1
|
Cross AH, Gelfand JM, Thebault S, Bennett JL, von Büdingen HC, Cameron B, Carruthers R, Edwards K, Fallis R, Gerstein R, Giacomini PS, Greenberg B, Hafler DA, Ionete C, Kaunzner UW, Kodama L, Lock C, Longbrake EE, Musch B, Pardo G, Piehl F, Weber MS, Yuen S, Ziemssen T, Bose G, Freedman MS, Anania VG, Ramesh A, Winger RC, Jia X, Herman A, Harp C, Bar-Or A. Emerging Cerebrospinal Fluid Biomarkers of Disease Activity and Progression in Multiple Sclerosis. JAMA Neurol 2024:2816158. [PMID: 38466277 DOI: 10.1001/jamaneurol.2024.0017] [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: 03/12/2024]
Abstract
Importance Biomarkers distinguishing nonrelapsing progressive disease biology from relapsing biology in multiple sclerosis (MS) are lacking. Cerebrospinal fluid (CSF) is an accessible fluid that most closely reflects central nervous system biology. Objective To identify CSF biological measures associated with progressive MS pathobiology. Design, Setting, and Participants This cohort study assessed data from 2 prospective MS cohorts: a test cohort provided serial CSF, clinical, and imaging assessments in a multicenter study of patients with relapsing MS (RMS) or primary progressive MS (PPMS) who were initiating anti-CD20 treatment (recruitment: 2016-2018; analysis: 2020-2023). A single-site confirmation cohort was used to assess CSF at baseline and long-term (>10 year) clinical follow-up (analysis: 2022-2023). Exposures Test-cohort participants initiated standard-of-care ocrelizumab treatment. Confirmation-cohort participants were untreated or received standard-of-care disease-modifying MS therapies. Main Outcomes and Measures Twenty-five CSF markers, including neurofilament light chain, neurofilament heavy chain, and glial fibrillary acid protein (GFAP); 24-week confirmed disability progression (CDP24); and brain magnetic resonance imaging measures reflecting focal injury, tissue loss, and progressive biology (slowly expanding lesions [SELs]). Results The test cohort (n = 131) included 100 patients with RMS (mean [SD] age, 36.6 [10.4] years; 68 [68%] female and 32 [32%] male; Expanded Disability Status Scale [EDSS] score, 0-5.5), and 31 patients with PPMS (mean [SD] age, 44.9 [7.4] years; 15 [48%] female and 16 [52%] male; EDSS score, 3.0-6.5). The confirmation cohort (n = 68) included 41 patients with RMS and 27 with PPMS enrolled at diagnosis (age, 40 years [range, 20-61 years]; 47 [69%] female and 21 [31%] male). In the test cohort, GFAP was correlated with SEL count (r = 0.33), greater proportion of T2 lesion volume from SELs (r = 0.24), and lower T1-weighted intensity within SELs (r = -0.33) but not with acute inflammatory measures. Neurofilament heavy chain was correlated with SEL count (r = 0.25) and lower T1-weighted intensity within SELs (r = -0.28). Immune markers correlated with measures of acute inflammation and, unlike GFAP, were impacted by anti-CD20. In the confirmation cohort, higher baseline CSF GFAP levels were associated with long-term CDP24 (hazard ratio, 2.1; 95% CI, 1.3-3.4; P = .002). Conclusions and Relevance In this study, activated glial markers (in particular GFAP) and neurofilament heavy chain were associated specifically with nonrelapsing progressive disease outcomes (independent of acute inflammatory activity). Elevated CSF GFAP was associated with long-term MS disease progression.
Collapse
Affiliation(s)
- Anne H Cross
- Washington University School of Medicine, St Louis, Missouri
| | | | - Simon Thebault
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | | | | | | | | | | | - Robert Fallis
- The Ohio State University Wexner Medical Center, Columbus
| | | | | | | | | | | | | | - Lay Kodama
- Genentech, South San Francisco, California
| | | | | | | | | | | | - Martin S Weber
- Institute of Neuropathology, Department of Neurology, University Medical Center, Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology, Göttingen, Germany
| | | | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Carl Gustav Carus University Clinic, Dresden, Germany
| | - Gauruv Bose
- Department of Medicine in Neurology, University of Ottawa, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Mark S Freedman
- Department of Medicine in Neurology, University of Ottawa, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | | | | | | | - Ann Herman
- Genentech, South San Francisco, California
| | | | - Amit Bar-Or
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| |
Collapse
|
2
|
Sumida TS, Cheru NT, Hafler DA. The regulation and differentiation of regulatory T cells and their dysfunction in autoimmune diseases. Nat Rev Immunol 2024:10.1038/s41577-024-00994-x. [PMID: 38374298 DOI: 10.1038/s41577-024-00994-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/15/2024] [Indexed: 02/21/2024]
Abstract
The discovery of FOXP3+ regulatory T (Treg) cells as a distinct cell lineage with a central role in regulating immune responses provided a deeper understanding of self-tolerance. The transcription factor FOXP3 serves a key role in Treg cell lineage determination and maintenance, but is not sufficient to enable the full potential of Treg cell suppression, indicating that other factors orchestrate the fine-tuning of Treg cell function. Moreover, FOXP3-independent mechanisms have recently been shown to contribute to Treg cell dysfunction. FOXP3 mutations in humans cause lethal fulminant systemic autoinflammation (IPEX syndrome). However, it remains unclear to what degree Treg cell dysfunction is contributing to the pathophysiology of common autoimmune diseases. In this Review, we discuss the origins of Treg cells in the periphery and the multilayered mechanisms by which Treg cells are induced, as well as the FOXP3-dependent and FOXP3-independent cellular programmes that maintain the suppressive function of Treg cells in humans and mice. Further, we examine evidence for Treg cell dysfunction in the context of common autoimmune diseases such as multiple sclerosis, inflammatory bowel disease, systemic lupus erythematosus and rheumatoid arthritis.
Collapse
Affiliation(s)
- Tomokazu S Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.
| | - Nardos T Cheru
- Department of Immunobiology, 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.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
3
|
Wei J, Moon J, Yasumizu Y, Zhang L, Radassi K, Buitrago-Pocasangre N, Deerhake ME, Strauli N, Chan A, Herman A, Pedotte R, Raposo C, Tackenberg B, Yim I, Pappalardo J, Longbrake EE, Sumida TS, Axisa PP, Hafler DA. Systems Analysis of Immune Changes after B-cell Depletion in Autoimmune Multiple Sclerosis. bioRxiv 2024:2024.02.07.576204. [PMID: 38370778 PMCID: PMC10871268 DOI: 10.1101/2024.02.07.576204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Multiple sclerosis (MS) is a complex genetically mediated autoimmune disease of the central nervous system where anti-CD20-mediated B cell depletion is remarkably effective in the treatment of early disease. While previous studies investigated the effect of B cell depletion on select immune cell subsets using flow cytometry-based methods, the therapeutic impact on patient immune landscape is unknown. In this study, we explored how a therapy-driven " in vivo perturbation " modulates the diverse immune landscape by measuring transcriptomic granularity with single-cell RNA sequencing (scRNAseq). We demonstrate that B cell depletion leads to cell type-specific changes in the abundance and function of CSF macrophages and peripheral blood monocytes. Specifically, a CSF-specific macrophage population with an anti-inflammatory transcriptomic signature and peripheral CD16 + monocytes increased in frequency post-B cell depletion. In addition, we observed increases in TNFα messenger RNA and protein in monocytes post-B cell depletion, consistent with the finding that anti-TNFα treatment exacerbates autoimmune activity in MS. In parallel, B cell depletion also induced changes in peripheral CD4 + T cell populations, including increases in the frequency of TIGIT + regulatory T cells and marked decreases in the frequency of myelin peptide loaded-tetramer binding CD4 + T cells. Collectively, this study provides an exhaustive transcriptomic map of immunological changes, revealing different mechanisms of action contributing to the high efficacy in B cell depletion treatment of MS.
Collapse
|
4
|
Ozonoff A, Jayavelu ND, Liu S, Melamed E, Milliren CE, Qi J, Geng LN, McComsey GA, Cairns CB, Baden LR, Schaenman J, Shaw AC, Samaha H, Seyfert-Margolis V, Krammer F, Rosen LB, Steen H, Syphurs C, Dandekar R, Shannon CP, Sekaly RP, Ehrlich LIR, Corry DB, Kheradmand F, Atkinson MA, Brakenridge SC, Higuita NIA, Metcalf JP, Hough CL, Messer WB, Pulendran B, Nadeau KC, Davis MM, Sesma AF, Simon V, van Bakel H, Kim-Schulze S, Hafler DA, Levy O, Kraft M, Bime C, Haddad EK, Calfee CS, Erle DJ, Langelier CR, Eckalbar W, Bosinger SE, Peters B, Kleinstein SH, Reed EF, Augustine AD, Diray-Arce J, Maecker HT, Altman MC, Montgomery RR, Becker PM, Rouphael N. Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study. Nat Commun 2024; 15:216. [PMID: 38172101 PMCID: PMC10764789 DOI: 10.1038/s41467-023-44090-5] [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: 03/17/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Post-acute sequelae of SARS-CoV-2 (PASC) is a significant public health concern. We describe Patient Reported Outcomes (PROs) on 590 participants prospectively assessed from hospital admission for COVID-19 through one year after discharge. Modeling identified 4 PRO clusters based on reported deficits (minimal, physical, mental/cognitive, and multidomain), supporting heterogenous clinical presentations in PASC, with sub-phenotypes associated with female sex and distinctive comorbidities. During the acute phase of disease, a higher respiratory SARS-CoV-2 viral burden and lower Receptor Binding Domain and Spike antibody titers were associated with both the physical predominant and the multidomain deficit clusters. A lower frequency of circulating B lymphocytes by mass cytometry (CyTOF) was observed in the multidomain deficit cluster. Circulating fibroblast growth factor 21 (FGF21) was significantly elevated in the mental/cognitive predominant and the multidomain clusters. Future efforts to link PASC to acute anti-viral host responses may help to better target treatment and prevention of PASC.
Collapse
Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Carly E Milliren
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Jingjing Qi
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Grace A McComsey
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | - Lindsey R Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Albert C Shaw
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | | | | | | | - Lindsey B Rosen
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - Hanno Steen
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Caitlin Syphurs
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Ravi Dandekar
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Casey P Shannon
- Centre for Heart Lung Innovation, Providence Research, St. Paul's Hospital, and the PROOF Centre of Excellence, Vancouver, BC, Canada
| | - Rafick P Sekaly
- Case Western Reserve University and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | - David B Corry
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Farrah Kheradmand
- Baylor College of Medicine, and the Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Mark A Atkinson
- University of Florida/University of South Florida, Tampa, FL, USA
| | | | | | - Jordan P Metcalf
- Oklahoma University Health Sciences Center, Oklahoma City, OK, USA
| | | | | | | | | | | | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - David A Hafler
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | | | | | - Elias K Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, USA
| | - Carolyn S Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - David J Erle
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Charles R Langelier
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Walter Eckalbar
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Steven H Kleinstein
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Elaine F Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Ruth R Montgomery
- Yale School of Medicine, and Yale School of Public Health, New Haven, CT, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | | |
Collapse
|
5
|
Zhu B, Wang Y, Ku LT, van Dijk D, Zhang L, Hafler DA, Zhao H. scNAT: a deep learning method for integrating paired single-cell RNA and T cell receptor sequencing profiles. Genome Biol 2023; 24:292. [PMID: 38111007 PMCID: PMC10726524 DOI: 10.1186/s13059-023-03129-y] [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: 05/30/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023] Open
Abstract
Many deep learning-based methods have been proposed to handle complex single-cell data. Deep learning approaches may also prove useful to jointly analyze single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor sequencing (scTCR-seq) data for novel discoveries. We developed scNAT, a deep learning method that integrates paired scRNA-seq and scTCR-seq data to represent data in a unified latent space for downstream analysis. We demonstrate that scNAT is capable of removing batch effects, and identifying cell clusters and a T cell migration trajectory from blood to cerebrospinal fluid in multiple sclerosis.
