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Hafler D, Lu B, Lucca L, Lewis W, Wang J, Nogeuira C, Heer S, Axisa PP, Buitrago-Pocasangre N, Pham G, Kojima M, Wei W, Aizenbud L, Bacchiocchi A, Zhang L, Walewski J, Chiang V, Olino K, Clune J, Halaban R, Kluger Y, Coyle A, Kisielow J, Obermair FJ, Kluger H. Circulating Tumor Reactive KIR+CD8+ T cells Suppress Anti-Tumor Immunity in Patients with Melanoma. Res Sq 2024:rs.3.rs-3956671. [PMID: 38464315 PMCID: PMC10925449 DOI: 10.21203/rs.3.rs-3956671/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Effective anti-tumor immunity is largely driven by cytotoxic CD8+ T cells that can specifically recognize tumor antigens. However, the factors which ultimately dictate successful tumor rejection remain poorly understood. Here we identify a subpopulation of CD8+ T cells which are tumor antigen-specific in patients with melanoma but resemble KIR+CD8+ T cells with a regulatory function (Tregs). These tumor antigen-specific KIR+CD8+ T cells are detectable in both the tumor and the blood, and higher levels of this population are associated with worse overall survival. Our findings therefore suggest that KIR+CD8+ Tregs are tumor antigen-specific but uniquely suppress anti-tumor immunity in patients with melanoma.
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2
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Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Nam J, Gao F, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq. Nat Biotechnol 2023; 41:1405-1409. [PMID: 36823353 PMCID: PMC10567548 DOI: 10.1038/s41587-023-01676-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 01/12/2023] [Indexed: 02/25/2023]
Abstract
In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Disease 2019 mRNA vaccine injection site.
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Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Hiromitsu Asashima
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Jungmin Nam
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Fu Gao
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | | | - Mary Tomayko
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT, USA
| | - Mina Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA
| | - David Hafler
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA.
- Department of Medicine, Yale School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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3
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Liu Y, DiStasio M, Su G, Asashima H, Enninful A, Qin X, Deng Y, Bordignon P, Cassano M, Tomayko M, Xu M, Halene S, Craft JE, Hafler D, Fan R. Spatial-CITE-seq: spatially resolved high-plex protein and whole transcriptome co-mapping. Res Sq 2022:rs.3.rs-1499315. [PMID: 35378748 PMCID: PMC8978952 DOI: 10.21203/rs.3.rs-1499315/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We present spatial-CITE-seq for high-plex protein and whole transcriptome co-mapping, which was firstly demonstrated for profiling 198 proteins and transcriptome in multiple mouse tissue types. It was then applied to human tissues to measure 283 proteins and transcriptome that revealed spatially distinct germinal center reaction in tonsil and early immune activation in skin at the COVID-19 mRNA vaccine injection site. Spatial-CITE-seq may find a range of applications in biomedical research.
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Affiliation(s)
- Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Marcello DiStasio
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Hiromitsu Asashima
- Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Pino Bordignon
- Lunaphore Technologies SA, Route de Lully 5c, 1131 Tolochenaz, Switzerland
| | - Marco Cassano
- Lunaphore Technologies SA, Route de Lully 5c, 1131 Tolochenaz, Switzerland
| | - Mary Tomayko
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mina Xu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Stephanie Halene
- Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Joseph E. Craft
- Department of Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
| | - David Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT 06520, USA
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4
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Hafler D, Sumida T, Dulberg S, Schupp J, Stillwell H, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo V. Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. Res Sq 2021:rs.3.rs-133494. [PMID: 34127967 PMCID: PMC8202434 DOI: 10.21203/rs.3.rs-133494/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection. Here we show that IFN-I regulates co-inhibitory receptor expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed unique regulators that control expression of co-inhibitory receptors. We found that the dynamic IFN-I response in vitro closely mirrored T cell features with IFN-I linked acute SARS-CoV-2 infection in human, with high LAG3 and decreased TIGIT expression. Finally, our gene regulatory network identified SP140 as a key regulator for differential LAG3 and TIGIT expression, which were validated at the level of protein expression. The construction of IFN-I regulatory networks with identification of unique transcription factors controlling co-inhibitory receptor expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.
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Affiliation(s)
| | | | | | | | | | | | - Michela Comi
- Department of Immunobiology, Yale University School of Medicine; Department of Neurology, Yale University School of Medicine
| | | | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
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Murray C, Miwa H, Dhar M, Park DE, Pao E, Martinez J, Kaanumale S, Loghin E, Graf J, Raddassi K, Kwok WW, Hafler D, Puleo C, Di Carlo D. Correction: Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting. Lab Chip 2018; 18:3703. [PMID: 30420988 DOI: 10.1039/c8lc90095g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Correction for 'Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting' by Coleman Murray et al., Lab Chip, 2018, 18, 2396-2409.
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Affiliation(s)
- Coleman Murray
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
| | - Hiromi Miwa
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
| | - Manjima Dhar
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
| | - Da Eun Park
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
| | - Edward Pao
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
| | | | | | | | - John Graf
- GE Global Research Centre, Niskayuna, NY, USA.
| | | | - William W Kwok
- Benaroya Research Institute, Virginia Mason, Seattle, WA, USA
| | - David Hafler
- Dept. of Neurology, Yale University, New Haven, CT, USA
| | - Chris Puleo
- GE Global Research Centre, Niskayuna, NY, USA.
| | - Dino Di Carlo
- Dept. of Bioengineering, University of California, Los Angeles, CA, USA
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Abstract
Multiple sclerosis (MS) is a genetically mediated autoimmune disease of the central nervous system. Allelic variants lead to lower thresholds of T-cell activation resulting in activation of autoreactive T cells. Environmental factors, including, among others, diet, vitamin D, and smoking, in combination with genetic predispositions, play a substantial role in disease development and activation of autoreactive T cells. FoxP3+ regulatory T cells (Tregs) have emerged as central in the control of autoreactive T cells. A consistent finding in patients with MS is defects in Treg cell function with reduced suppression of effector T cells and production of proinflammatory cytokines. Emerging data suggests that functional Tregs become effector-like T cells with loss of function associated with T-bet expression and interferon γ (IFN-γ) secretion.
