lymphocytes Using Non-Viral Vectors. Int J Mol Sci 2021; 22:8239. [PMID: 34361005 PMCID: PMC8347318 DOI: 10.3390/ijms22158239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 07/29/2021] [Accepted: 07/29/2021] [Indexed: 12/26/2022] Open
Abstract
Although the development of gene delivery systems based on non-viral vectors is advancing, it remains a challenge to deliver plasmid DNA into human blood cells. The current "gold standard", namely linear polyethyleneimine (l-PEI 25 kDa), in particular, is unable to produce transgene expression levels >5% in primary human B lymphocytes. Here, it is demonstrated that a well-defined 24-armed poly(2-dimethylamino) ethyl methacrylate (PDMAEMA, 755 kDa) nano-star is able to reproducibly elicit high transgene expression (40%) at sufficient residual viability (69%) in primary human B cells derived from tonsillar tissue. Moreover, our results indicate that the length of the mitogenic stimulation prior to transfection is an important parameter that must be established during the development of the transfection protocol. In our hands, four days of stimulation with rhCD40L post-thawing led to the best transfection results in terms of TE and cell survival. Most importantly, our data argue for an impact of the B cell subsets on the transfection outcomes, underlining that the complexity and heterogeneity of a given B cell population pre- and post-transfection is a critical parameter to consider in the multiparametric approach required for the implementation of the transfection protocol.
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Affiliation(s)
- Daniel Keim
- Process Biotechnology, University of Bayreuth, 95447 Bayreuth, Germany; (D.K.); (V.J.)
| | - Katrin Gollner
- Praxis am Schießgraben, Schießgraben 21, 95326 Kulmbach, Germany; (K.G.); (U.G.)
| | - Ulrich Gollner
- Praxis am Schießgraben, Schießgraben 21, 95326 Kulmbach, Germany; (K.G.); (U.G.)
| | - Valérie Jérôme
- Process Biotechnology, University of Bayreuth, 95447 Bayreuth, Germany; (D.K.); (V.J.)
| | - Ruth Freitag
- Process Biotechnology, University of Bayreuth, 95447 Bayreuth, Germany; (D.K.); (V.J.)
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30
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Faumont N, Taoui O, Collares D, Jais JP, Leroy K, Prévaud L, Jardin F, Molina TJ, Copie-Bergman C, Petit B, Gourin MP, Bordessoule D, Troutaud D, Baud V, Feuillard J. c-Rel Is the Pivotal NF-κB Subunit in Germinal Center Diffuse Large B-Cell Lymphoma: A LYSA Study. Front Oncol 2021; 11:638897. [PMID: 33959502 PMCID: PMC8095348 DOI: 10.3389/fonc.2021.638897] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Relationships between c-Rel and GCB-DLBCLs remain unclear. We found that strong c-Rel DNA-binding activity was mostly found in GCBs on two independent series of 48 DLBCLs and 66 DLBCLs, the latter issued from the GHEDI series. c-Rel DNA-binding activity was associated with increased REL mRNA expression. Extending the study to the whole GHEDI and Lenz DLBCL published series of 202 and 233 cases, it was found that the c-Rel gene expression profile (GEP) overlapped partially (12%) but only with the GCB GEP and not with the GEP of ABC-DLBCLs. Cases with both overexpression of REL mRNA and c-Rel GEP were defined as those having a c-Rel signature. These cases were GCBs in 88 and 83% of the GHEDI or Lenz's DLBCL series respectively. The c-Rel signature was also associated with various recurrent GCB-DLBCL genetic events, including REL gains, BCL2 translocation, MEF2B, EZH2, CREBBP, and TNFRSF14 mutations and with the EZB GCB genetic subtype. By CGH array, the c-Rel signature was specifically correlated with 2p15-16.1 amplification that includes XPO1, BCL11A, and USP34 and with the 22q11.22 deletion that covers IGLL5 and PRAME. The total number of gene copy number aberrations, so-called genomic imbalance complexity, was decreased in cases with the c-Rel signature. These cases exhibited a better overall survival. Functionally, overexpression of c-Rel induced its constitutive nuclear localization and protected cells against apoptosis while its repression tended to increase cell death. These results show that, clinically and biologically, c-Rel is the pivotal NF-κB subunit in the GCB-DLBCL subgroup. Functionally, c-Rel overexpression could directly promote DLBCL tumorigenesis without need for further activation signals.