Collapse
Affiliation(s)
- Biqing Zhu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Yuge Wang
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - Li-Ting Ku
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA
| | - David van Dijk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06511, USA
- Department of Computer Science, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Le Zhang
- Department of Neuroscience, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Department of Immunobiology, School of Medicine, Yale University, New Haven, CT, 06511, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, USA, MD , 20815
| | - Hongyu Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA.
- Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, 06511, USA.
| |
Collapse
|
6
|
Lee HJ, Zhao Y, Fleming I, Mehta S, Wang X, Wyk BV, Ronca SE, Kang H, Chou CH, Fatou B, Smolen KK, Levy O, Clish CB, Xavier RJ, Steen H, Hafler DA, Love JC, Shalek AK, Guan L, Murray KO, Kleinstein SH, Montgomery RR. Early cellular and molecular signatures correlate with severity of West Nile virus infection. iScience 2023; 26:108387. [PMID: 38047068 PMCID: PMC10692672 DOI: 10.1016/j.isci.2023.108387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/04/2023] [Accepted: 10/27/2023] [Indexed: 12/05/2023] Open
Abstract
Infection with West Nile virus (WNV) drives a wide range of responses, from asymptomatic to flu-like symptoms/fever or severe cases of encephalitis and death. To identify cellular and molecular signatures distinguishing WNV severity, we employed systems profiling of peripheral blood from asymptomatic and severely ill individuals infected with WNV. We interrogated immune responses longitudinally from acute infection through convalescence employing single-cell protein and transcriptional profiling complemented with matched serum proteomics and metabolomics as well as multi-omics analysis. At the acute time point, we detected both elevation of pro-inflammatory markers in innate immune cell types and reduction of regulatory T cell activity in participants with severe infection, whereas asymptomatic donors had higher expression of genes associated with anti-inflammatory CD16+ monocytes. Therefore, we demonstrated the potential of systems immunology using multiple cell-type and cell-state-specific analyses to identify correlates of infection severity and host cellular activity contributing to an effective anti-viral response.
Collapse
Affiliation(s)
- Ho-Joon Lee
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yujiao Zhao
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Ira Fleming
- The Institute of Medical Science and Engineering, Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Sameet Mehta
- Department of Genetics and Yale Center for Genome Analysis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiaomei Wang
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Brent Vander Wyk
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shannon E. Ronca
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
| | - Heather Kang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chih-Hung Chou
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benoit Fatou
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kinga K. Smolen
- Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Ofer Levy
- Department of Infectious Disease, Precision Vaccines Program, Boston Children’s Hospital, and Harvard Medical School, Boston, MA 02115, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Computational and Integrative Biology and Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hanno Steen
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
| | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - J. Christopher Love
- The Institute of Medical Science and Engineering, Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alex K. Shalek
- The Institute of Medical Science and Engineering, Department of Chemistry, and Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Leying Guan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06520, USA
| | - Kristy O. Murray
- Department of Pediatrics, National School of Tropical Medicine, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX 77030, USA
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | - Ruth R. Montgomery
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
7
|
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, Agudelo Higuita NI, Metcalf JP, Atkinson MA, Brakenridge SC, Corry D, Kheradmand F, Ehrlich LIR, Melamed E, McComsey GA, Sekaly R, Diray-Arce J, Peters B, Augustine AD, Reed EF, Altman MC, Becker PM, Rouphael N. Corrigendum to "Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study" [eBioMedicine 83 (2022) 104208]. EBioMedicine 2023; 98:104860. [PMID: 37918220 PMCID: PMC10643088 DOI: 10.1016/j.ebiom.2023.104860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Affiliation(s)
- Al Ozonoff
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Joanna Schaenman
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | | | - Carly E Milliren
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Carolyn S Calfee
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | - Lindsey R Baden
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Albert C Shaw
- Yale School of Medicine, Yale School of Public Health, New Haven, CT, USA
| | | | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Denise A Esserman
- Yale School of Medicine, Yale School of Public Health, New Haven, CT, USA
| | - Shanshan Liu
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | | | - Viviana Simon
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David A Hafler
- Yale School of Medicine, Yale School of Public Health, New Haven, CT, USA
| | - Ruth R Montgomery
- Yale School of Medicine, Yale School of Public Health, New Haven, CT, USA
| | | | - Ofer Levy
- Boston Clinical Site: Precision Vaccines Program, Boston Children's Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Elias K Haddad
- Drexel University/Tower Health Hospital, Philadelphia, PA, USA
| | - David J Erle
- University of California San Francisco School of Medicine, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Mark A Atkinson
- University of Florida, Gainesville and University of South Florida, Tampa, FL, USA
| | - Scott C Brakenridge
- University of Florida, Gainesville and University of South Florida, Tampa, FL, USA
| | - David Corry
- Baylor College of Medicine, The Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, USA
| | - Farrah Kheradmand
- Baylor College of Medicine, The Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey, Houston, TX, USA
| | | | | | | | | | - Joann Diray-Arce
- Clinical & Data Coordinating Center (CDCC), Precision Vaccines Program, Boston Children's Hospital, Boston, MA, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | - Elaine F Reed
- David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | | | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases/National Institutes of Health, Bethesda, MD, USA
| | | |
Collapse
|
8
|
Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Microfluidic Immuno-Serolomic Assay Reveals Systems Level Association with COVID-19 Pathology and Vaccine Protection. Small Methods 2023; 7:e2300594. [PMID: 37312418 PMCID: PMC10592458 DOI: 10.1002/smtd.202300594] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/23/2023] [Indexed: 06/15/2023]
Abstract
How to develop highly informative serology assays to evaluate the quality of immune protection against coronavirus disease-19 (COVID-19) has been a global pursuit over the past years. Here, a microfluidic high-plex immuno-serolomic assay is developed to simultaneously measure50 plasma or serum samples for50 soluble markers including 35proteins, 11 anti-spike/receptor binding domian (RBD) IgG antibodies spanningmajor variants, and controls. This assay demonstrates the quintuplicate test in a single run with high throughput, low sample volume, high reproducibilityand accuracy. It is applied to the measurement of 1012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein analysis reveals distinct immune mediator modules that exhibit a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies or receiving B cell depletion therapy. Serological analysis identifies that COVID-infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which can be associated with limited clonotype diversity and functional deficiency in B cells. These findings underscore the importance to individualize immunization strategies for these high-risk patients and provide an informative tool to monitor their responses at the systems level.
Collapse
Affiliation(s)
- Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Yuxin Liu
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Shalin Kothari
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Lohith Gowda
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jennifer M Kwan
- Cardiovascular Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | | | - Nikhil Lele
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
| | | | | | | | | | - Mary M Tomayko
- Departments of Dermatology, Yale University, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Erin E Longbrake
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
| | - David A Hafler
- Department of Neurology, Yale University, New Haven, CT, 06520, USA
- Department of Immunobiology, Yale University, New Haven, CT, 06520, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center and Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, 06520, USA
- Yale Cancer Center and Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
- Human and Translational Immunology, Yale School of Medicine, New Haven, CT, 06520, USA
| |
Collapse
|
9
|
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
|
10
|
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
|
11
|
Harroud A, Hafler DA. Common genetic factors among autoimmune diseases. Science 2023; 380:485-490. [PMID: 37141355 DOI: 10.1126/science.adg2992] [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: 05/06/2023]
Abstract
Autoimmune diseases display a high degree of comorbidity within individuals and families, suggesting shared risk factors. Over the past 15 years, genome-wide association studies have established the polygenic basis of these common conditions and revealed widespread sharing of genetic effects, indicative of a shared immunopathology. Despite ongoing challenges in determining the precise genes and molecular consequences of these risk variants, functional experiments and integration with multimodal genomic data are providing valuable insights into key immune cells and pathways driving these diseases, with potential therapeutic implications. Moreover, genetic studies of ancient populations are shedding light on the contribution of pathogen-driven selection pressures to the increased prevalence of autoimmune disease. This Review summarizes the current understanding of autoimmune disease genetics, including shared effects, mechanisms, and evolutionary origins.
Collapse
Affiliation(s)
- Adil Harroud
- Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
- The Neuro (Montreal Neurological Institute and Hospital), McGill University, Montréal, Quebec, Canada
| | - 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
- Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| |
Collapse
|
12
|
Abstract
Maintenance of peripheral tolerance by CD4+Foxp3+ regulatory T cells (Tregs) is essential for regulating autoreactive T cells. The loss of function of Foxp3 leads to autoimmune disease in both animals and humans. An example is the rare, X-linked recessive disorder known as IPEX (Immune Dysregulation, Polyendocrinopathy, Enteropathy X-linked) syndrome. In more common human autoimmune diseases, defects in Treg function are accompanied with aberrant effector cytokines such as IFNγ. It has recently become appreciated that Tregs plays an important role in not only maintaining immune homeostasis but also in establishing the tissue microenvironment and homeostasis of non-lymphoid tissues. Tissue resident Tregs show profiles that are unique to their local environments which are composed of both immune and non-immune cells. Core tissue-residence gene signatures are shared across different tissue Tregs and are crucial to homeostatic regulation and maintaining the tissue Treg pool in a steady state. Through interaction with immunocytes and non-immunocytes, tissue Tregs exert a suppressive function via conventional ways involving contact dependent and independent processes. In addition, tissue resident Tregs communicate with other tissue resident cells which allows Tregs to adopt to their local microenvironment. These bidirectional interactions are dependent on the specific tissue environment. Here, we summarize the recent advancements of tissue Treg studies in both human and mice, and discuss the molecular mechanisms that maintain tissue homeostasis and prevent pathogenesis.
