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Voisinne G, Locard-Paulet M, Froment C, Maturin E, Menoita MG, Girard L, Mellado V, Burlet-Schiltz O, Malissen B, Gonzalez de Peredo A, Roncagalli R. Kinetic proofreading through the multi-step activation of the ZAP70 kinase underlies early T cell ligand discrimination. Nat Immunol 2022; 23:1355-1364. [PMID: 36045187 PMCID: PMC9477740 DOI: 10.1038/s41590-022-01288-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/15/2022] [Indexed: 12/18/2022]
Abstract
T cells recognize a few high-affinity antigens among a vast array of lower affinity antigens. According to the kinetic proofreading model, antigen discrimination properties could be explained by the gradual amplification of small differences in binding affinities as the signal is transduced downstream of the T cell receptor. Which early molecular events are affected by ligand affinity, and how, has not been fully resolved. Here, we used time-resolved high-throughput proteomic analyses to identify and quantify the phosphorylation events and protein-protein interactions encoding T cell ligand discrimination in antigen-experienced T cells. Although low-affinity ligands induced phosphorylation of the Cd3 chains of the T cell receptor and the interaction of Cd3 with the Zap70 kinase as strongly as high-affinity ligands, they failed to activate Zap70 to the same extent. As a result, formation of the signalosome of the Lat adaptor was severely impaired with low- compared with high-affinity ligands, whereas formation of the signalosome of the Cd6 receptor was affected only partially. Overall, this study provides a comprehensive map of molecular events associated with T cell ligand discrimination.
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Affiliation(s)
- Guillaume Voisinne
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Marie Locard-Paulet
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Carine Froment
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France
| | - Emilie Maturin
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Marisa Goncalves Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Laura Girard
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Valentin Mellado
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Odile Burlet-Schiltz
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France. .,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, Marseille, France.
| | - Anne Gonzalez de Peredo
- Département Biologie Structural Biophysique, Institut de Pharmacologie et de Biologie Structurale, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR, Toulouse, France.
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.
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Locard‐Paulet M, Voisinne G, Froment C, Goncalves Menoita M, Ounoughene Y, Girard L, Gregoire C, Mori D, Martinez M, Luche H, Garin J, Malissen M, Burlet‐Schiltz O, Malissen B, Gonzalez de Peredo A, Roncagalli R. LymphoAtlas: a dynamic and integrated phosphoproteomic resource of TCR signaling in primary T cells reveals ITSN2 as a regulator of effector functions. Mol Syst Biol 2020; 16:e9524. [PMID: 32618424 PMCID: PMC7333348 DOI: 10.15252/msb.20209524] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 05/19/2020] [Accepted: 05/20/2020] [Indexed: 12/29/2022] Open
Abstract
T-cell receptor (TCR) ligation-mediated protein phosphorylation regulates the activation, cellular responses, and fates of T cells. Here, we used time-resolved high-resolution phosphoproteomics to identify, quantify, and characterize the phosphorylation dynamics of thousands of phosphorylation sites in primary T cells during the first 10 min after TCR stimulation. Bioinformatic analysis of the data revealed a coherent orchestration of biological processes underlying T-cell activation. In particular, functional modules associated with cytoskeletal remodeling, transcription, translation, and metabolic processes were mobilized within seconds after TCR engagement. Among proteins whose phosphorylation was regulated by TCR stimulation, we demonstrated, using a fast-track gene inactivation approach in primary lymphocytes, that the ITSN2 adaptor protein regulated T-cell effector functions. This resource, called LymphoAtlas, represents an integrated pipeline to further decipher the organization of the signaling network encoding T-cell activation. LymphoAtlas is accessible to the community at: https://bmm-lab.github.io/LymphoAtlas.
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Affiliation(s)
- Marie Locard‐Paulet
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, UPSToulouseFrance
- Present address:
Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Guillaume Voisinne
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
| | - Carine Froment
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, UPSToulouseFrance
| | | | - Youcef Ounoughene
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Laura Girard
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Claude Gregoire
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
| | - Daiki Mori
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Manuel Martinez
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Hervé Luche
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Jerôme Garin
- CEA, BIG, Biologie à Grande Echelle, INSERM, U1038Université Grenoble‐AlpesGrenobleFrance
| | - Marie Malissen
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Odile Burlet‐Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, UPSToulouseFrance
| | - Bernard Malissen
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
- Centre d'ImmunophénomiqueINSERM, CNRS UMRAix Marseille UniversitéMarseilleFrance
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale (IPBS)Université de Toulouse, CNRS, UPSToulouseFrance
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille‐LuminyINSERM, CNRSAix Marseille UniversitéMarseilleFrance
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Voisinne G, Kersse K, Chaoui K, Lu L, Chaix J, Zhang L, Goncalves Menoita M, Girard L, Ounoughene Y, Wang H, Burlet-Schiltz O, Luche H, Fiore F, Malissen M, Gonzalez de Peredo A, Liang Y, Roncagalli R, Malissen B. Quantitative interactomics in primary T cells unveils TCR signal diversification extent and dynamics. Nat Immunol 2019; 20:1530-1541. [PMID: 31591574 PMCID: PMC6859066 DOI: 10.1038/s41590-019-0489-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/05/2019] [Indexed: 12/17/2022]
Abstract
The activation of T cells by the T cell antigen receptor (TCR) results in the formation of signaling protein complexes (signalosomes), the composition of which has not been analyzed at a systems level. Here, we isolated primary CD4+ T cells from 15 gene-targeted mice, each expressing one tagged form of a canonical protein of the TCR-signaling pathway. Using affinity purification coupled with mass spectrometry, we analyzed the composition and dynamics of the signalosomes assembling around each of the tagged proteins over 600 s of TCR engagement. We showed that the TCR signal-transduction network comprises at least 277 unique proteins involved in 366 high-confidence interactions, and that TCR signals diversify extensively at the level of the plasma membrane. Integrating the cellular abundance of the interacting proteins and their interaction stoichiometry provided a quantitative and contextual view of each documented interaction, permitting anticipation of whether ablation of a single interacting protein can impinge on the whole TCR signal-transduction network.