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Affiliation(s)
- Nathalie Faumont
- CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Oussama Taoui
- CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Davi Collares
- Université de Paris, NF-κappaB, Differentiation and Cancer, Paris, France
| | | | - Karen Leroy
- UMRS1138, Centre de Recherche des Cordeliers, Paris Descartes University, CARPEM, Department of Genetics and Molecular Biology, Cochin Hospital, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Léa Prévaud
- CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
| | - Fabrice Jardin
- Inserm U1245 and Department of Henri-Becquerel Hematology Center and Normandie Univ UNIROUEN, Rouen, France
| | - Thierry J Molina
- Université de Paris, NF-κappaB, Differentiation and Cancer, Paris, France.,Pathology Department, Necker Hospital, Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Barbara Petit
- Pathology Department, CHU of Limoges, Limoges, France
| | - Marie-Pierre Gourin
- Regional Reference Structure of Limousin Lymphomas, Clinical Hematology Department, CHU of Limoges, Limoges, France
| | - Dominique Bordessoule
- CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France.,Regional Reference Structure of Limousin Lymphomas, Clinical Hematology Department, CHU of Limoges, Limoges, France
| | | | - Véronique Baud
- Université de Paris, NF-κappaB, Differentiation and Cancer, Paris, France
| | - Jean Feuillard
- CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France
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31
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Liu GJ, Jaritz M, Wöhner M, Agerer B, Bergthaler A, Malin SG, Busslinger M. Repression of the B cell identity factor Pax5 is not required for plasma cell development. J Exp Med 2021; 217:152012. [PMID: 32780801 PMCID: PMC7596824 DOI: 10.1084/jem.20200147] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 05/20/2020] [Accepted: 07/01/2020] [Indexed: 01/05/2023] Open
Abstract
B cell and plasma cell fates are controlled by different transcriptional networks, as exemplified by the mutually exclusive expression and cross-antagonism of the B cell identity factor Pax5 and the plasma cell regulator Blimp1. It has been postulated that repression of Pax5 by Blimp1 is essential for plasma cell development. Here, we challenged this hypothesis by analyzing the IghPax5/+ mouse, which expressed a Pax5 minigene from the immunoglobulin heavy-chain locus. Despite high Pax5 expression, plasma cells efficiently developed in young IghPax5/+ mice at steady state and upon immunization, while their number moderately declined in older mice. Although Pax5 significantly deregulated the plasma cell expression program, key plasma cell regulators were normally expressed in IghPax5/+ plasma cells. While IgM and IgA secretion by IghPax5/+ plasma cells was normal, IgG secretion was modestly decreased. Hence, Pax5 repression is not essential for robust plasma cell development and antibody secretion, although it is required for optimal IgG production and accumulation of long-lived plasma cells.
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Affiliation(s)
- Grace J Liu
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Miriam Wöhner
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Benedikt Agerer
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andreas Bergthaler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stephen G Malin
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Meinrad Busslinger
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
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32
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Berenguer J, Celià-Terrassa T. Cell memory of epithelial-mesenchymal plasticity in cancer. Curr Opin Cell Biol 2021; 69:103-110. [PMID: 33578288 DOI: 10.1016/j.ceb.2021.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 11/26/2022]
Abstract
Fundamental biological processes of cell identity and cell fate determination are controlled by complex regulatory networks. These processes require molecular mechanisms that confer cellular phenotypic memory and state persistence. In this minireview, we will summarize mechanisms of cell memory based on regulatory hysteretic feedback loops and explore epigenetic mechanisms widely represented in nature, with special focus on epithelial-to-mesenchymal plasticity. We will also discuss the functional consequences of cell memory and epithelial-to-mesenchymal plasticity dynamics during development and cancer metastasis.
