1
|
Asashima H, Kim D, Wang K, Lele N, Buitrago-Pocasangre NC, Lutz R, Cruz I, Raddassi K, Ruff WE, Racke MK, Wilson JE, Givens TS, Grifoni A, Weiskopf D, Sette A, Kleinstein SH, Montgomery RR, Shaw AC, Li F, Fan R, Hafler DA, Tomayko MM, Longbrake EE. Prior cycles of anti-CD20 antibodies affect antibody responses after repeated SARS-CoV-2 mRNA vaccination. JCI Insight 2023; 8:e168102. [PMID: 37606046 PMCID: PMC10543713 DOI: 10.1172/jci.insight.168102] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/06/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUNDWhile B cell depletion is associated with attenuated antibody responses to SARS-CoV-2 mRNA vaccination, responses vary among individuals. Thus, elucidating the factors that affect immune responses after repeated vaccination is an important clinical need.METHODSWe evaluated the quality and magnitude of the T cell, B cell, antibody, and cytokine responses to a third dose of BNT162b2 or mRNA-1273 mRNA vaccine in patients with B cell depletion.RESULTSIn contrast with control individuals (n = 10), most patients on anti-CD20 therapy (n = 48) did not demonstrate an increase in spike-specific B cells or antibodies after a third dose of vaccine. A third vaccine elicited significantly increased frequencies of spike-specific non-naive T cells. A small subset of B cell-depleted individuals effectively produced spike-specific antibodies, and logistic regression models identified time since last anti-CD20 treatment and lower cumulative exposure to anti-CD20 mAbs as predictors of those having a serologic response. B cell-depleted patients who mounted an antibody response to 3 vaccine doses had persistent humoral immunity 6 months later.CONCLUSIONThese results demonstrate that serial vaccination strategies can be effective for a subset of B cell-depleted patients.FUNDINGThe NIH (R25 NS079193, P01 AI073748, U24 AI11867, R01 AI22220, UM 1HG009390, P01 AI039671, P50 CA121974, R01 CA227473, U01CA260507, 75N93019C00065, K24 AG042489), NIH HIPC Consortium (U19 AI089992), the National Multiple Sclerosis Society (CA 1061-A-18, RG-1802-30153), the Nancy Taylor Foundation for Chronic Diseases, Erase MS, and the Claude D. Pepper Older Americans Independence Center at Yale (P30 AG21342).
Collapse
Affiliation(s)
- Hiromitsu Asashima
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kaicheng Wang
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Nikhil Lele
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Rachel Lutz
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Isabella Cruz
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Khadir Raddassi
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - William E. Ruff
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
- Repertoire Immune Medicines, Cambridge, Massachusetts, USA
| | | | | | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, UCSD, La Jolla, California, USA
| | - Steven H. Kleinstein
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | | | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal Medicine, and
| | - Fangyong Li
- Yale Center for Analytical Sciences, Yale School of Public Health, New Haven, Connecticut, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - David A. Hafler
- Department of Neurology, and
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Mary M. Tomayko
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Dermatology, Yale School of Medicine, New Haven, Connecticut, USA
| | | |
Collapse
|
2
|
Mann JE, Lucca L, Austin MR, Merkin RD, Robert ME, Al Bawardy B, Raddassi K, Aizenbud L, Joshi NS, Hafler DA, Abraham C, Herold KC, Kluger HM. ScRNA-seq defines dynamic T-cell subsets in longitudinal colon and peripheral blood samples in immune checkpoint inhibitor-induced colitis. J Immunother Cancer 2023; 11:e007358. [PMID: 37586769 PMCID: PMC10432652 DOI: 10.1136/jitc-2023-007358] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 08/18/2023] Open
Abstract
Immune checkpoint inhibitors (ICIs) are increasingly being used to manage multiple tumor types. Unfortunately, immune-related adverse events affect up to 60% of recipients, often leading to treatment discontinuation in settings where few alternative cancer therapies may be available. Checkpoint inhibitor induced colitis (ICI-colitis) is a common toxicity for which the underlying mechanisms are poorly defined. To better understand the changing colon-specific and peripheral immune environments over the course of progression and treatment of colitis, we collected blood and colon tissue from a patient with Merkel cell carcinoma who developed colitis on treatment with pembrolizumab. We performed single-cell RNA sequencing and T-cell receptor sequencing on samples collected before, during and after pembrolizumab and after various interventions to mitigate toxicity. We report T-cells populations defined by cytotoxicity, memory, and proliferation markers at various stages of colitis. We show preferential depletion of CD8+ T cells with biologic therapy and nominate both circulating and colon-resident T-cell subsets as potential drivers of inflammation and response to immune suppression. Our findings highlight the need for further exploration of the colon immune environment and rationalize future studies evaluating biologics for ICI-colitis, including in the context of ICI re-challenge.
Collapse
Affiliation(s)
- Jacqueline E Mann
- Department of Internal Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Liliana Lucca
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Matthew R Austin
- Department of Internal Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Ross D Merkin
- Department of Internal Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Marie E Robert
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Badr Al Bawardy
- Department of Internal Medicine (Digestive Diseases), Yale University, New Haven, Connecticut, USA
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Lilach Aizenbud
- Department of Internal Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Nikhil S Joshi
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Clara Abraham
- Department of Internal Medicine (Digestive Diseases), Yale University, New Haven, Connecticut, USA
| | - Kevan C Herold
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Internal Medicine (Endocrinology), Yale School of Medicine, New Haven, Connecticut, USA
| | - Harriet M Kluger
- Department of Internal Medicine (Medical Oncology), Yale School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
3
|
Asashima H, Mohanty S, Comi M, Ruff WE, Hoehn KB, Wong P, Klein J, Lucas C, Cohen I, Coffey S, Lele N, Greta L, Raddassi K, Chaudhary O, Unterman A, Emu B, Kleinstein SH, Montgomery RR, Iwasaki A, Dela Cruz CS, Kaminski N, Shaw AC, Hafler DA, Sumida TS. PD-1 highCXCR5 -CD4 + peripheral helper T cells promote CXCR3 + plasmablasts in human acute viral infection. Cell Rep 2023; 42:111895. [PMID: 36596303 PMCID: PMC9806868 DOI: 10.1016/j.celrep.2022.111895] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 06/15/2022] [Accepted: 12/08/2022] [Indexed: 01/03/2023] Open
Abstract
T cell-B cell interaction is the key immune response to protect the host from severe viral infection. However, how T cells support B cells to exert protective humoral immunity in humans is not well understood. Here, we use COVID-19 as a model of acute viral infections and analyze CD4+ T cell subsets associated with plasmablast expansion and clinical outcome. Peripheral helper T cells (Tph cells; denoted as PD-1highCXCR5-CD4+ T cells) are significantly increased, as are plasmablasts. Tph cells exhibit "B cell help" signatures and induce plasmablast differentiation in vitro. Interestingly, expanded plasmablasts show increased CXCR3 expression, which is positively correlated with higher frequency of activated Tph cells and better clinical outcome. Mechanistically, Tph cells help B cell differentiation and produce more interferon γ (IFNγ), which induces CXCR3 expression on plasmablasts. These results elucidate a role for Tph cells in regulating protective B cell response during acute viral infection.
Collapse
Affiliation(s)
- Hiromitsu Asashima
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Michela Comi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - William E Ruff
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Patrick Wong
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Jon Klein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Inessa Cohen
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Coffey
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nikhil Lele
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Leissa Greta
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Omkar Chaudhary
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Brinda Emu
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Department of Pathology, Yale School of Medicine, New Haven, CT, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA; Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tomokazu S Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
4
|
Asashima H, Axisa PP, Pham THG, Longbrake EE, Ruff WE, Lele N, Cohen I, Raddassi K, Sumida TS, Hafler DA. Impaired TIGIT expression on B cells drives circulating follicular helper T cell expansion in multiple sclerosis. J Clin Invest 2022; 132:156254. [PMID: 36250467 PMCID: PMC9566906 DOI: 10.1172/jci156254] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/25/2022] [Indexed: 11/17/2022] Open
Abstract
B cell depletion in patients with relapsing-remitting multiple sclerosis (RRMS) markedly prevents new MRI-detected lesions and disease activity, suggesting the hypothesis that altered B cell function leads to the activation of T cells driving disease pathogenesis. Here, we performed comprehensive analyses of CD40 ligand- (CD40L-) and IL-21-stimulated memory B cells from patients with MS and healthy age-matched controls, modeling the help of follicular helper T cells (Tfh cells), and found a differential gene expression signature in multiple B cell pathways. Most striking was the impaired TIGIT expression on MS-derived B cells mediated by dysregulation of the transcription factor TCF4. Activated circulating Tfh cells (cTfh cells) expressed CD155, the ligand of TIGIT, and TIGIT on B cells revealed their capacity to suppress the proliferation of IL-17-producing cTfh cells via the TIGIT/CD155 axis. Finally, CCR6+ cTfh cells were significantly increased in patients with MS, and their frequency was inversely correlated with that of TIGIT+ B cells. Together, these data suggest that the dysregulation of negative feedback loops between TIGIT+ memory B cells and cTfh cells in MS drives the activated immune system in this disease.
