1
|
Voutouri C, Hardin CC, Naranbhai V, Nikmaneshi MR, Khandekar MJ, Gainor JF, Stylianopoulos T, Munn LL, Jain RK. In silico clinical studies for optimal COVID-19 vaccination schedules in patients with cancer. Cell Rep Med 2024; 5:101436. [PMID: 38508146 PMCID: PMC10982978 DOI: 10.1016/j.xcrm.2024.101436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/25/2023] [Accepted: 01/29/2024] [Indexed: 03/22/2024]
Abstract
This study introduces a tailored COVID-19 model for patients with cancer, incorporating viral variants and immune-response dynamics. The model aims to optimize vaccination strategies, contributing to personalized healthcare for vulnerable groups.
Collapse
Affiliation(s)
- Chrysovalantis Voutouri
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
| | - C Corey Hardin
- Department of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Mohammad R Nikmaneshi
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Melin J Khandekar
- Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Triantafyllos Stylianopoulos
- Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus.
| | - Lance L Munn
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Rakesh K Jain
- Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
2
|
Schurz H, Naranbhai V, Yates TA, Gilchrist JJ, Parks T, Dodd PJ, Möller M, Hoal EG, Morris AP, Hill AVS. Multi-ancestry meta-analysis of host genetic susceptibility to tuberculosis identifies shared genetic architecture. eLife 2024; 13:e84394. [PMID: 38224499 PMCID: PMC10789494 DOI: 10.7554/elife.84394] [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: 10/23/2022] [Accepted: 11/23/2023] [Indexed: 01/17/2024] Open
Abstract
The heritability of susceptibility to tuberculosis (TB) disease has been well recognized. Over 100 genes have been studied as candidates for TB susceptibility, and several variants were identified by genome-wide association studies (GWAS), but few replicate. We established the International Tuberculosis Host Genetics Consortium to perform a multi-ancestry meta-analysis of GWAS, including 14,153 cases and 19,536 controls of African, Asian, and European ancestry. Our analyses demonstrate a substantial degree of heritability (pooled polygenic h2 = 26.3%, 95% CI 23.7-29.0%) for susceptibility to TB that is shared across ancestries, highlighting an important host genetic influence on disease. We identified one global host genetic correlate for TB at genome-wide significance (p<5 × 10-8) in the human leukocyte antigen (HLA)-II region (rs28383206, p-value=5.2 × 10-9) but failed to replicate variants previously associated with TB susceptibility. These data demonstrate the complex shared genetic architecture of susceptibility to TB and the importance of large-scale GWAS analysis across multiple ancestries experiencing different levels of infection pressure.
Collapse
Affiliation(s)
- Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Massachusetts General HospitalBostonUnited States
- Dana-Farber Cancer InstituteBostonUnited States
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Harvard Medical SchoolBostonUnited States
| | - Tom A Yates
- Division of Infection and Immunity, Faculty of Medical Sciences, University College LondonLondonUnited Kingdom
| | - James J Gilchrist
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Paediatrics, University of OxfordOxfordUnited Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Department of Infectious Diseases Imperial College LondonLondonUnited Kingdom
| | - Peter J Dodd
- School of Health and Related Research, University of SheffieldSheffieldUnited Kingdom
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Eileen G Hoal
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch UniversityCape TownSouth Africa
| | - Andrew P Morris
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of ManchesterManchesterUnited Kingdom
| | - Adrian VS Hill
- Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
- Jenner Institute, University of OxfordOxfordUnited Kingdom
| |
Collapse
|
3
|
Zonozi R, Walters LC, Shulkin A, Naranbhai V, Nithagon P, Sauvage G, Kaeske C, Cosgrove K, Nathan A, Tano-Menka R, Gayton AC, Getz MA, Senjobe F, Worrall D, Iafrate AJ, Fromson C, Montesi SB, Rao DA, Sparks JA, Wallace ZS, Farmer JR, Walker BD, Charles RC, Laliberte K, Niles JL, Gaiha GD. T cell responses to SARS-CoV-2 infection and vaccination are elevated in B cell deficiency and reduce risk of severe COVID-19. Sci Transl Med 2023; 15:eadh4529. [PMID: 38019932 DOI: 10.1126/scitranslmed.adh4529] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Individuals with primary and pharmacologic B cell deficiencies have high rates of severe disease and mortality from coronavirus disease 2019 (COVID-19), but the immune responses and clinical outcomes after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and vaccination have yet to be fully defined. Here, we evaluate the cellular immune responses after both SARS-CoV-2 infection and vaccination in patients receiving the anti-CD20 therapy rituximab (RTX) and those with low B cell counts due to common variable immune deficiency (CVID) disease. Assessment of effector and memory CD4+ and CD8+ T cell responses to SARS-CoV-2 revealed elevated reactivity and proliferative capacity after both infection and vaccination in B cell-deficient individuals, particularly within the CD8+ T cell compartment, in comparison with healthy controls. Evaluation of clinical outcomes demonstrates that vaccination of RTX-treated individuals was associated with about 4.8-fold reduced odds of moderate or severe COVID-19 in the absence of vaccine-induced antibodies. Analysis of T cell differentiation demonstrates that RTX administration increases the relative frequency of naïve CD8+ T cells, potentially by depletion of CD8+CD20dim T cells, which are primarily of an effector memory or terminal effector memory (TEMRA) phenotype. However, this also leads to a reduction in preexisting antiviral T cell immunity. Collectively, these data indicate that individuals with B cell deficiencies have enhanced T cell immunity after both SARS-CoV-2 infection and vaccination that potentially accounts for reduced hospitalization and severe disease from subsequent SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Reza Zonozi
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lucy C Walters
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA 02139, USA
| | - Aaron Shulkin
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Monash University, Melbourne, VIC 3022, Australia
| | - Pravarut Nithagon
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gabriel Sauvage
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Clarety Kaeske
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Katherine Cosgrove
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anusha Nathan
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Rhoda Tano-Menka
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Alton C Gayton
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Matthew A Getz
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Daniel Worrall
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Caroline Fromson
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Sydney B Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zachary S Wallace
- Division of Rheumatology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jocelyn R Farmer
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Allergy and Inflammation, Beth Israel Lahey Health, Boston, MA 02215, USA
| | - Bruce D Walker
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