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Affiliation(s)
- Alexandra Kitz
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Emily Singer
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520
| | - David Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut 06520
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7
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Murray C, Miwa H, Dhar M, Park DE, Pao E, Martinez J, Kaanumale S, Loghin E, Graf J, Rhaddassi K, Kwok WW, Hafler D, Puleo C, Di Carlo D. Unsupervised capture and profiling of rare immune cells using multi-directional magnetic ratcheting. Lab Chip 2018; 18:2396-2409. [PMID: 30039125 PMCID: PMC6095198 DOI: 10.1039/c8lc00518d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Immunotherapies (IT) require induction, expansion, and maintenance of specific changes to a patient's immune cell repertoire which yield a therapeutic benefit. Recently, mechanistic understanding of these changes at the cellular level has revealed that IT results in complex phenotypic transitions in target cells, and that therapeutic effectiveness may be predicted by monitoring these transitions during therapy. However, monitoring will require unique tools that enable capture, manipulation, and profiling of rare immune cell populations. In this study, we introduce a method of automated and unsupervised separation and processing of rare immune cells, using high-force and multidimensional magnetic ratcheting (MR). We demonstrate capture of target immune cells using samples with up to 1 : 10 000 target cell to background cell ratios from input volumes as small as 25 microliters (i.e. a low volume and low cell frequency sample sparing assay interface). Cell capture is shown to achieve up to 90% capture efficiency and purity, and captured cell analysis is shown using both on-chip culture/activity assays and off-chip ejection and nucleic acid analysis. These results demonstrate that multi-directional magnetic ratcheting offers a unique separation system for dealing with blood cell samples that contain either rare cells or significantly small volumes, and the "sample sparing" capability leads to an expanded spectrum of parameters that can be measured. These tools will be paramount to advancing techniques for immune monitoring under conditions in which both the sample volume and number of antigen-specific target cells are often exceedingly small, including during IT and treatment of allergy, asthma, autoimmunity, immunodeficiency, cell based therapy, transplantation, and infection.
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Affiliation(s)
- Coleman Murray
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Hiromi Miwa
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Manjima Dhar
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Da Eun Park
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | - Edward Pao
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
| | | | | | | | - John Graf
- GE Global Research Centre, Niskayuna, NY, USA
| | | | - William W Kwok
- Benaroya Research Institute, Virginia Mason, Seattle, WA, USA
| | - David Hafler
- Dept. of Neurology, Yale University, New Haven, CT, USA
| | - Chris Puleo
- GE Global Research Centre, Niskayuna, NY, USA
| | - Dino Di Carlo
- Dept. of Bioengineering; University of California, Los Angeles, CA, USA
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8
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9
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Pyne S, Lee SX, Wang K, Irish J, Tamayo P, Nazaire MD, Duong T, Ng SK, Hafler D, Levy R, Nolan GP, Mesirov J, McLachlan GJ. Joint modeling and registration of cell populations in cohorts of high-dimensional flow cytometric data. PLoS One 2014; 9:e100334. [PMID: 24983991 PMCID: PMC4077578 DOI: 10.1371/journal.pone.0100334] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 05/23/2014] [Indexed: 01/20/2023] Open
Abstract
In biomedical applications, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multivariate responses of a panel of markers such as from a signaling network. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While computational methods can identify cell populations in individual samples, without the ability to automatically match them across samples, it is difficult to compare and characterize the populations in typical experiments, such as those responding to various stimulations or distinctive of particular patients or time-points, especially when there are many samples. Joint Clustering and Matching (JCM) is a multi-level framework for simultaneous modeling and registration of populations across a cohort. JCM models every population with a robust multivariate probability distribution. Simultaneously, JCM fits a random-effects model to construct an overall batch template – used for registering populations across samples, and classifying new samples. By tackling systems-level variation, JCM supports practical biomedical applications involving large cohorts. Software for fitting the JCM models have been implemented in an R package EMMIX-JCM, available from http://www.maths.uq.edu.au/~gjm/mix_soft/EMMIX-JCM/.
