1
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Ren H, Lee AA, Lew LJN, DeGrandchamp JB, Groves JT. Positive feedback in Ras activation by full-length SOS arises from autoinhibition release mechanism. Biophys J 2024; 123:3295-3303. [PMID: 39021073 PMCID: PMC11480760 DOI: 10.1016/j.bpj.2024.07.014] [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: 03/24/2024] [Revised: 06/08/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024] Open
Abstract
Signaling through the Ras-MAPK pathway can exhibit switch-like activation, which has been attributed to the underlying positive feedback and bimodality in the activation of RasGDP to RasGTP by SOS. SOS contains both catalytic and allosteric Ras binding sites, and a common assumption is that allosteric activation selectively by RasGTP provides the mechanism of positive feedback. However, recent single-molecule studies have revealed that SOS catalytic rates are independent of the nucleotide state of Ras in the allosteric binding site, raising doubt about this as a positive feedback mechanism. Here, we perform detailed kinetic analyses of receptor-mediated recruitment of full-length SOS to the membrane while simultaneously monitoring its catalytic activation of Ras. These results, along with kinetic modeling, expose the autoinhibition release step in SOS, rather than either recruitment or allosteric activation, as the underlying mechanism giving rise to positive feedback in Ras activation.
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Affiliation(s)
- He Ren
- Department of Chemistry, University of California Berkeley, Berkeley, California
| | - Albert A Lee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California
| | - L J Nugent Lew
- Department of Chemistry, University of California Berkeley, Berkeley, California
| | | | - Jay T Groves
- Department of Chemistry, University of California Berkeley, Berkeley, California; Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California.
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2
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without deterministic bistability. SCIENCE ADVANCES 2024; 10:eadi0707. [PMID: 38905351 PMCID: PMC11192083 DOI: 10.1126/sciadv.adi0707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 05/15/2024] [Indexed: 06/23/2024]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of deterministic bistability but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts deterministic bistability and may be more resistant to pharmacological inhibition.
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Affiliation(s)
- Albert A. Lee
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Neil H. Kim
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Steven Alvarez
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Materials Science and Engineering, University of California, Berkeley, CA 94720, USA
| | - He Ren
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | - L. J. Nugent Lew
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Jay T. Groves
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
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3
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Fan S, Kang B, Li S, Li W, Chen C, Chen J, Deng L, Chen D, Zhou J. Exploring the multifaceted role of RASGRP1 in disease: immune, neural, metabolic, and oncogenic perspectives. Cell Cycle 2024; 23:722-746. [PMID: 38865342 PMCID: PMC11229727 DOI: 10.1080/15384101.2024.2366009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/25/2023] [Indexed: 06/14/2024] Open
Abstract
RAS guanyl releasing protein 1 (RASGRP1) is a guanine nucleotide exchange factor (GEF) characterized by the presence of a RAS superfamily GEF domain. It functions as a diacylglycerol (DAG)-regulated nucleotide exchange factor, specifically activating RAS through the exchange of bound GDP for GTP. Activation of RAS by RASGRP1 has a wide range of downstream effects at the cellular level. Thus, it is not surprising that many diseases are associated with RASGRP1 disorders. Here, we present an overview of the structure and function of RASGRP1, its crucial role in the development, expression, and regulation of immune cells, and its involvement in various signaling pathways. This review comprehensively explores the relationship between RASGRP1 and various diseases, elucidates the underlying molecular mechanisms of RASGRP1 in each disease, and identifies potential therapeutic targets. This study provides novel insights into the role of RASGRP1 in insulin secretion and highlights its potential as a therapeutic target for diabetes. The limitations and challenges associated with studying RASGRP1 in disease are also discussed.
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Affiliation(s)
- Shangzhi Fan
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Bo Kang
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Shaoqian Li
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Weiyi Li
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Canyu Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jixiang Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Lijing Deng
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Danjun Chen
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Jiecan Zhou
- The First Affiliated Hospital, Hunan Provincial Clinical Medical Research Center for Drug Evaluation of Major Chronic Diseases,Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Clinical Pharmacology Research Center, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Hengyang Key Laboratory of Clinical Pharmacology, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- The First Affiliated Hospital, Pharmacy Department, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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Funasaki S, Hatano A, Nakatsumi H, Koga D, Sugahara O, Yumimoto K, Baba M, Matsumoto M, Nakayama KI. A stepwise and digital pattern of RSK phosphorylation determines the outcome of thymic selection. iScience 2023; 26:107552. [PMID: 37646020 PMCID: PMC10460994 DOI: 10.1016/j.isci.2023.107552] [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: 12/12/2022] [Revised: 07/02/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
Developing CD4+CD8+ double-positive (DP) thymocytes with randomly generated T cell receptors (TCRs) undergo positive (maturation) or negative (apoptosis) selection on the basis of the strength of TCR stimulation. Selection fate is determined by engagement of TCR ligands with a subtle difference in affinity, but the molecular details of TCR signaling leading to the different selection outcomes have remained unclear. We performed phosphoproteome analysis of DP thymocytes and found that p90 ribosomal protein kinase (RSK) phosphorylation at Thr562 was induced specifically by high-affinity peptide ligands. Such phosphorylation of RSK triggered its translocation to the nucleus, where it phosphorylated the nuclear receptor Nur77 and thereby promoted its mitochondrial translocation for apoptosis induction. Inhibition of RSK activity protected DP thymocytes from antigen-induced cell death. We propose that RSK phosphorylation constitutes a mechanism by which DP thymocytes generate a stepwise and binary signal in response to exposure to TCR ligands with a graded affinity.
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Affiliation(s)
- Shintaro Funasaki
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Kumamoto 860-0811, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata 951-8510, Japan
| | - Hirokazu Nakatsumi
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Daisuke Koga
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Osamu Sugahara
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Kanae Yumimoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Masaya Baba
- Laboratory of Cancer Metabolism, International Research Center for Medical Sciences (IRCMS), Kumamoto University, Kumamoto, Kumamoto 860-0811, Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata 951-8510, Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
- Anticancer Strategies Laboratory, TMDU Advanced Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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5
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Lee AA, Kim NH, Alvarez S, Ren H, DeGrandchamp JB, Lew LJN, Groves JT. Bimodality in Ras signaling originates from processivity of the Ras activator SOS without classic kinetic bistability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549263. [PMID: 37503094 PMCID: PMC10370109 DOI: 10.1101/2023.07.17.549263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Ras is a small GTPase that is central to important functional decisions in diverse cell types. An important aspect of Ras signaling is its ability to exhibit bimodal, or switch-like activity. We describe the total reconstitution of a receptor-mediated Ras activation-deactivation reaction catalyzed by SOS and p120-RasGAP on supported lipid membrane microarrays. The results reveal a bimodal Ras activation response, which is not a result of classic kinetic bistability, but is rather driven by the distinct processivity of the Ras activator, SOS. Furthermore, the bimodal response is controlled by the condensation state of the scaffold protein, LAT, to which SOS is recruited. Processivity-driven bimodality leads to stochastic bursts of Ras activation even under strongly deactivating conditions. This behavior contrasts classic kinetic bistability and is distinctly more resistant to pharmacological inhibition.
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6
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A Focused Review of Ras Guanine Nucleotide-Releasing Protein 1 in Immune Cells and Cancer. Int J Mol Sci 2023; 24:ijms24021652. [PMID: 36675167 PMCID: PMC9864139 DOI: 10.3390/ijms24021652] [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: 11/14/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Four Ras guanine nucleotide-releasing proteins (RasGRP1 through 4) belong to the family of guanine nucleotide exchange factors (GEFs). RasGRPs catalyze the release of GDP from small GTPases Ras and Rap and facilitate their transition from an inactive GDP-bound to an active GTP-bound state. Thus, they regulate critical cellular responses via many downstream GTPase effectors. Similar to other RasGRPs, the catalytic module of RasGRP1 is composed of the Ras exchange motif (REM) and Cdc25 domain, and the EF hands and C1 domain contribute to its cellular localization and regulation. RasGRP1 can be activated by a diacylglycerol (DAG)-mediated membrane recruitment and protein kinase C (PKC)-mediated phosphorylation. RasGRP1 acts downstream of the T cell receptor (TCR), B cell receptors (BCR), and pre-TCR, and plays an important role in the thymocyte maturation and function of peripheral T cells, B cells, NK cells, mast cells, and neutrophils. The dysregulation of RasGRP1 is known to contribute to numerous disorders that range from autoimmune and inflammatory diseases and schizophrenia to neoplasia. Given its position at the crossroad of cell development, inflammation, and cancer, RASGRP1 has garnered interest from numerous disciplines. In this review, we outline the structure, function, and regulation of RasGRP1 and focus on the existing knowledge of the role of RasGRP1 in leukemia and other cancers.
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7
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Sheffels E, Kortum RL. The Role of Wild-Type RAS in Oncogenic RAS Transformation. Genes (Basel) 2021; 12:genes12050662. [PMID: 33924994 PMCID: PMC8146411 DOI: 10.3390/genes12050662] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The RAS family of oncogenes (HRAS, NRAS, and KRAS) are among the most frequently mutated protein families in cancers. RAS-mutated tumors were originally thought to proliferate independently of upstream signaling inputs, but we now know that non-mutated wild-type (WT) RAS proteins play an important role in modulating downstream effector signaling and driving therapeutic resistance in RAS-mutated cancers. This modulation is complex as different WT RAS family members have opposing functions. The protein product of the WT RAS allele of the same isoform as mutated RAS is often tumor-suppressive and lost during tumor progression. In contrast, RTK-dependent activation of the WT RAS proteins from the two non-mutated WT RAS family members is tumor-promoting. Further, rebound activation of RTK–WT RAS signaling underlies therapeutic resistance to targeted therapeutics in RAS-mutated cancers. The contributions of WT RAS to proliferation and transformation in RAS-mutated cancer cells places renewed interest in upstream signaling molecules, including the phosphatase/adaptor SHP2 and the RasGEFs SOS1 and SOS2, as potential therapeutic targets in RAS-mutated cancers.