- Broad Institute, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Karen Laliberte
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John L Niles
- Vasculitis and Glomerulonephritis Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav D Gaiha
- Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| |
Collapse
|
4
|
Fritschi N, Vaezipour N, Buettcher M, Portevin D, Naranbhai V, Ritz N. Ratios from full blood count as markers for TB diagnosis, treatment, prognosis: a systematic review. Int J Tuberc Lung Dis 2023; 27:822-832. [PMID: 37880883 DOI: 10.5588/ijtld.22.0598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND: The monocyte-to-lymphocyte (MLR) and neutrophil-to-lymphocyte (NLR) ratio are calculated from routine full blood counts. The aim of this study was to systematically review MLR and NLR as biomarkers for diagnosis, treatment response monitoring and prognostic biomarker for TB infection or disease.METHODS: A systematic literature search was conducted in Medline, Embase and the Cochrane Library on 12 January 2022. The following search terms were used: tuberculosis AND (monocyte OR neutrophils), AND lymphocytes AND (diagnostic OR prognostic OR treatment).RESULTS: A total of 2,314 studies were identified, of which 41, covering 11,952 individuals, were included in the final analysis. Studies enrolled a median of 154 individuals (IQR 108-301). Increased MLR and NLR were associated with TB disease when compared to healthy controls and individuals with TB infection. MLR was shown to be prognostic for progression to TB disease and to decrease in response to TB treatment. The cut-offs determined in the studies were highly variable for MLR and NLR, making it impractical to conduct a meta-analysis of sensitivity and specificity.CONCLUSION: Higher MLR and NLR are associated with TB disease and could be used as easy-to-obtain, low-cost additional diagnostic biomarkers. Further studies investigating these biomarkers are needed.
Collapse
Affiliation(s)
- N Fritschi
- Mycobacterial and Migrant Health Research Group, University of Basel Children's Hospital Basel, Basel, Department of Clinical Research, University of Basel, Basel, University Children's Hospital Basel, Basel
| | - N Vaezipour
- Mycobacterial and Migrant Health Research Group, University of Basel Children's Hospital Basel, Basel, Infectious Disease and Vaccinology Unit, University Children's Hospital Basel, University of Basel, Basel
| | - M Buettcher
- Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne, Paediatric Pharmacology and Pharmacometrics Research Center, University Children's Hospital Basel, University of Basel, Basel
| | - D Portevin
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, University of Basel, Basel, Switzerland
| | - V Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, Dana-Farber Cancer Institute, Boston, MA, USA, Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - N Ritz
- Mycobacterial and Migrant Health Research Group, University of Basel Children's Hospital Basel, Basel, Department of Clinical Research, University of Basel, Basel, Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne, Department of Paediatrics, The Royal Children's Hospital Melbourne, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
5
|
Thierauf JC, Kaluziak ST, Codd E, Dybel SN, Jobbagy S, Purohit R, Farahani AA, Dedeilia A, Naranbhai V, Hoang MP, Fisch AS, Ritterhouse L, Boland GM, Lennerz JK, Iafrate AJ. Prognostic biomarkers for survival in mucosal melanoma. Pigment Cell Melanoma Res 2023; 36:378-387. [PMID: 37390098 DOI: 10.1111/pcmr.13104] [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: 02/16/2023] [Revised: 05/17/2023] [Accepted: 05/29/2023] [Indexed: 07/02/2023]
Abstract
Mucosal melanoma (MM) is a rare subtype of melanoma with an aggressive clinical course. In cutaneous melanoma (CM), the absence of pigmentation and presence of NRAS/KRAS mutations are biomarkers indicating an aggressive clinical course with shorter overall survival. Similar data for MM are missing. We present the real-world outcome data in a cohort of genotyped MM patients and assessed the prognostic relevance of pigmentation- and NRAS/KRAS mutation status. We correlated pathological reports and clinical data with overall survival of patients with MM. Furthermore, we performed clinically integrated molecular genotyping and analyzed real world treatment regimens for covariates associated with clinical outcome. We identified 39 patients with available clinical and molecular data. Patients with amelanotic MM had a significantly shorter overall survival (p = .003). In addition, the presence of a NRAS or KRAS mutation was significantly associated with poor overall survival (NRAS or KRAS p = .024). Currently, it is unknown if the same prognostic relevance for the lack of pigmentation and RAS mutations in CM, exists in MM. Here we analyzed a cohort of MM for outcome measures and determined that two known prognostic biomarkers for CM are in fact novel prognosticators for MM.
Collapse
Affiliation(s)
- Julia C Thierauf
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital and Research Group Molecular Mechanisms of Head and Neck Tumors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan T Kaluziak
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Marine Science Center, Northeastern University, Nahant, Massachusetts, USA
| | - Elizabeth Codd
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Stacy N Dybel
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Soma Jobbagy
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rashi Purohit
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alex A Farahani
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | | | - Vivek Naranbhai
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mai P Hoang
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lauren Ritterhouse
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
6
|
Lin Z, Bashirova AA, Viard M, Garner L, Quastel M, Beiersdorfer M, Kasprzak WK, Akdag M, Yuki Y, Ojeda P, Das S, Andresson T, Naranbhai V, Horowitz A, McMichael AJ, Hoelzemer A, Gillespie GM, Garcia-Beltran WF, Carrington M. HLA class I signal peptide polymorphism determines the level of CD94/NKG2-HLA-E-mediated regulation of effector cell responses. Nat Immunol 2023; 24:1087-1097. [PMID: 37264229 PMCID: PMC10690437 DOI: 10.1038/s41590-023-01523-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/27/2023] [Indexed: 06/03/2023]
Abstract
Human leukocyte antigen (HLA)-E binds epitopes derived from HLA-A, HLA-B, HLA-C and HLA-G signal peptides (SPs) and serves as a ligand for CD94/NKG2A and CD94/NKG2C receptors expressed on natural killer and T cell subsets. We show that among 16 common classical HLA class I SP variants, only 6 can be efficiently processed to generate epitopes that enable CD94/NKG2 engagement, which we term 'functional SPs'. The single functional HLA-B SP, known as HLA-B/-21M, induced high HLA-E expression, but conferred the lowest receptor recognition. Consequently, HLA-B/-21M SP competes with other SPs for providing epitope to HLA-E and reduces overall recognition of target cells by CD94/NKG2A, calling for reassessment of previous disease models involving HLA-B/-21M. Genetic population data indicate a positive correlation between frequencies of functional SPs in humans and corresponding cytomegalovirus mimics, suggesting a means for viral escape from host responses. The systematic, quantitative approach described herein will facilitate development of prediction algorithms for accurately measuring the impact of CD94/NKG2-HLA-E interactions in disease resistance/susceptibility.