Collapse
Affiliation(s)
- Nardos Cheru
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - David A. Hafler
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, United States
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Tomokazu S. Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, United States
| |
Collapse
|
13
|
Hanin A, Cespedes J, Dorgham K, Pulluru Y, Gopaul M, Gorochov G, Hafler DA, Navarro V, Gaspard N, Hirsch LJ. Cytokines in New-Onset Refractory Status Epilepticus Predict Outcomes. Ann Neurol 2023. [PMID: 36871188 DOI: 10.1002/ana.26627] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/06/2023]
Abstract
OBJECTIVE The objective of this study was to investigate inflammation using cerebrospinal fluid (CSF) and serum cytokines/chemokines in patients with new-onset refractory status epilepticus (NORSE) to better understand the pathophysiology of NORSE and its consequences. METHODS Patients with NORSE (n = 61, including n = 51 cryptogenic), including its subtype with prior fever known as febrile infection-related epilepsy syndrome (FIRES), were compared with patients with other refractory status epilepticus (RSE; n = 37), and control patients without SE (n = 52). We measured 12 cytokines/chemokines in serum or CSF samples using multiplexed fluorescent bead-based immunoassay detection. Cytokine levels were compared between patients with and without SE, and between the 51 patients with cryptogenic NORSE (cNORSE) and the 47 patients with a known-etiology RSE (NORSE n = 10, other RSE n = 37), and correlated with outcomes. RESULTS A significant increase of IL-6, TNF-α, CXCL8/IL-8, CCL2, MIP-1α, and IL-12p70 pro-inflammatory cytokines/chemokines was observed in patients with SE compared with patients without SE, in serum and CSF. Serum innate immunity pro-inflammatory cytokines/chemokines (CXCL8, CCL2, and MIP-1α) were significantly higher in patients with cNORSE compared to non-cryptogenic RSE. Patients with NORSE with elevated innate immunity serum and CSF cytokine/chemokine levels had worse outcomes at discharge and at several months after the SE ended. INTERPRETATION We identified significant differences in innate immunity serum and CSF cytokine/chemokine profiles between patients with cNORSE and non-cryptogenic RSE. The elevation of innate immunity pro-inflammatory cytokines in patients with NORSE correlated with worse short- and long-term outcomes. These findings highlight the involvement of innate immunity-related inflammation, including peripherally, and possibly of neutrophil-related immunity in cNORSE pathogenesis and suggest the importance of utilizing specific anti-inflammatory interventions. ANN NEUROL 2023.
Collapse
Affiliation(s)
- Aurélie Hanin
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, United States.,Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France.,Department of Clinical Neurophysiology, Epilepsy Unit, DMU Neurosciences 6, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Jorge Cespedes
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, United States.,Universidad Autonoma de Centro America, School of Medicine, San Jose, Costa Rica
| | - Karim Dorgham
- Department of Immunology, Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Yashwanth Pulluru
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, United States.,Division of Epilepsy, Nebraska Medical Center, Omaha, NE, United States
| | - Margaret Gopaul
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Guy Gorochov
- Department of Immunology, Sorbonne Université, Inserm, Centre d'Immunologie et des Maladies Infectieuses, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - David A Hafler
- Department of Neurology and Immunobiology, Yale University School of Medicine, New Haven, CT, United States
| | - Vincent Navarro
- Sorbonne Université, Institut du Cerveau, Paris Brain Institute, ICM, Inserm, CNRS, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France.,Department of Clinical Neurophysiology, Epilepsy Unit, DMU Neurosciences 6, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France.,Center of Reference for Rare Epilepsies, AP-HP, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Nicolas Gaspard
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, United States.,Department of Neurology, Université Libre de Bruxelles, Hôpital Erasme, Brussels, Belgium
| | - Lawrence J Hirsch
- Comprehensive Epilepsy Center, Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
14
|
Zhang L, He CH, Coffey S, Yin D, Hsu IU, Su C, Ye Y, Zhang C, Spurrier J, Nicholson L, Rothlin CV, Ghosh S, Gopal PP, Hafler DA, Zhao H, Strittmatter SM. Single-cell transcriptomic atlas of Alzheimer's disease middle temporal gyrus reveals region, cell type and sex specificity of gene expression with novel genetic risk for MERTK in female. medRxiv 2023:2023.02.18.23286037. [PMID: 36865305 PMCID: PMC9980267 DOI: 10.1101/2023.02.18.23286037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Alzheimer's disease, the most common age-related neurodegenerative disease, is closely associated with both amyloid-ß plaque and neuroinflammation. Two thirds of Alzheimer's disease patients are females and they have a higher disease risk. Moreover, women with Alzheimer's disease have more extensive brain histological changes than men along with more severe cognitive symptoms and neurodegeneration. To identify how sex difference induces structural brain changes, we performed unbiased massively parallel single nucleus RNA sequencing on Alzheimer's disease and control brains focusing on the middle temporal gyrus, a brain region strongly affected by the disease but not previously studied with these methods. We identified a subpopulation of selectively vulnerable layer 2/3 excitatory neurons that that were RORB-negative and CDH9-expressing. This vulnerability differs from that reported for other brain regions, but there was no detectable difference between male and female patterns in middle temporal gyrus samples. Disease-associated, but sex-independent, reactive astrocyte signatures were also present. In clear contrast, the microglia signatures of diseased brains differed between males and females. Combining single cell transcriptomic data with results from genome-wide association studies (GWAS), we identified MERTK genetic variation as a risk factor for Alzheimer's disease selectively in females. Taken together, our single cell dataset revealed a unique cellular-level view of sex-specific transcriptional changes in Alzheimer's disease, illuminating GWAS identification of sex-specific Alzheimer's risk genes. These data serve as a rich resource for interrogation of the molecular and cellular basis of Alzheimer's disease.
Collapse
|
15
|
Côrte-Real BF, Hamad I, Arroyo Hornero R, Geisberger S, Roels J, Van Zeebroeck L, Dyczko A, van Gisbergen MW, Kurniawan H, Wagner A, Yosef N, Weiss SNY, Schmetterer KG, Schröder A, Krampert L, Haase S, Bartolomaeus H, Hellings N, Saeys Y, Dubois LJ, Brenner D, Kempa S, Hafler DA, Stegbauer J, Linker RA, Jantsch J, Müller DN, Kleinewietfeld M. Sodium perturbs mitochondrial respiration and induces dysfunctional Tregs. Cell Metab 2023; 35:299-315.e8. [PMID: 36754020 DOI: 10.1016/j.cmet.2023.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/10/2023]
Abstract
FOXP3+ regulatory T cells (Tregs) are central for peripheral tolerance, and their deregulation is associated with autoimmunity. Dysfunctional autoimmune Tregs display pro-inflammatory features and altered mitochondrial metabolism, but contributing factors remain elusive. High salt (HS) has been identified to alter immune function and to promote autoimmunity. By investigating longitudinal transcriptional changes of human Tregs, we identified that HS induces metabolic reprogramming, recapitulating features of autoimmune Tregs. Mechanistically, extracellular HS raises intracellular Na+, perturbing mitochondrial respiration by interfering with the electron transport chain (ETC). Metabolic disturbance by a temporary HS encounter or complex III blockade rapidly induces a pro-inflammatory signature and FOXP3 downregulation, leading to long-term dysfunction in vitro and in vivo. The HS-induced effect could be reversed by inhibition of mitochondrial Na+/Ca2+ exchanger (NCLX). Our results indicate that salt could contribute to metabolic reprogramming and that short-term HS encounter perturb metabolic fitness and long-term function of human Tregs with important implications for autoimmunity.
Collapse
Affiliation(s)
- Beatriz F Côrte-Real
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Ibrahim Hamad
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Rebeca Arroyo Hornero
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Sabrina Geisberger
- Experimental and Clinical Research Center, a joint cooperation of Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Integrative Proteomics and Metabolomics, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Joris Roels
- VIB-UGent Center for Inflammation Research, 9052 Gent, Belgium; VIB BioImaging Core, 9052 Gent, Belgium
| | - Lauren Van Zeebroeck
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Aleksandra Dyczko
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Marike W van Gisbergen
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Henry Kurniawan
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub Investigator, San Francisco, CA 94158, USA; Ragon Institute of Massachusetts General Hospital, MIT and Harvard University, Cambridge, MA 02139, USA; Department of Systems Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Susanne N Y Weiss
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg and University of Regensburg, 93053 Regensburg, Germany
| | - Klaus G Schmetterer
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg and University of Regensburg, 93053 Regensburg, Germany; Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Agnes Schröder
- Department of Orthodontics, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Luka Krampert
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg and University of Regensburg, 93053 Regensburg, Germany
| | - Stefanie Haase
- Department of Neurology, University of Regensburg, 93053 Regensburg, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a joint cooperation of Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany
| | - Niels Hellings
- Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Yvan Saeys
- VIB-UGent Center for Inflammation Research, 9052 Gent, Belgium
| | - Ludwig J Dubois
- The M-Lab, Department of Precision Medicine, GROW - School for Oncology and Developmental Biology, Maastricht University, 6200 MD Maastricht, the Netherlands
| | - Dirk Brenner
- Experimental & Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, 4354 Esch-sur-Alzette, Luxembourg; Odense Research Center for Anaphylaxis (ORCA), Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, 5230 Odense, Denmark
| | - Stefan Kempa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Integrative Proteomics and Metabolomics, 13125 Berlin, Germany
| | - 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
| | - Johannes Stegbauer
- Department of Nephrology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Ralf A Linker
- Department of Neurology, University of Regensburg, 93053 Regensburg, Germany
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg and University of Regensburg, 93053 Regensburg, Germany; Institute for Medical Microbiology, Immunology, and Hygiene, University Hospital Cologne and Faculty of Medicine, University of Cologne, 50935 Cologne, Germany
| | - Dominik N Müller
- Experimental and Clinical Research Center, a joint cooperation of Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Berlin, 10785 Berlin, Germany; Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Markus Kleinewietfeld
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, 3590 Diepenbeek, Belgium; Department of Immunology, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium.
| |
Collapse
|
16
|
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
|
17
|
Shinoda K, Li R, Rezk A, Mexhitaj I, Patterson KR, Kakara M, Zuroff L, Bennett JL, von Büdingen HC, Carruthers R, Edwards KR, Fallis R, Giacomini PS, Greenberg BM, Hafler DA, Ionete C, Kaunzner UW, Lock CB, Longbrake EE, Pardo G, Piehl F, Weber MS, Ziemssen T, Jacobs D, Gelfand JM, Cross AH, Cameron B, Musch B, Winger RC, Jia X, Harp CT, Herman A, Bar-Or A. Differential effects of anti-CD20 therapy on CD4 and CD8 T cells and implication of CD20-expressing CD8 T cells in MS disease activity. Proc Natl Acad Sci U S A 2023; 120:e2207291120. [PMID: 36634138 PMCID: PMC9934304 DOI: 10.1073/pnas.2207291120] [Citation(s) in RCA: 13] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A small proportion of multiple sclerosis (MS) patients develop new disease activity soon after starting anti-CD20 therapy. This activity does not recur with further dosing, possibly reflecting deeper depletion of CD20-expressing cells with repeat infusions. We assessed cellular immune profiles and their association with transient disease activity following anti-CD20 initiation as a window into relapsing disease biology. Peripheral blood mononuclear cells from independent discovery and validation cohorts of MS patients initiating ocrelizumab were assessed for phenotypic and functional profiles using multiparametric flow cytometry. Pretreatment CD20-expressing T cells, especially CD20dimCD8+ T cells with a highly inflammatory and central nervous system (CNS)-homing phenotype, were significantly inversely correlated with pretreatment MRI gadolinium-lesion counts, and also predictive of early disease activity observed after anti-CD20 initiation. Direct removal of pretreatment proinflammatory CD20dimCD8+ T cells had a greater contribution to treatment-associated changes in the CD8+ T cell pool than was the case for CD4+ T cells. Early disease activity following anti-CD20 initiation was not associated with reconstituting CD20dimCD8+ T cells, which were less proinflammatory compared with pretreatment. Similarly, this disease activity did not correlate with early reconstituting B cells, which were predominantly transitional CD19+CD24highCD38high with a more anti-inflammatory profile. We provide insights into the mode-of-action of anti-CD20 and highlight a potential role for CD20dimCD8+ T cells in MS relapse biology; their strong inverse correlation with both pretreatment and early posttreatment disease activity suggests that CD20-expressing CD8+ T cells leaving the circulation (possibly to the CNS) play a particularly early role in the immune cascades involved in relapse development.