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8
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T cells: a dedicated effector kinase pathways for every trait? Biochem J 2021; 478:1303-1307. [PMID: 33755101 DOI: 10.1042/bcj20210006] [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: 02/21/2021] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022]
Abstract
Signaling pathways play critical roles in regulating the activation of T cells. Recognition of foreign peptide presented by MHC to the T cell receptor (TCR) triggers a signaling cascade of proximal kinases and adapter molecules that lead to the activation of Effector kinase pathways. These effector kinase pathways play pivotal roles in T cell activation, differentiation, and proliferation. RNA sequencing-based methods have provided insights into the gene expression programs that support the above-mentioned cell biological responses. The proteome is often overlooked. A recent study by Damasio et al. [Biochem. J. (2021) 478, 79-98. doi:10.1042/BCJ20200661] focuses on characterizing the effect of extracellular signal-regulated kinase (ERK) on the remodeling of the proteome of activated CD8+ T cells using Mass spectrometric analysis. Surprisingly, the Effector kinase ERK pathway is responsible for only a select proportion of the proteome that restructures during T cell activation. The primary targets of ERK signaling are transcription factors, cytokines, and cytokine receptors. In this commentary, we discuss the recent findings by Damasio et al. [Biochem. J. (2021) 478, 79-98. doi:10.1042/BCJ20200661] in the context of different Effector kinase pathways in activated T cells.
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9
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Ma CY, Marioni JC, Griffiths GM, Richard AC. Stimulation strength controls the rate of initiation but not the molecular organisation of TCR-induced signalling. eLife 2020; 9:e53948. [PMID: 32412411 PMCID: PMC7308083 DOI: 10.7554/elife.53948] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/14/2020] [Indexed: 12/13/2022] Open
Abstract
Millions of naïve T cells with different TCRs may interact with a peptide-MHC ligand, but very few will activate. Remarkably, this fine control is orchestrated using a limited set of intracellular machinery. It remains unclear whether changes in stimulation strength alter the programme of signalling events leading to T cell activation. Using mass cytometry to simultaneously measure multiple signalling pathways during activation of murine CD8+ T cells, we found a programme of distal signalling events that is shared, regardless of the strength of TCR stimulation. Moreover, the relationship between transcription of early response genes Nr4a1 and Irf8 and activation of the ribosomal protein S6 is also conserved across stimuli. Instead, we found that stimulation strength dictates the rate with which cells initiate signalling through this network. These data suggest that TCR-induced signalling results in a coordinated activation program, modulated in rate but not organization by stimulation strength.
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MESH Headings
- Animals
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cells, Cultured
- Female
- Flow Cytometry
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/metabolism
- Kinetics
- Ligands
- Lymphocyte Activation/drug effects
- Male
- Mice, Inbred C57BL
- Mice, Transgenic
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- Ovalbumin/pharmacology
- Peptide Fragments/pharmacology
- Phosphorylation
- Receptors, Antigen, T-Cell/agonists
- Receptors, Antigen, T-Cell/metabolism
- Ribosomal Protein S6/metabolism
- Signal Transduction/drug effects
- Single-Cell Analysis
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Affiliation(s)
- Claire Y Ma
- Cambridge Institute for Medical Research, University of CambridgeCambridgeUnited Kingdom
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
- EMBL-European Bioinformatics Institute, Wellcome Genome CampusCambridgeUnited Kingdom
- Wellcome Sanger Institute, Wellcome Genome CampusCambridgeUnited Kingdom
| | - Gillian M Griffiths
- Cambridge Institute for Medical Research, University of CambridgeCambridgeUnited Kingdom
| | - Arianne C Richard
- Cambridge Institute for Medical Research, University of CambridgeCambridgeUnited Kingdom
- Cancer Research UK Cambridge Institute, University of CambridgeCambridgeUnited Kingdom
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10
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Bandaru P, Kondo Y, Kuriyan J. The Interdependent Activation of Son-of-Sevenless and Ras. Cold Spring Harb Perspect Med 2019; 9:cshperspect.a031534. [PMID: 29610148 DOI: 10.1101/cshperspect.a031534] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The guanine-nucleotide exchange factor (GEF) Son-of-Sevenless (SOS) plays a critical role in metazoan signaling by converting Ras•GDP (guanosine diphosphate) to Ras•GTP (guanosine triphosphate) in response to tyrosine kinase activation. Structural studies have shown that SOS differs from other Ras-specific GEFs in that SOS is itself activated by Ras•GTP binding to an allosteric site, distal to the site of nucleotide exchange. The activation of SOS involves membrane recruitment and conformational changes, triggered by lipid binding, that open the allosteric binding site for Ras•GTP. This is in contrast to other Ras-specific GEFs, which are activated by second messengers that more directly affect the active site. Allosteric Ras•GTP binding stabilizes SOS at the membrane, where it can turn over other Ras molecules processively, leading to an ultrasensitive response that is distinct from that of other Ras-specific GEFs.
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Affiliation(s)
- Pradeep Bandaru
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
| | - John Kuriyan
- Departments of Molecular and Cell Biology and of Chemistry, California Institute for Quantitative Biosciences, Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Howard Hughes Medical Institute, University of California, Berkeley, California 94720
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11
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Apavaloaei A, Brochu S, Dong M, Rouette A, Hardy MP, Villafano G, Murata S, Melichar HJ, Perreault C. PSMB11 Orchestrates the Development of CD4 and CD8 Thymocytes via Regulation of Gene Expression in Cortical Thymic Epithelial Cells. THE JOURNAL OF IMMUNOLOGY 2018; 202:966-978. [PMID: 30567730 DOI: 10.4049/jimmunol.1801288] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/16/2018] [Indexed: 12/16/2022]
Abstract
T cell development depends on sequential interactions of thymocytes with cortical thymic epithelial cells (cTECs) and medullary thymic epithelial cells. PSMB11 is a catalytic proteasomal subunit present exclusively in cTECs. Because proteasomes regulate transcriptional activity, we asked whether PSMB11 might affect gene expression in cTECs. We report that PSMB11 regulates the expression of 850 cTEC genes that modulate lymphostromal interactions primarily via the WNT signaling pathway. cTECs from Psmb11 -/- mice 1) acquire features of medullary thymic epithelial cells and 2) retain CD8 thymocytes in the thymic cortex, thereby impairing phase 2 of positive selection, 3) perturbing CD8 T cell development, and 4) causing dramatic oxidative stress leading to apoptosis of CD8 thymocytes. Deletion of Psmb11 also causes major oxidative stress in CD4 thymocytes. However, CD4 thymocytes do not undergo apoptosis because, unlike CD8 thymocytes, they upregulate expression of chaperones and inhibitors of apoptosis. We conclude that PSMB11 has pervasive effects on both CD4 and CD8 thymocytes via regulation of gene expression in cTECs.
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Affiliation(s)
- Anca Apavaloaei
- Institute for Research in Immunology and Cancer, Montreal, Quebec H3C 3J7, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Sylvie Brochu
- Institute for Research in Immunology and Cancer, Montreal, Quebec H3C 3J7, Canada
| | - Mengqi Dong
- Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada
| | - Alexandre Rouette
- Institute for Research in Immunology and Cancer, Montreal, Quebec H3C 3J7, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
| | - Marie-Pierre Hardy
- Institute for Research in Immunology and Cancer, Montreal, Quebec H3C 3J7, Canada
| | - Geno Villafano
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269; and
| | - Shigeo Murata
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo 113-0033, Japan
| | - Heather J Melichar
- Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada.,Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Montreal, Quebec H3C 3J7, Canada; .,Department of Medicine, University of Montreal, Montreal, Quebec H3C 3J7, Canada
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12
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Bolz S, Totzeck A, Amann K, Stettner M, Kleinschnitz C, Hagenacker T. CIDP, myasthenia gravis, and membranous glomerulonephritis - three autoimmune disorders in one patient: a case report. BMC Neurol 2018; 18:113. [PMID: 30107838 PMCID: PMC6092826 DOI: 10.1186/s12883-018-1120-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 08/06/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND We present a patient fulfilling the electrophysiological criteria for definite chronic inflammatory demyelinating polyneuropathy (CIDP), antibody-positive myasthenia gravis (MG), and membranous glomerulonephritis (MGN) confirmed by biopsy. To our knowledge, this is the first case of the concomitant appearance of these three autoimmune diseases in a single patient. CASE REPRESENTATION A 42-year-old Caucasian male presented with rapidly progressive gait disturbance, distal weakness of the lower extremities, ascending hypoesthesia, impaired fine motor skills, and beginning cranial nerve palsy showing dysarthrophonia, facial paralysis, and eye movement abnormalities and was diagnosed as rapid onset (atypical) CIDP. After 3 months, the patient complained of increasing physical exhaustion, reduction of his walking distance, worsening of the residual dysphagia, and dysarthria with an inability to swallow. AChR antibodies (17.0 nmol/L, RF < 0.4) and titin antibodies were positive and repetitive nerve stimulation showed an abnormal decrement matching the criteria of myasthenia gravis. Over time the patient developed severe acute-on-chronic renal failure with high-grade proteinuria resulting in generalized edema followed by secondary hyperparathyroidism and dialysis-dependent renal failure. Renal biopsy confirmed beginning anti-phospholipase A2 receptor antibody membranous nephropathy. CONCLUSION All three diseases are of autoimmune origin with distinctive immunopathogenetic mechanisms. The present case of CIDP, MG, and MGN occurring in one patient indicates a common underlying immune mechanism in these distinct conditions, including the involvement of autoantibodies and T cells.
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Affiliation(s)
- Saskia Bolz
- Department of Neurology, Essen University Hospital, Hufelandstrasse 55, 45147, Essen, Germany
| | - Andreas Totzeck
- Department of Neurology, Essen University Hospital, Hufelandstrasse 55, 45147, Essen, Germany
| | - Kerstin Amann
- Department of Nephropathology, University of Erlangen-Nürnberg, Krankenhausstr. 8-10, 91054, Erlangen, Germany
| | - Mark Stettner
- Department of Neurology, Essen University Hospital, Hufelandstrasse 55, 45147, Essen, Germany
| | - Christoph Kleinschnitz
- Department of Neurology, Essen University Hospital, Hufelandstrasse 55, 45147, Essen, Germany
| | - Tim Hagenacker
- Department of Neurology, Essen University Hospital, Hufelandstrasse 55, 45147, Essen, Germany.