Collapse
Affiliation(s)
- Zhansong Lin
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lee Garner
- Centre for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Max Quastel
- Centre for Immuno-Oncology, University of Oxford, Oxford, UK
| | - Maya Beiersdorfer
- Leibniz Institute of Virology, Hamburg, Germany
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Wojciech K Kasprzak
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Pedro Ojeda
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Sudipto Das
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thorkell Andresson
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Amir Horowitz
- Department of Oncological Sciences, Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, Germany
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | | | | | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| |
Collapse
|
7
|
Meador CB, Naranbhai V, Hambelton G, Rivera J, Nabel CS, Lewinsohn R, Sakhi M, Balazs AB, Iafrate AJ, Gainor JF. Brief Report: Declining Rates of SARS-CoV-2 Vaccine Uptake Among Patients With Thoracic Malignancies. Clin Lung Cancer 2023; 24:353-359. [PMID: 36792425 PMCID: PMC9876008 DOI: 10.1016/j.cllc.2023.01.007] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/08/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
•Patients with primary thoracic malignancies are at increased risk of complications and death from COVID-19. Multiple studies have demonstrated humoral immune responses to SARS-CoV-2 vaccinations in patients with cancer, though the degree of immunogenicity varies. Over the last year the United States CDC has issued recommendations for multiple additional ‘booster’ vaccine doses for patients with cancer for protection against severe disease. •In this study, we found that among 242 patients with primary thoracic malignancies who underwent initial vaccination against SARS-CoV-2, there was a marked decline in uptake of each subsequent additional vaccine dose. Specifically, among patients who received an initial mRNA-based vaccination series (mRNA-1273 or BNT162b2), 75% of eligible patients received the recommended third dose, 39% received the recommended fourth dose, and 5% received the recommended fifth dose at the time of data cutoff. Of note, we assessed serologic responses in a subset of patients receiving booster vaccinations and found that additional vaccinations increased humoral immunity, as expected. •With the recent CDC recommendation of novel bivalent mRNA-based vaccine booster doses for all individuals over the age of 12, our findings highlight the need for further understanding of the reasons behind decreased vaccine uptake and emphasize the importance of counseling by providers regarding public health recommendations for patients with lung cancer.
Collapse
Affiliation(s)
- Catherine B Meador
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Grace Hambelton
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Julia Rivera
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Christopher S Nabel
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Rebecca Lewinsohn
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Mustafa Sakhi
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Alejandro B Balazs
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA
| | - Justin F Gainor
- Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, MA.
| |
Collapse
|
8
|
Ravi A, Hellmann MD, Arniella MB, Holton M, Freeman SS, Naranbhai V, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin AT, Vokes NI, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde PM, Anagnostou V, Riess JW, Gibbons DL, Pennell NA, Velcheti V, Digumarthy SR, Mino-Kenudson M, Califano A, Heymach JV, Herbst RS, Brahmer JR, Schalper KA, Velculescu VE, Henick BS, Rizvi N, Jänne PA, Awad MM, Chow A, Greenbaum BD, Luksza M, Shaw AT, Wolchok J, Hacohen N, Getz G, Gainor JF. Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer. Nat Genet 2023; 55:807-819. [PMID: 37024582 PMCID: PMC10181943 DOI: 10.1038/s41588-023-01355-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [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: 07/19/2022] [Accepted: 02/24/2023] [Indexed: 04/08/2023]
Abstract
Anti-PD-1/PD-L1 agents have transformed the treatment landscape of advanced non-small cell lung cancer (NSCLC). To expand our understanding of the molecular features underlying response to checkpoint inhibitors in NSCLC, we describe here the first joint analysis of the Stand Up To Cancer-Mark Foundation cohort, a resource of whole exome and/or RNA sequencing from 393 patients with NSCLC treated with anti-PD-(L)1 therapy, along with matched clinical response annotation. We identify a number of associations between molecular features and outcome, including (1) favorable (for example, ATM altered) and unfavorable (for example, TERT amplified) genomic subgroups, (2) a prominent association between expression of inducible components of the immunoproteasome and response and (3) a dedifferentiated tumor-intrinsic subtype with enhanced response to checkpoint blockade. Taken together, results from this cohort demonstrate the complexity of biological determinants underlying immunotherapy outcomes and reinforce the discovery potential of integrative analysis within large, well-curated, cancer-specific cohorts.
Collapse
Affiliation(s)
- Arvind Ravi
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Monica B Arniella
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Mark Holton
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Samuel S Freeman
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
- Center for the AIDS Programme for Research in South Africa, Durban, South Africa
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Ignaty Leshchiner
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | | | - Yo Akiyama
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA
| | - Aaron T Griffin
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Natalie I Vokes
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, TX, USA
| | - Mustafa Sakhi
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Vashine Kamesan
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Patrick M Forde
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Don L Gibbons
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Nathan A Pennell
- Department of Hematology and Medical Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Vamsidhar Velcheti
- Department of Hematology and Oncology, NYU Langone Health, New York, NY, USA
| | - Subba R Digumarthy
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Mari Mino-Kenudson
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Califano
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- J.P. Sulzberger Columbia Genome Center, New York, NY, USA
| | - John V Heymach
- Department of Thoracic and Head and Neck Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Roy S Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Julie R Brahmer
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kurt A Schalper
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Victor E Velculescu
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian S Henick
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrew Chow
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Marta Luksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice T Shaw
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA
| | | | - Nir Hacohen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, USA.