Collapse
Affiliation(s)
- Koji Shinoda
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Rui Li
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ayman Rezk
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ina Mexhitaj
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Kristina R. Patterson
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Mihir Kakara
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Leah Zuroff
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jeffrey L. Bennett
- cDepartments of Neurology and Ophthalmology, Programs in Neuroscience and Immunology, University of Colorado School of Medicine, Aurora, CO80045
| | | | - Robert Carruthers
- eDepartment of Medicine, University of British Columbia, Vancouver, BCV6T 2B5, Canada
| | - Keith R. Edwards
- fMultiple Sclerosis Center of Northeastern New York, Comprehensive MS Care Center Affiliated with the National MS Society, Latham, NY12110
| | - Robert Fallis
- gDepartment of Neurology, Ohio State University Medical Center, Columbus, OH43210
| | - Paul S. Giacomini
- hDepartment of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QCH3A 2B4, Canada
| | - Benjamin M. Greenberg
- iDepartment of Neurology, University of Texas Southwestern Medical Center, Dallas, TX75390
| | - David A. Hafler
- jDepartments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT06510
| | - Carolina Ionete
- kDepartment of Neurology, University of Massachusetts Medical School, Worcester, MA01655
| | - Ulrike W. Kaunzner
- lJudith Jaffe Multiple Sclerosis Center, Weill Cornell Medicine, New York, NY10021
| | - Christopher B. Lock
- mDepartment of Neurology and Neurological Sciences, Stanford University, Palo Alto, CA94304
| | | | - Gabriel Pardo
- oOklahoma Medical Research Foundation, Multiple Sclerosis Center of Excellence, Oklahoma City, OK73104
| | - Fredrik Piehl
- pDepartment of Clinical Neuroscience, Karolinska Institute, SE-171 76Stockholm, Sweden
- qDepartment of Neurology, Karolinska University Hospital, SE-171 77Stockholm, Sweden
- rNeuroimmunology Unit, Center for Molecular Medicine, Karolinska University Hospital, Karolinska Institute, SE-171 77Stockholm, Sweden
| | - Martin S. Weber
- sInstitute of Neuropathology, University Medical Center, 37075Göttingen, Germany
- tDepartment of Neurology, University Medical Center, 37075Göttingen, Germany
- uFraunhofer-Institute for Translational Medicine and Pharmackology ITMP, 37075Göttingen, Germany
| | - Tjalf Ziemssen
- vDepartment of Neurology, Center of Clinical Neuroscience, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307Dresden, Germany
| | - Dina Jacobs
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jeffrey M. Gelfand
- wWeill Institute for Neurosciences, University of California, San Francisco, CA94158
- xDepartment of Neurology, University of California, San Francisco, CA94158
| | - Anne H. Cross
- yDepartment of Neurology, Washington University School of Medicine, Saint Louis, MO63110
| | | | - Bruno Musch
- zGenentech, Inc., South San Francisco, CA94080
| | | | | | | | - Ann Herman
- zGenentech, Inc., South San Francisco, CA94080
| | - Amit Bar-Or
- aDepartment of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- bCenter for Neuroinflammation and Experimental Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
- aaChildren's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA19104
- 1To whom correspondence may be addressed.
| |
Collapse
|
18
|
Qu R, Kluger Y, Yang J, Zhao J, Hafler DA, Krause DS, Bersenev A, Bosenberg M, Hurwitz M, Lucca L, Kluger HM. Longitudinal single-cell analysis of a patient receiving adoptive cell therapy reveals potential mechanisms of treatment failure. Mol Cancer 2022; 21:219. [PMID: 36514045 PMCID: PMC9749221 DOI: 10.1186/s12943-022-01688-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Adoptive cell therapy (ACT) using tumor infiltrating lymphocytes (TIL) is being studied in multiple tumor types. However, little is known about clonal cell expansion in vitro and persistence of the ACT product in vivo. We performed single-cell RNA and T-Cell Receptor (TCR) sequencing on serial blood and tumor samples from a patient undergoing ACT, who did not respond. We found that clonal expansion varied during preparation of the ACT product, and only one expanded clone was preserved in the ACT product. The TCR of the preserved clone which persisted and remained activated for five months was previously reported as specific for cytomegalovirus and had upregulation of granzyme family genes and genes associated with effector functions (HLA-DQB1, LAT, HLA-DQA1, and KLRD1). Clones that contracted during TIL preparation had features of exhaustion and apoptosis. At disease progression, all previously detected clonotypes were detected. New clonotypes appearing in blood or tumor at disease progression were enriched for genes associated with cytotoxicity or stemness (FGFBP2, GNLY, GZMH, GZMK, IL7R, SELL and KLF2), and these might be harnessed for alternative cellular therapy or cytokine therapy. In-depth single-cell analyses of serial samples from additional ACT-treated patients is warranted, and viral- versus tumor-specificity should be carefully analyzed.
Collapse
Affiliation(s)
- Rihao Qu
- grid.47100.320000000419368710Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Yuval Kluger
- grid.47100.320000000419368710Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Junchen Yang
- grid.47100.320000000419368710Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Jun Zhao
- grid.47100.320000000419368710Department of Pathology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - David A. Hafler
- grid.47100.320000000419368710Department of Neurology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Diane S. Krause
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Alexey Bersenev
- grid.47100.320000000419368710Department of Laboratory Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Marcus Bosenberg
- grid.47100.320000000419368710Department of Dermatology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA ,grid.47100.320000000419368710Department of Immunobiology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Michael Hurwitz
- grid.47100.320000000419368710Department of Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Liliana Lucca
- grid.47100.320000000419368710Department of Neurology, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| | - Harriet M. Kluger
- grid.47100.320000000419368710Department of Medicine, Yale School of Medicine, 333 Cedar St, New Haven, CT 06520 USA
| |
Collapse
|
19
|
Axisa PP, Yoshida TM, Lucca LE, Kasler HG, Lincoln MR, Pham GH, Del Priore D, Carpier JM, Lucas CL, Verdin E, Sumida TS, Hafler DA. A multiple sclerosis-protective coding variant reveals an essential role for HDAC7 in regulatory T cells. Sci Transl Med 2022; 14:eabl3651. [PMID: 36516268 DOI: 10.1126/scitranslmed.abl3651] [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: 12/15/2022]
Abstract
Genome-wide association studies identifying hundreds of susceptibility loci for autoimmune diseases indicate that genes active in immune cells predominantly mediate risk. However, identification and functional characterization of causal variants remain challenging. Here, we focused on the immunomodulatory role of a protective variant of histone deacetylase 7 (HDAC7). This variant (rs148755202, HDAC7.p.R166H) was identified in a study of low-frequency coding variation in multiple sclerosis (MS). Through transcriptomic analyses, we demonstrate that wild-type HDAC7 regulates genes essential for the function of Foxp3+ regulatory T cells (Tregs), an immunosuppressive subset of CD4 T cells that is generally dysfunctional in patients with MS. Moreover, Treg-specific conditional hemizygous deletion of HDAC7 increased the severity of experimental autoimmune encephalitis (EAE), a mouse model of neuroinflammation. In contrast, Tregs transduced with the protective HDAC7 R166H variant exhibited higher suppressive capacity in an in vitro functional assay, mirroring phenotypes previously observed in patient samples. In vivo modeling of the human HDAC7 R166H variant by generation of a knock-in mouse model bearing an orthologous R150H substitution demonstrated decreased EAE severity linked to transcriptomic alterations of brain-infiltrating Tregs, as assessed by single-cell RNA sequencing. Our data suggest that dysregulation of epigenetic modifiers, a distinct molecular class associated with disease risk, may influence disease onset. Last, our approach provides a template for the translation of genetic susceptibility loci to detailed functional characterization, using in vitro and in vivo modeling.
Collapse
Affiliation(s)
- Pierre-Paul Axisa
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Tomomi M Yoshida
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Liliana E Lucca
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | | | - Matthew R Lincoln
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - Giang H Pham
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Dante Del Priore
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jean-Marie Carpier
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Carrie L Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Tomokazu S Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT 06510, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA 02142, USA
| |
Collapse
|
20
|
Longbrake EE, Hua LH, Mowry EM, Gauthier SA, Alvarez E, Cross AH, Pei J, Priest J, Raposo C, Hafler DA, Winger RC. The CELLO trial: Protocol of a planned phase 4 study to assess the efficacy of Ocrelizumab in patients with radiologically isolated syndrome. Mult Scler Relat Disord 2022; 68:104143. [PMID: 36031693 PMCID: PMC9772048 DOI: 10.1016/j.msard.2022.104143] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/21/2022] [Accepted: 08/21/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Patients with radiologically isolated syndrome (RIS) exhibit CNS lesions suggestive of multiple sclerosis (MS) in the absence of overt neurological symptoms characteristic of the disease. They may have concurrent brain atrophy, subtle cognitive impairment, and intrathecal inflammation. At least half ultimately develop MS, cementing RIS as preclinical MS for many. However, high-quality data, including immunologic biomarkers, to guide treatment decisions in this population are lacking. Early intervention with ocrelizumab, a humanized monoclonal antibody approved for relapsing and primary progressive MS that targets CD20+ B-cells, may affect disease course and improve long-term outcomes. The objective of this study is to describe the protocol for CELLO, a clinical trial assessing the effect of ocrelizumab on RIS. METHODS The CELLO clinical trial, a phase 4, multicenter, randomized, double-blind, placebo-controlled study conducted as an academic-industry collaboration, aims to (1) assess the efficacy of ocrelizumab in patients with RIS and (2) identify biomarkers indicative of emerging autoimmunity as well as immune recovery after transient B-cell depletion. The study will enroll 100 participants across ≥15 sites. Participants will be aged 18 to 40 years, have RIS (defined as meeting 2017 revised McDonald criteria for dissemination in space), and have either been diagnosed with RIS within the last 5 years or have had new brain lesions identified within 5 years of study entry. A screening program of first-degree relatives of patients with MS will be used to boost recruitment. Eligible patients will be randomized 1:1 to receive 3 courses of ocrelizumab or placebo at baseline, week 24, and week 48. Patients will subsequently be followed up for ≥3 years. The primary outcome is time to development of new radiological or clinical evidence of MS. Secondary and exploratory objectives will investigate neuroimaging, serological and immunologic biomarkers, cognitive function, and patient-reported outcomes. A substudy using single-cell RNA sequencing to characterize blood and CSF immune cells will assess markers associated with conversion to clinical MS. CONCLUSION The CELLO study will improve the understanding of B-cell biology in early MS disease pathophysiology, characterize the emergence of CNS autoimmunity, and provide evidence to inform treatment decision-making for individuals with RIS. CLINICALTRIALS GOV: NCT04877457.