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Affiliation(s)
- Jordi Berenguer
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
| | - Toni Celià-Terrassa
- Cancer Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.
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33
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Merino Tejero E, Lashgari D, García-Valiente R, Gao X, Crauste F, Robert PA, Meyer-Hermann M, Martínez MR, van Ham SM, Guikema JEJ, Hoefsloot H, van Kampen AHC. Multiscale Modeling of Germinal Center Recapitulates the Temporal Transition From Memory B Cells to Plasma Cells Differentiation as Regulated by Antigen Affinity-Based Tfh Cell Help. Front Immunol 2021; 11:620716. [PMID: 33613551 PMCID: PMC7892951 DOI: 10.3389/fimmu.2020.620716] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023] Open
Abstract
Germinal centers play a key role in the adaptive immune system since they are able to produce memory B cells and plasma cells that produce high affinity antibodies for an effective immune protection. The mechanisms underlying cell-fate decisions are not well understood but asymmetric division of antigen, B-cell receptor affinity, interactions between B-cells and T follicular helper cells (triggering CD40 signaling), and regulatory interactions of transcription factors have all been proposed to play a role. In addition, a temporal switch from memory B-cell to plasma cell differentiation during the germinal center reaction has been shown. To investigate if antigen affinity-based Tfh cell help recapitulates the temporal switch we implemented a multiscale model that integrates cellular interactions with a core gene regulatory network comprising BCL6, IRF4, and BLIMP1. Using this model we show that affinity-based CD40 signaling in combination with asymmetric division of B-cells result in switch from memory B-cell to plasma cell generation during the course of the germinal center reaction. We also show that cell fate division is unlikely to be (solely) based on asymmetric division of Ag but that BLIMP1 is a more important factor. Altogether, our model enables to test the influence of molecular modulations of the CD40 signaling pathway on the production of germinal center output cells.
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Affiliation(s)
- Elena Merino Tejero
- Bioinformatics Laboratory, Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Danial Lashgari
- Bioinformatics Laboratory, Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Rodrigo García-Valiente
- Bioinformatics Laboratory, Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Xuefeng Gao
- Department of Hematology and Oncology, International Cancer Center, Shenzhen University General Hospital, Shenzhen University Health Science Center, Shenzhen, China
| | | | - Philippe A Robert
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - S Marieke van Ham
- Department of Immunopathology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands.,Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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34
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He S, Wang LH, Liu Y, Li YQ, Chen HT, Xu JH, Peng W, Lin GW, Wei PP, Li B, Xia X, Wang D, Bei JX, He X, Guo Z. Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs. Genome Biol 2020; 21:294. [PMID: 33287869 PMCID: PMC7720616 DOI: 10.1186/s13059-020-02210-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND As core units of organ tissues, cells of various types play their harmonious rhythms to maintain the homeostasis of the human body. It is essential to identify the characteristics of cells in human organs and their regulatory networks for understanding the biological mechanisms related to health and disease. However, a systematic and comprehensive single-cell transcriptional profile across multiple organs of a normal human adult is missing. RESULTS We perform single-cell transcriptomes of 84,363 cells derived from 15 tissue organs of one adult donor and generate an adult human cell atlas. The adult human cell atlas depicts 252 subtypes of cells, including major cell types such as T, B, myeloid, epithelial, and stromal cells, as well as novel COCH+ fibroblasts and FibSmo cells, each of which is distinguished by multiple marker genes and transcriptional profiles. These collectively contribute to the heterogeneity of major human organs. Moreover, T cell and B cell receptor repertoire comparisons and trajectory analyses reveal direct clonal sharing of T and B cells with various developmental states among different tissues. Furthermore, novel cell markers, transcription factors, and ligand-receptor pairs are identified with potential functional regulations in maintaining the homeostasis of human cells among tissues. CONCLUSIONS The adult human cell atlas reveals the inter- and intra-organ heterogeneity of cell characteristics and provides a useful resource in uncovering key events during the development of human diseases in the context of the heterogeneity of cells and organs.