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA, USA.
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
9
|
Naranbhai V, Ravi A, Hellmann M, Arniella M, Holton M, Freeman S, Stewart C, Leshchiner I, Kim J, Akiyama Y, Griffin A, Vokes N, Sakhi M, Kamesan V, Rizvi H, Ricciuti B, Forde P, Anagnostou V, Riess J, Gibbons D, Pennell N, Velcheti V, Digumarthy S, Mino-Kenudson M, Califano A, Heymach J, Herbst R, Brahmer J, Schalper K, Velculescu V, Henick B, Rizvi N, Janne P, Awad M, Chow A, Greenbaum B, Luksza M, Shaw A, Wolchok J, Hacohen N, Getz G, Gainor J. Abstract 3468: Immunoproteasome expression and checkpoint blockade response in advanced non-small cell lung cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3468] [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: 04/07/2023]
Abstract
Abstract
Responders to checkpoint blockade in Non Small Cell Lung Cancer (NSCLC) often feature an inflamed microenvironment prior to therapy. However, the complete set of molecular drivers connecting this histologic observation to enhanced tumor clearance remain enigmatic.
In updated analysis of the Stand Up 2 Cancer-Mark Foundation (SU2C-MARK) Cohort - a collection of 393 patients with whole exome and/or RNA sequencing along with matched checkpoint blockade response annotation - we identify a prominent predictive role for inducible components of the immunoproteasome, a non-canonical peptide processing complex upstream of antigen presentation. Notably, these subunits are enriched as predictors relative to interferon-inducible genes as well as proteasome components in general, and are consistently associated with objective response, progression-free survival and overall survival. Expression of Immunoproteasome subunits associates positively with TCR (but not BCR) burden, supporting a mechanistic model in which enhanced immunoproteasome processivity leads to superior T-cell recognition. Furthermore, although they are known to be targets of interferon gamma (IFNɣ), we demonstrate that their expression is better modeled via a combination of IFNɣ and tumor necrosis factor-α (TNFα) levels, suggesting they may act as integrators of multiple cytokine cascades.
Given the fact that the immunoproteasome can alter both antigen quantity as well as quality (including peptide cleavage site preference), the enhanced expression of this complex in the setting of checkpoint blockade response may have important implications for modeling of antigen presentation. These data also suggest novel strategies to enhance immune checkpoint blockade.
Citation Format: Vivek Naranbhai, Arvind Ravi, Matthew Hellmann, Monica Arniella, Mark Holton, Samuel Freeman, Chip Stewart, Ignaty Leshchiner, Jaegil Kim, Yo Akiyama, Aaron Griffin, Natalie Vokes, Mustafa Sakhi, Vashine Kamesan, Hira Rizvi, Biagio Ricciuti, Patrick Forde, Valsamo Anagnostou, Jonathan Riess, Don Gibbons, Nathan Pennell, Vamsidhar Velcheti, Subba Digumarthy, Mari Mino-Kenudson, Andrea Califano, John Heymach, Roy Herbst, Julie Brahmer, Kurt Schalper, Victor Velculescu, Brian Henick, Naiyer Rizvi, Pasi Janne, Mark Awad, Andrew Chow, Benjamin Greenbaum, Marta Luksza, Alice Shaw, Jedd Wolchok, Nir Hacohen, Gad Getz, Justin Gainor. Immunoproteasome expression and checkpoint blockade response in advanced non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3468.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Pasi Janne
- 8Dana-Farber Cancer Institute, Boston, MA
| | - Mark Awad
- 2DFCI/Harvard Medical School, Boston, MA
| | | | | | | | - Alice Shaw
- 1Massachusetts General Hospital, Boston, MA
| | | | | | | | | |
Collapse
|
10
|
Kissling M, Fritschi N, Baumann P, Buettcher M, Bonhoeffer J, Naranbhai V, Ritz N. Monocyte, Lymphocyte and Neutrophil Ratios - Easy-to-Use Biomarkers for the Diagnosis of Pediatric Tuberculosis. Pediatr Infect Dis J 2023; 42:520-527. [PMID: 36977187 DOI: 10.1097/inf.0000000000003901] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
BACKGROUND The neutrophil-to-lymphocyte-ratio (NLR), neutrophil-to-monocyte-plus-lymphocyte-ratio (NMLR) and monocyte-to-lymphocyte-ratio (MLR) may have diagnostic potential for tuberculosis (TB). METHODS Data of two prospective multicenter studies in Switzerland were used, which included children <18 years with TB exposure, infection or disease or with febrile non-TB lower-respiratory-tract infection (nTB-LRTI). RESULTS Of the 389 children included 25 (6.4%) had TB disease, 12 (3.1%) TB infection, 28 (7.2%) were healthy TB exposed and 324 (83.3%) nTB-LRTI. Median (IQR) NLR was highest with 2.0 (1.2, 2.2) in children with TB disease compared to TB exposed [0.8 (0.6, 1.3); P = 0.002] and nTB-LRTI [0.3 (0.1, 1.0); P < 0.001]. Median (IQR) NMLR was highest with 1.4 (1.2, 1.7) in children with TB disease compared to healthy exposed [0.7 (0.6, 1.1); P = 0.003] and children with nTB-LRTI [0.2 (0.1, 0.6); P < 0.001). Receiver operating characteristic curves to detect TB disease compared to nTB-LRTI for NLR and NMLR had an area under the curve of 0.82 and 0.86, the sensitivity of 88% and 88%, and specificity of 71% and 76%, respectively. CONCLUSION NLR and NMLR are promising, easy-to-obtain diagnostic biomarkers to differentiate children with TB disease from other lower respiratory tract infections. These results require validation in a larger study and in settings with high and low TB endemicity.