Collapse
|
5
|
Chou C, Mohanty S, Kang HA, Kong L, Avila‐Pacheco J, Joshi SR, Ueda I, Devine L, Raddassi K, Pierce K, Jeanfavre S, Bullock K, Meng H, Clish C, Santori FR, Shaw AC, Xavier RJ. Metabolomic and transcriptomic signatures of influenza vaccine response in healthy young and older adults. Aging Cell 2022; 21:e13682. [PMID: 35996998 PMCID: PMC9470889 DOI: 10.1111/acel.13682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/13/2022] [Indexed: 01/25/2023] Open
Abstract
Seasonal influenza causes mild to severe respiratory infections and significant morbidity, especially in older adults. Transcriptomic analysis in populations across multiple flu seasons has provided insights into the molecular determinants of vaccine response. Still, the metabolic changes that underlie the immune response to influenza vaccination remain poorly characterized. We performed untargeted metabolomics to analyze plasma metabolites in a cohort of younger and older subjects before and after influenza vaccination to identify vaccine-induced molecular signatures. Metabolomic and transcriptomic data were combined to define networks of gene and metabolic signatures indicative of high and low antibody response in these individuals. We observed age-related differences in metabolic baselines and signatures of antibody response to influenza vaccination and the abundance of α-linolenic and linoleic acids, sterol esters, fatty-acylcarnitines, and triacylglycerol metabolism. We identified a metabolomic signature associated with age-dependent vaccine response, finding increased tryptophan and decreased polyunsaturated fatty acids (PUFAs) in young high responders (HRs), while fatty acid synthesis and cholesteryl esters accumulated in older HRs. Integrated metabolomic and transcriptomic analysis shows that depletion of PUFAs, which are building blocks for prostaglandins and other lipid immunomodulators, in young HR subjects at Day 28 is related to a robust immune response to influenza vaccination. Increased glycerophospholipid levels were associated with an inflammatory response in older HRs to flu vaccination. This multi-omics approach uncovered age-related molecular markers associated with influenza vaccine response and provides insight into vaccine-induced metabolic responses that may help guide development of more effective influenza vaccines.
Collapse
Affiliation(s)
- Chih‐Hung Chou
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | | | - Lingjia Kong
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Samit R. Joshi
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ikuyo Ueda
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Lesley Devine
- Department of Laboratory MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Khadir Raddassi
- Department of NeurologyYale School of MedicineNew HavenConnecticutUSA
| | - Kerry Pierce
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | | | - Kevin Bullock
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Hailong Meng
- Department of PathologyYale School of MedicineNew HavenConnecticutUSA
| | - Clary Clish
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - Fabio R. Santori
- Center for Molecular MedicineUniversity of GeorgiaAthensGeorgiaUSA
| | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal MedicineYale School of MedicineNew HavenConnecticutUSA
| | - Ramnik J. Xavier
- Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
- Klarman Cell ObservatoryBroad Institute of Harvard and MITCambridgeMassachusettsUSA
- Center for Computational and Integrative Biology and Department of Molecular BiologyMassachusetts General Hospital and Harvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
6
|
Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N, Ozonoff A, Schaenman J, Jayavelu ND, Milliren CE, Calfee CS, Cairns CB, Kraft M, Baden LR, Shaw AC, Krammer F, van Bakel H, Esserman DA, Liu S, Sesma AF, Simon V, Hafler DA, Montgomery RR, Kleinstein SH, Levy O, Bime C, Haddad EK, Erle DJ, Pulendran B, Nadeau KC, Davis MM, Hough CL, Messer WB, Higuita NIA, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LI, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, McEnaney K, Barton B, Lentucci C, Saluvan M, Chang AC, Hoch A, Albert M, Shaheen T, Kho AT, Thomas S, Chen J, Murphy MD, Cooney M, Presnell S, Fragiadakis GK, Patel R, Guan L, Gygi J, Pawar S, Brito A, Khalil Z, Maguire C, Fourati S, Overton JA, Vita R, Westendorf K, Salehi-Rad R, Leligdowicz A, Matthay MA, Singer JP, Kangelaris KN, Hendrickson CM, Krummel MF, Langelier CR, Woodruff PG, Powell DL, Kim JN, Simmons B, Goonewardene IM, Smith CM, Martens M, Mosier J, Kimura H, Sherman AC, Walsh SR, Issa NC, Dela Cruz C, Farhadian S, Iwasaki A, Ko AI, Chinthrajah S, Ahuja N, Rogers AJ, Artandi M, Siegel SA, Lu Z, Drevets DA, Brown BR, Anderson ML, Guirgis FW, Thyagarajan RV, Rousseau JF, Wylie D, Busch J, Gandhi S, Triplett TA, Yendewa G, Giddings O, Anderson EJ, Mehta AK, Sevransky JE, Khor B, Rahman A, Stadlbauer D, Dutta J, Xie H, Kim-Schulze S, Gonzalez-Reiche AS, van de Guchte A, Farrugia K, Khan Z, Maecker HT, Elashoff D, Brook J, Ramires-Sanchez E, Llamas M, Rivera A, Perdomo C, Ward DC, Magyar CE, Fulcher JA, Abe-Jones Y, Asthana S, Beagle A, Bhide S, Carrillo SA, Chak S, Fragiadakis GK, Ghale R, Gonzalez A, Jauregui A, Jones N, Lea T, Lee D, Lota R, Milush J, Nguyen V, Pierce L, Prasad PA, Rao A, Samad B, Shaw C, Sigman A, Sinha P, Ward A, Willmore A, Zhan J, Rashid S, Rodriguez N, Tang K, Altamirano LT, Betancourt L, Curiel C, Sutter N, Paz MT, Tietje-Ulrich G, Leroux C, Connors J, Bernui M, Kutzler MA, Edwards C, Lee E, Lin E, Croen B, Semenza NC, Rogowski B, Melnyk N, Woloszczuk K, Cusimano G, Bell MR, Furukawa S, McLin R, Marrero P, Sheidy J, Tegos GP, Nagle C, Mege N, Ulring K, Seyfert-Margolis V, Conway M, Francisco D, Molzahn A, Erickson H, Wilson CC, Schunk R, Sierra B, Hughes T, Smolen K, Desjardins M, van Haren S, Mitre X, Cauley J, Li X, Tong A, Evans B, Montesano C, Licona JH, Krauss J, Chang JBP, Izaguirre N, Chaudhary O, Coppi A, Fournier J, Mohanty S, Muenker MC, Nelson A, Raddassi K, Rainone M, Ruff WE, Salahuddin S, Schulz WL, Vijayakumar P, Wang H, Wunder Jr. E, Young HP, Zhao Y, Saksena M, Altman D, Kojic E, Srivastava K, Eaker LQ, Bermúdez-González MC, Beach KF, Sominsky LA, Azad AR, Carreño JM, Singh G, Raskin A, Tcheou J, Bielak D, Kawabata H, Mulder LCF, Kleiner G, Lee AS, Do ED, Fernandes A, Manohar M, Hagan T, Blish CA, Din HN, Roque J, Yang S, Brunton A, Sullivan PE, Strnad M, Lyski ZL, Coulter FJ, Booth JL, Sinko LA, Moldawer LL, Borresen B, Roth-Manning B, Song LZ, Nelson E, Lewis-Smith M, Smith J, Tipan PG, Siles N, Bazzi S, Geltman J, Hurley K, Gabriele G, Sieg S, Vaysman T, Bristow L, Hussaini L, Hellmeister K, Samaha H, Cheng A, Spainhour C, Scherer EM, Johnson B, Bechnak A, Ciric CR, Hewitt L, Carter E, Mcnair N, Panganiban B, Huerta C, Usher J, Ribeiro SP, Altman MC, Becker PM, Rouphael N. Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study. EBioMedicine 2022; 83:104208. [PMID: 35952496 PMCID: PMC9359694 DOI: 10.1016/j.ebiom.2022.104208] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 07/11/2022] [Accepted: 07/25/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Better understanding of the association between characteristics of patients hospitalized with coronavirus disease 2019 (COVID-19) and outcome is needed to further improve upon patient management. METHODS Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) is a prospective, observational study of 1164 patients from 20 hospitals across the United States. Disease severity was assessed using a 7-point ordinal scale based on degree of respiratory illness. Patients were prospectively surveyed for 1 year after discharge for post-acute sequalae of COVID-19 (PASC) through quarterly surveys. Demographics, comorbidities, radiographic findings, clinical laboratory values, SARS-CoV-2 PCR and serology were captured over a 28-day period. Multivariable logistic regression was performed. FINDINGS The median age was 59 years (interquartile range [IQR] 20); 711 (61%) were men; overall mortality was 14%, and 228 (20%) required invasive mechanical ventilation. Unsupervised clustering of ordinal score over time revealed distinct disease course trajectories. Risk factors associated with prolonged hospitalization or death by day 28 included age ≥ 65 years (odds ratio [OR], 2.01; 95% CI 1.28-3.17), Hispanic ethnicity (OR, 1.71; 95% CI 1.13-2.57), elevated baseline creatinine (OR 2.80; 95% CI 1.63- 4.80) or troponin (OR 1.89; 95% 1.03-3.47), baseline lymphopenia (OR 2.19; 95% CI 1.61-2.97), presence of infiltrate by chest imaging (OR 3.16; 95% CI 1.96-5.10), and high SARS-CoV2 viral load (OR 1.53; 95% CI 1.17-2.00). Fatal cases had the lowest ratio of SARS-CoV-2 antibody to viral load levels compared to other trajectories over time (p=0.001). 589 survivors (51%) completed at least one survey at follow-up with 305 (52%) having at least one symptom consistent with PASC, most commonly dyspnea (56% among symptomatic patients). Female sex was the only associated risk factor for PASC. INTERPRETATION Integration of PCR cycle threshold, and antibody values with demographics, comorbidities, and laboratory/radiographic findings identified risk factors for 28-day outcome severity, though only female sex was associated with PASC. Longitudinal clinical phenotyping offers important insights, and provides a framework for immunophenotyping for acute and long COVID-19. FUNDING NIH.
Collapse
Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Carly E. Milliren
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Carolyn S. Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | - Charles B. Cairns
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - Monica Kraft
- University of Arizona, Tucson, AZ, United States
| | - Lindsey R. Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | - Albert C. Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Denise A. Esserman
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David A. Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ruth R. Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Steven H. Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, United States
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, United States
| | | | - Elias K. Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, United States
| | - David J. Erle
- University of California San Francisco School of Medicine, San Francisco, CA, United States
| | | | | | | | | | | | | | - Jordan P. Metcalf
- Oklahoma University Health Sciences Center, Oklahoma, OK, United States
| | - Mark A. Atkinson
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - Scott C. Brakenridge
- University of Florida, Gainesville and University of South Florida, Tampa, FL, United States
| | - David Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, United States
| | | | - Esther Melamed
- The University of Texas at Austin, Austin, TX, United States
| | | | - Rafick Sekaly
- Case Western Reserve University, Cleveland, OH, United States
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC); Precision Vaccines Program, Boston Children's Hospital, Boston, MA, United States
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alison D. Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
| | - Elaine F. Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, United States
| | | | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nat Commun 2022; 13:440. [PMID: 35064122 PMCID: PMC8782894 DOI: 10.1038/s41467-021-27716-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/03/2021] [Indexed: 02/06/2023] Open
Abstract
Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.