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Affiliation(s)
- Shuai He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Lin-He Wang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Yang Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Yi-Qi Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Hai-Tian Chen
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Jing-Hong Xu
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Wan Peng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Guo-Wang Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
- Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282 People’s Republic of China
| | - Pan-Pan Wei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Bo Li
- Department of Biochemistry and Molecular Biology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- RNA Biomedical Institute, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120 People’s Republic of China
| | - Xiaojun Xia
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Dan Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510060 People’s Republic of China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Xiaoshun He
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
| | - Zhiyong Guo
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080 People’s Republic of China
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35
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Wiggins KJ, Scharer CD. Roadmap to a plasma cell: Epigenetic and transcriptional cues that guide B cell differentiation. Immunol Rev 2020; 300:54-64. [PMID: 33278036 DOI: 10.1111/imr.12934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 12/11/2022]
Abstract
Antibody-secreting cells (ASCs) or plasma cells secrete antibodies and form a cornerstone of humoral immunity. B cells that receive activation signals in the presence or absence of T cells initiate a differentiation program that requires epigenetic and transcriptional reprogramming in order to ultimately form ASC. Reprogramming is accomplished through the interplay of transcription factors that initiate gene expression programs and epigenetic mechanisms that maintain these programs and cell fates. An important consideration is that all of these factors are operating in the context of cell division. Recent technical advances now allow mechanistic studies to move beyond genetic studies to identify the promoters and enhancer repertoires that are regulated by epigenetic mechanisms and transcription factors in rare cell types and differentiation stages in vivo. This review will detail efforts to integrate transcriptional and epigenetic changes during B cell differentiation with cell division in vivo. What has emerged is a multiphased differentiation model that requires distinct transcription factors and epigenetic programs at each step. The identification of markers that define each phase will help facilitate the manipulation of B cell differentiation for vaccine development or to treat diseases where antibodies are a component.
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Affiliation(s)
- Keenan J Wiggins
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Christopher D Scharer
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
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36
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Cocco M, Care MA, Saadi A, Al-Maskari M, Doody G, Tooze R. A dichotomy of gene regulatory associations during the activated B-cell to plasmablast transition. Life Sci Alliance 2020; 3:e202000654. [PMID: 32843533 PMCID: PMC7471511 DOI: 10.26508/lsa.202000654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/22/2023] Open
Abstract
The activated B-cell (ABC) to plasmablast transition encompasses the cusp of antibody-secreting cell (ASC) differentiation. We explore this transition with integrated analysis in human cells, focusing on changes that follow removal from CD40-mediated signals. Within hours of input signal loss, cell growth programs shift toward enhanced proliferation, accompanied by ER-stress response, and up-regulation of ASC features. Clustering of genomic occupancy for IRF4, BLIMP1, XBP1, and CTCF with histone marks identifies a dichotomy: XBP1 and IRF4 link to induced but not repressed gene modules in plasmablasts, whereas BLIMP1 links to modules of ABC genes that are repressed, but not to activated genes. Between ABC and plasmablast states, IRF4 shifts away from AP1/IRF composite elements while maintaining occupancy at IRF and ETS/IRF elements. This parallels the loss of BATF expression, which is identified as a potential BLIMP1 target. In plasmablasts, IRF4 acquires an association with CTCF, a feature maintained in plasma cell myeloma lines. Thus, shifting occupancy links IRF4 to both ABC and ASC gene expression, whereas BLIMP1 occupancy links to repression of the activation state.