Collapse
Affiliation(s)
- Mirjam Kissling
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
| | - Nora Fritschi
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
- University Children's Hospital Basel, Switzerland
| | - Philipp Baumann
- Department of Intensive Care Medicine and Neonatology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Infectious Disease and Vaccinology Unit, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael Buettcher
- Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne Switzerland
- Paediatric Pharmacology and Pharmacometrics Research Center, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Nicole Ritz
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
- University Children's Hospital Basel, Switzerland
- Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne Switzerland
- Department of Pediatrics, The Royal Children's Hospital Melbourne, The University of Melbourne, Australia
| |
Collapse
|
11
|
Hamilton F, Schurz H, Yates TA, Gilchrist JJ, Möller M, Naranbhai V, Ghazal P, Timpson NJ, Parks T, Pollara G. Altered IL-6 signalling and risk of tuberculosis disease: a meta-analysis and Mendelian randomisation study. medRxiv 2023:2023.02.07.23285472. [PMID: 36798349 PMCID: PMC9934798 DOI: 10.1101/2023.02.07.23285472] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
IL-6 responses are ubiquitous in Mycobacterium tuberculosis (Mtb) infections, but their role in determining human tuberculosis (TB) disease risk is unknown. We used single nucleotide polymorphisms (SNPs) in and near the IL-6 receptor (IL6R) gene, focusing on the non-synonymous variant, rs2228145, associated with reduced classical IL-6 signalling, to assess the effect of altered IL-6 activity on TB disease risk. We identified 16 genome wide association studies (GWAS) of TB disease collating 17,982 cases of TB disease and 972,389 controls across 4 continents. Meta-analyses and Mendelian randomisation analyses revealed that reduced classical IL-6 signalling was associated with lower odds of TB disease, a finding replicated using multiple, independent SNP instruments and 2 separate exposure variables. Our findings establish a causal relationship between IL-6 signalling and the outcome of Mtb infection, suggesting IL-6 antagonists do not increase the risk of TB disease and should be investigated as adjuncts in treatment.
Collapse
Affiliation(s)
- Fergus Hamilton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Haiko Schurz
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tom A. Yates
- Division of Infection and Immunity, University College London, London, UK
| | - James J. Gilchrist
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- Department of Paediatrics, University of Oxford, UK
| | - Marlo Möller
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- Massachusetts General Hospital, Boston, USA
- Dana-Farber Cancer Institute, Boston, USA
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Harvard Medical School, Boston, USA
| | | | | | - Tom Parks
- Wellcome Trust Centre for Human Genetics, Oxford, UK
- Department of Infectious Diseases Imperial College London, London, UK
| | - Gabriele Pollara
- Division of Infection and Immunity, University College London, London, UK
| |
Collapse
|
12
|
Voutouri C, Hardin CC, Naranbhai V, Nikmaneshi MR, Khandekar MJ, Gainor JF, Stylianopoulos T, Munn LL, Jain RK. Abstract A64: Mechanistic model for booster doses effectiveness in healthy, cancer and immunosuppressed patients infected with SARS-CoV-2. Cancer Immunol Res 2022. [DOI: 10.1158/2326-6074.tumimm22-a64] [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: 12/03/2022]
Abstract
Abstract
Introduction: Current SARS-CoV-2 vaccines are effective at preventing COVID-19 or limiting disease severity in healthy individuals, but effectiveness is lower among patients with cancer or immunosuppression. Vaccine effectiveness wanes with time and varies by vaccine type. Moreover, current vaccines are based on the ancestral SARS-CoV-2 spike protein sequence and emerging viral variants evade vaccine induced immunity. Booster doses partially overcome these issues, but there are limited clinical data on the durability of protection afforded by boosters – especially against SARS-CoV-2 variants.Methods: Here we describe a mechanistic mathematical model for vaccination-induced immunity and use it to predict vaccine effectiveness taking into account current and possible future viral, host and vaccine characteristics. Crucially, this allows predictions over time frames currently not reported in the clinical literature. The model incorporates the infection of lung epithelium by SARS-CoV-2, the response of innate and adaptive immune cells to infection, the production of pro-and anti-inflammatory cytokines, the activation of the coagulation cascade, as well as the effects of cancer cells on the lung and on the immune response. The model further accounts for the interactions between the virus, the immune cells and the tumor cells as well as for vaccination-induced immunity.Results: Model predictions were validated with clinical data. The model predicts that for healthy individuals vaccinated and boosted with mRNA-1273, BNT-162b2a, and Ad26.COV2.S, robust immunogenicity against the ancestral and delta variant extends beyond a year. Immunogenicity is also enhanced following booster vaccination in patients with cancer on various anti-cancer therapies, including immunotherapy, and for patients without cancer on immunosuppressive agents.Conclusion: Our model predicts that ³1 booster doses will be required for these individuals to maintain protective immunity. Furthermore, for immunosuppressed individuals, simulated new SARS-CoV2 variants with enhanced ability to bind to target cells, faster replication or reduced immunogenicity could lead to breakthrough infections even after a single booster dose. Modelling data such as these may be used to anticipate and plan for future vaccination needs.
Citation Format: Chrysovalantis Voutouri, Corey C Hardin, Vivek Naranbhai, Mohammad R. Nikmaneshi, Melin J. Khandekar, Justin F Gainor, Triantafyllos Stylianopoulos, Lance L. Munn, Rakesh K. Jain. Mechanistic model for booster doses effectiveness in healthy, cancer and immunosuppressed patients infected with SARS-CoV-2 [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A64.