Collapse
MESH Headings
- Adaptive Immunity/drug effects
- Adaptive Immunity/genetics
- Adaptive Immunity/immunology
- Aged
- Antibodies, Monoclonal, Humanized/therapeutic use
- CD4-Positive T-Lymphocytes/drug effects
- CD4-Positive T-Lymphocytes/immunology
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/drug effects
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- COVID-19/genetics
- COVID-19/immunology
- Cells, Cultured
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation/drug effects
- Gene Expression Regulation/immunology
- Humans
- Immunity, Innate/drug effects
- Immunity, Innate/genetics
- Immunity, Innate/immunology
- Male
- RNA-Seq/methods
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- SARS-CoV-2/drug effects
- SARS-CoV-2/immunology
- SARS-CoV-2/physiology
- Single-Cell Analysis/methods
- COVID-19 Drug Treatment
Collapse
Affiliation(s)
- Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA.
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel.
| | - Tomokazu S Sumida
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA.
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA.
| | - Nima Nouri
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Center for Medical Informatics, Yale School of Medicine, New Haven, CT, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Amy Y Zhao
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Victor Gasque
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Hiromitsu Asashima
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Carlos Cosme
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Wenxuan Deng
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ming Chen
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Micha Sam Brickman Raredon
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Guilin Wang
- Yale Center for Genome Analysis/Keck Biotechnology Resource Laboratory, Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Neal G Ravindra
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Patrick Wong
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - John Fournier
- School of Medicine, Yale University, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anne L Wyllie
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Anthony Melillo
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Yan Stein
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Maksym Minasyan
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Subhasis Mohanty
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - William E Ruff
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Inessa Cohen
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Laura E Niklason
- Departments of Anesthesiology & Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Ruth R Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Shelli F Farhadian
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - David van Dijk
- Department of Computer Science, Yale University, New Haven, CT, USA
- Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, Yale University, New Haven, CT, USA
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Steven H Kleinstein
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Inter-Departmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
- West Haven Veterans Affair Medical Center, West Haven, CT, USA
| |
Collapse
|
8
|
Jiang R, Meng H, Raddassi K, Fleming I, Hoehn KB, Dardick KR, Belperron AA, Montgomery RR, Shalek AK, Hafler DA, Kleinstein SH, Bockenstedt LK. Single-cell immunophenotyping of the skin lesion erythema migrans identifies IgM memory B cells. JCI Insight 2021; 6:148035. [PMID: 34061047 PMCID: PMC8262471 DOI: 10.1172/jci.insight.148035] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/19/2021] [Indexed: 11/17/2022] Open
Abstract
The skin lesion erythema migrans (EM) is an initial sign of the Ixodes tick-transmitted Borreliella spirochetal infection known as Lyme disease. T cells and innate immune cells have previously been shown to predominate the EM lesion and promote the reaction. Despite the established importance of B cells and antibodies in preventing infection, the role of B cells in the skin immune response to Borreliella is unknown. Here, we used single-cell RNA-Seq in conjunction with B cell receptor (BCR) sequencing to immunophenotype EM lesions and their associated B cells and BCR repertoires. We found that B cells were more abundant in EM in comparison with autologous uninvolved skin; many were clonally expanded and had circulating relatives. EM-associated B cells upregulated the expression of MHC class II genes and exhibited preferential IgM isotype usage. A subset also exhibited low levels of somatic hypermutation despite a gene expression profile consistent with memory B cells. Our study demonstrates that single-cell gene expression with paired BCR sequencing can be used to interrogate the sparse B cell populations in human skin and reveals that B cells in the skin infection site in early Lyme disease expressed a phenotype consistent with local antigen presentation and antibody production.
Collapse
Affiliation(s)
| | | | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ira Fleming
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | | | | | - Alexia A. Belperron
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Alex K. Shalek
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
- The Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, Massachusetts, USA
| | - David A. Hafler
- Department of Immunobiology
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, USA
- Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| | - Steven H. Kleinstein
- Department of Immunobiology
- Department of Pathology, and
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Linda K. Bockenstedt
- Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
9
|
Lucca LE, Axisa PP, Lu B, Harnett B, Jessel S, Zhang L, Raddassi K, Zhang L, Olino K, Clune J, Singer M, Kluger HM, Hafler DA. Circulating clonally expanded T cells reflect functions of tumor-infiltrating T cells. J Exp Med 2021; 218:e20200921. [PMID: 33651881 PMCID: PMC7933991 DOI: 10.1084/jem.20200921] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 05/07/2020] [Revised: 08/14/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Understanding the relationship between tumor and peripheral immune environments could allow longitudinal immune monitoring in cancer. Here, we examined whether T cells that share the same TCRαβ and are found in both tumor and blood can be interrogated to gain insight into the ongoing tumor T cell response. Paired transcriptome and TCRαβ repertoire of circulating and tumor-infiltrating T cells were analyzed at the single-cell level from matched tumor and blood from patients with metastatic melanoma. We found that in circulating T cells matching clonally expanded tumor-infiltrating T cells (circulating TILs), gene signatures of effector functions, but not terminal exhaustion, reflect those observed in the tumor. In contrast, features of exhaustion are displayed predominantly by tumor-exclusive T cells. Finally, genes associated with a high degree of blood-tumor TCR sharing were overexpressed in tumor tissue after immunotherapy. These data demonstrate that circulating TILs have unique transcriptional patterns that may have utility for the interrogation of T cell function in cancer immunotherapy.
Collapse
Affiliation(s)
- Liliana E. Lucca
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Pierre-Paul Axisa
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Benjamin Lu
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Brian Harnett
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Shlomit Jessel
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Le Zhang
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Khadir Raddassi
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Lin Zhang
- Department of Medicine, Yale School of Medicine, New Haven, CT
| | - Kelly Olino
- Department of Surgery, Yale School of Medicine, New Haven, CT
| | - James Clune
- Department of Surgery, Yale School of Medicine, New Haven, CT
| | - Meromit Singer
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | | | - David A. Hafler
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| |
Collapse
|
10
|
Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Transcriptomic and clonal characterization of T cells in the human central nervous system. Sci Immunol 2020; 5:eabb8786. [PMID: 32948672 PMCID: PMC8567322 DOI: 10.1126/sciimmunol.abb8786] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 03/24/2020] [Accepted: 08/26/2020] [Indexed: 08/04/2023]
Abstract
T cells provide critical immune surveillance to the central nervous system (CNS), and the cerebrospinal fluid (CSF) is thought to be a main route for their entry. Further characterization of the state of T cells in the CSF in healthy individuals is important for understanding how T cells provide protective immune surveillance without damaging the delicate environment of the CNS and providing tissue-specific context for understanding immune dysfunction in neuroinflammatory disease. Here, we have profiled T cells in the CSF of healthy human donors and have identified signatures related to cytotoxic capacity and tissue adaptation that are further exemplified in clonally expanded CSF T cells. By comparing profiles of clonally expanded T cells obtained from the CSF of patients with multiple sclerosis (MS) and healthy donors, we report that clonally expanded T cells from the CSF of patients with MS have heightened expression of genes related to T cell activation and cytotoxicity.
Collapse
Affiliation(s)
- Jenna L Pappalardo
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Le Zhang
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Maggie K Pecsok
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kelly Perlman
- Montreal Neurologic Institute, Montreal, Quebec, Canada
| | - Chrysoula Zografou
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Khadir Raddassi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Ahmad Abulaban
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Smita Krishnaswamy
- Departments of Genetics and Computer Science, Yale School of Medicine, New Haven, CT 06511, USA
| | - Jack Antel
- Montreal Neurologic Institute, Montreal, Quebec, Canada
| | - David van Dijk
- Departments of Internal Medicine (Cardiology), Cardiovascular Research Center, and Computer Science, New Haven, CT 06511, USA.
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| |
Collapse
|
11
|
Nassar SF, Raddassi K, Ubhi B, Doktorski J, Abulaban A. Precision Medicine: Steps along the Road to Combat Human Cancer. Cells 2020; 9:E2056. [PMID: 32916938 PMCID: PMC7563722 DOI: 10.3390/cells9092056] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 09/01/2020] [Indexed: 12/14/2022] Open
Abstract
The diagnosis and treatment of diseases such as cancer is becoming more accurate and specialized with the advent of precision medicine techniques, research and treatments. Reaching down to the cellular and even sub-cellular level, diagnostic tests can pinpoint specific, individual information from each patient, and guide providers to a more accurate plan of treatment. With this advanced knowledge, researchers and providers can better gauge the effectiveness of drugs, radiation, and other therapies, which is bound to lead to a more accurate, if not more positive, prognosis. As precision medicine becomes more established, new techniques, equipment, materials and testing methods will be required. Herein, we will examine the recent innovations in assays, devices and software, along with next generation sequencing in genomics diagnostics which are in use or are being developed for personalized medicine. So as to avoid duplication and produce the fullest possible benefit, all involved must be strongly encouraged to collaborate, across national borders, public and private sectors, science, medicine and academia alike. In this paper we will offer recommendations for tools, research and development, along with ideas for implementation. We plan to begin with discussion of the lessons learned to date, and the current research on pharmacogenomics. Given the steady stream of advances in imaging mass spectrometry and nanoLC-MS/MS, and use of genomic, proteomic and metabolomics biomarkers to distinguish healthy tissue from diseased cells, there is great potential to utilize pharmacogenomics to tailor a drug or drugs to a particular cohort of patients. Such efforts very well may bring increased hope for small groups of non-responders and those who have demonstrated adverse reactions to current treatments.