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Affiliation(s)
- Saumyadipta Pyne
- CR Rao Advanced Institute of Mathematics, Statistics and Computer Science, Hyderabad, Andhra Pradesh, India
| | - Sharon X. Lee
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
| | - Kui Wang
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
| | - Jonathan Irish
- Division of Oncology, Stanford Medical School, Stanford, California, United States of America
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America
- Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Pablo Tamayo
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Marc-Danie Nazaire
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Tarn Duong
- Molecular Mechanisms of Intracellular Transport, Unit Mixte de Recherche 144 Centre National de la Recherche Scientifique/Institut Curie, Paris, France
| | - Shu-Kay Ng
- School of Medicine, Griffith University, Meadowbrook, Queensland, Australia
| | - David Hafler
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Ronald Levy
- Division of Oncology, Stanford Medical School, Stanford, California, United States of America
| | - Garry P. Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, California, United States of America
| | - Jill Mesirov
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, United States of America
| | - Geoffrey J. McLachlan
- Department of Mathematics, University of Queensland, St. Lucia, Queensland, Australia
- * E-mail:
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Sampson JH, Vlahovic G, Desjardins A, Friedman HS, Baehring JM, Hafler D, Rollin L, Coric V, Perez SN, Reardon DA. Randomized phase IIb study of nivolumab (anti-PD-1; BMS-936558, ONO-4538) alone or in combination with ipilimumab versus bevacizumab in patients (pts) with recurrent glioblastoma (GBM). J Clin Oncol 2014. [DOI: 10.1200/jco.2014.32.15_suppl.tps2101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- John Howard Sampson
- The Preston Robert Tisch Brain Tumor Center at Duke University Medical Center, Durham, NC
| | - Gordana Vlahovic
- Divisions of Oncology and Neurosurgery at Duke University Medical Center, Durham, NC
| | - Annick Desjardins
- The Preston Robert Tisch Brain Tumor Center at Duke University Medical Center, Durham, NC
| | - Henry S. Friedman
- The Preston Robert Tisch Brain Tumor Center at Duke University Medical Center, Durham, NC
| | - Joachim M. Baehring
- Yale Brain Tumor Center, Department of Neurology at Yale School of Medicine, New Haven, CT
| | - David Hafler
- Departments of Immunobiology and Neurology at Yale School of Medicine, New Haven, CT
| | | | | | | | - David A. Reardon
- Center for Neuro-Oncology at Dana-Farber Cancer Institute, Boston, MA
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11
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Beecham AH, Patsopoulos NA, Xifara DK, Davis MF, Kemppinen A, Cotsapas C, Shah TS, Spencer C, Booth D, Goris A, Oturai A, Saarela J, Fontaine B, Hemmer B, Martin C, Zipp F, D'Alfonso S, Martinelli-Boneschi F, Taylor B, Harbo HF, Kockum I, Hillert J, Olsson T, Ban M, Oksenberg JR, Hintzen R, Barcellos LF, Agliardi C, Alfredsson L, Alizadeh M, Anderson C, Andrews R, Søndergaard HB, Baker A, Band G, Baranzini SE, Barizzone N, Barrett J, Bellenguez C, Bergamaschi L, Bernardinelli L, Berthele A, Biberacher V, Binder TMC, Blackburn H, Bomfim IL, Brambilla P, Broadley S, Brochet B, Brundin L, Buck D, Butzkueven H, Caillier SJ, Camu W, Carpentier W, Cavalla P, Celius EG, Coman I, Comi G, Corrado L, Cosemans L, Cournu-Rebeix I, Cree BAC, Cusi D, Damotte V, Defer G, Delgado SR, Deloukas P, di Sapio A, Dilthey AT, Donnelly P, Dubois B, Duddy M, Edkins S, Elovaara I, Esposito F, Evangelou N, Fiddes B, Field J, Franke A, Freeman C, Frohlich IY, Galimberti D, Gieger C, Gourraud PA, Graetz C, Graham A, Grummel V, Guaschino C, Hadjixenofontos A, Hakonarson H, Halfpenny C, Hall G, Hall P, Hamsten A, Harley J, Harrower T, Hawkins C, Hellenthal G, Hillier C, Hobart J, Hoshi M, Hunt SE, Jagodic M, Jelčić I, Jochim A, Kendall B, Kermode A, Kilpatrick T, Koivisto K, Konidari I, Korn T, Kronsbein H, Langford C, Larsson M, Lathrop M, Lebrun-Frenay C, Lechner-Scott J, Lee MH, Leone MA, Leppä V, Liberatore G, Lie BA, Lill CM, Lindén M, Link J, Luessi F, Lycke J, Macciardi F, Männistö S, Manrique CP, Martin R, Martinelli V, Mason D, Mazibrada G, McCabe C, Mero IL, Mescheriakova J, Moutsianas L, Myhr KM, Nagels G, Nicholas R, Nilsson P, Piehl F, Pirinen M, Price SE, Quach H, Reunanen M, Robberecht W, Robertson NP, Rodegher M, Rog D, Salvetti M, Schnetz-Boutaud NC, Sellebjerg F, Selter RC, Schaefer C, Shaunak S, Shen L, Shields S, Siffrin V, Slee M, Sorensen PS, Sorosina M, Sospedra M, Spurkland A, Strange A, Sundqvist E, Thijs V, Thorpe J, Ticca A, Tienari P, van Duijn C, Visser EM, Vucic S, Westerlind H, Wiley JS, Wilkins A, Wilson JF, Winkelmann J, Zajicek J, Zindler E, Haines JL, Pericak-Vance MA, Ivinson AJ, Stewart G, Hafler D, Hauser SL, Compston A, McVean G, De Jager P, Sawcer SJ, McCauley JL. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet 2013; 45:1353-60. [PMID: 24076602 PMCID: PMC3832895 DOI: 10.1038/ng.2770] [Citation(s) in RCA: 980] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022]
Abstract
Using the ImmunoChip custom genotyping array, we analyzed 14,498 subjects with multiple sclerosis and 24,091 healthy controls for 161,311 autosomal variants and identified 135 potentially associated regions (P < 1.0 × 10(-4)). In a replication phase, we combined these data with previous genome-wide association study (GWAS) data from an independent 14,802 subjects with multiple sclerosis and 26,703 healthy controls. In these 80,094 individuals of European ancestry, we identified 48 new susceptibility variants (P < 5.0 × 10(-8)), 3 of which we found after conditioning on previously identified variants. Thus, there are now 110 established multiple sclerosis risk variants at 103 discrete loci outside of the major histocompatibility complex. With high-resolution Bayesian fine mapping, we identified five regions where one variant accounted for more than 50% of the posterior probability of association. This study enhances the catalog of multiple sclerosis risk variants and illustrates the value of fine mapping in the resolution of GWAS signals.
