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Fu C, Wang J, Ma T, Yin C, Zhou L, Clausen BE, Mi QS, Jiang A. β-Catenin in Dendritic Cells Negatively Regulates CD8 T Cell Immune Responses through the Immune Checkpoint Molecule Tim-3. Vaccines (Basel) 2024; 12:460. [PMID: 38793711 PMCID: PMC11125945 DOI: 10.3390/vaccines12050460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Recent studies have demonstrated that β-catenin in dendritic cells (DCs) serves as a key mediator in promoting both CD4 and CD8 T cell tolerance, although the mechanisms underlying how β-catenin exerts its functions remain incompletely understood. Here, we report that activation of β-catenin leads to the up-regulation of inhibitory molecule T-cell immunoglobulin and mucin domain 3 (Tim-3) in type 1 conventional DCs (cDC1s). Using a cDC1-targeted vaccine model with anti-DEC-205 engineered to express the melanoma antigen human gp100 (anti-DEC-205-hgp100), we demonstrated that CD11c-β-cateninactive mice exhibited impaired cross-priming and memory responses of gp100-specific CD8 T (Pmel-1) cells upon immunization with anti-DEC-205-hgp100. Single-cell RNA sequencing (scRNA-seq) analysis revealed that β-catenin in DCs negatively regulated transcription programs for effector function and proliferation of primed Pmel-1 cells, correlating with suppressed CD8 T cell immunity in CD11c-β-cateninactive mice. Further experiments showed that treating CD11c-β-cateninactive mice with an anti-Tim-3 antibody upon anti-DEC-205-hgp100 vaccination led to restored cross-priming and memory responses of gp100-specific CD8 T cells, suggesting that anti-Tim-3 treatment likely synergizes with DC vaccines to improve their efficacy. Indeed, treating B16F10-bearing mice with DC vaccines using anti-DEC-205-hgp100 in combination with anti-Tim-3 treatment resulted in significantly reduced tumor growth compared with treatment with the DC vaccine alone. Taken together, we identified the β-catenin/Tim-3 axis as a potentially novel mechanism to inhibit anti-tumor CD8 T cell immunity and that combination immunotherapy of a DC-targeted vaccine with anti-Tim-3 treatment leads to improved anti-tumor efficacy.
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Affiliation(s)
- Chunmei Fu
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Jie Wang
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Tianle Ma
- Department of Computer Science and Engineering, School of Engineering and Computer Science, Oakland University, Rochester, MI 48309, USA;
| | - Congcong Yin
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Li Zhou
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Internal Medicine, Henry Ford Health, Detroit, MI 48202, USA
| | - Björn E. Clausen
- Institute for Molecular Medicine, Paul Klein Center for Immune Intervention, University Medical Center of the Johannes Gutenberg-University Mainz, Langenbeckstrasse 1, 55131 Mainz, Germany;
| | - Qing-Sheng Mi
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
- Department of Internal Medicine, Henry Ford Health, Detroit, MI 48202, USA
| | - Aimin Jiang
- Center for Cutaneous Biology and Immunology, Department of Dermatology, Henry Ford Health, Detroit, MI 48202, USA; (C.F.); (J.W.); (C.Y.); (L.Z.)
- Immunology Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI 48202, USA
- College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
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2
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Karnaukhov VK, Le Gac AL, Bilonda Mutala L, Darbois A, Perrin L, Legoux F, Walczak AM, Mora T, Lantz O. Innate-like T cell subset commitment in the murine thymus is independent of TCR characteristics and occurs during proliferation. Proc Natl Acad Sci U S A 2024; 121:e2311348121. [PMID: 38530897 PMCID: PMC10998581 DOI: 10.1073/pnas.2311348121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 02/09/2024] [Indexed: 03/28/2024] Open
Abstract
How T-cell receptor (TCR) characteristics determine subset commitment during T-cell development is still unclear. Here, we addressed this question for innate-like T cells, mucosal-associated invariant T (MAIT) cells, and invariant natural killer T (iNKT) cells. MAIT and iNKT cells have similar developmental paths, leading in mice to two effector subsets, cytotoxic (MAIT1/iNKT1) and IL17-secreting (MAIT17/iNKT17). For iNKT1 vs iNKT17 fate choice, an instructive role for TCR affinity was proposed but recent data argue against this model. Herein, we examined TCR role in MAIT and iNKT subset commitment through scRNAseq and TCR repertoire analysis. In our dataset of thymic MAIT cells, we found pairs of T-cell clones with identical amino acid TCR sequences originating from distinct precursors, one of which committed to MAIT1 and the other to MAIT17 fates. Quantitative in silico simulations indicated that the number of such cases is best explained by lineage choice being independent of TCR characteristics. Comparison of TCR features of MAIT1 and MAIT17 clonotypes demonstrated that the subsets cannot be distinguished based on TCR sequence. To pinpoint the developmental stage associated with MAIT sublineage choice, we demonstrated that proliferation takes place both before and after MAIT fate commitment. Altogether, we propose a model of MAIT cell development in which noncommitted, intermediate-stage MAIT cells undergo a first round of proliferation, followed by TCR characteristics-independent commitment to MAIT1 or MAIT17 lineage, followed by an additional round of proliferation. Reanalyzing a published iNKT TCR dataset, we showed that this model is also relevant for iNKT cell development.