Collapse
Affiliation(s)
- Samuel F. Nassar
- Department of Biology, Brandeis University, Waltham, MA 02453, USA
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511, USA;
| | | | | | - Ahmad Abulaban
- Department of Neurology, Yale School of Medicine, New Haven, CT 06511, USA;
- Department of Medicine, King Saud Bin-Abdulaziz University, King Abdulaziz Medical City-National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| |
Collapse
|
12
|
Lucca LE, Lerner BA, Park C, DeBartolo D, Harnett B, Kumar VP, Ponath G, Raddassi K, Huttner A, Hafler DA, Pitt D. Differential expression of the T-cell inhibitor TIGIT in glioblastoma and MS. Neurol Neuroimmunol Neuroinflamm 2020; 7:e712. [PMID: 32269065 PMCID: PMC7188477 DOI: 10.1212/nxi.0000000000000712] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/07/2020] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To identify coinhibitory immune pathways important in the brain, we hypothesized that comparison of T cells in lesions from patients with MS with tumor-infiltrating T cells (TILs) from patients with glioblastoma multiforme may reveal novel targets for immunotherapy. METHODS We collected fresh surgical resections and matched blood from patients with glioblastoma, blood and unmatched postmortem CNS tissue from patients with MS, and blood from healthy donors. The expression of TIGIT, CD226, and their shared ligand CD155 as well as PD-1 and PDL1 was assessed by both immunohistochemistry and flow cytometry. RESULTS We found that TIGIT was highly expressed on glioblastoma-infiltrating T cells, but was near-absent from MS lesions. Conversely, lymphocytic expression of PD-1/PD-L1 was comparable between the 2 diseases. Moreover, TIGIT was significantly upregulated in circulating lymphocytes of patients with glioblastoma compared with healthy controls, suggesting recirculation of TILs. Expression of CD226 was also increased in glioblastoma, but this costimulatory receptor was expressed alongside TIGIT in the majority of tumor-infiltrating T cells, suggesting functional counteraction. CONCLUSIONS The opposite patterns of TIGIT expression in the CNS between MS and glioblastoma reflects the divergent features of the immune response in these 2 CNS diseases. These data raise the possibility that anti-TIGIT therapy may be beneficial for patients with glioblastoma.
Collapse
Affiliation(s)
- Liliana E Lucca
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Benjamin A Lerner
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Calvin Park
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Danielle DeBartolo
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Brian Harnett
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Varun P Kumar
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Gerald Ponath
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Khadir Raddassi
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - Anita Huttner
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - David A Hafler
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT
| | - David Pitt
- From the Departments of Neurology (L.E.L., B.A.L., C.P., D.D., B.H., V.P.K., G.P., K.R., D.A.H., D.P.); Immunobiology (L.E.L., B.A.L., B.H., K.R., D.A.H.); and Pathology (A.H.), Yale School of Medicine, New Haven, CT.
| |
Collapse
|
13
|
Choileáin SN, Kleinewietfeld M, Raddassi K, Hafler DA, Ruff WE, Longbrake EE. CXCR3+ T cells in multiple sclerosis correlate with reduced diversity of the gut microbiome. J Transl Autoimmun 2019; 3:100032. [PMID: 32743517 PMCID: PMC7388357 DOI: 10.1016/j.jtauto.2019.100032] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/11/2019] [Accepted: 12/13/2019] [Indexed: 12/25/2022] Open
Abstract
Multiple sclerosis (MS) is a genetically mediated autoimmune disease characterized by inflammation in the central nervous system (CNS). Disease onset is thought to occur when autoreactive T cells orchestrate a cascade of events in the CNS resulting in white and grey matter inflammation and axonal degeneration. It is unclear what triggers the activation of CNS-reactive T cells and their polarization into inflammatory subsets. Mounting evidence from animal and human studies supports the hypothesis that the gut microbiome affects MS pathogenesis. We investigated the association between the gut microbiome and inflammatory T cell subsets in relapsing-remitting MS patients and healthy controls. Gut microbiome composition was characterized by sequencing the V4 region of the 16S rRNA gene from fecal DNA, and inflammatory T cell subsets were characterized by flow cytometry. We identified an altered gut microbiome in MS patients, including decreased abundance of Coprococcus, Clostridium, and an unidentified Ruminococcaceae genus. Among circulating immune cells, patients had increased expression of CXCR3 in both CD4 and CD8 T cells, and both CD4+CXCR3+ and CD8+CXCR3+ populations expressing the gut-homing α4β7 integrin receptor were increased. Finally, we show that alpha diversity inversely correlated with a CXCR3+ Th1 phenotype in MS. These findings indicate the presence of an aberrant gut-immune axis in patients with MS.
Collapse
Affiliation(s)
- Siobhán Ní Choileáin
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Markus Kleinewietfeld
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), UHasselt, Campus Diepenbeek, Hasselt, Belgium
| | - Khadir Raddassi
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - David A. Hafler
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - William E. Ruff
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Erin E. Longbrake
- Department of Neurology, Yale University School of Medicine, New Haven, CT, 06511, USA
- Center for Neuroepidemiology and Clinical Neurological Research, Yale School of Medicine, Yale University, New Haven, CT, USA
| |
Collapse
|
14
|
Dominguez-Villar M, Raddassi K, Danielsen AC, Guarnaccia J, Hafler DA. Corrigendum to "Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo" [Yjaut 96C (2019) 40-49]. J Autoimmun 2019; 102:179. [PMID: 31109655 DOI: 10.1016/j.jaut.2019.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Joseph Guarnaccia
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Dominguez-Villar M, Raddassi K, Danielsen AC, Guarnaccia J, Hafler DA. Fingolimod modulates T cell phenotype and regulatory T cell plasticity in vivo. J Autoimmun 2018; 96:40-49. [PMID: 30122421 DOI: 10.1016/j.jaut.2018.08.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 08/06/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
Fingolimod is an approved therapeutic option for patients with relapsing-remitting multiple sclerosis that primarily functions by sequestering T cells in lymph nodes inhibiting their egress to the central nervous system. However, recent data suggests that Fingolimod may also directly affect the immune cell function. Here we examined the in vivo effects of Fingolimod in modulating the phenotype and function of T cell and Foxp3 regulatory T cell populations in patients with multiple sclerosis under Fingolimod treatment. Besides decreasing the cell numbers in peripheral blood and sera levels of pro-inflammatory cytokines, Fingolimod inhibited the expression of Th1 and Th17 cytokines on CD4+ T cells and increased the expression of exhaustion markers. Furthermore, treatment increased the frequency of regulatory T cells in blood and inhibited the Th1-like phenotype that is characteristic of patients with multiple sclerosis, augmenting the expression of markers associated with increased suppressive function. Overall, our data suggest that Fingolimod performs other important immunomodulatory functions besides altering T cell migratory capacities, with consequences for other autoimmune pathologies characterized by excessive Th1/Th17 responses and Th1-like regulatory T cell effector phenotypes.
Collapse
Affiliation(s)
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - Joseph Guarnaccia
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| |
Collapse
|
17
|
Shaham U, Stanton KP, Zhao J, Li H, Raddassi K, Montgomery R, Kluger Y. Removal of batch effects using distribution-matching residual networks. Bioinformatics 2018; 33:2539-2546. [PMID: 28419223 DOI: 10.1093/bioinformatics/btx196] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/31/2017] [Indexed: 11/12/2022] Open
Abstract
Motivation Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument and random measurement errors. Several novel biological technologies, such as mass cytometry and single-cell RNA-seq (scRNA-seq), are plagued with systematic errors that may severely affect statistical analysis if the data are not properly calibrated. Results We propose a novel deep learning approach for removing systematic batch effects. Our method is based on a residual neural network, trained to minimize the Maximum Mean Discrepancy between the multivariate distributions of two replicates, measured in different batches. We apply our method to mass cytometry and scRNA-seq datasets, and demonstrate that it effectively attenuates batch effects. Availability and Implementation our codes and data are publicly available at https://github.com/ushaham/BatchEffectRemoval.git. Contact yuval.kluger@yale.edu. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Uri Shaham
- Department of Statistics, Yale University, New Haven, CT 06511, USA
| | - Kelly P Stanton
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA.,Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Jun Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Huamin Li
- Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| | | | - Ruth Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Yuval Kluger
- Department of Pathology, Yale School of Medicine, New Haven, CT 06510, USA.,Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.,Applied Mathematics Program, Yale University, New Haven, CT 06511, USA
| |
Collapse
|
18
|
Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Correction: Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog 2017; 13:e1006646. [PMID: 28950012 PMCID: PMC5614647 DOI: 10.1371/journal.ppat.1006646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
19
|
Goods BA, Hernandez AL, Lowther DE, Lucca LE, Lerner BA, Gunel M, Raddassi K, Coric V, Hafler DA, Love JC. Functional differences between PD-1+ and PD-1- CD4+ effector T cells in healthy donors and patients with glioblastoma multiforme. PLoS One 2017; 12:e0181538. [PMID: 28880903 PMCID: PMC5589094 DOI: 10.1371/journal.pone.0181538] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 02/09/2017] [Accepted: 07/03/2017] [Indexed: 11/19/2022] Open
Abstract
Immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) have been highly successful in the treatment of cancer. While PD-1 expression has been widely investigated, its role in CD4+ effector T cells in the setting of health and cancer remains unclear, particularly in the setting of glioblastoma multiforme (GBM), the most aggressive and common form of brain cancer. We examined the functional and molecular features of PD-1+CD4+CD25-CD127+Foxp3-effector cells in healthy subjects and in patients with GBM. In healthy subjects, we found that PD-1+CD4+ effector cells are dysfunctional: they do not proliferate but can secrete large quantities of IFNγ. Strikingly, blocking antibodies against PD-1 did not rescue proliferation. RNA-sequencing revealed features of exhaustion in PD-1+ CD4 effectors. In the context of GBM, tumors were enriched in PD-1+ CD4+ effectors that were similarly dysfunctional and unable to proliferate. Furthermore, we found enrichment of PD-1+TIM-3+ CD4+ effectors in tumors, suggesting that co-blockade of PD-1 and TIM-3 in GBM may be therapeutically beneficial. RNA-sequencing of blood and tumors from GBM patients revealed distinct differences between CD4+ effectors from both compartments with enrichment in multiple gene sets from tumor infiltrating PD-1-CD4+ effectors cells. Enrichment of these gene sets in tumor suggests a more metabolically active cell state with signaling through other co-receptors. PD-1 expression on CD4 cells identifies a dysfunctional subset refractory to rescue with PD-1 blocking antibodies, suggesting that the influence of immune checkpoint inhibitors may involve recovery of function in the PD-1-CD4+ T cell compartment. Additionally, co-blockade of PD-1 and TIM-3 in GBM may be therapeutically beneficial.