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12
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Baranzini S, Khankhanian P, Patsopoulos N, Li M, Stankovich J, Cotsapas C, Søndergaard H, Ban M, Barizzone N, Bergamaschi L, Booth D, Buck D, Cavalla P, Celius E, Comabella M, Comi G, Compston A, Cournu-Rebeix I, D’alfonso S, Damotte V, Din L, Dubois B, Elovaara I, Esposito F, Fontaine B, Franke A, Goris A, Gourraud PA, Graetz C, Guerini F, Guillot-Noel L, Hafler D, Hakonarson H, Hall P, Hamsten A, Harbo H, Hemmer B, Hillert J, Kemppinen A, Kockum I, Koivisto K, Larsson M, Lathrop M, Leone M, Lill C, Macciardi F, Martin R, Martinelli V, Martinelli-Boneschi F, McCauley J, Myhr KM, Naldi P, Olsson T, Oturai A, Pericak-Vance M, Perla F, Reunanen M, Saarela J, Saker-Delye S, Salvetti M, Sellebjerg F, Sørensen P, Spurkland A, Stewart G, Taylor B, Tienari P, Winkelmann J, Zipp F, Ivinson A, Haines J, Sawcer S, DeJager P, Hauser S, Oksenberg J. Network-based multiple sclerosis pathway analysis with GWAS data from 15,000 cases and 30,000 controls. Am J Hum Genet 2013; 92:854-65. [PMID: 23731539 DOI: 10.1016/j.ajhg.2013.04.019] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 04/04/2013] [Accepted: 04/23/2013] [Indexed: 02/03/2023] Open
Abstract
Multiple sclerosis (MS) is an inflammatory CNS disease with a substantial genetic component, originally mapped to only the human leukocyte antigen (HLA) region. In the last 5 years, a total of seven genome-wide association studies and one meta-analysis successfully identified 57 non-HLA susceptibility loci. Here, we merged nominal statistical evidence of association and physical evidence of interaction to conduct a protein-interaction-network-based pathway analysis (PINBPA) on two large genetic MS studies comprising a total of 15,317 cases and 29,529 controls. The distribution of nominally significant loci at the gene level matched the patterns of extended linkage disequilibrium in regions of interest. We found that products of genome-wide significantly associated genes are more likely to interact physically and belong to the same or related pathways. We next searched for subnetworks (modules) of genes (and their encoded proteins) enriched with nominally associated loci within each study and identified those modules in common between the two studies. We demonstrate that these modules are more likely to contain genes with bona fide susceptibility variants and, in addition, identify several high-confidence candidates (including BCL10, CD48, REL, TRAF3, and TEC). PINBPA is a powerful approach to gaining further insights into the biology of associated genes and to prioritizing candidates for subsequent genetic studies of complex traits.
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Scheuermann R, Finak G, Ramey J, Taghiyar J, Stanton R, Brandes A, De Jager P, Qiu P, McCoy J, Hafler D, Maecker H, Mosmann T, Brinkman R, Gottardo R. FlowCAP: comparison of automated and manual gating of standardized lyoplate flow cytometry data (P3374). The Journal of Immunology 2013. [DOI: 10.4049/jimmunol.190.supp.135.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Standardization of immunological assays, including flow cytometry, in terms of reagents, sample handling, instrument setup, and data analysis, is essential for successful cross-study and cross-center analysis in order to mitigate the effects of technical variability in assay results. The Human Immunology Project and the Federation of Clinical Immunology Societies (FOCIS) have partnered to develop five standardized, lyophilized, eight-color staining reagent panels (termed lyoplates) for this purpose. In collaboration with the FlowCAP consortium, standardized samples (Cytotrol control cells) were distributed to nine participating centers and analyzed by flow cytometry using the lyoplate reagents and SOP's to minimize experimental variability. Data from two of these panels (T-cell and B-cell) were entered into the FlowCAP-III challenge, where participants analyzed the data using automated gating methods for comparison against cell population statistics for major T and B-cell subsets as defined by a consensus manual gating scheme. This evaluation showed that several automated gating algorithms could successfully recapitulate centralized manual gating statistics for T-cell and B-cell subsets with little statistical bias, and with within-center and between-center variability as low or lower than centralized manual gating. These results demonstrate that automated gating algorithms are ready for use in performing reproducible analyses and comparisons of immunological data.
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Affiliation(s)
| | - Greg Finak
- 2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - John Ramey
- 2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jafar Taghiyar
- 3Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Rick Stanton
- 1Informatics, J. Craig Venter Institute, San Diego, CA
| | - Aaron Brandes
- 4Program in Medical & Population Genetics, Broad Institute of Harvard University, Cambridge, MA
| | - Philip De Jager
- 4Program in Medical & Population Genetics, Broad Institute of Harvard University, Cambridge, MA
| | - Peng Qiu
- 5Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX
| | - J. McCoy
- 6Center for Human Immunology, National Heart, Lung and Blood Institute, Bethesda, MD
| | - David Hafler
- 7Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Holden Maecker
- 8Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Palo Alto, CA
| | - Tim Mosmann
- 9School of Medicine and Dentistry, University of Rochester, Rochester, NY
| | - Ryan Brinkman
- 3Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Raphael Gottardo
- 2Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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14
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Astier A, Kickler K, Ni Choileain S, Stephen J, Hafler D, Jabbour H. Prostaglandin E2 affects T cell responses through modulation of CD46 expression. (178.8). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.178.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The complement regulator CD46 controls T cell activation and differentiation. CD46-mediated differentiation pathway is defective in several chronic inflammatory diseases, underlying the importance of CD46 in controlling T cell function and the need to understand its regulatory mechanisms. Using an RNAi-based screening approach in primary T cells, we have identified that two members of the G-protein coupled receptor (GPCR) kinase family were involved in regulating CD46 expression at the T cell surface. We have investigated the role of prostaglandin E2 (PGE2), which binds to GPCRs, in the regulation of CD46 expression and function. Conflicting roles of PGE2 in T cell functions have been reported, and the reasons for these apparent discrepancies are not well understood. We show that: i) addition of PGE2 strongly downregulates CD46 expression in activated T cells, ii) PGE2 differentially affects T cell activation, cytokine production and phenotype depending on the activation signals received by the T cells, iii) this was correlated with a distinct pattern of the EP2-EP4 PGE2 receptors induced, with EP4 being preferentially expressed upon CD46, and iv) addition of an EP4 antagonist could reverse the effects observed on cytokine production upon CD46 costimulation. These data demonstrate a novel role of the PGE2-EP4-GRK axis in CD46 functions, which might partly explain the diverse roles of PGE2 in T cell functions.