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Affiliation(s)
- Mario Cocco
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Matthew A Care
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Bioinformatics Group, Institute of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Amel Saadi
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Muna Al-Maskari
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Gina Doody
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Reuben Tooze
- Division of Immunology and Haematology, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
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37
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Bone marrow stromal cell-mediated degradation of CD20 leads to primary rituximab resistance in mantle cell lymphoma. Leukemia 2020; 35:1506-1510. [PMID: 32929128 DOI: 10.1038/s41375-020-01035-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/11/2020] [Accepted: 08/19/2020] [Indexed: 12/22/2022]
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38
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Functional interplay of Epstein-Barr virus oncoproteins in a mouse model of B cell lymphomagenesis. Proc Natl Acad Sci U S A 2020; 117:14421-14432. [PMID: 32522871 DOI: 10.1073/pnas.1921139117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epstein-Barr virus (EBV) is a B cell transforming virus that causes B cell malignancies under conditions of immune suppression. EBV orchestrates B cell transformation through its latent membrane proteins (LMPs) and Epstein-Barr nuclear antigens (EBNAs). We here identify secondary mutations in mouse B cell lymphomas induced by LMP1, to predict and identify key functions of other EBV genes during transformation. We find aberrant activation of early B cell factor 1 (EBF1) to promote transformation of LMP1-expressing B cells by inhibiting their differentiation to plasma cells. EBV EBNA3A phenocopies EBF1 activities in LMP1-expressing B cells, promoting transformation while inhibiting differentiation. In cells expressing LMP1 together with LMP2A, EBNA3A only promotes lymphomagenesis when the EBNA2 target Myc is also overexpressed. Collectively, our data support a model where proproliferative activities of LMP1, LMP2A, and EBNA2 in combination with EBNA3A-mediated inhibition of terminal plasma cell differentiation critically control EBV-mediated B cell lymphomagenesis.
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39
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Hashiguchi M, Kashiwakura Y, Kanno Y, Kojima H, Kobata T. IL-21 and IL-5 coordinately induce surface IgA + cells. Immunol Lett 2020; 224:21-27. [PMID: 32492473 DOI: 10.1016/j.imlet.2020.05.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/07/2020] [Accepted: 05/26/2020] [Indexed: 11/17/2022]
Abstract
Intestinal IgA is induced by microbes and food antigens. Peyer's patches (PPs) are known as one of the inductive sites for intestinal IgA production. However, the precise mechanism of IgA induction is as yet unknown. IgA secretion was induced from IgD+ B cells in vitro by stimulus with lipopolysaccharide in the presence of only retinoic acid (RA) and low doses of TGF-β1. Surface IgA+ cells were effectively induced from IgD+ B cells in vitro by the mixture of RA and the cytokines TGF-β1, APRIL, IL-5 and IL-21. rIL-21 upregulated surface IgA+ but impaired the proliferation of stimulated B cells in the presence of rTGF-β1, RA and rAPRIL, in vitro. The addition of rIL-5 restored the impaired proliferation by rIL-21, resulting in the expansion of IgA+ cells. rIL-21 induced the expression of Aicda and Prdm1, and impaired Rel in IgD+ B cells. Blockade of IL-21R signaling by a neutralizing mAb in vivo led to lower frequencies of IgA+ and IgG2b+ cells and lower germinal center B cells in PPs in a homeostatic condition. Although amounts of small intestinal IgA and titers of anti-dsDNA, the major target of intestinal IgA, in these mice were not altered, anti-OVA IgA titers induced by OVA drinking in OVA-specific T-cell receptor (TCR) transgenic mice were decreased. PP-deficient TCR transgenic mice showed diminished anti-OVA IgA induction. Blockade of IL-5R signaling in vivo led to similar results with relatively weaker effects than that of IL-21R mAb administration. These results suggest that IL-21 and IL-5 play cooperative roles in surface expression of IgA in PPs.