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13
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Li L, Xu GK, Song F. Impact of lipid rafts on the T-cell-receptor and peptide-major-histocompatibility-complex interactions under different measurement conditions. Phys Rev E 2017; 95:012403. [PMID: 28208397 DOI: 10.1103/physreve.95.012403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Indexed: 01/02/2023]
Abstract
The interactions between T-cell receptor (TCR) and peptide-major-histocompatibility complex (pMHC), which enable T-cell development and initiate adaptive immune responses, have been intensively studied. However, a central issue of how lipid rafts affect the TCR-pMHC interactions remains unclear. Here, by using a statistical-mechanical membrane model, we show that the binding affinity of TCR and pMHC anchored on two apposing cell membranes is significantly enhanced because of the lipid raft-induced signaling protein aggregation. This finding may provide an alternative insight into the mechanism of T-cell activation triggered by very low densities of pMHC. In the case of cell-substrate adhesion, our results indicate that the loss of lateral mobility of the proteins on the solid substrate leads to the inhibitory effect of lipid rafts on TCR-pMHC interactions. Our findings help to understand why different experimental methods for measuring the impact of lipid rafts on the receptor-ligand interactions have led to contradictory conclusions.
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Affiliation(s)
- Long Li
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Guang-Kui Xu
- International Center for Applied Mechanics, State Key Laboratory for Strength and Vibration of Mechanical Structures, School of Aerospace, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics (LNM) and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, 100190, China.,School of Engineering Science, University of Chinese Academy of Sciences, Beijing 100049, China
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14
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Hatano A, Matsumoto M, Nakayama KI. Phosphoproteomics analyses show subnetwork systems in T-cell receptor signaling. Genes Cells 2016; 21:1095-1112. [DOI: 10.1111/gtc.12406] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/02/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Atsushi Hatano
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Masaki Matsumoto
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Keiichi I. Nakayama
- Department of Molecular and Cellular Biology; Medical Institute of Bioregulation; Kyushu University; 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
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15
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Allison KA, Sajti E, Collier JG, Gosselin D, Troutman TD, Stone EL, Hedrick SM, Glass CK. Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. eLife 2016; 5. [PMID: 27376549 PMCID: PMC4931909 DOI: 10.7554/elife.10134] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 05/20/2016] [Indexed: 12/18/2022] Open
Abstract
Affinity and dose of T cell receptor (TCR) interaction with antigens govern the magnitude of CD4+ T cell responses, but questions remain regarding the quantitative translation of TCR engagement into downstream signals. We find that while the response of mouse CD4+ T cells to antigenic stimulation is bimodal, activated cells exhibit analog responses proportional to signal strength. Gene expression output reflects TCR signal strength, providing a signature of T cell activation. Expression changes rely on a pre-established enhancer landscape and quantitative acetylation at AP-1 binding sites. Finally, we show that graded expression of activation genes depends on ERK pathway activation, suggesting that an ERK-AP-1 axis plays an important role in translating TCR signal strength into proportional activation of enhancers and genes essential for T cell function. DOI:http://dx.doi.org/10.7554/eLife.10134.001 T helper cells recognize and respond to bacteria, viruses and other invading microbes and thus play a central role in the adaptive immune system. These cells have a receptor on their surface that binds to fragments of proteins – known as oligopeptides – from the microbes that have been digested and presented on the surfaces of other immune cells. Once active, T helper cells multiply, grow and release signals that regulate genes in other cells to promote immune responses. Previous studies suggest that a T helper cell’s response is binary – that is, either on or off. However, this does not explain how the strength of the T cell response to infection can vary. Allison et al. used a technique called high-throughput sequencing to examine the activity of genes in T helper cells from mice that had been genetically engineered to only produce one type of T cell receptor. For the experiments, the T cells were exposed to various concentrations of different peptides known to bind either well or poorly to the receptor. Allison et al. found that, once activated, the response of an individual T cell was not binary, but instead was related to the strength of the signal it received through its receptor. Further experiments showed that although a subset of the genes activated in T helper cells do respond in a binary fashion, the activities of many other genes involved in immune responses and cell metabolism were related to the strength of the signal from the receptor. This “analog” gene activation depends on the level of activity of the MAP kinase signaling pathway. Together, Allison et al.’s findings help us to understand how T cells are able to fine-tune immune responses to invading microbes. The next challenge will be to investigate the mechanisms underlying binary and analog gene activity in T cells. DOI:http://dx.doi.org/10.7554/eLife.10134.002
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Affiliation(s)
- Karmel A Allison
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Bioinformatics and Systems Biology Program, University of California, San Diego, United States
| | - Eniko Sajti
- Department of Pediatrics, University of California, San Diego, United States.,Rady Children's Hospital, San Diego, United States
| | - Jana G Collier
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - David Gosselin
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Ty Dale Troutman
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States
| | - Erica L Stone
- Molecular Biology Section, Division of Biological Science, University of California, San Diego, United States.,Translational Tumor Immunology Program, Wistar Institute Cancer Center, Philadelphia, United States
| | - Stephen M Hedrick
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Molecular Biology Section, Division of Biological Science, University of California, San Diego, United States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, United States.,Department of Medicine, University of California, San Diego, United States
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16
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Trinquand A, Dos Santos NR, Tran Quang C, Rocchetti F, Zaniboni B, Belhocine M, Da Costa de Jesus C, Lhermitte L, Tesio M, Dussiot M, Cosset FL, Verhoeyen E, Pflumio F, Ifrah N, Dombret H, Spicuglia S, Chatenoud L, Gross DA, Hermine O, Macintyre E, Ghysdael J, Asnafi V. Triggering the TCR Developmental Checkpoint Activates a Therapeutically Targetable Tumor Suppressive Pathway in T-cell Leukemia. Cancer Discov 2016; 6:972-85. [PMID: 27354269 DOI: 10.1158/2159-8290.cd-15-0675] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 06/24/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED Cancer onset and progression involves the accumulation of multiple oncogenic hits, which are thought to dominate or bypass the physiologic regulatory mechanisms in tissue development and homeostasis. We demonstrate in T-cell acute lymphoblastic leukemia (T-ALL) that, irrespective of the complex oncogenic abnormalities underlying tumor progression, experimentally induced, persistent T-cell receptor (TCR) signaling has antileukemic properties and enforces a molecular program resembling thymic negative selection, a major developmental event in normal T-cell development. Using mouse models of T-ALL, we show that induction of TCR signaling by high-affinity self-peptide/MHC or treatment with monoclonal antibodies to the CD3ε chain (anti-CD3) causes massive leukemic cell death. Importantly, anti-CD3 treatment hampered leukemogenesis in mice transplanted with either mouse- or patient-derived T-ALLs. These data provide a strong rationale for targeted therapy based on anti-CD3 treatment of patients with TCR-expressing T-ALL and demonstrate that endogenous developmental checkpoint pathways are amenable to therapeutic intervention in cancer cells. SIGNIFICANCE T-ALLs are aggressive malignant lymphoid proliferations of T-cell precursors characterized by high relapse rates and poor prognosis, calling for the search for novel therapeutic options. Here, we report that the lineage-specific TCR/CD3 developmental checkpoint controlling cell death in normal T-cell progenitors remains switchable to induce massive tumor cell apoptosis in T-ALL and is amenable to preclinical therapeutic intervention. Cancer Discov; 6(9); 972-85. ©2016 AACR.See related commentary by Lemonnier and Mak, p. 946This article is highlighted in the In This Issue feature, p. 932.
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Affiliation(s)
- Amélie Trinquand
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Nuno R Dos Santos
- Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal. Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France
| | - Christine Tran Quang
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France. Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay, France
| | - Francesca Rocchetti
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France. Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay, France
| | - Benedetta Zaniboni
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France. Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay, France
| | - Mohamed Belhocine
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France. Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, Marseille, France
| | - Cindy Da Costa de Jesus
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France. Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay, France
| | - Ludovic Lhermitte
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Melania Tesio
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Michael Dussiot
- INSERM UMR 1163 and CNRS ERL 8654, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, Laboratory of Excellence GR-Ex, Imagine Institute and Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - François-Loïc Cosset
- CIRI, EVIR Team, INSERM U1111, CNRS UMR 5308, Université de Lyon-1, ENS de Lyon, Lyon, France
| | - Els Verhoeyen
- CIRI, EVIR Team, INSERM U1111, CNRS UMR 5308, Université de Lyon-1, ENS de Lyon, Lyon, France. INSERM U1065, C3M, Equipe "Contrôle Métabolique des Morts Cellulaires," Nice, France
| | - Françoise Pflumio
- Laboratoire des Cellules Souches Hématopoïétiques et Leucémiques, UMR 967, INSERM, Commissariat à l'Energie Atomique, Université Paris Diderot, Université Paris 11, Institut de Radiobiologie Cellulaire et Moléculaire, équipe labellisée Ligue Nationale contre le Cancer, Fontenay-aux-Roses, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers service des Maladies du Sang et INSERM U892, Angers, France
| | - Hervé Dombret
- Université Paris 7, Hôpital Saint-Louis, AP-HP, Department of Hematology and Institut Universitaire d'Hématologie, Paris, France
| | - Salvatore Spicuglia
- Technological Advances for Genomics and Clinics (TAGC), INSERM U1090, Université de la Méditerranée, Marseille, France
| | - Lucienne Chatenoud
- Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Hôpital Necker-Enfants Malades, Paris, France, and Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - David-Alexandre Gross
- Institut Necker Enfants Malades, INSERM U1151, CNRS UMR 8253, Hôpital Necker-Enfants Malades, Paris, France, and Université Paris Descartes Sorbonne Paris Cité, Paris, France
| | - Olivier Hermine
- INSERM UMR 1163 and CNRS ERL 8654, Laboratory of Cellular and Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, Laboratory of Excellence GR-Ex, Imagine Institute and Paris Descartes University, Sorbonne Paris Cité, Paris, France. Department of Clinical Hematology, Hôpital Necker, Assistance publique hôpitaux de Paris, Paris, France
| | - Elizabeth Macintyre
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France
| | - Jacques Ghysdael
- Institut Curie, PSL Research University, CNRS UMR 3348, Orsay, France. Université Paris Sud, Université Paris-Saclay, CNRS UMR 3348, Orsay, France.
| | - Vahid Asnafi
- Université Paris Descartes Sorbonne Cité, Institut Necker-Enfants Malades (INEM), Institut national de recherche médicale (INSERM) U1151, and Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Necker Enfants-Malades, Paris, France.