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Affiliation(s)
- Anne Astier
- 1MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- 2Centre for MS research, University of Edinburgh, Edinburgh, United Kingdom
| | - Karoline Kickler
- 1MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Siobhan Ni Choileain
- 1MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
- 2Centre for MS research, University of Edinburgh, Edinburgh, United Kingdom
| | - Jillian Stephen
- 1MRC Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - David Hafler
- 3Department of Neurology, Yale School of Medicine, New Haven, CT
| | - Henry Jabbour
- 4MRC Human Reproduction Unit, University of Edinburgh, Edinburgh, United Kingdom
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15
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Kleinewietfeld M, Manzel A, Wu C, Titze J, Kuchroo V, Linker R, Muller D, Hafler D. High salt induces pathogenic Th17 cells and exacerbates autoimmune diseases (60.13). The Journal of Immunology 2012. [DOI: 10.4049/jimmunol.188.supp.60.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Interleukin (IL)-17 producing CD4+ helper T cells (Th17 cells) play a pivotal role in autoimmune diseases. Apart from their importance for the control of certain pathogens, IL-23 dependent Th17 cells have been shown to be critical for the development of experimental autoimmune encephalomyelitis (EAE). Moreover, genetic risk factors associated with multiple sclerosis (MS) are linked to the IL23/Th17 pathway. Besides genetic factors, the increased incidence of autoimmune diseases like MS in developed countries is also believed to be related to environmental risk factors. However, how environmental risk factors such as changes in diet, sun exposure or medications could directly influence the development of pathogenic Th17 cells is not well established. Here we show that increased salt (sodium chloride; NaCl) concentrations dramatically boost the induction of murine and human Th17 cells in vitro. Moreover, mice fed with a high salt diet develop a very severe form of EAE, dependent on the induction of highly pathogenic Th17 cells. The generation of Th17 cells under high salt conditions is well regulated on the molecular level and seems to be dependent on specific pathways. Thus, increased salt intake, which may represents one of the biggest contributors to changes in diet during the last half century and accounts for cardiovascular disease, might also represent an environmental risk factor for autoimmune diseases through the exacerbated induction of pathogenic Th17 cells.
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Affiliation(s)
- Markus Kleinewietfeld
- 1Neurology, Yale School of Medicine, New Haven, CT
- 2Broad Institute, Broad Institute of MIT and Harvard, Boston, MA
| | | | - Chuan Wu
- 5CND, Harvard Medical School, Boston, MA
| | - Jens Titze
- 4UK, University of Erlangen, Erlangen, Germany
- 6Clinical Pharmacology, Vanderbilt University, Nashville, TN
| | | | - Ralf Linker
- 4UK, University of Erlangen, Erlangen, Germany
| | - Dominik Muller
- 3MDC, Max-Delbrueck-Center, Berlin, Germany
- 4UK, University of Erlangen, Erlangen, Germany
| | - David Hafler
- 1Neurology, Yale School of Medicine, New Haven, CT
- 2Broad Institute, Broad Institute of MIT and Harvard, Boston, MA
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Abstract
Autoimmune diseases have a complex etiology and despite great progress having been made in our comprehension of these disorders, there has been limited success in the development of approved medications based on these insights. Development of drugs and strategies for application in translational research and medicine are hampered by an inadequate molecular definition of the human autoimmune phenotype and the organizational models that are necessary to clarify this definition.
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Affiliation(s)
- Richard S Blumberg
- Division of Gastroenterology and Hepatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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17
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Maecker HT, McCoy JP, Amos M, Elliott J, Gaigalas A, Wang L, Aranda R, Banchereau J, Boshoff C, Braun J, Korin Y, Reed E, Cho J, Hafler D, Davis M, Fathman CG, Robinson W, Denny T, Weinhold K, Desai B, Diamond B, Gregersen P, Di Meglio P, DiMeglio P, Nestle FO, Nestle F, Peakman M, Villanova F, Villnova F, Ferbas J, Field E, Kantor A, Kawabata T, Komocsar W, Lotze M, Nepom J, Ochs H, O'Lone R, Phippard D, Plevy S, Rich S, Roederer M, Rotrosen D, Yeh JH. A model for harmonizing flow cytometry in clinical trials. Nat Immunol 2010; 11:975-8. [PMID: 20959798 PMCID: PMC3400260 DOI: 10.1038/ni1110-975] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Complexities in sample handling, instrument setup and data analysis are barriers to the effective use of flow cytometry to monitor immunological parameters in clinical trials. The novel use of a central laboratory may help mitigate these issues.
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Affiliation(s)
- Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, California, USA.