Collapse
Affiliation(s)
- Erin E Longbrake
- Department of Neurology, Yale School of Medicine, New Haven, CT.
| | - Le H Hua
- Lou Ruvo Center for Brain Health, Cleveland Clinic, Las Vegas, NV
| | - Ellen M Mowry
- The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Enrique Alvarez
- Rocky Mountain Multiple Sclerosis Center at Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Anne H Cross
- Washington University School of Medicine, St Louis, MO
| | | | | | | | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT
| | | |
Collapse
|
21
|
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
|
22
|
Kim D, Biancon G, Bai Z, VanOudenhove J, Liu Y, Kothari S, Gowda L, Kwan JM, Buitrago-Pocasangre NC, Lele N, Asashima H, Racke MK, Wilson JE, Givens TS, Tomayko MM, Schulz WL, Longbrake EE, Hafler DA, Halene S, Fan R. Microfluidic immuno-serology assay revealed a limited diversity of protection against COVID-19 in patients with altered immunity. bioRxiv 2022:2022.08.31.506117. [PMID: 36093346 PMCID: PMC9460970 DOI: 10.1101/2022.08.31.506117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The immune response to SARS-CoV-2 for patients with altered immunity such as hematologic malignancies and autoimmune disease may differ substantially from that in general population. These patients remain at high risk despite wide-spread adoption of vaccination. It is critical to examine the differences at the systems level between the general population and the patients with altered immunity in terms of immunologic and serological responses to COVID-19 infection and vaccination. Here, we developed a novel microfluidic chip for high-plex immuno-serological assay to simultaneously measure up to 50 plasma or serum samples for up to 50 soluble markers including 35 plasma proteins, 11 anti-spike/RBD IgG antibodies spanning all major variants, and controls. Our assay demonstrated the quintuplicate test in a single run with high throughput, low sample volume input, high reproducibility and high accuracy. It was applied to the measurement of 1,012 blood samples including in-depth analysis of sera from 127 patients and 21 healthy donors over multiple time points, either with acute COVID infection or vaccination. The protein association matrix analysis revealed distinct immune mediator protein modules that exhibited a reduced degree of diversity in protein-protein cooperation in patients with hematologic malignancies and patients with autoimmune disorders receiving B cell depletion therapy. Serological analysis identified that COVID infected patients with hematologic malignancies display impaired anti-RBD antibody response despite high level of anti-spike IgG, which could be associated with limited clonotype diversity and functional deficiency in B cells and was further confirmed by single-cell BCR and transcriptome sequencing. These findings underscore the importance to individualize immunization strategy for these high-risk patients and provide an informative tool to monitor their responses at the systems level.
Collapse
Affiliation(s)
- Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Jennifer VanOudenhove
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuxin Liu
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Shalin Kothari
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lohith Gowda
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jennifer M Kwan
- Cardiovascular Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Nikhil Lele
- Department of Neurology, Yale University, New Haven, CT 06520, USA
| | | | | | | | | | - Mary M Tomayko
- Departments of Dermatology, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Wade L Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Erin E Longbrake
- Department of Neurology, Yale University, New Haven, CT 06520, USA
| | - David A Hafler
- Department of Neurology, Yale University, New Haven, CT 06520, USA
- Department of Immunobiology, Yale University, New Haven, CT 06520, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Center for RNA Science and Medicine, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
23
|
Hafler DA, Sansing LH. Neuroimmune interactions in health and disease. Semin Immunopathol 2022; 44:565-567. [PMID: 36171280 DOI: 10.1007/s00281-022-00963-3] [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: 11/24/2022]
Affiliation(s)
- David A Hafler
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06520, USA. .,Department of Neurology, Yale School of Medicine, New Haven, CT, 06520, USA.
| | - Lauren H Sansing
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06520, USA. .,Department of Neurology, Yale School of Medicine, New Haven, CT, 06520, USA.
| |
Collapse
|
24
|
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
|
25
|
Abstract
Cellular metabolic remodeling is intrinsically linked to the development, activation, differentiation, function, and survival of T cells. T cells transition from a catabolic, naïve state to an anabolic effector state upon T cell activation. Subsequently, specialization of T cells into T helper (Th) subsets, including regulatory T cells (Treg), requires fine-tuning of metabolic programs that better support and optimize T cell functions for that particular environment. Increasingly, studies have shown that changes in nutrient availability at both the cellular and organismal level during disease states can alter T cell function, highlighting the importance of better characterizing metabolic-immune axes in both physiological and disease settings. In support of these data, a growing body of evidence is emerging that shows specific lipid species are capable of altering the inflammatory functional phenotypes of T cells. In this review we summarize the metabolic programs shown to support naïve and effector T cells, and those driving Th subsets. We then discuss changes to lipid profiles in patients with multiple sclerosis, and focus on how the presence of specific lipid species can alter cellular metabolism and function of T cells.
Collapse
Affiliation(s)
- Saige L. Pompura
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, United States
| | | |
Collapse
|
26
|
Sumida TS, Hafler DA. Population genetics meets single-cell sequencing. Science 2022; 376:134-135. [PMID: 35389792 DOI: 10.1126/science.abq0426] [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: 11/02/2022]
Abstract
Single-cell technology can be used to understand the genetic basis of human diseases.
Collapse
Affiliation(s)
- Tomokazu S Sumida
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - David A Hafler
- Department of Neurology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.,Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
27
|
Sumida TS, Dulberg S, Schupp JC, Lincoln MR, Stillwell HA, Axisa PP, Comi M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Type I interferon transcriptional network regulates expression of coinhibitory receptors in human T cells. Nat Immunol 2022; 23:632-642. [PMID: 35301508 PMCID: PMC8989655 DOI: 10.1038/s41590-022-01152-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/03/2022] [Indexed: 12/15/2022]
Abstract
Although inhibition of T cell coinhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. In the present study, we show that type 1 interferon (IFN-I) regulates coinhibitory receptor expression on human T cells, inducing PD-1/TIM-3/LAG-3 while inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses established the dynamic regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors (TFs) and TF footprint analysis revealed two regulator modules with different temporal kinetics that control expression of coinhibitory receptors and IFN-I response genes, with SP140 highlighted as one of the key regulators that differentiates LAG-3 and TIGIT expression. Finally, we found that the dynamic IFN-I response in vitro closely mirrored T cell features in acute SARS-CoV-2 infection. The identification of unique TFs controlling coinhibitory receptor expression under IFN-I response may provide targets for enhancement of immunotherapy in cancer, infectious diseases and autoimmunity.
Collapse
Affiliation(s)
- Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| | - Shai Dulberg
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, 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, Hannover, Germany
| | - Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Medicine, Division of Neurology, University of Toronto, Toronto, Ontario, Canada
| | - Helen A Stillwell
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Michela Comi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv University, Tel Aviv, Israel
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
28
|
Pauken KE, Lagattuta KA, Lu BY, Lucca LE, Daud AI, Hafler DA, Kluger HM, Raychaudhuri S, Sharpe AH. TCR-sequencing in cancer and autoimmunity: barcodes and beyond. Trends Immunol 2022; 43:180-194. [PMID: 35090787 PMCID: PMC8882139 DOI: 10.1016/j.it.2022.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 11/29/2021] [Revised: 01/04/2022] [Accepted: 01/04/2022] [Indexed: 01/21/2023]
Abstract
The T cell receptor (TCR) endows T cells with antigen specificity and is central to nearly all aspects of T cell function. Each naïve T cell has a unique TCR sequence that is stably maintained during cell division. In this way, the TCR serves as a molecular barcode that tracks processes such as migration, differentiation, and proliferation of T cells. Recent technological advances have enabled sequencing of the TCR from single cells alongside deep molecular phenotypes on an unprecedented scale. In this review, we discuss strengths and limitations of TCR sequences as molecular barcodes and their application to study immune responses following Programmed Death-1 (PD-1) blockade in cancer. Additionally, we consider applications of TCR data beyond use as a barcode.
Collapse
Affiliation(s)
- Kristen E. Pauken
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA.,Correspondence: (A. H. Sharpe); (K. E. Pauken)
| | - Kaitlyn A. Lagattuta
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Benjamin Y. Lu
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Liliana E. Lucca
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Current Address: Cancer Research Center of Toulouse, Toulouse, France
| | - Adil I. Daud
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David A. Hafler
- Department of Neurology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women’s Hospital, Boston, MA, USA.,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9PL, UK
| | - Arlene H. Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Correspondence: (A. H. Sharpe); (K. E. Pauken)
| |
Collapse
|
29
|
Nowak RJ, Coffey CS, Goldstein JM, Dimachkie MM, Benatar M, Kissel JT, Wolfe GI, Burns TM, Freimer ML, Nations S, Granit V, Smith AG, Richman DP, Ciafaloni E, Al-Lozi MT, Sams LA, Quan D, Ubogu E, Pearson B, Sharma A, Yankey JW, Uribe L, Shy M, Amato AA, Conwit R, O'Connor KC, Hafler DA, Cudkowicz ME, Barohn RJ. Phase 2 Trial of Rituximab in Acetylcholine Receptor Antibody-Positive Generalized Myasthenia Gravis: The BeatMG Study. Neurology 2022; 98:e376-e389. [PMID: 34857535 PMCID: PMC8793103 DOI: 10.1212/wnl.0000000000013121] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/19/2021] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE To determine whether rituximab is safe and potentially beneficial, warranting further investigation in an efficacy trial for acetylcholine receptor antibody-positive generalized MG (AChR-Ab+ gMG). METHODS The B-Cell Targeted Treatment in MG (BeatMG) study was a randomized, double-blind, placebo-controlled, multicenter phase-2 trial that utilized a futility design. Individuals 21-90 years of age, with AChR-Ab+ gMG (MG Foundation of America Class II-IV) and receiving prednisone ≥15 mg/day were eligible. The primary outcome was a measure of steroid-sparing effect, defined as the proportion achieving ≥75% reduction in mean daily prednisone dose in the 4-weeks prior to week 52 and with clinical improvement or no significant worsening as compared to the 4-week period prior to randomization. The co-primary outcome was safety. Secondary outcomes included MG-specific clinical assessments. Fifty-two individuals were randomized (1:1) to either a two-cycle rituximab/placebo regimen, with follow-up through 52-weeks. RESULTS Of the 52 participants included, mean (±SD) age at enrollment was 55.1 (±17.1) years; 23 (44.2%) were female, and 31 (59.6%) were MGFA Class II. The mean (±SD) baseline prednisone dose was 22.1 (±9.7) mg/day. The primary steroid-sparing outcome was achieved in 60% of those on rituximab vs. 56% on placebo. The study reached its futility endpoint (p=0.03) suggesting that the pre-defined clinically meaningful improvement of 30% due to rituximab over placebo was unlikely to be achieved in a subsequent, larger trial. No safety issues identified. CONCLUSIONS While rituximab was safe and well-tolerated, these results suggest that there is a low probability of observing the defined clinically meaningful steroid-sparing effect over a 12-month period in a phase-3 trial of mild-moderately symptomatic AChR-Ab+ gMG. CLASSIFICATION OF EVIDENCE This study provides Class I evidence that for mild-to-moderate AChR-Ab+ gMG, compared with placebo, rituximab is safe but unlikely to reduce steroid use by an absolute difference of at least 30% at 1 year. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT02110706.