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17
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Prill RJ, Vogel R, Cecchi GA, Altan-Bonnet G, Stolovitzky G. Noise-driven causal inference in biomolecular networks. PLoS One 2015; 10:e0125777. [PMID: 26030907 PMCID: PMC4452541 DOI: 10.1371/journal.pone.0125777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 03/26/2015] [Indexed: 11/18/2022] Open
Abstract
Single-cell RNA and protein concentrations dynamically fluctuate because of stochastic ("noisy") regulation. Consequently, biological signaling and genetic networks not only translate stimuli with functional response but also random fluctuations. Intuitively, this feature manifests as the accumulation of fluctuations from the network source to the target. Taking advantage of the fact that noise propagates directionally, we developed a method for causation prediction that does not require time-lagged observations and therefore can be applied to data generated by destructive assays such as immunohistochemistry. Our method for causation prediction, "Inference of Network Directionality Using Covariance Elements (INDUCE)," exploits the theoretical relationship between a change in the strength of a causal interaction and the associated changes in the single cell measured entries of the covariance matrix of protein concentrations. We validated our method for causation prediction in two experimental systems where causation is well established: in an E. coli synthetic gene network, and in MEK to ERK signaling in mammalian cells. We report the first analysis of covariance elements documenting noise propagation from a kinase to a phosphorylated substrate in an endogenous mammalian signaling network.
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Affiliation(s)
- Robert J. Prill
- IBM T. J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, N.Y. 10598, United States of America
| | - Robert Vogel
- ImmunoDynamics Group, Program in Computational Biology and Immunology, Memorial Sloan- Kettering Cancer Center, 1275 York Avenue, Box 460, New York, N.Y. 10065, United States of America
| | - Guillermo A. Cecchi
- IBM T. J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, N.Y. 10598, United States of America
| | - Grégoire Altan-Bonnet
- ImmunoDynamics Group, Program in Computational Biology and Immunology, Memorial Sloan- Kettering Cancer Center, 1275 York Avenue, Box 460, New York, N.Y. 10065, United States of America
| | - Gustavo Stolovitzky
- IBM T. J. Watson Research Center, 1101 Kitchawan Road, Route 134, Yorktown Heights, N.Y. 10598, United States of America
- * E-mail:
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18
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Depeille P, Henricks LM, van de Ven RAH, Lemmens E, Wang CY, Matli M, Werb Z, Haigis KM, Donner D, Warren R, Roose JP. RasGRP1 opposes proliferative EGFR-SOS1-Ras signals and restricts intestinal epithelial cell growth. Nat Cell Biol 2015; 17:804-15. [PMID: 26005835 PMCID: PMC4652934 DOI: 10.1038/ncb3175] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/08/2015] [Indexed: 02/08/2023]
Abstract
The character of EGFR signals can influence cell fate but mechanistic insights into intestinal EGFR-Ras signalling are limited. Here we show that two distinct Ras nucleotide exchange factors, RasGRP1 and SOS1, lie downstream of EGFR but act in functional opposition. RasGRP1 is expressed in intestinal crypts where it restricts epithelial growth. High RasGRP1 expression in colorectal cancer (CRC) patient samples correlates with a better clinical outcome. Biochemically, we find that RasGRP1 creates a negative feedback loop that limits proliferative EGFR-SOS1-Ras signals in CRC cells. Genetic Rasgrp1 depletion from mice with either an activating mutation in KRas or with aberrant Wnt signalling due to a mutation in Apc resulted in both cases in exacerbated Ras-ERK signalling and cell proliferation. The unexpected opposing cell biological effects of EGFR-RasGRP1 and EGFR-SOS1 signals in the same cell shed light on the intricacy of EGFR-Ras signalling in normal epithelium and carcinoma.
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Affiliation(s)
- Philippe Depeille
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Linda M. Henricks
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Robert A. H. van de Ven
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Ed Lemmens
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Chih-Yang Wang
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Mary Matli
- Department of Surgery, University of California, San Francisco, San Francisco, California 94143, USA
| | - Zena Werb
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
| | - Kevin M. Haigis
- Molecular Pathology Unit, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
| | - David Donner
- Department of Surgery, University of California, San Francisco, San Francisco, California 94143, USA
| | - Robert Warren
- Department of Surgery, University of California, San Francisco, San Francisco, California 94143, USA
| | - Jeroen P. Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, California 94143, USA
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19
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The role of T cell receptor signaling thresholds in guiding T cell fate decisions. Curr Opin Immunol 2015; 33:43-8. [PMID: 25660212 DOI: 10.1016/j.coi.2015.01.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 11/21/2022]
Abstract
Canonical T cell receptor signal transduction has been extensively studied and dissected in cell lines and primary lymphocytes. However, a static depiction of this signaling cascade fails to capture the complex and dynamic process by which individual T cells discriminate TCR:peptide-MHC affinity, then integrate signals over time to drive discrete cellular behaviors such as thymic selection, proliferation, and cytokine production. Recent technological advances have made it possible to study complex lymphocyte behavior on a single cell level and are revealing how T cells interpret information about affinity and abundance of antigen in order to make life-and-death cell fate decisions individually and collectively.
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20
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Janardhan SV, Marks R, Gajewski TF. Primary murine CD4+ T cells fail to acquire the ability to produce effector cytokines when active Ras is present during Th1/Th2 differentiation. PLoS One 2014; 9:e112831. [PMID: 25397617 PMCID: PMC4232516 DOI: 10.1371/journal.pone.0112831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 10/16/2014] [Indexed: 01/10/2023] Open
Abstract
Constitutive Ras signaling has been shown to augment IL-2 production, reverse anergy, and functionally replace many aspects of CD28 co-stimulation in CD4+ T cells. These data raise the possibility that introduction of active Ras into primary T cells might result in improved functionality in pathologic situations of T cell dysfunction, such as cancer or chronic viral infection. To test the biologic effects of active Ras in primary T cells, CD4+ T cells from Coxsackie-Adenovirus Receptor Transgenic mice were transduced with an adenovirus encoding active Ras. As expected, active Ras augmented IL-2 production in naive CD4+ T cells. However, when cells were cultured for 4 days under conditions to promote effector cell differentiation, active Ras inhibited the ability of CD4+ T cells to acquire a Th1 or Th2 effector cytokine profile. This differentiation defect was not due to deficient STAT4 or STAT6 activation by IL-12 or IL-4, respectively, nor was it associated with deficient induction of T-bet and GATA-3 expression. Impaired effector cytokine production in active Ras-transduced cells was associated with deficient demethylation of the IL-4 gene locus. Our results indicate that, despite augmenting acute activation of naïve T cells, constitutive Ras signaling inhibits the ability of CD4+ T cells to properly differentiate into Th1/Th2 effector cytokine-producing cells, in part by interfering with epigenetic modification of effector gene loci. Alternative strategies to potentiate Ras pathway signaling in T cells in a more regulated fashion should be considered as a therapeutic approach to improve immune responses in vivo.
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Affiliation(s)
- Sujit V. Janardhan
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Reinhard Marks
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Thomas F. Gajewski
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
- Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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21
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Stepanek O, Prabhakar AS, Osswald C, King CG, Bulek A, Naeher D, Beaufils-Hugot M, Abanto ML, Galati V, Hausmann B, Lang R, Cole DK, Huseby ES, Sewell AK, Chakraborty AK, Palmer E. Coreceptor scanning by the T cell receptor provides a mechanism for T cell tolerance. Cell 2014; 159:333-45. [PMID: 25284152 PMCID: PMC4304671 DOI: 10.1016/j.cell.2014.08.042] [Citation(s) in RCA: 131] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 07/14/2014] [Accepted: 08/29/2014] [Indexed: 12/11/2022]
Abstract
In the thymus, high-affinity, self-reactive thymocytes are eliminated from the pool of developing T cells, generating central tolerance. Here, we investigate how developing T cells measure self-antigen affinity. We show that very few CD4 or CD8 coreceptor molecules are coupled with the signal-initiating kinase, Lck. To initiate signaling, an antigen-engaged T cell receptor (TCR) scans multiple coreceptor molecules to find one that is coupled to Lck; this is the first and rate-limiting step in a kinetic proofreading chain of events that eventually leads to TCR triggering and negative selection. MHCII-restricted TCRs require a shorter antigen dwell time (0.2 s) to initiate negative selection compared to MHCI-restricted TCRs (0.9 s) because more CD4 coreceptors are Lck-loaded compared to CD8. We generated a model (Lck come&stay/signal duration) that accurately predicts the observed differences in antigen dwell-time thresholds used by MHCI- and MHCII-restricted thymocytes to initiate negative selection and generate self-tolerance.
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Affiliation(s)
- Ondrej Stepanek
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland.
| | - Arvind S Prabhakar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Celine Osswald
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Carolyn G King
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Anna Bulek
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Dieter Naeher
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Marina Beaufils-Hugot
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Michael L Abanto
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Virginie Galati
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Barbara Hausmann
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - Rosemarie Lang
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland
| | - David K Cole
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Andrew K Sewell
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science, Departments of Physics, Chemistry, and Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ed Palmer
- Departments of Biomedicine and Nephrology, University Hospital Basel and University of Basel, 4031 Basel, Switzerland.