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Affiliation(s)
- Masaaki Hashiguchi
- Department of Immunology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, Japan.
| | - Yuji Kashiwakura
- Department of Immunology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, Japan
| | - Yumiko Kanno
- Department of Immunology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, Japan
| | - Hidefumi Kojima
- Department of Immunology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, Japan
| | - Tetsuji Kobata
- Department of Immunology, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, Japan
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40
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Cook SL, Franke MC, Sievert EP, Sciammas R. A Synchronous IRF4-Dependent Gene Regulatory Network in B and Helper T Cells Orchestrating the Antibody Response. Trends Immunol 2020; 41:614-628. [PMID: 32467029 DOI: 10.1016/j.it.2020.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/04/2020] [Accepted: 05/05/2020] [Indexed: 12/18/2022]
Abstract
Control of diverse pathogens requires an adaptive antibody response, dependent on cellular division of labor to allocate antigen-dependent B- and CD4+ T-cell fates that collaborate to control the quantity and quality of antibody. This is orchestrated by the dynamic action of key transcriptional regulators mediating gene expression programs in response to pathogen-specific environmental inputs. We describe a conserved, likely ancient, gene regulatory network that intriguingly operates contemporaneously in B and CD4+ T cells to control their cell fate dynamics and thus, the character of the antibody response. The remarkable output of this network derives from graded expression, designated by antigen receptor signal strength, of a pivotal transcription factor that regulates alternate cell fate choices.
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Affiliation(s)
- Sarah L Cook
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA.
| | - Marissa C Franke
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Evelyn P Sievert
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
| | - Roger Sciammas
- Center for Immunology and Infectious Diseases, University of California Davis, Davis, CA 95616, USA
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41
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Regulation of B-cell function by NF-kappaB c-Rel in health and disease. Cell Mol Life Sci 2020; 77:3325-3340. [PMID: 32130429 DOI: 10.1007/s00018-020-03488-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/03/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
B cells mediate humoral immune response and contribute to the regulation of cellular immune response. Members of the Nuclear Factor kappaB (NF-κB) family of transcription factors play a major role in regulating B-cell functions. NF-κB subunit c-Rel is predominantly expressed in lymphocytes, and in B cells, it is required for survival, proliferation, and antibody production. Dysregulation of c-Rel expression and activation alters B-cell homeostasis and is associated with B-cell lymphomas and autoimmune pathologies. Based on its essential roles, c-Rel may serve as a potential prognostic and therapeutic target. This review summarizes the current understanding of the multifaceted role of c-Rel in B cells and B-cell diseases.
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42
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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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Single-Cell Expression Variability Implies Cell Function. Cells 2019; 9:cells9010014. [PMID: 31861624 PMCID: PMC7017299 DOI: 10.3390/cells9010014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/27/2019] [Indexed: 12/11/2022] Open
Abstract
As single-cell RNA sequencing (scRNA-seq) data becomes widely available, cell-to-cell variability in gene expression, or single-cell expression variability (scEV), has been increasingly appreciated. However, it remains unclear whether this variability is functionally important and, if so, what are its implications for multi-cellular organisms. Here, we analyzed multiple scRNA-seq data sets from lymphoblastoid cell lines (LCLs), lung airway epithelial cells (LAECs), and dermal fibroblasts (DFs) and, for each cell type, selected a group of homogenous cells with highly similar expression profiles. We estimated the scEV levels for genes after correcting the mean-variance dependency in that data and identified 465, 466, and 364 highly variable genes (HVGs) in LCLs, LAECs, and DFs, respectively. Functions of these HVGs were found to be enriched with those biological processes precisely relevant to the corresponding cell type’s function, from which the scRNA-seq data used to identify HVGs were generated—e.g., cytokine signaling pathways were enriched in HVGs identified in LCLs, collagen formation in LAECs, and keratinization in DFs. We repeated the same analysis with scRNA-seq data from induced pluripotent stem cells (iPSCs) and identified only 79 HVGs with no statistically significant enriched functions; the overall scEV in iPSCs was of negligible magnitude. Our results support the “variation is function” hypothesis, arguing that scEV is required for cell type-specific, higher-level system function. Thus, quantifying and characterizing scEV are of importance for our understating of normal and pathological cellular processes.