Collapse
Affiliation(s)
- Chrysovalantis Voutouri
- 1aEdwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA bCancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus, Boston, MA,
| | - Corey C Hardin
- 2Department of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United Kingdom,
| | - Vivek Naranbhai
- 3dMassachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA,
| | - Mohammad R. Nikmaneshi
- 4Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA,
| | - Melin J. Khandekar
- 5hDepartment of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA,
| | - Justin F Gainor
- 3dMassachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA,
| | - Triantafyllos Stylianopoulos
- 6bCancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
| | - Lance L. Munn
- 4Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA,
| | - Rakesh K. Jain
- 4Edwin L Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA,
| |
Collapse
|
13
|
Gregory DJ, Vannier A, Duey AH, Roady TJ, Dzeng RK, Pavlovic MN, Chapin MH, Mukherjee S, Wilmot H, Chronos N, Charles RC, Ryan ET, LaRocque RC, Miller TE, Garcia-Beltran WF, Thierauf JC, Iafrate AJ, Mullenbrock S, Stump MD, Wetzel RK, Polakiewicz RD, Naranbhai V, Poznansky MC. Repertoires of SARS-CoV-2 epitopes targeted by antibodies vary according to severity of COVID-19. Virulence 2022; 13:890-902. [PMID: 35587156 PMCID: PMC9122311 DOI: 10.1080/21505594.2022.2073025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/28/2022] [Indexed: 02/08/2023] Open
Abstract
Antibodies to SARS-CoV-2 are central to recovery and immunity from COVID-19. However, the relationship between disease severity and the repertoire of antibodies against specific SARS-CoV-2 epitopes an individual develops following exposure remains incompletely understood. Here, we studied seroprevalence of antibodies to specific SARS-CoV-2 and other betacoronavirus antigens in a well-annotated, community sample of convalescent and never-infected individuals obtained in August 2020. One hundred and twenty-four participants were classified into five groups: previously exposed but without evidence of infection, having no known exposure or evidence of infection, seroconverted without symptoms, previously diagnosed with symptomatic COVID-19, and recovered after hospitalization with COVID-19. Prevalence of IgGs specific to the following antigens was compared between the five groups: recombinant SARS-CoV-2 and betacoronavirus spike and nucleocapsid protein domains, peptides from a tiled array of 22-mers corresponding to the entire spike and nucleocapsid proteins, and peptides corresponding to predicted immunogenic regions from other proteins of SARS-CoV-2. Antibody abundance generally correlated positively with severity of prior illness. A number of specific immunogenic peptides and some that may be associated with milder illness or protection from symptomatic infection were identified. No convincing association was observed between antibodies to Receptor Binding Domain(s) (RBDs) of less pathogenic betacoronaviruses HKU1 or OC43 and COVID-19 severity. However, apparent cross-reaction with SARS-CoV RBD was evident and some predominantly asymptomatic individuals had antibodies to both MERS-CoV and SARS-CoV RBDs. Findings from this pilot study may inform development of diagnostics, vaccines, and therapeutic antibodies, and provide insight into viral pathogenic mechanisms.
Collapse
Affiliation(s)
- David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
- Pediatric Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Augustin Vannier
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Akiro H. Duey
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Tyler J. Roady
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Richard K. Dzeng
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Maia N. Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Michael H. Chapin
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | - Sonia Mukherjee
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Richelle C. Charles
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Edward T. Ryan
- Cardiology Care Clinics, Eatonton, GA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Regina C. LaRocque
- Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital Boston, Boston, MA, USA
| | - Tyler E. Miller
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Wilfredo F. Garcia-Beltran
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Julia C. Thierauf
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - A. John Iafrate
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | | | | | | | - Vivek Naranbhai
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| |
Collapse
|
14
|
Groha S, Alaiwi SA, Xu W, Naranbhai V, Nassar AH, Bakouny Z, El Zarif T, Saliby RM, Wan G, Rajeh A, Adib E, Nuzzo PV, Schmidt AL, Labaki C, Ricciuti B, Alessi JV, Braun DA, Shukla SA, Keenan TE, Van Allen E, Awad MM, Manos M, Rahma O, Zubiri L, Villani AC, Fairfax B, Hammer C, Khan Z, Reynolds K, Semenov Y, Schrag D, Kehl KL, Freedman ML, Choueiri TK, Gusev A. Germline variants associated with toxicity to immune checkpoint blockade. Nat Med 2022; 28:2584-2591. [PMID: 36526723 PMCID: PMC10958775 DOI: 10.1038/s41591-022-02094-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [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: 04/05/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
Immune checkpoint inhibitors (ICIs) have yielded remarkable responses but often lead to immune-related adverse events (irAEs). Although germline causes for irAEs have been hypothesized, no individual variant associated with developing irAEs has been identified. We carried out a genome-wide association study of 1,751 patients on ICIs across 12 cancer types. We investigated two irAE phenotypes: (1) high-grade (3-5) and (2) all-grade events. We identified 3 genome-wide significant associations (P < 5 × 10-8) in the discovery cohort associated with all-grade irAEs: rs16906115 near IL7 (combined P = 3.6 × 10-11; hazard ratio (HR) = 2.1); rs75824728 near IL22RA1 (combined P = 3.5 × 10-8; HR = 1.8); and rs113861051 on 4p15 (combined P = 1.2 × 10-8, HR = 2.0); rs16906115 was replicated in 3 independent studies. The association near IL7 colocalized with the gain of a new cryptic exon for IL7, a critical regulator of lymphocyte homeostasis. Patients carrying the IL7 germline variant exhibited significantly increased lymphocyte stability after ICI initiation, which was itself predictive of downstream irAEs and improved survival.