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22
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Loads bias genetic and signaling switches in synthetic and natural systems. PLoS Comput Biol 2014; 10:e1003533. [PMID: 24676102 PMCID: PMC3967935 DOI: 10.1371/journal.pcbi.1003533] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/29/2014] [Indexed: 01/05/2023] Open
Abstract
Biological protein interactions networks such as signal transduction or gene transcription networks are often treated as modular, allowing motifs to be analyzed in isolation from the rest of the network. Modularity is also a key assumption in synthetic biology, where it is similarly expected that when network motifs are combined together, they do not lose their essential characteristics. However, the interactions that a network module has with downstream elements change the dynamical equations describing the upstream module and thus may change the dynamic and static properties of the upstream circuit even without explicit feedback. In this work we analyze the behavior of a ubiquitous motif in gene transcription and signal transduction circuits: the switch. We show that adding an additional downstream component to the simple genetic toggle switch changes its dynamical properties by changing the underlying potential energy landscape, and skewing it in favor of the unloaded side, and in some situations adding loads to the genetic switch can also abrogate bistable behavior. We find that an additional positive feedback motif found in naturally occurring toggle switches could tune the potential energy landscape in a desirable manner. We also analyze autocatalytic signal transduction switches and show that a ubiquitous positive feedback switch can lose its switch-like properties when connected to a downstream load. Our analysis underscores the necessity of incorporating the effects of downstream components when understanding the physics of biochemical network motifs, and raises the question as to how these effects are managed in real biological systems. This analysis is particularly important when scaling synthetic networks to more complex organisms. Cells rely on complex networks of protein-protein interactions in order to carry out life functions. Scientists believe that these networks are organized in a modular fashion; that is they are made up of functionally distinct parts like an electronic circuit. Modularity implies that just as we put together electronic parts to make an amplifier that we can use in many different circuits, we can put together biochemical reactions to make an amplifier, or a switch or an oscillator, which perform the same function in different organisms. This assumption is important in synthetic biology, where we engineer and assemble synthetic genetic circuits in living organisms in a modular fashion. We show that for important modules like genetic and signaling switches, the assumption of modularity has a crucial limitation. We show that if one simply connects a biological switch to another downstream circuit, the presence of the connection changes the operation of the switch, which in some cases may stop behaving like a switch. Our work underscores the importance of taking into account these downstream connections and suggests that natural systems may be balancing some of these components in order to ensure that despite diversity, modules continue to work in different systems with fidelity.
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23
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Sawicka M, Stritesky GL, Reynolds J, Abourashchi N, Lythe G, Molina-París C, Hogquist KA. From pre-DP, post-DP, SP4, and SP8 Thymocyte Cell Counts to a Dynamical Model of Cortical and Medullary Selection. Front Immunol 2014; 5:19. [PMID: 24592261 PMCID: PMC3924582 DOI: 10.3389/fimmu.2014.00019] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/15/2014] [Indexed: 01/15/2023] Open
Abstract
Cells of the mature αβ T cell repertoire arise from the development in the thymus of bone marrow precursors (thymocytes). αβ T cell maturation is characterized by the expression of thousands of copies of identical αβ T cell receptors and the CD4 and/or CD8 co-receptors on the surface of thymocytes. The maturation stages of a thymocyte are: (1) double negative (DN) (TCR−, CD4− and CD8−), (2) double positive (DP) (TCR+, CD4+ and CD8+), and (3) single positive (SP) (TCR+, CD4+ or CD8+). Thymic antigen presenting cells provide the appropriate micro-architecture for the maturation of thymocytes, which “sense” the signaling environment via their randomly generated TCRs. Thymic development is characterized by (i) an extremely low success rate, and (ii) the selection of a functional and self-tolerant T cell repertoire. In this paper, we combine recent experimental data and mathematical modeling to study the selection events that take place in the thymus after the DN stage. The stable steady state of the model for the pre-DP, post-DP, and SP populations is identified with the experimentally measured cell counts from 5.5- to 17-week-old mice. We make use of residence times in the cortex and the medulla for the different populations, as well as recently reported asymmetric death rates for CD4 and CD8 SP thymocytes. We estimate that 65.8% of pre-DP thymocytes undergo death by neglect. In the post-DP compartment, 91.7% undergo death by negative selection, 4.7% become CD4 SP, and 3.6% become CD8 SP. Death by negative selection in the medulla removes 8.6% of CD4 SP and 32.1% of CD8 SP thymocytes. Approximately 46.3% of CD4 SP and 27% of CD8 SP thymocytes divide before dying or exiting the thymus.
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Affiliation(s)
- Maria Sawicka
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Gretta L Stritesky
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota , Minneapolis, MN , USA
| | - Joseph Reynolds
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Niloufar Abourashchi
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Grant Lythe
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Carmen Molina-París
- Department of Applied Mathematics, School of Mathematics, University of Leeds , Leeds , UK
| | - Kristin A Hogquist
- Department of Laboratory Medicine and Pathology, Center for Immunology, University of Minnesota , Minneapolis, MN , USA
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24
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Abstract
The peripheral T cell repertoire is sculpted from prototypic T cells in the thymus bearing randomly generated T cell receptors (TCR) and by a series of developmental and selection steps that remove cells that are unresponsive or overly reactive to self-peptide–MHC complexes. The challenge of understanding how the kinetics of T cell development and the statistics of the selection processes combine to provide a diverse but self-tolerant T cell repertoire has invited quantitative modeling approaches, which are reviewed here.
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Affiliation(s)
- Andrew J Yates
- Departments of Systems and Computational Biology, Microbiology and Immunology, Albert Einstein College of Medicine , New York, NY , USA
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25
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Lim S, Park J, Lee N, Jeong J, Toh S, Watanabe A, Kim J, Kang H, Kim DH, Kawakami N, Choi G. ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. THE PLANT CELL 2013. [PMID: 24326588 DOI: 10.1105/tpc.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Seeds monitor the environment to germinate at the proper time, but different species respond differently to environmental conditions, particularly light and temperature. In Arabidopsis thaliana, light promotes germination but high temperature suppresses germination. We previously reported that light promotes germination by repressing SOMNUS (SOM). Here, we examined whether high temperature also regulates germination through SOM and found that high temperature activates SOM expression. Consistent with this, som mutants germinated more frequently than the wild type at high temperature. The induction of SOM mRNA at high temperature required abscisic acid (ABA) and gibberellic acid biosynthesis, and ABA-insensitive3 (ABI3), ABI5, and DELLAs positively regulated SOM expression. Chromatin immunoprecipitation assays indicated that ABI3, ABI5, and DELLAs all target the SOM promoter. At the protein level, ABI3, ABI5, and DELLAs all interact with each other, suggesting that they form a complex on the SOM promoter to activate SOM expression at high temperature. We found that high-temperature-inducible genes frequently have RY motifs and ABA-responsive elements in their promoters, some of which are targeted by ABI3, ABI5, and DELLAs in vivo. Taken together, our data indicate that ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
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Affiliation(s)
- Soohwan Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
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26
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Lim S, Park J, Lee N, Jeong J, Toh S, Watanabe A, Kim J, Kang H, Kim DH, Kawakami N, Choi G. ABA-insensitive3, ABA-insensitive5, and DELLAs Interact to activate the expression of SOMNUS and other high-temperature-inducible genes in imbibed seeds in Arabidopsis. THE PLANT CELL 2013; 25:4863-78. [PMID: 24326588 PMCID: PMC3903992 DOI: 10.1105/tpc.113.118604] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/07/2013] [Accepted: 11/16/2013] [Indexed: 05/18/2023]
Abstract
Seeds monitor the environment to germinate at the proper time, but different species respond differently to environmental conditions, particularly light and temperature. In Arabidopsis thaliana, light promotes germination but high temperature suppresses germination. We previously reported that light promotes germination by repressing SOMNUS (SOM). Here, we examined whether high temperature also regulates germination through SOM and found that high temperature activates SOM expression. Consistent with this, som mutants germinated more frequently than the wild type at high temperature. The induction of SOM mRNA at high temperature required abscisic acid (ABA) and gibberellic acid biosynthesis, and ABA-insensitive3 (ABI3), ABI5, and DELLAs positively regulated SOM expression. Chromatin immunoprecipitation assays indicated that ABI3, ABI5, and DELLAs all target the SOM promoter. At the protein level, ABI3, ABI5, and DELLAs all interact with each other, suggesting that they form a complex on the SOM promoter to activate SOM expression at high temperature. We found that high-temperature-inducible genes frequently have RY motifs and ABA-responsive elements in their promoters, some of which are targeted by ABI3, ABI5, and DELLAs in vivo. Taken together, our data indicate that ABI3, ABI5, and DELLAs mediate high-temperature signaling to activate the expression of SOM and other high-temperature-inducible genes, thereby inhibiting seed germination.
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Affiliation(s)
- Soohwan Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Jeongmoo Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Nayoung Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Jinkil Jeong
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Shigeo Toh
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Asuka Watanabe
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Junghyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Hyojin Kang
- National Institute of Supercomputing and Networking, Korea Institute of Science and Technology Information, Daejeon 305-806, Korea
| | - Dong Hwan Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
| | - Naoto Kawakami
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Giltsu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Korea
- Address correspondence to
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27
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Mukherjee S, Seok SC, Vieland VJ, Das J. Data-driven quantification of the robustness and sensitivity of cell signaling networks. Phys Biol 2013; 10:066002. [PMID: 24164951 DOI: 10.1088/1478-3975/10/6/066002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the experimentally observed cell-to-cell variations of protein abundances and cell functions or contain ad hoc assumptions. We propose and apply a data-driven maximum entropy based method to quantify robustness and sensitivity of Escherichia coli (E. coli) chemotaxis signaling network. Our analysis correctly rank orders different models of E. coli chemotaxis based on their robustness and suggests that parameters regulating cell signaling are evolutionary selected to vary in individual cells according to their abilities to perturb cell functions. Furthermore, predictions from our approach regarding distribution of protein abundances and properties of chemotactic responses in individual cells based on cell population averaged data are in excellent agreement with their experimental counterparts. Our approach is general and can be used to evaluate robustness as well as generate predictions of single cell properties based on population averaged experimental data in a wide range of cell signaling systems.