Collapse
Affiliation(s)
- Richard J Nowak
- Department of Neurology, Yale University School of Medicine, New Haven, CT
| | - Christopher S Coffey
- Clinical Trials Statistical & Data Management Center, University of Iowa, Iowa City, IA
| | | | - Mazen M Dimachkie
- Department of Neurology, Kansas University School of Medicine, Kansas City, KS
| | - Michael Benatar
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL
| | - John T Kissel
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Gil I Wolfe
- Department of Neurology, University at Buffalo Jacobs School of Medicine & Biomedical Sciences, Buffalo, NY
| | - Ted M Burns
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA
| | - Miriam L Freimer
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH
| | - Sharon Nations
- Department of Neurology, University of Texas Southwestern Medical School, Dallas, TX
| | - Volkan Granit
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL
| | - A Gordon Smith
- Department of Neurology, University of Utah School of Medicine, Salt Lake City, UT
| | - David P Richman
- Department of Neurology, University of California Davis School of Medicine, Sacramento, CA
| | - Emma Ciafaloni
- Department of Neurology, University of Rochester School of Medicine & Dentistry, Rochester, NY
| | - Muhammad T Al-Lozi
- Department of Neurology, Washington University School of Medicine, St. Louis, MO
| | - Laura Ann Sams
- Department of Neurology, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Dianna Quan
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO
| | - Eroboghene Ubogu
- Department of Neurology, The University of Alabama at Birmingham School of Medicine, Birmingham, AL
| | - Brenda Pearson
- Clinical Trials Statistical & Data Management Center, University of Iowa, Iowa City, IA
| | - Aditi Sharma
- Department of Neurology, Yale University School of Medicine, New Haven, CT
- Department of Neurology, University of Iowa, Iowa City, IA
| | - Jon W Yankey
- Clinical Trials Statistical & Data Management Center, University of Iowa, Iowa City, IA
| | - Liz Uribe
- Clinical Trials Statistical & Data Management Center, University of Iowa, Iowa City, IA
| | - Michael Shy
- Department of Neurology, University of Iowa, Carver College of Medicine, Iowa City, IA
| | - Anthony A Amato
- Department of Neurology, Brigham and Women's Hospital, Boston, MA
| | - Robin Conwit
- Division of Clinical Research, National Institute of Neurological Disorders and Stroke, Rockville, MD
| | - Kevin C O'Connor
- Department of Neurology, Yale University School of Medicine, New Haven, CT
| | - David A Hafler
- Department of Neurology, Yale University School of Medicine, New Haven, CT
| | | | - Richard J Barohn
- Department of Neurology, Kansas University School of Medicine, Kansas City, KS
- Department of Neurology, University of Missouri, Columbia, MO
| |
Collapse
|
30
|
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
|
31
|
Abstract
[Figure: see text].
Collapse
Affiliation(s)
- Juhi R Kuchroo
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.,Evergrande Center for Immunological Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, USA.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Liliana E Lucca
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| |
Collapse
|
32
|
Pompura SL, Wagner A, Kitz A, LaPerche J, Yosef N, Dominguez-Villar M, Hafler DA. Oleic acid restores suppressive defects in tissue-resident FOXP3 Tregs from patients with multiple sclerosis. J Clin Invest 2021; 131:138519. [PMID: 33170805 DOI: 10.1172/jci138519] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [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: 03/26/2020] [Accepted: 11/05/2020] [Indexed: 12/21/2022] Open
Abstract
FOXP3+ Tregs rely on fatty acid β-oxidation-driven (FAO-driven) oxidative phosphorylation (OXPHOS) for differentiation and function. Recent data demonstrate a role for Tregs in the maintenance of tissue homeostasis, with tissue-resident Tregs possessing tissue-specific transcriptomes. However, specific signals that establish tissue-resident Treg programs remain largely unknown. Tregs metabolically rely on FAO, and considering the lipid-rich environments of tissues, we hypothesized that environmental lipids drive Treg homeostasis. First, using human adipose tissue to model tissue residency, we identified oleic acid as the most prevalent free fatty acid. Mechanistically, oleic acid amplified Treg FAO-driven OXPHOS metabolism, creating a positive feedback mechanism that increased the expression of FOXP3 and phosphorylation of STAT5, which enhanced Treg-suppressive function. Comparing the transcriptomic program induced by oleic acid with proinflammatory arachidonic acid, we found that Tregs sorted from peripheral blood and adipose tissue of healthy donors transcriptomically resembled the Tregs treated in vitro with oleic acid, whereas Tregs from patients with multiple sclerosis (MS) more closely resembled an arachidonic acid transcriptomic profile. Finally, we found that oleic acid concentrations were reduced in patients with MS and that exposure of MS Tregs to oleic acid restored defects in their suppressive function. These data demonstrate the importance of fatty acids in regulating tissue inflammatory signals.
Collapse
Affiliation(s)
- Saige L Pompura
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Allon Wagner
- Department of Electrical Engineering and Computer Science, and the Center for Computational Biology, University of California Berkeley, Berkeley, California, USA
| | - Alexandra Kitz
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Jacob LaPerche
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Nir Yosef
- Department of Electrical Engineering and Computer Science, and the Center for Computational Biology, University of California Berkeley, Berkeley, California, USA.,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology (MIT) and Harvard University, Boston, Massachusetts, USA.,Chan-Zuckerberg Biohub, San Francisco, California, USA
| | - Margarita Dominguez-Villar
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA.,Faculty of Medicine, Imperial College London, London, United Kingdom
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, Connecticut, USA.,Broad Institute of MIT and Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
33
|
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
|
34
|
Hoehn KB, Ramanathan P, Unterman A, Sumida TS, Asashima H, Hafler DA, Kaminski N, Dela Cruz CS, Sealfon SC, Bukreyev A, Kleinstein SH. Cutting Edge: Distinct B Cell Repertoires Characterize Patients with Mild and Severe COVID-19. J Immunol 2021; 206:2785-2790. [PMID: 34049971 PMCID: PMC8627528 DOI: 10.4049/jimmunol.2100135] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022]
Abstract
Protective immunity against COVID-19 likely depends on the production of SARS-CoV-2-specific plasma cells and memory B cells postinfection or postvaccination. Previous work has found that germinal center reactions are disrupted in severe COVID-19. This may adversely affect long-term immunity against reinfection. Consistent with an extrafollicular B cell response, patients with severe COVID-19 have elevated frequencies of clonally expanded, class-switched, unmutated plasmablasts. However, it is unclear whether B cell populations in individuals with mild COVID-19 are similarly skewed. In this study, we use single-cell RNA sequencing of B cells to show that in contrast to patients with severe COVID-19, subjects with mildly symptomatic COVID-19 have B cell repertoires enriched for clonally diverse, somatically hypermutated memory B cells ∼30 d after the onset of symptoms. This provides evidence that B cell responses are less disrupted in mild COVID-19 and result in the production of memory B cells.
Collapse
Affiliation(s)
- Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT
| | - Palaniappan Ramanathan
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX
| | - Avraham Unterman
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT
- Pulmonary Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Tomokazu S Sumida
- Department of Neurology, School of Medicine, Yale University, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Hiromitsu Asashima
- Department of Neurology, School of Medicine, Yale University, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - David A Hafler
- Department of Neurology, School of Medicine, Yale University, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT
| | - Stuart C Sealfon
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexander Bukreyev
- Department of Pathology, The University of Texas Medical Branch at Galveston, Galveston, TX
- Galveston National Laboratory, The University of Texas Medical Branch at Galveston, Galveston, TX
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, TX; and
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT;
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| |
Collapse
|
35
|
He L, Davila-Velderrain J, Sumida TS, Hafler DA, Kellis M, Kulminski AM. NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data. Commun Biol 2021; 4:629. [PMID: 34040149 PMCID: PMC8155058 DOI: 10.1038/s42003-021-02146-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 10/09/2020] [Accepted: 04/19/2021] [Indexed: 11/18/2022] Open
Abstract
The increasing availability of single-cell data revolutionizes the understanding of biological mechanisms at cellular resolution. For differential expression analysis in multi-subject single-cell data, negative binomial mixed models account for both subject-level and cell-level overdispersions, but are computationally demanding. Here, we propose an efficient NEgative Binomial mixed model Using a Large-sample Approximation (NEBULA). The speed gain is achieved by analytically solving high-dimensional integrals instead of using the Laplace approximation. We demonstrate that NEBULA is orders of magnitude faster than existing tools and controls false-positive errors in marker gene identification and co-expression analysis. Using NEBULA in Alzheimer's disease cohort data sets, we found that the cell-level expression of APOE correlated with that of other genetic risk factors (including CLU, CST3, TREM2, C1q, and ITM2B) in a cell-type-specific pattern and an isoform-dependent manner in microglia. NEBULA opens up a new avenue for the broad application of mixed models to large-scale multi-subject single-cell data.
Collapse
Affiliation(s)
- Liang He
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Tomokazu S Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Cardiovascular Medicine, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
| |
Collapse
|
36
|
Dumbrava EE, Dougan ML, Gupta S, Cappelli L, Katsumoto TR, Rahma OE, Painter J, Wang Y, Suarez-Almazor ME, Reid P, Wesley SF, Hafler DA, Bingham CO, Warner BM, Chung L, Ott PA, Kluger HM, Khosroshahi A, Tawbi HAH, Sharon E. A phase 1b study of nivolumab in patients with autoimmune disorders and advanced malignancies (AIM-NIVO). J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.tps2676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
TPS2676 Background: Nivolumab is an anti-PD1 monoclonal antibody approved for treatment of an increasing number of solid tumors and hematological malignancies. However, patients (pts) with history of autoimmune disorders are excluded from the majority of clinical trials testing immune-checkpoint inhibitors (ICI) such as anti-PD1/anti-PD-L1 antibodies. Consequently, the risks of flare ups, worsening of pre-existing autoimmune disorders or risk of de-novo immune related adverse events (irAEs) in pts with dysfunctional immune systems and tumor types who otherwise stand to benefit from ICI therapy are largely unknown, posing a challenge for oncologists. We are conducting a phase Ib study to test the hypothesis that nivolumab can be safely administered to pts with varying severity of Dermatomyositis, Systemic Sclerosis, Rheumatoid Arthritis, Systemic Lupus Erythematosus, Inflammatory Bowel Disease, Multiple Sclerosis and other autoimmune disorders (AIM-Nivo). Methods: AIM-Nivo is an open-label, multi-center ongoing phase Ib study with nivolumab 480mg IV every 28 days in pts with autoimmune diseases and advanced malignancies (NCT03816345). The study has autoimmune disease-specific cohorts overseen by a multidisciplinary group of experts. The primary objective is to assess the overall safety and toxicity profile of nivolumab in pts with autoimmune disorders and advanced malignancies. Secondary objectives are to evaluate the antitumor efficacy; the impact of nivolumab on the autoimmune disease severity indices; and to explore potential biomarkers of response, resistance, or toxicity for each of the autoimmune disease-specific cohorts. Key overall inclusion criteria include age ≥18 years, histologically confirmed advanced or metastatic malignancies in which ICI are approved or have shown clinical activity. Key overall exclusion criteria include prior therapy with anti-PD-1/PD-L1 antibodies. Specific eligibility criteria are defined for each disease-specific cohort. For each autoimmune disorder, severity level of the disease as defined by disease-specific severity indices will be assessed, and up to a total of 12 pts will be included in each disease cohort at each severity level (max 36 pts per cohort). Primary endpoints are dose-limiting toxicities, adverse events (AEs) and serious AEs. Continuous monitoring of toxicity will be conducted. Key secondary endpoints are best objective response per RECIST1.1; progression free and overall survival; and cohort specific tumor tissue, blood, and non-tumor tissue-based biomarkers. The AIM-Nivo trial opened in May 2019 and is enrolling pts through the National Cancer Institute Experimental Therapeutics Clinical Trials Network (ETCTN), Early Drug Development Opportunity Program (EDDOP), and Create Access to Targeted Cancer Therapy for Underserved Populations (CATCH-UP) sites. Clinical trial information: NCT03816345.