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The Unsolved Puzzle of c-Rel in B Cell Lymphoma. Cancers (Basel) 2019; 11:cancers11070941. [PMID: 31277480 PMCID: PMC6678315 DOI: 10.3390/cancers11070941] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 01/04/2023] Open
Abstract
Aberrant constitutive activation of Rel/NF-κB transcription factors is a hallmark of numerous cancers. Of the five Rel family members, c-Rel has the strongest direct links to tumorigenesis. c-Rel is the only member that can malignantly transform lymphoid cells in vitro. Furthermore, c-Rel is implicated in human B cell lymphoma through the frequent occurrence of REL gene locus gains and amplifications. In normal physiology, high c-Rel expression predominates in the hematopoietic lineage and a diverse range of stimuli can trigger enhanced expression and activation of c-Rel. Both expression and activation of c-Rel are tightly regulated on multiple levels, indicating the necessity to keep its functions under control. In this review we meta-analyze and integrate studies reporting gene locus aberrations to provide an overview on the frequency of REL gains in human B cell lymphoma subtypes, namely follicular lymphoma, diffuse large B cell lymphoma, primary mediastinal B cell lymphoma, and classical Hodgkin lymphoma. We also summarize current knowledge on c-Rel expression and protein localization in these human B cell lymphomas and discuss the co-amplification of BCL11A with REL. In addition, we highlight and illustrate key pathways of c-Rel activation and regulation with a specific focus on B cell biology.
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Mitchell S, Mercado EL, Adelaja A, Ho JQ, Cheng QJ, Ghosh G, Hoffmann A. An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Front Immunol 2019; 10:1425. [PMID: 31293585 PMCID: PMC6604663 DOI: 10.3389/fimmu.2019.01425] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Accepted: 06/05/2019] [Indexed: 01/22/2023] Open
Abstract
Nuclear factor kappa B (NFκB) is a transcription factor that controls inflammation and cell survival. In clinical histology, elevated NFκB activity is a hallmark of poor prognosis in inflammatory disease and cancer, and may be the result of a combination of diverse micro-environmental constituents. While previous quantitative studies of NFκB focused on its signaling dynamics in single cells, we address here how multiple stimuli may combine to control tissue level NFκB activity. We present a novel, simplified model of NFκB (SiMoN) that functions as an NFκB activity calculator. We demonstrate its utility by exploring how type I and type II interferons modulate NFκB activity in macrophages. Whereas, type I IFNs potentiate NFκB activity by inhibiting translation of IκBα and by elevating viral RNA sensor (RIG-I) expression, type II IFN amplifies NFκB activity by increasing the degradation of free IκB through transcriptional induction of proteasomal cap components (PA28). Both cross-regulatory mechanisms amplify NFκB activation in response to weaker (viral) inducers, while responses to stronger (bacterial or cytokine) inducers remain largely unaffected. Our work demonstrates how the NFκB calculator can reveal distinct mechanisms of crosstalk on NFκB activity in interferon-containing microenvironments.
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Affiliation(s)
- Simon Mitchell
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Ellen L Mercado
- Signaling Systems Laboratory, San Diego Center for Systems Biology, La Jolla, CA, United States
| | - Adewunmi Adelaja
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Jessica Q Ho
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Quen J Cheng
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States
| | - Gourisankar Ghosh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
| | - Alexander Hoffmann
- Signaling Systems Laboratory, Institute for Quantitative and Computational Biosciences, Department of Microbiology, Immunology, and Molecular Genetics, and Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, United States.,Signaling Systems Laboratory, San Diego Center for Systems Biology, La Jolla, CA, United States
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Koike T, Harada K, Horiuchi S, Kitamura D. The quantity of CD40 signaling determines the differentiation of B cells into functionally distinct memory cell subsets. eLife 2019; 8:44245. [PMID: 31225793 PMCID: PMC6636905 DOI: 10.7554/elife.44245] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 06/14/2019] [Indexed: 12/15/2022] Open
Abstract
In mice, memory B (Bmem) cells can be divided into two subpopulations: CD80hi Bmem cells, which preferentially differentiate into plasma cells; and CD80lo Bmem cells, which become germinal center (GC) B cells during a recall response. We demonstrate that these distinct responses can be B-cell-intrinsic and essentially independent of B-cell receptor (BCR) isotypes. Furthermore, we find that the development of CD80hi Bmem cells in the primary immune response requires follicular helper T cells, a relatively strong CD40 signal and a high-affinity BCR on B cells, whereas the development of CD80lo Bmem cells does not. Quantitative differences in CD40 stimulation were enough to recapitulate the distinct B cell fate decisions in an in vitro culture system. The quantity of CD40 signaling appears to be translated into NF-κB activation, followed by BATF upregulation that promotes Bmem cell differentiation from GC B cells.