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Affiliation(s)
- Sayak Mukherjee
- Battelle Center for Mathematical Medicine, The Research Institute at the Nationwide Children's Hospital, The Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA. Department of Pediatrics, The Ohio State University, 700 Children's Drive, Columbus, OH 43205, USA
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28
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Jun JE, Rubio I, Roose JP. Regulation of ras exchange factors and cellular localization of ras activation by lipid messengers in T cells. Front Immunol 2013; 4:239. [PMID: 24027568 PMCID: PMC3762125 DOI: 10.3389/fimmu.2013.00239] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 08/02/2013] [Indexed: 11/17/2022] Open
Abstract
The Ras-MAPK signaling pathway is highly conserved throughout evolution and is activated downstream of a wide range of receptor stimuli. Ras guanine nucleotide exchange factors (RasGEFs) catalyze GTP loading of Ras and play a pivotal role in regulating receptor-ligand induced Ras activity. In T cells, three families of functionally important RasGEFs are expressed: RasGRF, RasGRP, and Son of Sevenless (SOS)-family GEFs. Early on it was recognized that Ras activation is critical for T cell development and that the RasGEFs play an important role herein. More recent work has revealed that nuances in Ras activation appear to significantly impact T cell development and selection. These nuances include distinct biochemical patterns of analog versus digital Ras activation, differences in cellular localization of Ras activation, and intricate interplays between the RasGEFs during distinct T cell developmental stages as revealed by various new mouse models. In many instances, the exact nature of these nuances in Ras activation or how these may result from fine-tuning of the RasGEFs is not understood. One large group of biomolecules critically involved in the control of RasGEFs functions are lipid second messengers. Multiple, yet distinct lipid products are generated following T cell receptor (TCR) stimulation and bind to different domains in the RasGRP and SOS RasGEFs to facilitate the activation of the membrane-anchored Ras GTPases. In this review we highlight how different lipid-based elements are generated by various enzymes downstream of the TCR and other receptors and how these dynamic and interrelated lipid products may fine-tune Ras activation by RasGEFs in developing T cells.
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Affiliation(s)
- Jesse E Jun
- Department of Anatomy, University of California San Francisco , San Francisco, CA , USA
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29
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Iwig JS, Vercoulen Y, Das R, Barros T, Limnander A, Che Y, Pelton JG, Wemmer DE, Roose JP, Kuriyan J. Structural analysis of autoinhibition in the Ras-specific exchange factor RasGRP1. eLife 2013; 2:e00813. [PMID: 23908768 PMCID: PMC3728621 DOI: 10.7554/elife.00813] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/18/2013] [Indexed: 11/13/2022] Open
Abstract
RasGRP1 and SOS are Ras-specific nucleotide exchange factors that have distinct roles in lymphocyte development. RasGRP1 is important in some cancers and autoimmune diseases but, in contrast to SOS, its regulatory mechanisms are poorly understood. Activating signals lead to the membrane recruitment of RasGRP1 and Ras engagement, but it is unclear how interactions between RasGRP1 and Ras are suppressed in the absence of such signals. We present a crystal structure of a fragment of RasGRP1 in which the Ras-binding site is blocked by an interdomain linker and the membrane-interaction surface of RasGRP1 is hidden within a dimerization interface that may be stabilized by the C-terminal oligomerization domain. NMR data demonstrate that calcium binding to the regulatory module generates substantial conformational changes that are incompatible with the inactive assembly. These features allow RasGRP1 to be maintained in an inactive state that is poised for activation by calcium and membrane-localization signals. DOI:http://dx.doi.org/10.7554/eLife.00813.001 Individual cells within the human body must grow, divide or specialize to perform the tasks required of them. The fates of these cells are often directed by proteins in the Ras family, which detect signals from elsewhere in the body and orchestrate responses within each cell. The activities of these proteins must be tightly controlled, because cancers and developmental diseases can result if Ras proteins are not properly regulated. Binding to the small molecule GTP activates Ras and causes conformational changes that allow it to interact with other proteins in various signaling pathways in the cell. GTP is loaded into Ras by proteins called nucleotide exchange factors, which can replace ‘used’ nucleotides with ‘fresh’ ones to activate Ras. These nucleotide exchange factors are also tightly regulated. For example, the genes for many exchange factors are only switched on after particular signals are received, which can restrict their presence to defined times and locations (e.g., cells or tissues). Also, when activating signals are absent, nucleotide exchange factors commonly reside in the cytoplasm, whereas the Ras proteins remain bound to lipid membranes inside the cell. RasGRP1 is a nucleotide exchange factor that controls the development of immune cells, and leukemia and lupus can result if it is not regulated correctly. However, many questions about RasGRP1 remain unanswered, including how it is able to remain inactive, and how it is activated by various different signals. Iwig et al. have now revealed the mechanisms through which RasGRP1 suppresses Ras signaling in immune cells by solving the structures of two fragments of RasGRP1 and then using a combination of structural, biochemical and cell-based methods to explore how it is activated. These analyses revealed that inactive RasGRP1 adopts a conformation in which one of its regulatory elements blocks access to the Ras binding site. Surprisingly, RasGRP1 can form dimers; this hides the portions of the protein that associate with the membrane and thereby keeps RasGRP1 away from Ras. Iwig et al. also found that two signals, calcium ions and a lipid called diacylglycerol, overcome these inhibitory mechanisms by changing the conformation of RasGRP1 and recruiting it to the membrane. These studies provide a framework for understanding how disease-associated mutations in RasGRP1 bypass the regulatory mechanisms that insure proper immune cell development, and will be critical for developing therapeutic agents that inhibit RasGRP1 activity. DOI:http://dx.doi.org/10.7554/eLife.00813.002
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Affiliation(s)
- Jeffrey S Iwig
- Department of Molecular and Cell Biology , University of California, Berkeley , Berkeley , United States ; California Institute for Quantitative Biosciences , University of California, Berkeley , Berkeley , United States
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30
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Bains I, van Santen HM, Seddon B, Yates AJ. Models of self-peptide sampling by developing T cells identify candidate mechanisms of thymic selection. PLoS Comput Biol 2013; 9:e1003102. [PMID: 23935465 PMCID: PMC3723501 DOI: 10.1371/journal.pcbi.1003102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 05/01/2013] [Indexed: 11/18/2022] Open
Abstract
Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC (pMHC) ligands. This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self. Regulatory T cells are thought to lie at the higher end of the spectrum of acceptable self-reactivity and play a crucial role in the control of autoimmunity and tolerance to innocuous antigens. While many studies have elucidated key elements influencing lineage commitment, we still lack a full understanding of how thymocytes integrate signals obtained by sampling self-peptides to make fate decisions. To address this problem, we apply stochastic models of signal integration by T cells to data from a study quantifying the development of the two lineages using controllable levels of agonist peptide in the thymus. We find two models are able to explain the observations; one in which T cells continually re-assess fate decisions on the basis of multiple summed proximal signals from TCR-pMHC interactions; and another in which TCR sensitivity is modulated over time, such that contact with the same pMHC ligand may lead to divergent outcomes at different stages of development. Neither model requires that T(conv) and T(reg) are differentially susceptible to deletion or that the two lineages need qualitatively different signals for development, as have been proposed. We find additional support for the variable-sensitivity model, which is able to explain apparently paradoxical observations regarding the effect of partial and strong agonists on T(conv) and T(reg) development.
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Affiliation(s)
- Iren Bains
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
| | - Hisse M. van Santen
- Centro Biologia Molecular Severo Ochoa, CSIC/Universidad Autonoma de Madrid, Madrid, Spain
| | - Benedict Seddon
- Immune Cell Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
| | - Andrew J. Yates
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, New York, United States of America
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, New York, United States of America
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31
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Activation of Extracellular Signal-Regulated Kinase but Not of p38 Mitogen-Activated Protein Kinase Pathways in Lymphocytes Requires Allosteric Activation of SOS. Mol Cell Biol 2013; 33:2470-84. [DOI: 10.1128/mcb.01593-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
Thymocytes convert graded T cell receptor (TCR) signals into positive selection or deletion, and activation of extracellular signal-related kinase (ERK), p38, and Jun N-terminal protein kinase (JNK) mitogen-activated protein kinases (MAPKs) has been postulated to play a discriminatory role. Two families of Ras guanine nucleotide exchange factors (RasGEFs), SOS and RasGRP, activate Ras and the downstream RAF-MEK-ERK pathway. The pathways leading to lymphocyte p38 and JNK activation are less well defined. We previously described how RasGRP alone induces analog Ras-ERK activation while SOS and RasGRP cooperate to establish bimodal ERK activation. Here we employed computational modeling and biochemical experiments with model cell lines and thymocytes to show that TCR-induced ERK activation grows exponentially in thymocytes and that a W729E allosteric pocket mutant, SOS1, can only reconstitute analog ERK signaling. In agreement with RasGRP allosterically priming SOS, exponential ERK activation is severely decreased by pharmacological or genetic perturbation of the phospholipase Cγ (PLCγ)-diacylglycerol-RasGRP1 pathway. In contrast, p38 activation is not sharply thresholded and requires high-level TCR signal input. Rac and p38 activation depends on SOS1 expression but not allosteric activation. Based on computational predictions and experiments exploring whether SOS functions as a RacGEF or adaptor in Rac-p38 activation, we established that the presence of SOS1, but not its enzymatic activity, is critical for p38 activation.
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32
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Hartzell C, Ksionda O, Lemmens E, Coakley K, Yang M, Dail M, Harvey RC, Govern C, Bakker J, Lenstra TL, Ammon K, Boeter A, Winter SS, Loh M, Shannon K, Chakraborty AK, Wabl M, Roose JP. Dysregulated RasGRP1 responds to cytokine receptor input in T cell leukemogenesis. Sci Signal 2013; 6:ra21. [PMID: 23532335 DOI: 10.1126/scisignal.2003848] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enhanced signaling by the small guanosine triphosphatase Ras is common in T cell acute lymphoblastic leukemia/lymphoma (T-ALL), but the underlying mechanisms are unclear. We identified the guanine nucleotide exchange factor RasGRP1 (Rasgrp1 in mice) as a Ras activator that contributes to leukemogenesis. We found increased RasGRP1 expression in many pediatric T-ALL patients, which is not observed in rare early T cell precursor T-ALL patients with KRAS and NRAS mutations, such as K-Ras(G12D). Leukemia screens in wild-type mice, but not in mice expressing the mutant K-Ras(G12D) that encodes a constitutively active Ras, yielded frequent retroviral insertions that led to increased Rasgrp1 expression. Rasgrp1 and oncogenic K-Ras(G12D) promoted T-ALL through distinct mechanisms. In K-Ras(G12D) T-ALLs, enhanced Ras activation had to be uncoupled from cell cycle arrest to promote cell proliferation. In mouse T-ALL cells with increased Rasgrp1 expression, we found that Rasgrp1 contributed to a previously uncharacterized cytokine receptor-activated Ras pathway that stimulated the proliferation of T-ALL cells in vivo, which was accompanied by dynamic patterns of activation of effector kinases downstream of Ras in individual T-ALLs. Reduction of Rasgrp1 abundance reduced cytokine-stimulated Ras signaling and decreased the proliferation of T-ALL in vivo. The position of RasGRP1 downstream of cytokine receptors as well as the different clinical outcomes that we observed as a function of RasGRP1 abundance make RasGRP1 an attractive future stratification marker for T-ALL.