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Affiliation(s)
- Vadim K. Karnaukhov
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Anne-Laure Le Gac
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Linda Bilonda Mutala
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Aurélie Darbois
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Laetitia Perrin
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
| | - Francois Legoux
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- INSERM Equipe de Recherche Labellisée 1305, CNRSUMR6290, Université de Rennes, Institut de Génétique & Développement de Rennes35000, France
| | - Aleksandra M. Walczak
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Thierry Mora
- Laboratoire de Physique de l’École Normale Supérieure, Paris Sciences & Lettres University, CNRS, Sorbonne Université and Université Paris Cité, Paris75005, France
| | - Olivier Lantz
- Institut Curie, Paris Sciences & Lettres University, Inserm U932, Immunity and Cancer, Paris75005, France
- Laboratoire d’Immunologie Clinique, Département de médecine diagnostique et théranostique, Institut Curie, Paris75005, France
- Centre d’Investigation Clinique en Biothérapie Gustave-Roussy Institut Curie (CIC-BT1428), Paris75005, France
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3
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Liu R, Xu R, Yan S, Li P, Jia C, Sun H, Sheng K, Wang Y, Zhang Q, Guo J, Xin X, Li X, Guo D. Hi-C, a chromatin 3D structure technique advancing the functional genomics of immune cells. Front Genet 2024; 15:1377238. [PMID: 38586584 PMCID: PMC10995239 DOI: 10.3389/fgene.2024.1377238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 03/13/2024] [Indexed: 04/09/2024] Open
Abstract
The functional performance of immune cells relies on a complex transcriptional regulatory network. The three-dimensional structure of chromatin can affect chromatin status and gene expression patterns, and plays an important regulatory role in gene transcription. Currently available techniques for studying chromatin spatial structure include chromatin conformation capture techniques and their derivatives, chromatin accessibility sequencing techniques, and others. Additionally, the recently emerged deep learning technology can be utilized as a tool to enhance the analysis of data. In this review, we elucidate the definition and significance of the three-dimensional chromatin structure, summarize the technologies available for studying it, and describe the research progress on the chromatin spatial structure of dendritic cells, macrophages, T cells, B cells, and neutrophils.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Dianhao Guo
- School of Clinical and Basic Medical Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, China
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4
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Cui G, Abe S, Kato R, Ikuta K. Insights into the heterogeneity of iNKT cells: tissue-resident and circulating subsets shaped by local microenvironmental cues. Front Immunol 2024; 15:1349184. [PMID: 38440725 PMCID: PMC10910067 DOI: 10.3389/fimmu.2024.1349184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
Invariant natural killer T (iNKT) cells are a distinct subpopulation of innate-like T lymphocytes. They are characterized by semi-invariant T cell receptors (TCRs) that recognize both self and foreign lipid antigens presented by CD1d, a non-polymorphic MHC class I-like molecule. iNKT cells play a critical role in stimulating innate and adaptive immune responses, providing an effective defense against infections and cancers, while also contributing to chronic inflammation. The functions of iNKT cells are specific to their location, ranging from lymphoid to non-lymphoid tissues, such as the thymus, lung, liver, intestine, and adipose tissue. This review aims to provide insights into the heterogeneity of development and function in iNKT cells. First, we will review the expression of master transcription factors that define subsets of iNKT cells and their production of effector molecules such as cytokines and granzymes. In this article, we describe the gene expression profiles contributing to the kinetics, distribution, and cytotoxicity of iNKT cells across different tissue types. We also review the impact of cytokine production in distinct immune microenvironments on iNKT cell heterogeneity, highlighting a recently identified circulating iNKT cell subset. Additionally, we explore the potential of exploiting iNKT cell heterogeneity to create potent immunotherapies for human cancers in the future.