Collapse
Affiliation(s)
- Brittany A. Goods
- Departments of Biological Engineering and Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Amanda L. Hernandez
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Daniel E. Lowther
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Liliana E. Lucca
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Benjamin A. Lerner
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Murat Gunel
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Khadir Raddassi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Vlad Coric
- Bristol-Myers Squibb, Wallingford, Connecticut, United States of America
| | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - J. Christopher Love
- Departments of Biological Engineering and Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
- The Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| |
Collapse
|
20
|
Askenase MH, Goods BA, Steinschneider AF, Raddassi K, Beatty H, Hafler DA, Love JC, Sansing LH. Abstract 213: Hematoma-infiltrating Macrophages Transition From Inflammatory to Reparative Programs in Patients After Intracerebral Hemorrhage. Stroke 2017. [DOI: 10.1161/str.48.suppl_1.213] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Intracerebral hemorrhage (ICH) causes rapid recruitment of circulating leukocytes to the injury; however, the roles of these cells in disease progression and repair in the brain are poorly understood. Findings from animal models have failed to translate into effective therapies for ICH, emphasizing the importance of studying the ICH immune response in the patient population. To gain insight into the inflammatory response in patient hematomas, we are utilizing mass cytometry, flow cytometry, and RNA-seq to characterize hematoma-infiltrating leukocytes isolated from ICH patients over a 5 day period, in conjunction with the ongoing MISTIE III trial for surgical evacuation of ICH. We have found that the hematoma immune infiltrate is predominantly composed of neutrophils and macrophages recruited from the circulation, rather than CNS-resident microglia. We have observed that hematoma macrophages have acquired a distinct phenotype differing from phagocyte populations in the peripheral blood, suggesting that their gene expression is controlled by local signals in the hematoma. Preliminary transcriptional analysis of hematoma macrophages 24-50 hours post-ICH has revealed an inflammatory profile characterized by increased expression of antigen presentation, TLR signaling, glycolytic metabolism, and prostaglandin production pathways (Figure 1). Intriguingly, by 100 hours post-ICH, macrophages downregulated these pathways and engaged a wound healing program characterized by TGF-beta signaling, fatty acid metabolism, and collagen deposition (Figure 1). These findings, in agreement with our previous results in animal models of ICH, suggest that recruited macrophages may contribute not only to initial inflammatory damage, but also to clearance of the hematoma and resolution of inflammation, making them potentially ideal targets for therapeutic intervention.
Collapse
Affiliation(s)
| | - Brittany A Goods
- Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA
| | | | | | | | | | | | | |
Collapse
|
21
|
Lindow JC, Wunder EA, Popper SJ, Min JN, Mannam P, Srivastava A, Yao Y, Hacker KP, Raddassi K, Lee PJ, Montgomery RR, Shaw AC, Hagan JE, Araújo GC, Nery N, Relman DA, Kim CC, Reis MG, Ko AI. Cathelicidin Insufficiency in Patients with Fatal Leptospirosis. PLoS Pathog 2016; 12:e1005943. [PMID: 27812211 PMCID: PMC5094754 DOI: 10.1371/journal.ppat.1005943] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 06/02/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
Leptospirosis causes significant morbidity and mortality worldwide; however, the role of the host immune response in disease progression and high case fatality (>10-50%) is poorly understood. We conducted a multi-parameter investigation of patients with acute leptospirosis to identify mechanisms associated with case fatality. Whole blood transcriptional profiling of 16 hospitalized Brazilian patients with acute leptospirosis (13 survivors, 3 deceased) revealed fatal cases had lower expression of the antimicrobial peptide, cathelicidin, and chemokines, but more abundant pro-inflammatory cytokine receptors. In contrast, survivors generated strong adaptive immune signatures, including transcripts relevant to antigen presentation and immunoglobulin production. In an independent cohort (23 survivors, 22 deceased), fatal cases had higher bacterial loads (P = 0.0004) and lower anti-Leptospira antibody titers (P = 0.02) at the time of hospitalization, independent of the duration of illness. Low serum cathelicidin and RANTES levels during acute illness were independent risk factors for higher bacterial loads (P = 0.005) and death (P = 0.04), respectively. To investigate the mechanism of cathelicidin in patients surviving acute disease, we administered LL-37, the active peptide of cathelicidin, in a hamster model of lethal leptospirosis and found it significantly decreased bacterial loads and increased survival. Our findings indicate that the host immune response plays a central role in severe leptospirosis disease progression. While drawn from a limited study size, significant conclusions include that poor clinical outcomes are associated with high systemic bacterial loads, and a decreased antibody response. Furthermore, our data identified a key role for the antimicrobial peptide, cathelicidin, in mounting an effective bactericidal response against the pathogen, which represents a valuable new therapeutic approach for leptospirosis.
Collapse
Affiliation(s)
- Janet C. Lindow
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Elsio A. Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Stephen J. Popper
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jin-na Min
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Praveen Mannam
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Anup Srivastava
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Yi Yao
- Section of Rheumatology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Kathryn P. Hacker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Patty J. Lee
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Ruth R. Montgomery
- Section of Rheumatology, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Albert C. Shaw
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jose E. Hagan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Guilherme C. Araújo
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Nivison Nery
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - David A. Relman
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America; Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
| | - Charles C. Kim
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Mitermayer G. Reis
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz, Ministério da Saúde, Salvador, Bahia, Brazil
| |
Collapse
|
22
|
Lowther DE, Goods BA, Lucca LE, Lerner BA, Raddassi K, van Dijk D, Hernandez AL, Duan X, Gunel M, Coric V, Krishnaswamy S, Love JC, Hafler DA. PD-1 marks dysfunctional regulatory T cells in malignant gliomas. JCI Insight 2016; 1. [PMID: 27182555 DOI: 10.1172/jci.insight.85935] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Immunotherapies targeting the immune checkpoint receptor programmed cell death protein 1 (PD-1) have shown remarkable efficacy in treating cancer. CD4+CD25hiFoxP3+ Tregs are critical regulators of immune responses in autoimmunity and malignancies, but the functional status of human Tregs expressing PD-1 remains unclear. We examined functional and molecular features of PD-1hi Tregs in healthy subjects and patients with glioblastoma multiforme (GBM), combining functional assays, RNA sequencing, and cytometry by time of flight (CyTOF). In both patients with GBM and healthy subjects, circulating PD-1hi Tregs displayed reduced suppression of CD4+ effector T cells, production of IFN-γ, and molecular signatures of exhaustion. Transcriptional profiling of tumor-resident Tregs revealed that several genes coexpressed with PD-1 and associated with IFN-γ production and exhaustion as well as enrichment in exhaustion signatures compared with circulating PD-1hi Tregs. CyTOF analysis of circulating and tumor-infiltrating Tregs from patients with GBM treated with PD-1-blocking antibodies revealed that treatment shifts the profile of circulating Tregs toward a more exhausted phenotype reminiscent of that of tumor-infiltrating Tregs, further increasing IFN-γ production. Thus, high PD-1 expression on human Tregs identifies dysfunctional, exhausted Tregs secreting IFN-γ that exist in healthy individuals and are enriched in tumor infiltrates, possibly losing function as they attempt to modulate the antitumoral immune responses.
Collapse
Affiliation(s)
- Daniel E Lowther
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Brittany A Goods
- Departments of Biological Engineering and Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Liliana E Lucca
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Benjamin A Lerner
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Khadir Raddassi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - David van Dijk
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Amanda L Hernandez
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Xiangguo Duan
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Murat Gunel
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA; Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Vlad Coric
- Bristol-Myers Squibb, Wallingford, Connecticut, USA
| | - Smita Krishnaswamy
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - J Christopher Love
- Departments of Biological Engineering and Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| |
Collapse
|
23
|
Cao Y, Goods BA, Raddassi K, Nepom GT, Kwok WW, Love JC, Hafler DA. Functional inflammatory profiles distinguish myelin-reactive T cells from patients with multiple sclerosis. Sci Transl Med 2016; 7:287ra74. [PMID: 25972006 DOI: 10.1126/scitranslmed.aaa8038] [Citation(s) in RCA: 215] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Myelin-reactive T cells have been identified in patients with multiple sclerosis (MS) and healthy subjects with comparable frequencies, but the contribution of these autoreactive T cells to disease pathology remains unknown. A total of 13,324 T cell libraries generated from blood of 23 patients and 22 healthy controls were interrogated for reactivity to myelin antigens. Libraries derived from CCR6(+) myelin-reactive T cells from patients with MS exhibited significantly enhanced production of interferon-γ (IFN-γ), interleukin-17 (IL-17), and granulocyte-macrophage colony-stimulating factor (GM-CSF) compared to healthy controls. Single-cell clones isolated by major histocompatibility complex/peptide tetramers from CCR6(+) T cell libraries also secreted more proinflammatory cytokines, whereas clones isolated from controls secreted more IL-10. The transcriptomes of myelin-specific CCR6(+) T cells from patients with MS were distinct from those derived from healthy controls and, notably, were enriched in T helper cell 17 (TH17)-induced experimental autoimmune encephalitis gene signatures, and gene signatures derived from TH17 cells isolated other human autoimmune diseases. These data, although not causal, imply that functional differences between antigen-specific T cells from MS and healthy controls are fundamental to disease development and support the notion that IL-10 production from myelin-reactive T cells may act to limit disease progression or even pathogenesis.