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18
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Surolia I, Pirnie SP, Chellappa V, Taylor KN, Cariappa A, Moya J, Liu H, Bell DW, Driscoll DR, Diederichs S, Haider K, Netravali I, Le S, Elia R, Dow E, Lee A, Freudenberg J, De Jager PL, Chretien Y, Varki A, MacDonald ME, Gillis T, Behrens TW, Bloch D, Collier D, Korzenik J, Podolsky DK, Hafler D, Murali M, Sands B, Stone JH, Gregersen PK, Pillai S. Functionally defective germline variants of sialic acid acetylesterase in autoimmunity. Nature 2010; 466:243-7. [PMID: 20555325 PMCID: PMC2900412 DOI: 10.1038/nature09115] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Accepted: 04/22/2010] [Indexed: 01/05/2023]
Abstract
Sialic acid acetylesterase (SIAE) is an enzyme that negatively regulates B lymphocyte antigen receptor signaling and is required for the maintenance of immunological tolerance in mice1, 2. Heterozygous loss-of-function germline rare variants and a homozygous defective polymorphic variant of SIAE were identified in 24/923 Caucasian subjects with relatively common autoimmune disorders and in 2/648 Caucasian controls. All heterozygous loss-of-function SIAE mutations tested were capable of functioning in a dominant negative manner. A homozygous secretion-defective polymorphic variant of SIAE was catalytically active, lacked the ability to function in a dominant negative manner, and was seen in 8 autoimmune subjects but in no control subjects. The Odds Ratio for inheriting defective SIAE alleles was 8.6 in all autoimmune subjects, 8.3 in subjects with rheumatoid arthritis, and 7.9 in subjects with type I diabetes. Functionally defective SIAE rare and polymorphic variants represent a strong genetic link to susceptibility in relatively common human autoimmune disorders.
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Affiliation(s)
- Ira Surolia
- Cancer Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
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19
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Dominguez-Villar M, Hafler D, Baecher-Allan C. IL-12 induces human CD4+CD45RA-CD25hiCD127low/neg regulatory T cells to secrete IFNγ and IL-10 and acquire a non-regulatory effector phenotype (138.9). The Journal of Immunology 2010. [DOI: 10.4049/jimmunol.184.supp.138.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Regulatory T cells (Treg) play a pivotal role in maintaining a balance between the immune response and peripheral tolerance. Recent evidence indicates that regulatory T cells are more functionally plastic than originally thought. Not only does the cytokine milieu modulate their capacity to suppress, but it can also induce Tregs to secrete cytokines (IL-17). The IL-12 family of cytokines (IL-12, IL-23, IL-27, IL-35) are key players in the regulation of T cell responses. We have studied the distinct effects that these cytokines (IL-12, IL-23 and IL-27) exert on human Treg function and phenotype. RESULTS: Surprisingly, we have found that IL-12 induces memory CD127lo Tregs to express T-bet and produce IFN-gamma and IL-10. Furthermore, in this state, these Tregs not only exhibit a non-regulatory effector phenotype, but they are also markedly less able to suppress the activation of co-cultured CD4 T cells. Importantly, although these IL-12-treated Tregs are less suppressive, their Foxp3 expression is not significantly altered. Additional data indicates that this is a transient state of reduced Treg suppression.. Thus this represents a way for the immune system to inactivate Treg function to allow an immune response to proceed.
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Affiliation(s)
| | - David Hafler
- 2Yale School of Medicine, New Haven, CT
- 1Neurology, Harvard Medical School, Boston, MA
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20
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Castillo IW, Lui Q, Ottoboni L, Briskin R, Alter G, Hafler D, De Jager P. The PhenoGenetic Project: A Living Biobank Enabling the Study of Human Genetic and Immunologic Variation. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Gordo S, Schubert D, Vardhana S, Seth N, Pyrdol J, Raddassi K, Hafler D, Dustin M, Wucherpfennig K. Efficient Activation of Self-reactive T Cells from MS Patients with Altered Synapse Formation. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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22
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Ottoboni L, Mousissian N, Castillo IW, Hafler D, De Jager P. Dissecting the Functional Consequences of the Validated Multiple Sclerosis Susceptibility Allele in TNFRSF1A. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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23
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Bradshaw E, Elyaman W, Raddassi K, Mousissian N, Greer A, Orban T, Gottlieb P, Kent S, Hafler D. Monocytes from Patients with Type 1 Diabetes Have Increased Gene Expression of Pro-inflammatory Cytokines or IL-10. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Surolia I, Pirnie S, Chellappa V, Annaiah C, Moya J, Bell D, Haider K, Taylor K, De Jager P, Behrens T, Hafler D, Sands B, Murali M, Gregersen P, Pillai S. Regulation of Immunological Tolerance and Autoimmunity by the Enzyme Sialic Acid Acetylesterase (SIAE). Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Schubert D, Gordo S, Vardhana S, Pyrdol J, Seth N, Raddassi K, Hafler D, Dustin M, Wucherpfennig K. Altered Synapse Formation by Self-reactive T Cells from MS Patients. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Beriou G, Bradshaw E, Lozano E, Baecher-Allan C, Hafler D. Interleukin-9 Secretion by Human Th17 Cells is Inducible by TGF-β and Proinflammatory Cytokines and is Increased in Autoimmune Diabetes. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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27