Collapse
Affiliation(s)
- Stefan Groha
- Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Wenxin Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Amin H Nassar
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziad Bakouny
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Talal El Zarif
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Renee Maria Saliby
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Guihong Wan
- Harvard Medical School, Boston, MA, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Ahmad Rajeh
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Elio Adib
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Pier V Nuzzo
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genoa, Genoa, Italy
| | - Andrew L Schmidt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chris Labaki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Joao Victor Alessi
- Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genoa, Genoa, Italy
| | - David A Braun
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Sachet A Shukla
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Tanya E Keenan
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber/Brigham and Women's Cancer Center, Boston, MA, USA
| | - Eliezer Van Allen
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mark M Awad
- Department of Internal Medicine and Medical Specialties, School of Medicine, University of Genoa, Genoa, Italy
| | - Michael Manos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Osama Rahma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Alexandra-Chloe Villani
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Zia Khan
- Genentech, South San Francisco, CA, USA
| | - Kerry Reynolds
- Harvard Medical School, Boston, MA, USA
- Division of Medical Oncology, Bartlett, Massachusetts General Hospital, Boston, MA, USA
| | - Yevgeniy Semenov
- Harvard Medical School, Boston, MA, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA
| | - Deborah Schrag
- Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kenneth L Kehl
- Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew L Freedman
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Toni K Choueiri
- Harvard Medical School, Boston, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander Gusev
- Division of Population Sciences, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard & MIT, Cambridge, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA.
| |
Collapse
|
15
|
Taylor CA, Watson RA, Tong O, Ye W, Nassiri I, Gilchrist JJ, de Los Aires AV, Sharma PK, Koturan S, Cooper RA, Woodcock VK, Jungkurth E, Shine B, Coupe N, Payne MJ, Church DN, Naranbhai V, Groha S, Emery P, Mankia K, Freedman ML, Choueiri TK, Middleton MR, Gusev A, Fairfax BP. IL7 genetic variation and toxicity to immune checkpoint blockade in patients with melanoma. Nat Med 2022; 28:2592-2600. [PMID: 36526722 PMCID: PMC9800275 DOI: 10.1038/s41591-022-02095-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 04/06/2022] [Accepted: 10/18/2022] [Indexed: 12/23/2022]
Abstract
Treatment with immune checkpoint blockade (ICB) frequently triggers immune-related adverse events (irAEs), causing considerable morbidity. In 214 patients receiving ICB for melanoma, we observed increased severe irAE risk in minor allele carriers of rs16906115, intronic to IL7. We found that rs16906115 forms a B cell-specific expression quantitative trait locus (eQTL) to IL7 in patients. Patients carrying the risk allele demonstrate increased pre-treatment B cell IL7 expression, which independently associates with irAE risk, divergent immunoglobulin expression and more B cell receptor mutations. Consistent with the role of IL-7 in T cell development, risk allele carriers have distinct ICB-induced CD8+ T cell subset responses, skewing of T cell clonality and greater proportional repertoire occupancy by large clones. Finally, analysis of TCGA data suggests that risk allele carriers independently have improved melanoma survival. These observations highlight key roles for B cells and IL-7 in both ICB response and toxicity and clinical outcomes in melanoma.
Collapse
Affiliation(s)
- Chelsea A Taylor
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Robert A Watson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Orion Tong
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Weiyu Ye
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Isar Nassiri
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - James J Gilchrist
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Paediatrics, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alba Verge de Los Aires
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Piyush Kumar Sharma
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Surya Koturan
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Rosalin A Cooper
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Victoria K Woodcock
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Elsita Jungkurth
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Department of Oncology, University of Oxford, Oxford, UK
| | - Brian Shine
- Department of Clinical Biochemistry, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Nicholas Coupe
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - Miranda J Payne
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
| | - David N Church
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Stefan Groha
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Kulveer Mankia
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
- National Institute for Health Research Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
| | - Toni K Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark R Middleton
- Department of Oncology, University of Oxford, Oxford, UK
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard & MIT, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Benjamin P Fairfax
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Department of Oncology, University of Oxford, Oxford, UK.
- Oxford Cancer and Haematology Centre, Oxford University Hospitals NHS Foundation Trust, Churchill Hospital, Oxford, UK.
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.
| |
Collapse
|
16
|
Le TK, Brown I, Goldberg R, Taylor MT, Deng J, Parthasarathy V, Bordeaux ZA, Alphonse MP, Kwatra MM, Naranbhai V, Gusev A, Alhariri J, LeBoeuf NR, Reynolds KL, Cappelli LC, Naidoo J, Brahmer JR, Kang S, Semenov YR, Kwatra SG. Cutaneous Toxicities Associated with Immune Checkpoint Inhibitors: An Observational, Pharmacovigilance Study. J Invest Dermatol 2022; 142:2896-2908.e4. [PMID: 35605659 PMCID: PMC10796162 DOI: 10.1016/j.jid.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/20/2022] [Accepted: 04/20/2022] [Indexed: 11/19/2022]
Abstract
Cutaneous immune-related adverse events (cirAEs) are the most prevalent complication to arise from immunotherapy and cause significant morbidity. We aimed to determine the spectrum, timing, clinical features, and outcomes of cirAEs by conducting an observational pharmacovigilance study using VigiBase, the World Health Organization's global database of individual case safety reports from over 130 member countries (ClinicalTrials.gov, number NCT04898751). We compared adverse event reporting in patients who received immune checkpoint inhibitors (91,323 adverse events) with those of the full reporting database (18,919,358 adverse events). There were 10,933 cases of cirAEs within 51 distinct dermatologic types, with 27 specific eruptions with disproportionate signal represented (information component [IC]025 > 0). Of these 27 eruptions, there were eight cirAEs with n > 100 reports, including vitiligo (IC025 = 4.87), bullous pemphigoid (IC025 = 4.08), lichenoid dermatitis (IC025 = 3.69), erythema multiforme (IC025 = 1.03), toxic epidermal necrolysis (IC025 = 0.95), Stevens‒Johnson syndrome (IC025 = 0.41), drug eruption (IC025 = 0.11), and eczematous dermatitis (IC025 = 0.11). There were differences in time to onset after immune checkpoint inhibitor initiation, with a median of approximately 1 month (erythema multiforme, Stevens‒Johnson syndrome, and toxic epidermal necrolysis), 2 months (drug eruption and eczematous dermatitis), 4 months (lichenoid dermatitis), and 5‒6 months (bullous pemphigoid and vitiligo). CirAEs are diverse, dependent on cancer type, and have distinct and different onset times that are linked to the cirAE subtype.