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Affiliation(s)
- Catherine Hartzell
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
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33
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Kortum RL, Rouquette-Jazdanian AK, Samelson LE. Ras and extracellular signal-regulated kinase signaling in thymocytes and T cells. Trends Immunol 2013; 34:259-68. [PMID: 23506953 DOI: 10.1016/j.it.2013.02.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/04/2013] [Accepted: 02/12/2013] [Indexed: 12/22/2022]
Abstract
Extracellular signal-regulated kinase (ERK) activation is important for both thymocyte development and T cell function. Classically, signal transduction from the T cell antigen receptor (TCR) to ERK is thought to be regulated by signaling from Ras guanine nucleotide exchange factors (GEFs), through the small G protein Ras, to the three-tiered Raf-MAPK/ERK kinase (MEK)-ERK kinase cascade. Developing and mature T cells express four members of two RasGEF families, RasGRP1, RasGRP4, son of sevenless 1 (Sos1), and Sos2, and several models describing combined signaling from these RasGEFs have been proposed. However, recent studies suggest that existing models need revision to include both distinct and overlapping roles of multiple RasGEFs during thymocyte development and novel, Ras-independent signals to ERK that have been identified in peripheral T cells.
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Affiliation(s)
- Robert L Kortum
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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34
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Phenotypic model for early T-cell activation displaying sensitivity, specificity, and antagonism. Proc Natl Acad Sci U S A 2013; 110:E888-97. [PMID: 23431198 DOI: 10.1073/pnas.1300752110] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Early T-cell activation is selected by evolution to discriminate a few foreign peptides rapidly from a vast excess of self-peptides, and it is unclear in quantitative terms how this is possible. We show that a generic proofreading cascade supplemented by a single negative feedback mediated by the Src homology 2 domain phosphatase-1 (SHP-1) accounts quantitatively for early T-cell activation, including the effects of antagonists. Modulation of the negative feedback with SHP-1 concentration explains counterintuitive experimental observations, such as the nonmonotonic behavior of receptor activity on agonist concentration, the digital vs. continuous behavior on certain parameters, and the loss of response for high SHP-1 concentration. New experiments validate predictions on the nontrivial joint dependence on binding time and concentration for the relative effect of two antagonists: We explain why strong antagonists behave as partial agonists at low concentration and predict that the relative effect of antagonists can invert as their concentrations are varied. By focusing on the phenotype, our model quantitatively fits a body of experimental data with minimal variables and parameters.
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Lee DM, Lee SH, Jeong KT, Hwang SJ, Park JH. SDS3 interacts with ARNT in an AhR ligand-specific manner regulating expression of cKrox and S100A4 in CD4+CD8+ DPK thymocytes differentiation. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2012; 34:858-868. [PMID: 22981438 DOI: 10.1016/j.etap.2012.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 07/02/2012] [Accepted: 08/24/2012] [Indexed: 06/01/2023]
Abstract
To study mechanisms underlying differential effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and benzo(a)pyrene (B(a)P) on thymocyte differentiation, we examined effects of AhR ligands on the differentiation of DPK cells, a CD4(+)CD8(+) thymic lymphoma cell line which can differentiate into CD4(+)CD8(-) thymocytes. In contrast to TCDD, which inhibited the differentiation, B(a)P showed little effect. Antigen-mediated up-regulation of S100A4, S100A6, galectin-1, and TRAF5-like protein was remarkably suppressed by TCDD, but slightly by B(a)P. Immunoprecipitation using anti-ARNT Ab revealed that SDS3, a component of the Sin3/HDAC repressor complex, was associated with ARNT only when DPK cells were incubated with TCDD. Expression of cKrox S100A4 was derepressed when SDS3 protein was reduced. These results indicate that although it is generally known that many AhR ligands such as TCDD and B(a)P function mainly by the AhR/ARNT complex, ligand-specific interaction between SDS3 and ARNT exerts differential effects on the expression of genes associated with thymocyte differentiation.
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Affiliation(s)
- Dong-Min Lee
- Department of Biology, Changwon National University, Changwon, Kyungnam 641-773, South Korea
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36
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Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. BMC SYSTEMS BIOLOGY 2012; 6:109. [PMID: 22920937 PMCID: PMC3484110 DOI: 10.1186/1752-0509-6-109] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 07/27/2012] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cell-to-cell variability in protein expression can be large, and its propagation through signaling networks affects biological outcomes. Here, we apply deterministic and probabilistic models and biochemical measurements to study how network topologies and cell-to-cell protein abundance variations interact to shape signaling responses. RESULTS We observe bimodal distributions of extracellular signal-regulated kinase (ERK) responses to epidermal growth factor (EGF) stimulation, which are generally thought to indicate bistable or ultrasensitive signaling behavior in single cells. Surprisingly, we find that a simple MAPK/ERK-cascade model with negative feedback that displays graded, analog ERK responses at a single cell level can explain the experimentally observed bimodality at the cell population level. Model analysis suggests that a conversion of graded input-output responses in single cells to digital responses at the population level is caused by a broad distribution of ERK pathway activation thresholds brought about by cell-to-cell variability in protein expression. CONCLUSIONS Our results show that bimodal signaling response distributions do not necessarily imply digital (ultrasensitive or bistable) single cell signaling, and the interplay between protein expression noise and network topologies can bring about digital population responses from analog single cell dose responses. Thus, cells can retain the benefits of robustness arising from negative feedback, while simultaneously generating population-level on/off responses that are thought to be critical for regulating cell fate decisions.
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Affiliation(s)
- Marc R Birtwistle
- Dept. of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, NY 10029, USA
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TCR-mediated Erk activation does not depend on Sos and Grb2 in peripheral human T cells. EMBO Rep 2012; 13:386-91. [PMID: 22344067 DOI: 10.1038/embor.2012.17] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 02/07/2023] Open
Abstract
Sos proteins are ubiquitously expressed activators of Ras. Lymphoid cells also express RasGRP1, another Ras activator. Sos and RasGRP1 are thought to cooperatively control full Ras activation upon T-cell receptor triggering. Using RNA interference, we evaluated whether this mechanism operates in primary human T cells. We found that T-cell antigen receptor (TCR)-mediated Erk activation requires RasGRP1, but not Grb2/Sos. Conversely, Grb2/Sos—but not RasGRP1—are required for IL2-mediated Erk activation. Thus, RasGRP1 and Grb2/Sos are insulators of signals that lead to Ras activation induced by different stimuli, rather than cooperating downstream of the TCR.
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Abstract
Thymocytes must transit at least two distinct developmental checkpoints, governed by signals that emanate from either the pre-T cell receptor (pre-TCR) or the TCR to the small G protein Ras before emerging as functional T lymphocytes. Recent studies have shown a role for the Ras guanine exchange factor (RasGEF) Sos1 at the pre-TCR checkpoint. At the second checkpoint, the quality of signaling through the TCR is interrogated to ensure the production of an appropriate T cell repertoire. Although RasGRP1 is the only confirmed RasGEF required at the TCR checkpoint, current models suggest that the intensity and character of Ras activation, facilitated by both Sos and RasGRP1, will govern the boundary between survival (positive selection) and death (negative selection) at this stage. Using mouse models, we have assessed the independent and combined roles for the RasGEFs Sos1, Sos2, and RasGRP1 during thymocyte development. Although Sos1 was the dominant RasGEF at the pre-TCR checkpoint, combined Sos1/RasGRP1 deletion was required to effectively block development at this stage. Conversely, while RasGRP1 deletion efficiently blocked positive selection, combined RasGRP1/Sos1 deletion was required to block negative selection. This functional redundancy in RasGEFs during negative selection may act as a failsafe mechanism ensuring appropriate central tolerance.
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Whitacre JM, Lin J, Harding A. T Cell Adaptive Immunity Proceeds through Environment-Induced Adaptation from the Exposure of Cryptic Genetic Variation. Front Genet 2012; 3:5. [PMID: 22363338 PMCID: PMC3275780 DOI: 10.3389/fgene.2012.00005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/06/2012] [Indexed: 01/10/2023] Open
Abstract
Evolution is often characterized as a process involving incremental genetic changes that are slowly discovered and fixed in a population through genetic drift and selection. However, a growing body of evidence is finding that changes in the environment frequently induce adaptations that are much too rapid to occur by an incremental genetic search process. Rapid evolution is hypothesized to be facilitated by mutations present within the population that are silent or "cryptic" within the first environment but are co-opted or "exapted" to the new environment, providing a selective advantage once revealed. Although cryptic mutations have recently been shown to facilitate evolution in RNA enzymes, their role in the evolution of complex phenotypes has not been proven. In support of this wider role, this paper describes an unambiguous relationship between cryptic genetic variation and complex phenotypic responses within the immune system. By reviewing the biology of the adaptive immune system through the lens of evolution, we show that T cell adaptive immunity constitutes an exemplary model system where cryptic alleles drive rapid adaptation of complex traits. In naive T cells, normally cryptic differences in T cell receptor reveal diversity in activation responses when the cellular population is presented with a novel environment during infection. We summarize how the adaptive immune response presents a well studied and appropriate experimental system that can be used to confirm and expand upon theoretical evolutionary models describing how seemingly small and innocuous mutations can drive rapid cellular evolution.
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Affiliation(s)
| | - Joseph Lin
- Department of Biology, Sonoma State UniversityRohnert Park, CA, USA
| | - Angus Harding
- Princess Alexandra Hospital, The University of Queensland Diamantina InstituteWoolloongabba, QLD, Australia
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Prasad A. Computational modeling of signal transduction networks: a pedagogical exposition. Methods Mol Biol 2012; 880:219-41. [PMID: 23361987 DOI: 10.1007/978-1-61779-833-7_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
We give a pedagogical introduction to computational modeling of signal transduction networks, starting from explaining the representations of chemical reactions by differential equations via the law of mass action. We discuss elementary biochemical reactions such as Michaelis-Menten enzyme kinetics and cooperative binding, and show how these allow the representation of large networks as systems of differential equations. We discuss the importance of looking for simpler or reduced models, such as network motifs or dynamical motifs within the larger network, and describe methods to obtain qualitative behavior by bifurcation analysis, using freely available continuation software. We then discuss stochastic kinetics and show how to implement easy-to-use methods of rule-based modeling for stochastic simulations. We finally suggest some methods for comprehensive parameter sensitivity analysis, and discuss the insights that it could yield. Examples, including code to try out, are provided based on a paper that modeled Ras kinetics in thymocytes.