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Cvetanovich G, Bradshaw E, Beriou G, Mousissian N, Baecher-Allan C, Hafler D. IL-1 Receptor Expression on Human Regulatory T Cells and IL-1β's Role in Reducing Suppression. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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28
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Dominguez-Villar M, Hafler D, Baecher-Allan C. IL-12 Induces Human CD4+CD45RA-CD25hiCD127low/neg Regulatory T Cells to Secrete IFNγ and IL-10 and Acquire a Non-regulatory Effector Phenotype. Clin Immunol 2010. [DOI: 10.1016/j.clim.2010.03.400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Ashley C, Hafler D, Baecher-Allan C. S.119. CD127 and HLA DR Define Functionally Distinct Human Tregs- One Subsets Exhibits Decreased Activity in Multiple Sclerosis. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Bradshaw E, Raddassi K, Elyaman W, Orban T, Gottlieb P, Kent S, Hafler D. T.22. Monocytes from Patients with Type 1 Diabetes Spontaneously Secrete Pro-inflammatory Cytokines Inducing Th17 Cells. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Costantino C, Ploegh H, Hafler D. S.132. Cathepsin S Regulates MHC Class II Processing in Human CD4+HLA-DR+T Cells. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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32
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Raddassi K, Yang J, Kent S, Bradshaw E, Bourcier K, Seyfert-Margolis V, Kwok W, Hafler D. S.67. Detection of Myelin Reactive CD4+Cells in the Peripheral Blood of Patients with Multiple Sclerosis using MHC Class II Tetramers. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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33
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Willis S, Almendinger S, Lovato L, Hafler D, O'Connor K. F.89. Elucidating the Antigen Specificity of B Cells Present within the CNS Lesions of Patients with MS. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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34
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Kent S, Bradshaw E, Han Q, Varadarajan N, Greer A, Love J, Hafler D. OR.39. Enumeration and Phenotype of Autoreactive B Cells in Pancreatic Draining Lymph Nodes from Type 1 Diabetes Subjects. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Costantino C, Beriou G, Ashley C, Hafler D, Baecher-Allan C. OR.4. Cellular Senescence in Terminally Differentiated Human CD4+CD25hi IL-7Rneg HLA-DR+Regulatory T Cells. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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36
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Lovato L, Almendinger S, Willis S, Rodig S, Hafler D, O'Connor K. OR.43. Comparative Analysis of B Cell Repertoires Among Lesions and Normal Appearing White Matter in the Multiple Sclerosis Central Nervous System. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Neilson DE, Adams MD, Orr CMD, Schelling DK, Eiben RM, Kerr DS, Anderson J, Bassuk AG, Bye AM, Childs AM, Clarke A, Crow YJ, Di Rocco M, Dohna-Schwake C, Dueckers G, Fasano AE, Gika AD, Gionnis D, Gorman MP, Grattan-Smith PJ, Hackenberg A, Kuster A, Lentschig MG, Lopez-Laso E, Marco EJ, Mastroyianni S, Perrier J, Schmitt-Mechelke T, Servidei S, Skardoutsou A, Uldall P, van der Knaap MS, Goglin KC, Tefft DL, Aubin C, de Jager P, Hafler D, Warman ML. Infection-triggered familial or recurrent cases of acute necrotizing encephalopathy caused by mutations in a component of the nuclear pore, RANBP2. Am J Hum Genet 2009; 84:44-51. [PMID: 19118815 DOI: 10.1016/j.ajhg.2008.12.009] [Citation(s) in RCA: 234] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Revised: 12/09/2008] [Accepted: 12/12/2008] [Indexed: 01/05/2023] Open
Abstract
Acute necrotizing encephalopathy (ANE) is a rapidly progressive encephalopathy that can occur in otherwise healthy children after common viral infections such as influenza and parainfluenza. Most ANE is sporadic and nonrecurrent (isolated ANE). However, we identified a 7 Mb interval containing a susceptibility locus (ANE1) in a family segregating recurrent ANE as an incompletely penetrant, autosomal-dominant trait. We now report that all affected individuals and obligate carriers in this family are heterozygous for a missense mutation (c.1880C-->T, p.Thr585Met) in the gene encoding the nuclear pore protein Ran Binding Protein 2 (RANBP2). To determine whether this mutation is the susceptibility allele, we screened controls and other patients with ANE who are unrelated to the index family. Patients from 9 of 15 additional kindreds with familial or recurrent ANE had the identical mutation. It arose de novo in two families and independently in several other families. Two other patients with familial ANE had different RANBP2 missense mutations that altered conserved residues. None of the three RANBP2 missense mutations were found in 19 patients with isolated ANE or in unaffected controls. We conclude that missense mutations in RANBP2 are susceptibility alleles for familial and recurrent cases of ANE.
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Affiliation(s)
- Derek E Neilson
- Department of Genetics, Case Western Reserve University School of Medicine, University Hospitals Case Medical Center, Cleveland, OH 44106, USA.