Collapse
Affiliation(s)
| | | | - Sarthak Gupta
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | | | | | | | - Jeane Painter
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yinghong Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Maria E. Suarez-Almazor
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Sarah F. Wesley
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | | | - Blake M Warner
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | - Lorinda Chung
- Stanford University School of Medicine, Palo Alto, CA
| | | | - Harriet M. Kluger
- Yale School of Medicine and Smilow Cancer Center, Yale New Haven Hospital, New Haven, CT
| | | | | | | |
Collapse
|
37
|
Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children. Immunity 2021; 54:1083-1095.e7. [PMID: 33891889 PMCID: PMC8043654 DOI: 10.1016/j.immuni.2021.04.003] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [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: 11/20/2020] [Revised: 02/10/2021] [Accepted: 04/07/2021] [Indexed: 12/26/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening post-infectious complication occurring unpredictably weeks after mild or asymptomatic SARS-CoV-2 infection. We profiled MIS-C, adult COVID-19, and healthy pediatric and adult individuals using single-cell RNA sequencing, flow cytometry, antigen receptor repertoire analysis, and unbiased serum proteomics, which collectively identified a signature in MIS-C patients that correlated with disease severity. Despite having no evidence of active infection, MIS-C patients had elevated S100A-family alarmins and decreased antigen presentation signatures, indicative of myeloid dysfunction. MIS-C patients showed elevated expression of cytotoxicity genes in NK and CD8+ T cells and expansion of specific IgG-expressing plasmablasts. Clinically severe MIS-C patients displayed skewed memory T cell TCR repertoires and autoimmunity characterized by endothelium-reactive IgG. The alarmin, cytotoxicity, TCR repertoire, and plasmablast signatures we defined have potential for application in the clinic to better diagnose and potentially predict disease severity early in the course of MIS-C.
Collapse
Affiliation(s)
- Anjali Ramaswamy
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA
| | - Nina N Brodsky
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA; Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Tomokazu S Sumida
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA; Department of Neurology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Michela Comi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA; Department of Neurology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Hiromitsu Asashima
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA; Department of Neurology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Ningshan Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Aagam Shah
- Department of Internal Medicine (Cardiology), Yale University School of Medicine, New Haven, CT, 06510, USA; Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Neal G Ravindra
- Department of Internal Medicine (Cardiology), Yale University School of Medicine, New Haven, CT, 06510, USA; Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Jason Bishai
- Department of Internal Medicine (Cardiology), Yale University School of Medicine, New Haven, CT, 06510, USA; Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Alamzeb Khan
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - William Lau
- NIH Center for Human Immunology (CHI), NIAID, NIH, Bethesda, MD, 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Brian Sellers
- NIH Center for Human Immunology (CHI), NIAID, NIH, Bethesda, MD, 20892, USA
| | - Neha Bansal
- NIH Center for Human Immunology (CHI), NIAID, NIH, Bethesda, MD, 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Pamela Guerrerio
- Food Allergy Research Section, Laboratory of Allergic Diseases, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New, Haven, CT, 06520, USA
| | - Victoria Habet
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Andrew J Rice
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA
| | - Jason Catanzaro
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Harsha Chandnani
- Department of Pediatrics, Loma Linda School of Medicine, Loma Linda, CA, 92354, USA
| | - Merrick Lopez
- Department of Pediatrics, Loma Linda School of Medicine, Loma Linda, CA, 92354, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New, Haven, CT, 06520, USA
| | - Charles S Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New, Haven, CT, 06520, USA
| | - John S Tsang
- NIH Center for Human Immunology (CHI), NIAID, NIH, Bethesda, MD, 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, 20892, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA; Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, 06520, USA; Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
| | - David van Dijk
- Department of Internal Medicine (Cardiology), Yale University School of Medicine, New Haven, CT, 06510, USA; Department of Computer Science, Yale University, New Haven, CT, 06520, USA
| | - Richard W Pierce
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - David A Hafler
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA; Department of Neurology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Carrie L Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, 06519, USA.
| |
Collapse
|
38
|
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
|
39
|
Ramaswamy A, Brodsky NN, Sumida TS, Comi M, Asashima H, Hoehn KB, Li N, Liu Y, Shah A, Ravindra NG, Bishai J, Khan A, Lau W, Sellers B, Bansal N, Guerrerio P, Unterman A, Habet V, Rice AJ, Catanzaro J, Chandnani H, Lopez M, Kaminski N, Dela Cruz CS, Tsang JS, Wang Z, Yan X, Kleinstein SH, van Dijk D, Pierce RW, Hafler DA, Lucas CL. Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity. medRxiv 2021. [PMID: 33300011 DOI: 10.1101/2020.12.01.20241364] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening post-infectious complication occurring unpredictably weeks after mild or asymptomatic SARS-CoV2 infection in otherwise healthy children. Here, we define immune abnormalities in MIS-C compared to adult COVID-19 and pediatric/adult healthy controls using single-cell RNA sequencing, antigen receptor repertoire analysis, unbiased serum proteomics, and in vitro assays. Despite no evidence of active infection, we uncover elevated S100A-family alarmins in myeloid cells and marked enrichment of serum proteins that map to myeloid cells and pathways including cytokines, complement/coagulation, and fluid shear stress in MIS-C patients. Moreover, NK and CD8 T cell cytotoxicity genes are elevated, and plasmablasts harboring IgG1 and IgG3 are expanded. Consistently, we detect elevated binding of serum IgG from severe MIS-C patients to activated human cardiac microvascular endothelial cells in culture. Thus, we define immunopathology features of MIS-C with implications for predicting and managing this SARS-CoV2-induced critical illness in children.
Collapse
|
40
|
Sumida TS, Dulberg S, Schupp J, Stillwell HA, Axisa PP, Comi M, Lincoln M, Unterman A, Kaminski N, Madi A, Kuchroo VK, Hafler DA. Type I Interferon Transcriptional Network Regulates Expression of Coinhibitory Receptors in Human T cells. bioRxiv 2020:2020.10.30.362947. [PMID: 33140047 PMCID: PMC7605554 DOI: 10.1101/2020.10.30.362947] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
While inhibition of T cell co-inhibitory receptors has revolutionized cancer therapy, the mechanisms governing their expression on human T cells have not been elucidated. Type 1 interferon (IFN-I) modulates T cell immunity in viral infection, autoimmunity, and cancer, and may facilitate induction of T cell exhaustion in chronic viral infection 1,2 . Here we show that IFN-I regulates co-inhibitory receptors expression on human T cells, inducing PD-1/TIM-3/LAG-3 while surprisingly inhibiting TIGIT expression. High-temporal-resolution mRNA profiling of IFN-I responses enabled the construction of dynamic transcriptional regulatory networks uncovering three temporal transcriptional waves. Perturbation of key transcription factors on human primary T cells revealed both canonical and non-canonical IFN-I transcriptional regulators, and identified unique regulators that control expression of co-inhibitory receptors. To provide direct in vivo evidence for the role of IFN-I on co-inhibitory receptors, we then performed single cell RNA-sequencing in subjects infected with SARS-CoV-2, where viral load was strongly associated with T cell IFN-I signatures. We found that the dynamic IFN-I response in vitro closely mirrored T cell features with acute IFN-I linked viral infection, with high LAG3 and decreased TIGIT expression. Finally, our gene regulatory network identified SP140 as a key regulator for differential LAG3 and TIGIT expression. The construction of co-inhibitory regulatory networks induced by IFN-I with identification of unique transcription factors controlling their expression may provide targets for enhancement of immunotherapy in cancer, infectious diseases, and autoimmunity.
Collapse
Affiliation(s)
- Tomokazu S. Sumida
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Shai Dulberg
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonas Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Helen A. Stillwell
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pierre-Paul Axisa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Michela Comi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Matthew Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Avraham Unterman
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine Section, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Asaf Madi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
| | - Vijay K. Kuchroo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David A. Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| |
Collapse
|
41
|
Nakatsuka N, Patterson N, Patsopoulos NA, Altemose N, Tandon A, Beecham AH, McCauley JL, Isobe N, Hauser S, De Jager PL, Hafler DA, Oksenberg JR, Reich D. Two genetic variants explain the association of European ancestry with multiple sclerosis risk in African-Americans. Sci Rep 2020; 10:16902. [PMID: 33037294 PMCID: PMC7547691 DOI: 10.1038/s41598-020-74035-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 09/24/2020] [Indexed: 12/31/2022] Open
Abstract
Epidemiological studies have suggested differences in the rate of multiple sclerosis (MS) in individuals of European ancestry compared to African ancestry, motivating genetic scans to identify variants that could contribute to such patterns. In a whole-genome scan in 899 African-American cases and 1155 African-American controls, we confirm that African-Americans who inherit segments of the genome of European ancestry at a chromosome 1 locus are at increased risk for MS [logarithm of odds (LOD) = 9.8], although the signal weakens when adding an additional 406 cases, reflecting heterogeneity in the two sets of cases [logarithm of odds (LOD) = 2.7]. The association in the 899 individuals can be fully explained by two variants previously associated with MS in European ancestry individuals. These variants tag a MS susceptibility haplotype associated with decreased CD58 gene expression (odds ratio of 1.37; frequency of 84% in Europeans and 22% in West Africans for the tagging variant) as well as another haplotype near the FCRL3 gene (odds ratio of 1.07; frequency of 49% in Europeans and 8% in West Africans). Controlling for all other genetic and environmental factors, the two variants predict a 1.44-fold higher rate of MS in European-Americans compared to African-Americans.
Collapse
Affiliation(s)
- Nathan Nakatsuka
- Department of Genetics, Harvard Medical School, New Research Building, Boston, MA, 02115, USA. .,Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA
| | - Nikolaos A Patsopoulos
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA.,Systems Biology and Computer Science Program, Department of Neurology, Ann Romney Center for Neurological Diseases, Brigham & Women's Hospital, Boston, MA, 02115, USA.,Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California Berkeley, San Francisco, Berkeley, CA, 94720, USA
| | - Arti Tandon
- Department of Genetics, Harvard Medical School, New Research Building, Boston, MA, 02115, USA.,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA
| | - Ashley H Beecham
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.,Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Noriko Isobe
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, CA, 94158, USA.,Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Stephen Hauser
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, CA, 94158, USA
| | - Philip L De Jager
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA.,Department of Neurology, Center for Translational & Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - David A Hafler
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA.,Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco School of Medicine, San Francisco, CA, 94158, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, New Research Building, Boston, MA, 02115, USA. .,Department of Human Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA. .,Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, 02141, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
42
|
Lincoln MR, Axisa PP, Hafler DA. Epigenetic fine-mapping: identification of causal mechanisms for autoimmunity. Curr Opin Immunol 2020; 67:50-56. [PMID: 32977183 DOI: 10.1016/j.coi.2020.09.002] [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] [Received: 07/01/2020] [Revised: 08/28/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022]
Abstract
Genome-wide association studies (GWAS) have identified genetic susceptibility loci for a variety of autoimmune and inflammatory diseases. These studies confirm the fundamental genetic basis of individual autoimmune diseases, and also point to shared etiological mechanisms across the spectrum of autoimmunity. While hundreds of genetic loci have been implicated in autoimmune diseases, the translation of individual susceptibility loci into specific molecular mechanisms for individual diseases remains difficult. This review highlights recent advances in the genetics of autoimmune disease, and the emerging use of epigenetic techniques to identify pathogenic cell types and causal molecular mechanisms of autoimmunity.