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Affiliation(s)
- Guangwei Cui
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shinya Abe
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Ryoma Kato
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Faculty of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Koichi Ikuta
- Laboratory of Immune Regulation, Department of Virus Research, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
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5
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Maas-Bauer K, Köhler N, Stell AV, Zwick M, Acharya S, Rensing-Ehl A, König C, Kroll J, Baker J, Koßmann S, Pradier A, Wang S, Docquier M, Lewis DB, Negrin RS, Simonetta F. Single-cell transcriptomics reveal different maturation stages and sublineage commitment of human thymic invariant natural killer T cells. J Leukoc Biol 2024; 115:401-409. [PMID: 37742056 PMCID: PMC10799303 DOI: 10.1093/jleuko/qiad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 07/08/2023] [Accepted: 08/29/2023] [Indexed: 09/25/2023] Open
Abstract
Invariant natural killer T cells are a rare, heterogeneous T-cell subset with cytotoxic and immunomodulatory properties. During thymic development, murine invariant natural killer T cells go through different maturation stages differentiating into distinct sublineages, namely, invariant natural killer T1, 2, and 17 cells. Recent reports indicate that invariant natural killer T2 cells display immature properties and give rise to other subsets, whereas invariant natural killer T1 cells seem to be terminally differentiated. Whether human invariant natural killer T cells follow a similar differentiation model is still unknown. To define the maturation stages and assess the sublineage commitment of human invariant natural killer T cells during thymic development, in this study, we performed single-cell RNA sequencing analysis on human Vα24+Vβ11+ invariant natural killer T cells isolated from thymocytes. We show that these invariant natural killer T cells displayed heterogeneity, and our unsupervised analysis identified 5 clusters representing different maturation stages, from an immature profile with high expression of genes important for invariant natural killer T cell development and proliferation to a mature, fully differentiated profile with high levels of cytotoxic effector molecules. Evaluation of expression of sublineage-defining gene sets revealed mainly cells with an invariant natural killer T2 signature in the most immature cluster, whereas the more differentiated ones displayed an invariant natural killer T1 signature. Combined analysis with a publicly available single-cell RNA sequencing data set of human invariant natural killer T cells from peripheral blood suggested that the 2 main subsets exist both in thymus and in the periphery, while a third more immature one was restricted to the thymus. Our data point to the existence of different maturation stages of human thymic invariant natural killer T cells and provide evidence for sublineage commitment of invariant natural killer T cells in the human thymus.
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Affiliation(s)
- Kristina Maas-Bauer
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Natalie Köhler
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
- CIBSS—Centre for Integrative Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, Freiburg 79104, Germany
| | - Anna-Verena Stell
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Melissa Zwick
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Swati Acharya
- Sean N. Parker Center for Asthma and Allergy Research, Department of Medicine, Stanford University, 240 Pasteur Dr, Stanford, CA 94304, United States
| | - Anne Rensing-Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Str. 115, Freiburg 79106, Germany
| | - Christoph König
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, Medical Center-University of Freiburg, Faculty of Medicine, Breisacher Str. 115, Freiburg 79106, Germany
- Faculty of Biology, University of Freiburg, Schänzlestr. 1, Freiburg 79104, Germany
| | - Johannes Kroll
- Department of Cardiovascular Surgery, Heart Center Freiburg University, Hugstetter Straße 55, Freiburg 79106, Germany
| | - Jeanette Baker
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
| | - Stefanie Koßmann
- Department of Hematology, Oncology, and Stem Cell Transplantation, Medical Center—University of Freiburg, Faculty of Medicine, Hugstetter Str. 55, Freiburg 79106, Germany
| | - Amandine Pradier
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva 1205, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - Sisi Wang
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
- Department of Genetics & Evolution, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
| | - David B Lewis
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, Stanford University School of Medicine, 240 Pasteur Dr, Stanford, CA 94304, United States
| | - Robert S Negrin
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
| | - Federico Simonetta
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University, Center for Clinical Sciences Research Building, 269 W. Campus Drive, Stanford, CA 94305, United States
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, Geneva 1205, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Rue Michel-Servet 1, Geneva 1211, Switzerland
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Loh L, Carcy S, Krovi HS, Domenico J, Spengler A, Lin Y, Torres J, Palmer W, Norman PJ, Stone M, Brunetti T, Meyer HV, Gapin L. Unraveling the Phenotypic States of Human innate-like T Cells: Comparative Insights with Conventional T Cells and Mouse Models. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570707. [PMID: 38105962 PMCID: PMC10723458 DOI: 10.1101/2023.12.07.570707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity, having the ability to mount rapid responses following activation. In mice, this ability is acquired during thymic development. We explored the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single cell RNA sequencing and flow cytometry. We reveal that in human blood, the majority of Tinn cells, including iNKT, MAIT, and Vδ2+Vγ9+ T cells, share an effector program characterized by the expression of unique chemokine and cytokine receptors, and cytotoxic molecules. This program is driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type I/type III effector potential. To conduct a comprehensive cross-species analysis, we constructed a murine Tinn developmental atlas and uncovered additional species-specific distinctions, including the absence of type II Tinn cells in humans, which implies distinct immune regulatory mechanisms across species. The study provides insights into the development and functionality of Tinn cells, emphasizing their role in immune responses and their potential as targets for therapeutic interventions.
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Affiliation(s)
- Liyen Loh
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Salomé Carcy
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | | | - Yong Lin
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshua Torres
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - William Palmer
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Paul J. Norman
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | | | - Tonya Brunetti
- University of Colorado Anschutz Medical Campus, Aurora, USA
| | - Hannah V. Meyer
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Laurent Gapin
- University of Colorado Anschutz Medical Campus, Aurora, USA
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