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Affiliation(s)
- Guillaume Voisinne
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Kristof Kersse
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, Département Biologie Structurale Biophysique, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR 5089, Toulouse, France
| | - Liaoxun Lu
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China.,Laboratory of Mouse Genetics, Institute of Psychiatry and Neuroscience, Xinxiang Medical University, Xinxiang, China
| | - Julie Chaix
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Lichen Zhang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Marisa Goncalves Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Laura Girard
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, Marseille, France
| | - Youcef Ounoughene
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France
| | - Hui Wang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Département Biologie Structurale Biophysique, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR 5089, Toulouse, France
| | - Hervé Luche
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, Marseille, France.,Laboratory of Immunophenomics, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Frédéric Fiore
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, Marseille, France
| | - Marie Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, Marseille, France.,Laboratory of Immunophenomics, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale, Département Biologie Structurale Biophysique, Protéomique Génopole Toulouse Midi Pyrénées CNRS UMR 5089, Toulouse, France
| | - Yinming Liang
- School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China. .,Laboratory of Immunophenomics, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China.
| | - Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France.
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, Marseille, France. .,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS UMR, Marseille, France. .,Laboratory of Immunophenomics, School of Laboratory Medicine, Xinxiang Medical University, Xinxiang, China.
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Roncagalli R, Cucchetti M, Jarmuzynski N, Grégoire C, Bergot E, Audebert S, Baudelet E, Menoita MG, Joachim A, Durand S, Suchanek M, Fiore F, Zhang L, Liang Y, Camoin L, Malissen M, Malissen B. The scaffolding function of the RLTPR protein explains its essential role for CD28 co-stimulation in mouse and human T cells. J Exp Med 2016; 213:2437-2457. [PMID: 27647348 PMCID: PMC5068240 DOI: 10.1084/jem.20160579] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/17/2016] [Indexed: 12/26/2022] Open
Abstract
In two complementary papers, Casanova, Malissen, and collaborators report the discovery of human RLTPR deficiency, the first primary immunodeficiency of the human CD28 pathway in T cells. Together, the two studies elucidate the largely (but not completely) overlapping roles of RLTPR in CD28 signaling in T and B cells of humans and mice. The RLTPR cytosolic protein, also known as CARMIL2, is essential for CD28 co-stimulation in mice, but its importance in human T cells and mode of action remain elusive. Here, using affinity purification followed by mass spectrometry analysis, we showed that RLTPR acts as a scaffold, bridging CD28 to the CARD11/CARMA1 cytosolic adaptor and to the NF-κB signaling pathway, and identified proteins not found before within the CD28 signaling pathway. We further demonstrated that RLTPR is essential for CD28 co-stimulation in human T cells and that its noncanonical pleckstrin-homology domain, leucine-rich repeat domain, and proline-rich region were mandatory for that task. Although RLTPR is thought to function as an actin-uncapping protein, this property was dispensable for CD28 co-stimulation in both mouse and human. Our findings suggest that the scaffolding role of RLTPR predominates during CD28 co-stimulation and underpins the similar function of RLTPR in human and mouse T cells. Along that line, the lack of functional RLTPR molecules impeded the differentiation toward Th1 and Th17 fates of both human and mouse CD4+ T cells. RLTPR was also expressed in both human and mouse B cells. In the mouse, RLTPR did not play, however, any detectable role in BCR-mediated signaling and T cell-independent B cell responses.
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Affiliation(s)
- Romain Roncagalli
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Margot Cucchetti
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Nicolas Jarmuzynski
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Claude Grégoire
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Elise Bergot
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Stéphane Audebert
- CRCM, Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille Université, INSERM, CNRS, 13009 Marseille, France
| | - Emilie Baudelet
- CRCM, Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille Université, INSERM, CNRS, 13009 Marseille, France
| | - Marisa Goncalves Menoita
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Anais Joachim
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Stéphane Durand
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | | | - Frédéric Fiore
- Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Lichen Zhang
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France.,School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Yinming Liang
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France.,School of Laboratory Medicine, Xinxiang Medical University, Xinxiang 453003, China
| | - Luc Camoin
- CRCM, Marseille Protéomique, Institut Paoli-Calmettes, Aix Marseille Université, INSERM, CNRS, 13009 Marseille, France
| | - Marie Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France .,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
| | - Bernard Malissen
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France .,Centre d'Immunophénomique, Aix Marseille Université, INSERM, CNRS, 13288 Marseille, France
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