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Beriou G, Costantino C, Baecher-Allan C, Hafler D. OR.55. Transforming Growth Factor-beta is Crucial for the Differentiation and Regulation of Interleukin 9-producing Human CD4+T Cells. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D. Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet 2008; 4:e1000287. [PMID: 19043577 PMCID: PMC2583954 DOI: 10.1371/journal.pgen.1000287] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Accepted: 10/29/2008] [Indexed: 11/30/2022] Open
Abstract
Lymphoblastoid cell lines (LCLs), originally collected as renewable sources of DNA, are now being used as a model system to study genotype–phenotype relationships in human cells, including searches for QTLs influencing levels of individual mRNAs and responses to drugs and radiation. In the course of attempting to map genes for drug response using 269 LCLs from the International HapMap Project, we evaluated the extent to which biological noise and non-genetic confounders contribute to trait variability in LCLs. While drug responses could be technically well measured on a given day, we observed significant day-to-day variability and substantial correlation to non-genetic confounders, such as baseline growth rates and metabolic state in culture. After correcting for these confounders, we were unable to detect any QTLs with genome-wide significance for drug response. A much higher proportion of variance in mRNA levels may be attributed to non-genetic factors (intra-individual variance—i.e., biological noise, levels of the EBV virus used to transform the cells, ATP levels) than to detectable eQTLs. Finally, in an attempt to improve power, we focused analysis on those genes that had both detectable eQTLs and correlation to drug response; we were unable to detect evidence that eQTL SNPs are convincingly associated with drug response in the model. While LCLs are a promising model for pharmacogenetic experiments, biological noise and in vitro artifacts may reduce power and have the potential to create spurious association due to confounding. The use of lymphoblastoid cell lines (LCLs) has evolved from a renewable source of DNA to an in vitro model system to study the genetics of gene expression, drug response, and other traits in a controlled laboratory setting. While convincing relationships between SNPs and mRNA levels (eQTLs) have been described, the degree to which non-genetic variables also influence phenotypes in LCLs is less well characterized. In the course of attempting to map genes for drug responses in vitro, we evaluated the reproducibility of in vitro traits across replicates, the impact of the EBV virus used to transform B cells into cell lines, and the effect of in vitro culture conditions. We found that responses to at least some drugs and levels of many mRNAs can be technically well measured, but vary both across experiments and with non-genetic confounders such as growth rates, EBV levels, and ATP levels. The influence of such non-genetic factors can both decrease power to detect true relationships between DNA variation and traits and create the potential for non-genetic confounding and spurious associations between DNA variants and traits.
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Affiliation(s)
- Edwin Choy
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Hematology Oncology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Roman Yelensky
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Harvard–MIT Division of Health Sciences and Technology, Cambridge, Massachusetts, United States of America
| | - Sasha Bonakdar
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Robert M. Plenge
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Richa Saxena
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Philip L. De Jager
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Harvard Medical School–Partners Healthcare Center for Genetics and Genomics, Boston, Massachusetts, United States of America
| | - Stanley Y. Shaw
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Systems Biology and Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Cara S. Wolfish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Jacqueline M. Slavik
- Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
- Biomedical Research Institute, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Chris Cotsapas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Manuel Rivas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United Sates of America
| | | | - Ellen Cahir-McFarland
- Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Laboratory and Infectious Disease Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Elliott Kieff
- Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Laboratory and Infectious Disease Division, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - David Hafler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Mark J. Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Altshuler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Diabetes Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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Anderson D, Yang L, Baecher-Allan C, Bettelli E, Oukka M, Kuchroo V, Hafler D. OR.41. IL-21 and TGF-β are Required for Differentiation of Human Th17 Cells. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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41
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Baecher-Allan C, Ashley C, Hafler D. Sa.114. IL-10 and Granzyme B Inhibits Suppression by Human DR+ Effector nTregs. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Maier L, Severson C, Jager PD, Hafler D. Sa.109. Allelic and Phenotypic Heterogeneity at the Autoimmune Susceptibility Locus IL2RA. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Astier A, Beriou G, Eisenhaure T, Hafler D, Hacohen N. Flt3, a New Regulator of IL-10 Production by Human T Cells, Identified Using an RNAi Library. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Ottoboni L, Young E, Yelensky R, Hafler D, Daly M, Jager PD. F.33. Genetic Variants that Control the Expression of MHC Genes Do Not Affect Susceptibility to Multiple Sclerosis. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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45
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Hastings W, Anderson D, Kuchroo V, Hafler D. Sa.102. Discovery and Characterization of Novel Human TIM-3 Splice Variants. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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46
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Baecher-Allan C, Maier L, Beriou G, Ashley C, Hafler D. Sa.115. IL7R and HLA-Class II selected FoxP3+ Natural Regulatory T Cells (nTregs) Represent Effector nTregs, Precursor nTregs, and Induced nTregs. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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47
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Beriou G, Ashley C, Constantino C, Hafler D, Baecher-Allan C. OR.39. Differentiation of Natural Human CD4+CD25high Tregs to Th17 Effector Cells. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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48
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Jager PD, Kivisäkk P, Hu X, Soler-Ferran D, Izmailova E, O'Brien C, Hafler D, Weiner H, Khoury S. F.34. Changes in the CD8dimCD4- Cell Population Parallel Disease Activity in Treated Multiple Sclerosis Subjects. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Bradshaw E, Kent S, Greer A, Elyaman W, Raddassi K, Love JC, Orban T, Hafler D. Sa.77. Ex Vivo Activated State of Type 1 Diabetic Monocytes. Clin Immunol 2008. [DOI: 10.1016/j.clim.2008.03.298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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50
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Wucherpfennig KW, Allen PM, Celada F, Cohen IR, De Boer R, Garcia KC, Goldstein B, Greenspan R, Hafler D, Hodgkin P, Huseby ES, Krakauer DC, Nemazee D, Perelson AS, Pinilla C, Strong RK, Sercarz EE. Polyspecificity of T cell and B cell receptor recognition. Semin Immunol 2007; 19:216-24. [PMID: 17398114 PMCID: PMC2034306 DOI: 10.1016/j.smim.2007.02.012] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 02/26/2007] [Indexed: 02/06/2023]
Abstract
A recent workshop discussed the recognition of multiple distinct ligands by individual T cell and B cell receptors and the implications of this discovery for lymphocyte biology. The workshop recommends general use of the term polyspecificity because it emphasizes two fundamental aspects, the inherent specificity of receptor recognition and the ability to recognize multiple ligands. Many different examples of polyspecificity and the structural mechanisms were discussed, and the group concluded that polyspecificity is a general, inherent feature of TCR and antibody recognition. This review summarizes the relevance of polyspecificity for lymphocyte development, activation and disease processes.
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Affiliation(s)
- Kai W Wucherpfennig
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA.
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