Collapse
Affiliation(s)
- Yonghao Cao
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Brittany A Goods
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Khadir Raddassi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gerald T Nepom
- Benaroya Research Institute, Virginia Mason Research Center, Seattle, WA 98101, USA
| | - William W Kwok
- Benaroya Research Institute, Virginia Mason Research Center, Seattle, WA 98101, USA. Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - J Christopher Love
- Department of Chemical Engineering, Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA. The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| |
Collapse
|
24
|
Finak G, Langweiler M, Jaimes M, Malek M, Taghiyar J, Korin Y, Raddassi K, Devine L, Obermoser G, Pekalski ML, Pontikos N, Diaz A, Heck S, Villanova F, Terrazzini N, Kern F, Qian Y, Stanton R, Wang K, Brandes A, Ramey J, Aghaeepour N, Mosmann T, Scheuermann RH, Reed E, Palucka K, Pascual V, Blomberg BB, Nestle F, Nussenblatt RB, Brinkman RR, Gottardo R, Maecker H, McCoy JP. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium. Sci Rep 2016; 6:20686. [PMID: 26861911 PMCID: PMC4748244 DOI: 10.1038/srep20686] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [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: 08/19/2015] [Accepted: 01/05/2016] [Indexed: 01/21/2023] Open
Abstract
Standardization of immunophenotyping requires careful attention to reagents, sample handling, instrument setup, and data analysis, and is essential for successful cross-study and cross-center comparison of data. Experts developed five standardized, eight-color panels for identification of major immune cell subsets in peripheral blood. These were produced as pre-configured, lyophilized, reagents in 96-well plates. We present the results of a coordinated analysis of samples across nine laboratories using these panels with standardized operating procedures (SOPs). Manual gating was performed by each site and by a central site. Automated gating algorithms were developed and tested by the FlowCAP consortium. Centralized manual gating can reduce cross-center variability, and we sought to determine whether automated methods could streamline and standardize the analysis. Within-site variability was low in all experiments, but cross-site variability was lower when central analysis was performed in comparison with site-specific analysis. It was also lower for clearly defined cell subsets than those based on dim markers and for rare populations. Automated gating was able to match the performance of central manual analysis for all tested panels, exhibiting little to no bias and comparable variability. Standardized staining, data collection, and automated gating can increase power, reduce variability, and streamline analysis for immunophenotyping.
Collapse
Affiliation(s)
- Greg Finak
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA
| | - Marc Langweiler
- Hematology Branch, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Mehrnoush Malek
- Terry Fox Laboratory , British Columbia Cancer Agency, V3J 4W6, Canada
| | - Jafar Taghiyar
- Terry Fox Laboratory , British Columbia Cancer Agency, V3J 4W6, Canada
| | - Yael Korin
- UCLA Pathology and Laboratory Medicine, Los Angeles, CA
| | | | - Lesley Devine
- Dept of Neurology, Yale School of Medicine, New Haven, CT
| | | | - Marcin L. Pekalski
- University of Cambridge, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Cambridge, UK
| | - Nikolas Pontikos
- University of Cambridge, JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Cambridge, UK
| | - Alain Diaz
- Dept Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Susanne Heck
- Guys and St Thomas Hospital, Guy’s Hospital, London, UK
| | | | - Nadia Terrazzini
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, United Kingdom
| | - Florian Kern
- Brighton and Sussex Medical School, Division of Medicine, Brighton, BN1 9PS, United Kingdom
| | - Yu Qian
- Department of Informatics, J. Craig Venter Institute, La Jolla, 92037, CA
| | - Rick Stanton
- Department of Informatics, J. Craig Venter Institute, La Jolla, 92037, CA
| | - Kui Wang
- School of Mathematics and Physics, University of Queensland, Brisbane, Australia
| | - Aaron Brandes
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John Ramey
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA
| | - Nima Aghaeepour
- Terry Fox Laboratory , British Columbia Cancer Agency, V3J 4W6, Canada
- Baxter Laboratory in Stem Cell Biology, Stanford University, Stanford, California, 94305, USA
| | - Tim Mosmann
- Hematology Branch, National Institutes of Health, Bethesda, Maryland, USA
- University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, 14642, NY
| | | | - Elaine Reed
- UCLA Pathology and Laboratory Medicine, Los Angeles, CA
| | | | | | - Bonnie B. Blomberg
- Dept Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL
| | - Frank Nestle
- Guys and St Thomas Hospital, Guy’s Hospital, London, UK
| | - Robert B. Nussenblatt
- Laboratory of Immunology, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ryan Remy Brinkman
- Terry Fox Laboratory , British Columbia Cancer Agency, V3J 4W6, Canada
- Department of Medical Genetics, University of British Columbia, Canada
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA
| | - Holden Maecker
- Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, 94305, CA
| | | |
Collapse
|
25
|
Tooley JE, Vudattu N, Choi J, Cotsapas C, Devine L, Raddassi K, Ehlers MR, McNamara JG, Harris KM, Kanaparthi S, Phippard D, Herold KC. Changes in T-cell subsets identify responders to FcR-nonbinding anti-CD3 mAb (teplizumab) in patients with type 1 diabetes. Eur J Immunol 2015; 46:230-41. [PMID: 26518356 DOI: 10.1002/eji.201545708] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 04/01/2015] [Revised: 08/30/2015] [Accepted: 10/16/2015] [Indexed: 12/15/2022]
Abstract
The mechanisms whereby immune therapies affect progression of type 1 diabetes (T1D) are not well understood. Teplizumab, an FcR nonbinding anti-CD3 mAb, has shown efficacy in multiple randomized clinical trials. We previously reported an increase in the frequency of circulating CD8(+) central memory (CD8CM) T cells in clinical responders, but the generalizability of this finding and the molecular effects of teplizumab on these T cells have not been evaluated. We analyzed data from two randomized clinical studies of teplizumab in patients with new- and recent-onset T1D. At the conclusion of therapy, clinical responders showed a significant reduction in circulating CD4(+) effector memory T cells. Afterward, there was an increase in the frequency and absolute number of CD8CM T cells. In vitro, teplizumab expanded CD8CM T cells by proliferation and conversion of non-CM T cells. Nanostring analysis of gene expression of CD8CM T cells from responders and nonresponders versus placebo-treated control subjects identified decreases in expression of genes associated with immune activation and increases in expression of genes associated with T-cell differentiation and regulation. We conclude that CD8CM T cells with decreased activation and regulatory gene expression are associated with clinical responses to teplizumab in patients with T1D.
Collapse
Affiliation(s)
- James E Tooley
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Nalini Vudattu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jinmyung Choi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Chris Cotsapas
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | - Lesley Devine
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA
| | | | - James G McNamara
- National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, MD, USA
| | | | | | | | - Kevan C Herold
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
26
|
Lowther DE, Weinhold K, Reap E, Vlahovic G, Omuro A, Sahebjam S, Baehring J, Voloschin A, Cloughesy T, Lim M, Coric V, Latek R, Simon J, Lerner B, Raddassi K, Hafler DA, Sampson J. CBM-06IMMUNE BIOMARKER RESULTS FROM A TRIAL OF NIVOLUMAB ± IPILIMUMAB IN PATIENTS WITH RECURRENT GLIOBLASTOMA: CHECKMATE-143. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov211.06] [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: 11/14/2022] Open
|
27
|
Lucca L, Goods BA, Lowther DE, Hernandez A, Lerner B, Gunel M, Raddassi K, Simon J, Latek R, Coric V, Love JC, Hafler DA. CBM-04PD-1 EXPRESSION IDENTIFIES EXHAUSTED TUMOR INFILTRATING REGULATORY T CELLS IN GLIOBLASTOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov211.04] [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: 11/14/2022] Open
|
28
|
Goods BA, Lowther DE, Lucca L, Hernandez A, Lerner B, Gunel M, Raddassi K, Simon J, Coric V, Love JC, Hafler DA. CBM-05FUNCTIONAL DIFFERENCES BETWEEN PD-1 +AND PD-1 –CD4 +T EFFECTOR CELLS IN HEALTHY DONORS AND PATIENTS WITH GLIOBLASTOMA. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov211.05] [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: 11/12/2022] Open
|
29
|
Mohanty S, Joshi SR, Ueda I, Wilson J, Blevins TP, Siconolfi B, Meng H, Devine L, Raddassi K, Tsang S, Belshe RB, Hafler DA, Kaech SM, Kleinstein SH, Trentalange M, Allore HG, Shaw AC. Prolonged proinflammatory cytokine production in monocytes modulated by interleukin 10 after influenza vaccination in older adults. J Infect Dis 2014; 211:1174-84. [PMID: 25367297 DOI: 10.1093/infdis/jiu573] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We evaluated in vivo innate immune responses in monocyte populations from 67 young (aged 21-30 years) and older (aged ≥65 years) adults before and after influenza vaccination. CD14(+)CD16(+) inflammatory monocytes were induced after vaccination in both young and older adults. In classical CD14(+)CD16(-) and inflammatory monocytes, production of tumor necrosis factor α and interleukin 6, as measured by intracellular staining, was strongly induced after vaccination. Cytokine production was strongly associated with influenza vaccine antibody response; the highest levels were found as late as day 28 after vaccination in young subjects and were substantially diminished in older subjects. Notably, levels of the anti-inflammatory cytokine interleukin 10 (IL-10) were markedly elevated in monocytes from older subjects before and after vaccination. In purified monocytes, we found age-associated elevation in phosphorylated signal transducer and activator of transcription-3, and decreased serine 359 phosphorylation of the negative IL-10 regulator dual-specificity phosphatase 1. These findings for the first time implicate dysregulated IL-10 production in impaired vaccine responses in older adults.