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Affiliation(s)
- Ashok Prasad
- Chemical and Biological Engineering, School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA.
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Abstract
Ras guanyl nucleotide releasing proteins (RasGRPs) are guanyl nucleotide exchange factors that activate Ras and related GTPases such as Rap. Like Sos proteins, RasGRPs have a catalytic region composed of a Ras exchange motif (REM) and a CDC25 domain. RasGRPs also possess a pair of atypical EF hands that may bind calcium in vivo and a C1 domain resembling the diacylglycerol (DAG)-binding domain of protein kinase C. DAG directly activates RasGRPs by a membrane recruitment mechanism as well as indirectly by PKC-mediated phosphorylation. RasGRPs are prominently expressed in blood cells. RasGRP1 acts downstream of TCR, while RasGRP1 and RasGRP3 both act downstream of BCR. Together, they regulate Ras in adaptive immune cells. RasGRP2, through Rap, plays a role in controlling platelet adhesion, while RasGRP4 controls Ras activation in mast cells. RasGRP malfunction likely contributes to autoimmunity and may contribute to blood malignancies. RasGRPs might prove to be viable drug targets. The intracellular site of RasGRP action and the relationship between RasGRPs and other Ras regulatory mechanisms are subjects of lively debate.
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Affiliation(s)
- James C Stone
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
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42
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Stites EC, Ravichandran KS. Mechanistic modeling to investigate signaling by oncogenic Ras mutants. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 4:117-27. [PMID: 21766467 DOI: 10.1002/wsbm.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Mathematical models based on biochemical reaction mechanisms can be a powerful complement to experimental investigations of cell signaling networks. In principle, such models have the potential to find the behaviors that result from well-understood component interactions and their measurable properties, such as concentrations and rate constants. As cancer results from the acquisition of mutations that alter the expression level and/or the biochemistry of proteins encoded by mutated genes, mathematical models of cell signaling networks would also seem to have the potential to predict how these changes alter cell signaling to produce a cancer phenotype. Ras is commonly found in cancer and has been extensively characterized at the level of detail needed to develop such models. Here, we consider how biochemical mechanism-based models have been used to study mutant Ras signaling. These models demonstrate that it is clearly possible to use observable properties of individual reactions to predict how the entire system behaves to produce the high levels of signal that drive the cancer phenotype. These models also demonstrate differences in how models are developed and studied. Their evaluation suggests which approaches are most promising for future work.
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Affiliation(s)
- Edward C Stites
- Clinical Translational Research Division, The Translational Genomics Research Institute, Phoenix, AZ, USA.
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Targeted Sos1 deletion reveals its critical role in early T-cell development. Proc Natl Acad Sci U S A 2011; 108:12407-12. [PMID: 21746917 DOI: 10.1073/pnas.1104295108] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Activation of the small G protein Ras is required for thymocyte differentiation. In thymocytes, Ras is activated by the Ras guanine exchange factors (RasGEFs) Sos1, Sos2, and RasGRP1. We report the development of a floxed allele of sos1 to assess the role of Sos1 during thymocyte development. Sos1 was required for pre-T-cell receptor (pre-TCR)- but not TCR-stimulated developmental signals. Sos1 deletion led to a partial block at the DN-to-DP transition. Sos1-deficient thymocytes showed reduced pre-TCR-stimulated proliferation, differentiation, and ERK phosphorylation. In contrast, TCR-stimulated positive selection, and negative selection under strong stimulatory conditions, remained intact in Sos1-deficient mice. Comparison of RasGEF expression at different developmental stages showed that relative to Sos2 and RasGRP1, Sos1 is most abundant in DN thymocytes, but least abundant in DP thymocytes. These data reveal that Sos1 is uniquely positioned to affect signal transduction early in thymocyte development.
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Cao Y, Li H, Liu H, Zhang M, Hua Z, Ji H, Liu X. LKB1 regulates TCR-mediated PLCγ1 activation and thymocyte positive selection. EMBO J 2011; 30:2083-93. [PMID: 21487392 DOI: 10.1038/emboj.2011.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 03/14/2011] [Indexed: 11/09/2022] Open
Abstract
The serine/threonine kinase LKB1 is a tumour suppressor that regulates cell growth, polarity, and proliferation in many different cell types. We previously demonstrated that LKB1 controls thymocyte survival via regulation of AMPK activation. In this study, we show that LKB1 was also involved in thymocyte positive selection through regulation of T cell receptor (TCR) signalling. Both Lck-Cre- and CD4-Cre-mediated deletion of LKB1 impaired the generation of mature CD4 and CD8 single positive (SP) thymocytes that might have resulted from the attenuated tyrosine phosphorylation of phospholipase C-γ 1 (PLCγ1) in the absence of LKB1. We found that LKB1 was directly phosphorylated by Lck at tyrosine residues 36, 261, and 365 and predominately interacted with LAT and PLCγ1 following TCR stimulation. Loss of LKB1 led to impaired recruitment of PLCγ1 to the LAT signalosome. Correlatively, LKB1-deficient thymocytes failed to upregulate lineage-specifying factors, and to differentiate into SP thymocytes even if their impaired survival was rescued. These observations indicated that LKB1 is a critical component involved in TCR signalling, and our studies provide novel insights into the mechanisms of LKB1-mediated thymocyte development.
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Affiliation(s)
- Yonghao Cao
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Artomov M, Kardar M, Chakraborty AK. Only signaling modules that discriminate sharply between stimulatory and nonstimulatory inputs require basal signaling for fast cellular responses. J Chem Phys 2011; 133:105101. [PMID: 20849190 DOI: 10.1063/1.3482813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In many types of cells, binding of molecules to their receptors enables cascades of intracellular chemical reactions to take place (signaling). However, a low level of signaling also occurs in most unstimulated cells. Such basal signaling in resting cells can have many functions, one of which is that it is thought to be required for fast cellular responses to external stimuli. A mechanistic understanding of why this is true and which features of cellular signaling networks make basal signaling necessary for fast responses is unknown. We address this issue by obtaining the time required for activation of common types of cell signaling modules with and without basal signaling. Our results show that the absence of basal signaling does not have any dramatic effects on the response time for signaling modules that exhibit a graded response to increasing stimulus levels. In sharp contrast, signaling modules that exhibit sharp dose-response curves which discriminate sensitively between stimuli to which the cell needs to respond and low-grade inputs (or stochastic noise) require basal signaling for fast cellular responses. In such cases, we find that an optimal level of basal signaling balances the requirements for fast cellular responses while minimizing spurious activation without appropriate stimulation.
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Affiliation(s)
- Mykyta Artomov
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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47
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Abstract
Higher organisms, such as humans, have an adaptive immune system that usually enables them to successfully combat diverse (and evolving) microbial pathogens. The adaptive immune system is not preprogrammed to respond to prescribed pathogens. Yet it mounts pathogen-specific responses against diverse microbes and establishes memory of past infections (the basis of vaccination). Although major advances have been made in understanding pertinent molecular and cellular phenomena, the mechanistic principles that govern many aspects of an immune response are not known. We illustrate how complementary approaches from the physical and life sciences can help confront this challenge. Specifically, we describe work that brings together statistical mechanics and cell biology to shed light on how key molecular/cellular components of the adaptive immune system are selected to enable pathogen-specific responses. We hope these examples encourage physical chemists to work at this crossroad of disciplines where fundamental discoveries with implications for human health might be made.
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Affiliation(s)
- Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
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48
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Groves JT, Kuriyan J. Molecular mechanisms in signal transduction at the membrane. Nat Struct Mol Biol 2010; 17:659-65. [PMID: 20495561 PMCID: PMC3703790 DOI: 10.1038/nsmb.1844] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Signal transduction originates at the membrane, where the clustering of signaling proteins is a key step in transmitting a message. Membranes are difficult to study, and their influence on signaling is still only understood at the most rudimentary level. Recent advances in the biophysics of membranes, surveyed in this review, have highlighted a variety of phenomena that are likely to influence signaling activity, such as local composition heterogeneities and long-range mechanical effects. We discuss recent mechanistic insights into three signaling systems-Ras activation, Ephrin signaling and the control of actin nucleation-where the active role of membrane components is now appreciated and for which experimentation on the membrane is required for further understanding.
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Affiliation(s)
- Jay T Groves
- Departments of Chemistry, University of California, Berkeley, California, USA.
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49
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Hu Q, Sader A, Parkman JC, Baldwin TA. Bim-mediated apoptosis is not necessary for thymic negative selection to ubiquitous self-antigens. THE JOURNAL OF IMMUNOLOGY 2010; 183:7761-7. [PMID: 19933852 DOI: 10.4049/jimmunol.0902181] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
T cell education in the thymus is critical for establishing a functional, yet self-tolerant, T cell repertoire. Negative selection is a key process in enforcing self-tolerance. There are many questions that surround the mechanism of negative selection, but it is currently held that apoptosis initiated by Bim and/or Nur77 is critical for negative selection. Recent studies, however, have questioned the necessity of Bim in maintaining both central and peripheral T cell tolerance. To reconcile these apparently contradictory findings, we examined the role of Bim in negative selection in the well-characterized, physiological HY(cd4) mouse model. We found that while Bim expression was required for CD4(+)CD8(+) double-positive thymocyte apoptosis, it was not required for negative selection. Furthermore, Bim deficiency did not alter the frequency or affinity of male reactive cells that escape negative selection in an oligoclonal repertoire. Collectively, these studies indicate that negative selection occurs efficiently in the absence of apoptosis and suggest that the current paradigm of negative selection requiring apoptosis be revisited.
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Affiliation(s)
- Qian Hu
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
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50
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Chakraborty AK, Das J. Pairing computation with experimentation: a powerful coupling for understanding T cell signalling. Nat Rev Immunol 2010; 10:59-71. [DOI: 10.1038/nri2688] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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