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Affiliation(s)
- Takuya Koike
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
| | - Koshi Harada
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
| | - Shu Horiuchi
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
| | - Daisuke Kitamura
- Division of Molecular Biology, Research Institute for Biomedical Sciences (RIBS), Tokyo University of Science, Noda, Japan
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Willis SN, Nutt SL. New players in the gene regulatory network controlling late B cell differentiation. Curr Opin Immunol 2019; 58:68-74. [DOI: 10.1016/j.coi.2019.04.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 04/19/2019] [Indexed: 02/07/2023]
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Stone SL, Peel JN, Scharer CD, Risley CA, Chisolm DA, Schultz MD, Yu B, Ballesteros-Tato A, Wojciechowski W, Mousseau B, Misra RS, Hanidu A, Jiang H, Qi Z, Boss JM, Randall TD, Brodeur SR, Goldrath AW, Weinmann AS, Rosenberg AF, Lund FE. T-bet Transcription Factor Promotes Antibody-Secreting Cell Differentiation by Limiting the Inflammatory Effects of IFN-γ on B Cells. Immunity 2019; 50:1172-1187.e7. [PMID: 31076359 PMCID: PMC6929688 DOI: 10.1016/j.immuni.2019.04.004] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 01/04/2019] [Accepted: 04/12/2019] [Indexed: 01/07/2023]
Abstract
Although viral infections elicit robust interferon-γ (IFN-γ) and long-lived antibody-secreting cell (ASC) responses, the roles for IFN-γ and IFN-γ-induced transcription factors (TFs) in ASC development are unclear. We showed that B cell intrinsic expression of IFN-γR and the IFN-γ-induced TF T-bet were required for T-helper 1 cell-induced differentiation of B cells into ASCs. IFN-γR signaling induced Blimp1 expression in B cells but also initiated an inflammatory gene program that, if not restrained, prevented ASC formation. T-bet did not affect Blimp1 upregulation in IFN-γ-activated B cells but instead regulated chromatin accessibility within the Ifng and Ifngr2 loci and repressed the IFN-γ-induced inflammatory gene program. Consistent with this, B cell intrinsic T-bet was required for formation of long-lived ASCs and secondary ASCs following viral, but not nematode, infection. Therefore, T-bet facilitates differentiation of IFN-γ-activated inflammatory effector B cells into ASCs in the setting of IFN-γ-, but not IL-4-, induced inflammatory responses.
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Affiliation(s)
- Sara L Stone
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jessica N Peel
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | | | - Christopher A Risley
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Danielle A Chisolm
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Michael D Schultz
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Wojciech Wojciechowski
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Betty Mousseau
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
| | - Adedayo Hanidu
- Boerhinger Ingelheim Pharmaceutical Inc., Ridgefield, CT 06877, USA
| | - Huiping Jiang
- Boerhinger Ingelheim Pharmaceutical Inc., Ridgefield, CT 06877, USA
| | - Zhenhao Qi
- Boerhinger Ingelheim Pharmaceutical Inc., Ridgefield, CT 06877, USA
| | - Jeremy M Boss
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Troy D Randall
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Scott R Brodeur
- Boerhinger Ingelheim Pharmaceutical Inc., Ridgefield, CT 06877, USA
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amy S Weinmann
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Alexander F Rosenberg
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA; Informatics Institute, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Frances E Lund
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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