Collapse
Affiliation(s)
| | - Samit R Joshi
- Section of Infectious Diseases, Department of Internal Medicine
| | - Ikuyo Ueda
- Section of Infectious Diseases, Department of Internal Medicine
| | - Jean Wilson
- Section of Infectious Diseases, Department of Internal Medicine
| | - Tamara P Blevins
- Department of Center for Vaccine Development, Saint Louis University, Missouri
| | | | | | | | | | - Sui Tsang
- Section of Infectious Diseases, Department of Internal Medicine
| | - Robert B Belshe
- Department of Center for Vaccine Development, Saint Louis University, Missouri
| | | | | | - Steven H Kleinstein
- Department of Pathology Department of Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut
| | | | | | - Albert C Shaw
- Section of Infectious Diseases, Department of Internal Medicine
| |
Collapse
|
30
|
Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N. Common genetic variants modulate pathogen-sensing responses in human dendritic cells. Science 2014; 343:1246980. [PMID: 24604203 DOI: 10.1126/science.1246980] [Citation(s) in RCA: 317] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Little is known about how human genetic variation affects the responses to environmental stimuli in the context of complex diseases. Experimental and computational approaches were applied to determine the effects of genetic variation on the induction of pathogen-responsive genes in human dendritic cells. We identified 121 common genetic variants associated in cis with variation in expression responses to Escherichia coli lipopolysaccharide, influenza, or interferon-β (IFN-β). We localized and validated causal variants to binding sites of pathogen-activated STAT (signal transducer and activator of transcription) and IRF (IFN-regulatory factor) transcription factors. We also identified a common variant in IRF7 that is associated in trans with type I IFN induction in response to influenza infection. Our results reveal common alleles that explain interindividual variation in pathogen sensing and provide functional annotation for genetic variants that alter susceptibility to inflammatory diseases.
Collapse
Affiliation(s)
- Mark N Lee
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA 02142, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Vargas-Lowy D, Kivisäkk P, Gandhi R, Raddassi K, Soltany P, Gorman MP, Khoury SJ, Chitnis T. Increased Th17 response to myelin peptides in pediatric MS. Clin Immunol 2012; 146:176-84. [PMID: 23352968 DOI: 10.1016/j.clim.2012.12.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 11/02/2012] [Accepted: 12/18/2012] [Indexed: 12/21/2022]
Abstract
Studies of the underlying immune mechanisms of multiple sclerosis (MS) in children may shed light on the initial events of MS pathogenesis. We studied T cell responses to myelin peptides in 10 pediatric MS patients (PMS), 10 pediatric healthy controls (PHC), 10 adult MS patients (AMS) and 10 adult healthy controls (AHC). A significantly higher proportion of divided CD4+ T cell responses in response to myelin peptides by the CFSE assay in PMS compared to PHC at both concentrations of myelin peptide tested (t test, 95% CI, p=0.0067 for MP1; p=0.0086 for MP10), and between PMS and AMS (p=0.0012 at 1 μg/mL of myelin peptides, p<0.0001 at 10 μg/mL) was found. In addition, T cells with a central memory phenotype producing IL-17 were increased in PMS compared to PHC (p<0.05). IL-7 levels in culture supernatants were elevated in PMS compared to PHC and AMS (t test<0.01).
Collapse
Affiliation(s)
- David Vargas-Lowy
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Vargas-Lowy D, Kivisaak P, Ghandi R, Raddassi K, Gorman M, Khoury S, Chitnis T. Increased Th17 Central Memory Response to Myelin Peptides in Pediatric Multiple Sclerosis (S60.005). Neurology 2012. [DOI: 10.1212/wnl.78.1_meetingabstracts.s60.005] [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: 11/15/2022] Open
|
33
|
Raddassi K, Kent SC, Yang J, Bourcier K, Bradshaw EM, Seyfert-Margolis V, Nepom GT, Kwok WW, Hafler DA. Increased frequencies of myelin oligodendrocyte glycoprotein/MHC class II-binding CD4 cells in patients with multiple sclerosis. J Immunol 2011; 187:1039-46. [PMID: 21653833 DOI: 10.4049/jimmunol.1001543] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by infiltration of pathogenic immune cells in the CNS resulting in destruction of the myelin sheath and surrounding axons. We and others have previously measured the frequency of human myelin-reactive T cells in peripheral blood. Using T cell cloning techniques, a modest increase in the frequency of myelin-reactive T cells in patients as compared with control subjects was observed. In this study, we investigated whether myelin oligodendrocyte glycoprotein (MOG)-specific T cells could be detected and their frequency was measured using DRB1*0401/MOG(97-109(107E-S)) tetramers in MS subjects and healthy controls expressing HLA class II DRB1*0401. We defined the optimal culture conditions for expansion of MOG-reactive T cells upon MOG peptide stimulation of PMBCs. MOG(97-109)-reactive CD4(+) T cells, isolated with DRB1*0401/MOG(97-109) tetramers, and after a short-term culture of PMBCs with MOG(97-109) peptides, were detected more frequently from patients with MS as compared with healthy controls. T cell clones from single cell cloning of DRB1*0401/MOG(97-109(107E-S)) tetramer(+) cells confirmed that these T cell clones were responsive to both the native and the substituted MOG peptide. These data indicate that autoantigen-specific T cells can be detected and enumerated from the blood of subjects using class II tetramers, and the frequency of MOG(97-109)-reactive T cells is greater in patients with MS as compared with healthy controls.
Collapse
Affiliation(s)
- Khadir Raddassi
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510-8018, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Lv H, Havari E, Pinto S, Gottumukkala RVSRK, Cornivelli L, Raddassi K, Matsui T, Rosenzweig A, Bronson RT, Smith R, Fletcher AL, Turley SJ, Wucherpfennig K, Kyewski B, Lipes MA. Impaired thymic tolerance to α-myosin directs autoimmunity to the heart in mice and humans. J Clin Invest 2011; 121:1561-73. [PMID: 21436590 DOI: 10.1172/jci44583] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 01/19/2011] [Indexed: 01/25/2023] Open
Abstract
Autoimmunity has long been linked to myocarditis and its sequela, dilated cardiomyopathy, the leading causes of heart failure in young patients. However, the underlying mechanisms are poorly defined, with most clinical investigations focused on humoral autoimmunity as the target for intervention. Here, we show that the α-isoform of myosin heavy chain (α-MyHC, which is encoded by the gene Myh6) is the pathogenic autoantigen for CD4+ T cells in a spontaneous mouse model of myocarditis. Further, we found that Myh6 transcripts were absent in mouse medullary thymic epithelial cells (mTECs) and peripheral lymphoid stromal cells, which have been implicated in mediating central and peripheral T cell tolerance, respectively. Transgenic expression of α-MyHC in thymic epithelium conferred tolerance to cardiac myosin and prevented myocarditis, demonstrating that α-MyHC is a primary autoantigen in this disease process. Remarkably, we found that humans also lacked α-MyHC in mTECs and had high frequencies of α-MyHC-specific T cells in peripheral blood, with markedly augmented T cell responses to α-MyHC in patients with myocarditis. Since α-MyHC constitutes a small fraction of MyHC in human heart, these findings challenge the longstanding notion that autoimmune targeting of MyHC is due to its cardiac abundance and instead suggest that it is targeted as a result of impaired T cell tolerance mechanisms. These results thus support a role for T cell-specific therapies for myocarditis.
Collapse
Affiliation(s)
- Huijuan Lv
- Joslin Diabetes Center, Boston, Massachusetts 02215, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Song Q, Han Q, Bradshaw EM, Kent SC, Raddassi K, Nilsson B, Nepom GT, Hafler DA, Love JC. On-chip activation and subsequent detection of individual antigen-specific T cells. Anal Chem 2010; 82:473-7. [PMID: 20000848 DOI: 10.1021/ac9024363] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The frequencies of antigen-specific CD4+ T cells in samples of human tissue have been difficult to determine accurately ex vivo, particularly for autoimmune diseases such as multiple sclerosis or type 1 diabetes. Conventional approaches involve the expansion of primary T cells in vitro to increase the numbers of cells, and a subsequent assessment of the frequencies of antigen-specific T cells in the expanded population by limiting dilution or by using fluorescently labeled tetramers of peptide-loaded major histocompatibility complex (MHC) receptors. Here we describe an alternative approach that uses arrays of subnanoliter wells coated with recombinant peptide-loaded MHC class II monomers to isolate and stimulate individual CD4+ T cells in an antigen-specific manner. In these experiments, activation was monitored using microengraving to capture two cytokines (IFNgamma and IL-17) released from single cells. This new method should enable direct enumeration of antigen-specific CD4+ T cells ex vivo from clinical samples.
Collapse
Affiliation(s)
- Qing Song
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
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]
|
37
|
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]
|
38
|
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]
|
39
|
Bradshaw EM, Raddassi K, Elyaman W, Orban T, Gottlieb PA, Kent SC, Hafler DA. Monocytes from patients with type 1 diabetes spontaneously secrete proinflammatory cytokines inducing Th17 cells. J Immunol 2009; 183:4432-9. [PMID: 19748982 DOI: 10.4049/jimmunol.0900576] [Citation(s) in RCA: 199] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Autoimmune diseases including type 1 diabetes (T1D) are thought to have a Th1/Th17 bias. The underlying mechanisms driving the activation and differentiation of these proinflammatory T cells are unknown. We examined the monocytes isolated directly from the blood of T1D patients and found they spontaneously secreted the proinflammatory cytokines IL-1beta and IL-6, which are known to induce and expand Th17 cells. Moreover, these in vivo-activated monocytes from T1D subjects induced more IL-17-secreting cells from memory T cells compared with monocytes from healthy control subjects. The induction of IL-17-secreting T cells by monocytes from T1D subjects was reduced in vitro with a combination of an IL-6-blocking Ab and IL-1R antagonist. In this study, we report a significant although modest increase in the frequency of IL-17-secreting cells in lymphocytes from long-term patients with T1D compared with healthy controls. These data suggest that the innate immune system in T1D may drive the adaptive immune system by expanding the Th17 population of effector T cells.