Collapse
Affiliation(s)
- Matthew R Lincoln
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Pierre-Paul Axisa
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA.
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| |
Collapse
|
43
|
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
|
44
|
Ileana Dumbrava EE, Suarez-Almazor M, Painter J, Johanns TM, Dougan ML, Cappelli L, Wang Y, Bingham C, Gupta S, Warner BM, Rahma O, Naidoo J, Ott PA, Hafler DA, Kluger H, Khosroshahi A, Naqash R, Chung L, Katsumoto TR, Kummar S, Tawbi H, Sharon E. Abstract CT249: A phase 1b study of nivolumab in patients with autoimmune disorders and advanced malignancies (AIM-NIVO). Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-ct249] [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
Abstract
Background: Immune checkpoint inhibitors (ICI) such as anti-PD-1/PD-L1 antibodies have rapidly become a pivotal approach to cancer therapy. Nivolumab is an anti-PD1 antibody approved for treatment of melanoma, lung, renal cell, head and neck squamous, urothelial and increasing number of other solid and hematological malignancies. However, patients with history of autoimmune disorders are excluded from the majority of clinical trials testing ICI. Consequently, the risks of flare ups and worsening of pre-existing autoimmune disorders in patients with tumor types who otherwise stand to benefit from ICI therapy are largely unknown, posing a challenge for oncologists. We are conducting a phase Ib study to test the hypothesis that nivolumab can be safely administered to patients with varying severity of Dermatomyositis, Systemic Sclerosis, Rheumatoid Arthritis, Systemic Lupus Erythematosus, Inflammatory Bowel Disease, Multiple Sclerosis and others autoimmune disorders (AIM-Nivo). Methods: AIM-Nivo is an open-label, multi-center ongoing phase Ib study with nivolumab 480mg IV every 28 days in patients with autoimmune diseases and advanced or metastatic solid tumors. The study has autoimmune disease-specific cohorts overseen by a multidisciplinary group of experts. The primary objective is to assess the overall safety and toxicity profile of nivolumab in patients with autoimmune disorders and advanced or metastatic solid tumors. Secondary objectives are to evaluate the antitumor efficacy, the impact of nivolumab on the autoimmune disease severity indices, and to explore potential biomarkers of response, resistance or toxicity. Key overall inclusion criteria include age ≥18 years, histologically confirmed advanced or metastatic solid tumors in which ICI are approved or have shown clinical activity, Eastern Cooperative Oncology Group (ECOG) performance status 0-2. Key overall exclusion criteria include prior therapy with an anti-PD-1/PD-L1 antibodies. Specific eligibility criteria are defined for each disease-specific cohort. For each autoimmune disorder, severity level of the disease as defined by disease-specific severity indices will be assessed, and up to a total of 12 patients will be included in each disease cohort at each severity level. Primary endpoints are dose-limiting toxicities defined for each autoimmune disease-specific cohort, adverse events (AEs) and serious AEs. Continuous monitoring of toxicity will be conducted. Key secondary endpoints are best objective response, progression free and overall survival and cohort specific tumor tissue, blood and non-tumor tissue-based biomarkers. The AIM-Nivo trial opened in May 2019 and is currently enrolling patients in the participating sites through the National Cancer Institute Experimental Therapeutics Clinical Trials Network (ETCTN). Clinical trial information: NCT03816345.
Citation Format: Ecaterina E. Ileana Dumbrava, Maria Suarez-Almazor, Jeane Painter, Tanner M. Johanns, Michael L. Dougan, Laura Cappelli, Yinghong Wang, Clifton Bingham, Sarthak Gupta, Blake M. Warner, Osama Rahma, Jarushka Naidoo, Patrick A. Ott, David A. Hafler, Harriet Kluger, Arezou Khosroshahi, Rafeh Naqash, Lorinda Chung, Tamiko R. Katsumoto, Shivaani Kummar, Hussein Tawbi, Elad Sharon. A phase 1b study of nivolumab in patients with autoimmune disorders and advanced malignancies (AIM-NIVO) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT249.
Collapse
Affiliation(s)
| | | | - Jeane Painter
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Michael L. Dougan
- 3Massachusetts General Hospital/Dana-Farber Cancer Institute, Boston, MA
| | - Laura Cappelli
- 4Johns Hopkins University School of Medicine, Baltimore, MD
| | - Yinghong Wang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Sarthak Gupta
- 5National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Blake M. Warner
- 6National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | | | | | | | | | | | | | | | - Lorinda Chung
- 11Stanford University School of Medicine, Stanford, CA
| | | | | | - Hussein Tawbi
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | |
Collapse
|
45
|
Ileana Dumbrava EE, Suarez-Almazor ME, Painter J, Johanns T, Dougan ML, Cappelli L, Bingham CO, Wang Y, Gupta S, Warner BM, Rahma OE, Naidoo J, Ott PA, Hafler DA, Kluger HM, Khosroshahi A, Katsumoto TR, Kummar S, Sharon E, Tawbi HAH. A phase Ib study of nivolumab in patients with autoimmune disorders and advanced malignancies (AIM-NIVO). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.tps3158] [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: 11/20/2022] Open
Abstract
TPS3158 Background: Immune checkpoint inhibitors (ICI) such as anti-PD-1/PD-L1 antibodies have become a pivotal approach to cancer therapy. Nivolumab is an anti-PD1 antibody approved for an increasing number of solid tumors and hematological malignancies. However, patients (pts) with history of autoimmune disorders are excluded from the majority of clinical trials testing ICI. Consequently, the risks of flares and worsening of pre-existing autoimmune disorders in pts with tumor types who otherwise stand to benefit from ICI therapy are largely unknown, posing a challenge for oncologists. We are conducting a phase Ib study to test the hypothesis that nivolumab can be safely administered to pts with varying severity of Dermatomyositis, Systemic Sclerosis, Rheumatoid Arthritis, Systemic Lupus Erythematosus, Inflammatory Bowel Disease, Multiple Sclerosis, Sjögren's Syndrome and Other Autoimmune Disorders (AIM-Nivo). Methods: AIM-Nivo is an open-label, multi-center ongoing phase Ib study with nivolumab 480mg IV every 28 days in pts with autoimmune diseases and advanced malignancies (NCT03816345). The study has autoimmune disease-specific cohorts overseen by a multidisciplinary group of experts. The primary objective is to assess the overall safety and toxicity profile of nivolumab in pts with autoimmune disorders and advanced malignancies. Secondary objectives are to evaluate the antitumor efficacy, the impact of nivolumab on the autoimmune disease severity indices, and to explore potential biomarkers of response, resistance or toxicity. Key overall inclusion criteria include age ≥18 years, histologically confirmed advanced malignancies in which ICI are approved or have shown clinical activity. Key overall exclusion criteria include prior therapy with anti-PD-1/PD-L1 antibodies. Specific eligibility criteria are defined for each disease-specific cohort. For each autoimmune disorder, severity level of the disease as defined by disease-specific severity indices will be assessed, and up to a total of 12 pts will be included in each disease cohort at each severity level. Primary endpoints are dose-limiting toxicities, adverse events (AEs) and serious AEs. Continuous monitoring of toxicity will be conducted. Key secondary endpoints are best objective response, progression free and overall survival and cohort specific tumor tissue, blood and non-tumor tissue-based biomarkers. The AIM-Nivo trial opened in May 2019 and is enrolling pts through the National Cancer Institute Experimental Therapeutics Clinical Trials Network (ETCTN). Clinical trial information: NCT03816345 .
Collapse
Affiliation(s)
| | - Maria E. Suarez-Almazor
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeane Painter
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Yinghong Wang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarthak Gupta
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD
| | - Blake M Warner
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | | | | | | | | | - Harriet M. Kluger
- Yale School of Medicine and Smilow Cancer Center, Yale New Haven Hospital, New Haven, CT
| | | | | | - Shivaani Kummar
- Stanford Cancer Institute, Stanford University, Palo Alto, CA
| | | | | |
Collapse
|
46
|
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: 15] [Impact Index Per Article: 3.8] [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
|
47
|
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: 13] [Impact Index Per Article: 2.6] [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
|
48
|
Abstract
Progressive multiple sclerosis (PMS) causes slow accumulation of neurologic disability and has been refractory to treatment with the immunomodulatory medications that effectively control relapsing MS. Siponimod modestly slowed the rate of disability progression among PMS patients who had inflammatory disease activity, evidenced by new or gadolinium-enhancing MRI lesions. To view this Bench to Bedside, open or download the PDF.
Collapse
|
49
|
Kitz A, de Marcken M, Gautron AS, Mitrovic M, Hafler DA, Dominguez-Villar M. AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease. EMBO Rep 2019; 20:e48624. [PMID: 31379130 PMCID: PMC6680151 DOI: 10.15252/embr.201948624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2023] Open
Abstract
[Image: see text]
Collapse
|
50
|
Mitrovič M, Patsopoulos NA, Beecham AH, Dankowski T, Goris A, Dubois B, D’hooghe MB, Lemmens R, Van Damme P, Søndergaard HB, Sellebjerg F, Sorensen PS, Ullum H, Thørner LW, Werge T, Saarela J, Cournu-Rebeix I, Damotte V, Fontaine B, Guillot-Noel L, Lathrop M, Vukusik S, Gourraud PA, Andlauer TF, Pongratz V, Buck D, Gasperi C, Bayas A, Heesen C, Kümpfel T, Linker R, Paul F, Stangel M, Tackenberg B, Bergh FT, Warnke C, Wiendl H, Wildemann B, Zettl U, Ziemann U, Tumani H, Gold R, Grummel V, Hemmer B, Knier B, Lill CM, Luessi F, Dardiotis E, Agliardi C, Barizzone N, Mascia E, Bernardinelli L, Comi G, Cusi D, Esposito F, Ferrè L, Comi C, Galimberti D, Leone MA, Sorosina M, Mescheriakova J, Hintzen R, van Duijn C, Teunissen CE, Bos SD, Myhr KM, Celius EG, Lie BA, Spurkland A, Comabella M, Montalban X, Alfredsson L, Stridh P, Hillert J, Jagodic M, Piehl F, Jelčić I, Martin R, Sospedra M, Ban M, Hawkins C, Hysi P, Kalra S, Karpe F, Khadake J, Lachance G, Neville M, Santaniello A, Caillier SJ, Calabresi PA, Cree BA, Cross A, Davis MF, Haines JL, de Bakker PI, Delgado S, Dembele M, Edwards K, Fitzgerald KC, Hakonarson H, Konidari I, Lathi E, Manrique CP, Pericak-Vance MA, Piccio L, Schaefer C, McCabe C, Weiner H, Goldstein J, Olsson T, Hadjigeorgiou G, Taylor B, Tajouri L, Charlesworth J, Booth DR, Harbo HF, Ivinson AJ, Hauser SL, Compston A, Stewart G, Zipp F, Barcellos LF, Baranzini SE, Martinelli-Boneschi F, D’Alfonso S, Ziegler A, Oturai A, McCauley JL, Sawcer SJ, Oksenberg JR, De Jager PL, Kockum I, Hafler DA, Cotsapas C. Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk. Cell 2019; 178:262. [PMID: 31251915 PMCID: PMC6602362 DOI: 10.1016/j.cell.2019.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|