Collapse
Affiliation(s)
- Elizabeth M Bradshaw
- Division of Molecular Immunology, Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
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]
|
41
|
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]
|
42
|
Starossom S, Imitola J, Raddassi K, Elyaman W, Rabinovich G, Khoury S. OR.29. Galectin-1 Modulates Microglia Activation and Promotes Regeneration in a Model of Multiple Sclerosis. Clin Immunol 2009. [DOI: 10.1016/j.clim.2009.03.036] [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: 11/26/2022]
|
43
|
Asare AL, Kolchinsky SA, Gao Z, Wang R, Raddassi K, Bourcier K, Seyfert-Margolis V. Differential gene expression profiles are dependent upon method of peripheral blood collection and RNA isolation. BMC Genomics 2008; 9:474. [PMID: 18847473 PMCID: PMC2573897 DOI: 10.1186/1471-2164-9-474] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 10/10/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA isolation and purification steps greatly influence the results of gene expression profiling. There are two commercially available products for whole blood RNA collection, PAXgene and Tempus blood collection tubes, and each comes with their own RNA purification method. In both systems the blood is immediately lysed when collected into the tube and RNA stabilized using proprietary reagents. Both systems enable minimal blood handling procedures thus minimizing the risk of inducing changes in gene expression through blood handling or processing. Because the RNA purification steps could influence the total RNA pool, we examined the impact of RNA isolation, using the PAXgene or Tempus method, on gene expression profiles. RESULTS Using microarrays as readout of RNA from stimulated whole blood we found a common set of expressed transcripts in RNA samples from either PAXgene or Tempus. However, we also found several to be uniquely expressed depending on the type of collection tube, suggesting that RNA purification methods impact results of differential gene expression profiling. Specifically, transcripts for several known PHA-inducible genes, including IFNgamma, IL13, IL2, IL3, and IL4 were found to be upregulated in stimulated vs. control samples when RNA was isolated using the ABI Tempus method, but not using the PAXgene method (p < 0.01, FDR corrected). Sequenom Quantiative Gene Expression (QGE) (SanDiego, CA) measures confirmed IL2, IL4 and IFNgamma up-regulation in Tempus purified RNA from PHA stimulated cells while only IL2 was up-regulated using PAXgene purified (p < 0.05). CONCLUSION Here, we demonstrate that peripheral blood RNA isolation methods can critically impact differential expression results, particularly in the clinical setting where fold-change differences are typically small and there is inherent variability within biological cohorts. A modified method based upon the Tempus system was found to provide high yield, good post-hybridization array quality, low variability in expression measures and was shown to produce differential expression results consistent with the predicted immunologic effects of PHA stimulation.
Collapse
Affiliation(s)
- Adam L Asare
- University of California, San Francisco, Immune Tolerance Network, 3 Bethesda Metro Suite 400, Bethesda, MD 20814, USA.
| | | | | | | | | | | | | |
Collapse
|
44
|
Elyaman W, Kivisäkk P, Reddy J, Chitnis T, Raddassi K, Imitola J, Bradshaw E, Kuchroo VK, Yagita H, Sayegh MH, Khoury SJ. Distinct functions of autoreactive memory and effector CD4+ T cells in experimental autoimmune encephalomyelitis. Am J Pathol 2008; 173:411-22. [PMID: 18583313 DOI: 10.2353/ajpath.2008.080142] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The persistence of human autoimmune diseases is thought to be mediated predominantly by memory T cells. We investigated the phenotype and migration of memory versus effector T cells in vivo in experimental autoimmune encephalomyelitis (EAE). We found that memory CD4(+) T cells up-regulated the activation marker CD44 as well as CXCR3 and ICOS, proliferated more and produced more interferon-gamma and less interleukin-17 compared to effector T cells. Moreover, adoptive transfer of memory T cells into T cell receptor (TCR)alphabeta(-/-) recipients induced more severe disease than did effector CD4(+) T cells with marked central nervous system inflammation and axonal damage. The uniqueness of disease mediated by memory T cells was confirmed by the differential susceptibility to immunomodulatory therapies in vivo. CD28-B7 T cell costimulatory signal blockade by CTLA4Ig suppressed effector cell-mediated EAE but had minimal effects on disease induced by memory cells. In contrast, ICOS-B7h blockade exacerbated effector T cell-induced EAE but protected from disease induced by memory T cells. However, blockade of the OX40 (CD134) costimulatory pathway ameliorated disease mediated by both memory and effector T cells. Our data extend the understanding of the pathogenicity of autoreactive memory T cells and have important implications for the development of novel therapies for human autoimmune diseases.
Collapse
Affiliation(s)
- Wassim Elyaman
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
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]
|
46
|
Chitnis T, Imitola J, Wang Y, Elyaman W, Chawla P, Sharuk M, Raddassi K, Bronson RT, Khoury SJ. Elevated neuronal expression of CD200 protects Wlds mice from inflammation-mediated neurodegeneration. Am J Pathol 2007; 170:1695-712. [PMID: 17456775 PMCID: PMC1854964 DOI: 10.2353/ajpath.2007.060677] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/16/2007] [Indexed: 02/05/2023]
Abstract
Axonal damage secondary to inflammation is likely the substrate of chronic disability in multiple sclerosis and is found in the animal model of experimental autoimmune encephalomyelitis (EAE). Wld(s) mice have a triplication of the fusion gene Ube4b/Nmnat and a phenotype of axon protection. Wld(s) mice develop an attenuated disease course of EAE, with decreased demyelination, reduced axonal pathology, and decreased central nervous system (CNS) macrophage and microglial accumulation. We show that attenuated disease in Wld(s) mice was associated with robust constitutive expression of the nonsignaling CD200 molecule on neurons in the CNS compared with control mice. CD200 interacts with its signaling receptor CD200R, which we found to be expressed on microglia, astrocytes, and oligodendrocytes at similar levels in control and Wld(s) mice. Administration of blocking anti-CD200 antibody to Wld(s) mice abrogated disease attenuation and was associated with increased CNS inflammation and neurodegeneration. In vitro, Wld(s) neuronal cultures were protected from microglial-induced neurotoxicity compared with control cultures, but protection was abrogated by anti-CD200 antibody. The CD200-CD200R pathway plays a critical role in attenuating EAE and reducing inflammation-mediated damage in the CNS. Strategies that up-regulate the expression of CD200 in the CNS or molecules that ligate the CD200R may be relevant as neuroprotective strategies in multiple sclerosis.
Collapse
MESH Headings
- Animals
- Antigens, CD/biosynthesis
- Blotting, Western
- Cell Proliferation
- Demyelinating Diseases/metabolism
- Demyelinating Diseases/pathology
- Encephalomyelitis, Autoimmune, Experimental/immunology
- Encephalomyelitis, Autoimmune, Experimental/metabolism
- Encephalomyelitis, Autoimmune, Experimental/pathology
- Enzyme-Linked Immunosorbent Assay
- Female
- Flow Cytometry
- Fluorescent Antibody Technique
- Immunoprecipitation
- Inflammation/immunology
- Inflammation/metabolism
- Inflammation/pathology
- Interleukin-6/metabolism
- Interleukins/metabolism
- Macrophage Activation/immunology
- Membrane Glycoproteins/metabolism
- Mice
- Microscopy, Confocal
- Microscopy, Electron, Transmission
- Nerve Degeneration/immunology
- Nerve Degeneration/physiopathology
- Neuroglia/metabolism
- Neurons/metabolism
- Neurons/pathology
- Spinal Cord/pathology
Collapse
Affiliation(s)
- Tanuja Chitnis
- Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Raddassi K, Bouchier K, Estevam J, Seyfert-Margolis V, Hafler D. Elifacs: A Multiplex Assay to Detect Antigen Specific T Cells and to Monitor the Immune Response. Clin Immunol 2007. [DOI: 10.1016/j.clim.2007.03.538] [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]
|
48
|
Raddassi K, Bourcier K, Estevam J, Seyfert-Margolis V, Hafler D. Improving Elispot to Detect Antigen Specific T Cells. Clin Immunol 2007. [DOI: 10.1016/j.clim.2007.03.078] [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: 11/30/2022]
|
49
|
Raddassi K, Estevam J, Bourcier K, Gisler T, Hafler D, Seyfert-Margolis V. Sa.128. Comparison of Two Methods to Isolate Mononuclear Cells from Peripheral Blood On Viability and Function of Freshly and Cryopreserved PBMCS. Clin Immunol 2006. [DOI: 10.1016/j.clim.2006.04.360] [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: 11/26/2022]
|
50
|
Kutok JL, Yang X, Folkerth RD, Imitola J, Raddassi K, Yano Y, Salahuddin S, Lawitts J, Imboden H, Chinami M, Shirakawa T, Turner H, Khoury S, Sayegh MH, Scadden D, Adra C. The cell cycle associated protein, HTm4, is expressed in differentiating cellsof the hematopoietic and central nervous system in mice. J Mol Histol 2005; 36:77-87. [PMID: 15704002 DOI: 10.1007/s10735-004-3913-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 07/23/2004] [Revised: 09/15/2004] [Indexed: 11/28/2022]
Abstract
HTm4 is a member of a newly defined family of human and murine proteins, the MS4 (membrane-spanning four) protein group, which has a distinctive four-transmembrane structure. MS4 protein functions include roles as cell surface signaling receptors and intracellular adapter proteins. We have previously demonstrated that HTm4 regulates the function of the KAP phosphatase, a key regulator of cell cycle progression. In humans, the expression of HTm4 is largely restricted to cells of the hematopoietic lineage, possibly reflecting a causal role for this molecule in differentiation/proliferation of hematopoietic lineage cells. In this study, we show that, like the human homologue, murine HTm4 is also predominantly a hematopoietic protein with distinctive expression patterns in developing murine embryos and in adult animals. In addition, we observed that murine HTm4 is highly expressed in the developing and adult murine nervous system, suggesting a previously unrecognized role in central and peripheral nervous system development.
Collapse
Affiliation(s)
- Jeffery L Kutok
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|