Collapse
Affiliation(s)
- Thomas K Le
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Isabelle Brown
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rebecca Goldberg
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew T Taylor
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Junwen Deng
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Varsha Parthasarathy
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zachary A Bordeaux
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Martin Prince Alphonse
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Madan M Kwatra
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Vivek Naranbhai
- Department of Oncology, Mass General Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander Gusev
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jihad Alhariri
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nicole R LeBoeuf
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Cutaneous Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Kerry L Reynolds
- Division of Hematology and Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Laura C Cappelli
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jarushka Naidoo
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Julie R Brahmer
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; The Bloomberg-Kimmel Institute for Cancer Immunotherapy, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sewon Kang
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA; Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| |
Collapse
|
17
|
Denault E, Nakajima E, Naranbhai V, Hutchinson JA, Mortensen L, Neihoff E, Barabell C, Comander A, Juric D, Kuter I, Mulvey T, Peppercorn J, Rosenstock AS, Shin J, Vidula N, Wander SA, Moy B, Ellisen LW, Isakoff SJ, Iafrate AJ, Gainor JF, Bardia A, Spring LM. Immunogenicity of SARS-CoV-2 vaccines in patients with breast cancer. Ther Adv Med Oncol 2022; 14:17588359221119370. [PMID: 36051470 PMCID: PMC9425892 DOI: 10.1177/17588359221119370] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/25/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose To explore the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines in patients with breast cancer based on type of anticancer treatment. Methods Patients with breast cancer had anti-spike antibody concentrations measured ⩾14 days after receiving a full SARS-CoV-2 vaccination series. The primary endpoint was IgA/G/M anti-spike antibody concentration. Multiple regression analysis was used to analyze log10-transformed antibody titer concentrations. Results Between 29 April and 20 July 2021, 233 patients with breast cancer were enrolled, of whom 212 were eligible for the current analysis. Patients who received mRNA-1273 (Moderna) had the highest antibody concentrations [geometric mean concentration (GMC) in log10: 3.0 U/mL], compared to patients who received BNT162b2 (Pfizer) (GMC: 2.6 U/mL) (multiple regression adjusted p = 0.013) and Ad26.COV2.S (Johnson & Johnson/Janssen) (GMC: 2.6 U/mL) (p = 0.071). Patients receiving cytotoxic therapy had a significantly lower antibody titer GMC (2.5 U/mL) compared to patients on no therapy or endocrine therapy alone (3.0 U/mL) (p = 0.005). Patients on targeted therapies (GMC: 2.7 U/mL) also had a numerically lower GMC compared to patients not receiving therapy/on endocrine therapy alone, although this result was not significant (p = 0.364). Among patients who received an additional dose of vaccine (n = 31), 28 demonstrated an increased antibody response that ranged from 0.2 to >4.4 U/ mL. Conclusion Most patients with breast cancer generate detectable anti-spike antibodies following SARS-CoV-2 vaccination, though systemic treatments and vaccine type impact level of response. Further studies are needed to better understand the clinical implications of different antibody levels, the effectiveness of additional SARS-CoV-2 vaccine doses, and the risk of breakthrough infections among patients with breast cancer.
Collapse
Affiliation(s)
| | | | - Vivek Naranbhai
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Amy Comander
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Dejan Juric
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Irene Kuter
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Theresa Mulvey
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jeffrey Peppercorn
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Aron S Rosenstock
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Jennifer Shin
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Neelima Vidula
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Seth A Wander
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Beverly Moy
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Leif W Ellisen
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Steven J Isakoff
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Aditya Bardia
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Laura M Spring
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| |
Collapse
|
18
|
Gilchrist JJ, Auckland K, Parks T, Mentzer AJ, Goldblatt L, Naranbhai V, Band G, Rockett KA, Toure OB, Konate S, Sissoko S, Djimdé AA, Thera MA, Doumbo OK, Sow S, Floyd S, Pönnighaus JM, Warndorff DK, Crampin AC, Fine PEM, Fairfax BP, Hill AVS. Genome-wide association study of leprosy in Malawi and Mali. PLoS Pathog 2022; 18:e1010312. [PMID: 36121873 PMCID: PMC9624411 DOI: 10.1371/journal.ppat.1010312] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 01/31/2022] [Revised: 11/01/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022] Open
Abstract
Leprosy is a chronic infection of the skin and peripheral nerves caused by Mycobacterium leprae. Despite recent improvements in disease control, leprosy remains an important cause of infectious disability globally. Large-scale genetic association studies in Chinese, Vietnamese and Indian populations have identified over 30 susceptibility loci for leprosy. There is a significant burden of leprosy in Africa, however it is uncertain whether the findings of published genetic association studies are generalizable to African populations. To address this, we conducted a genome-wide association study (GWAS) of leprosy in Malawian (327 cases, 436 controls) and Malian (247 cases, 368 controls) individuals. In that analysis, we replicated four risk loci previously reported in China, Vietnam and India; MHC Class I and II, LACC1 and SLC29A3. We further identified a novel leprosy susceptibility locus at 10q24 (rs2015583; combined p = 8.81 × 10-9; OR = 0.51 [95% CI 0.40 - 0.64]). Using publicly-available data we characterise regulatory activity at this locus, identifying ACTR1A as a candidate mediator of leprosy risk. This locus shows evidence of recent positive selection and demonstrates pleiotropy with established risk loci for inflammatory bowel disease and childhood-onset asthma. A shared genetic architecture for leprosy and inflammatory bowel disease has been previously described. We expand on this, strengthening the hypothesis that selection pressure driven by leprosy has shaped the evolution of autoimmune and atopic disease in modern populations. More broadly, our data highlights the importance of defining the genetic architecture of disease across genetically diverse populations, and that disease insights derived from GWAS in one population may not translate to all affected populations.
Collapse
Affiliation(s)
- James J. Gilchrist
- Department of Paediatrics, University of Oxford, Oxford, United Kingdom
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Vivek Naranbhai
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kirk A. Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ousmane B. Toure
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sibiri Sissoko
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimdé
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou A. Thera
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Ogobara K. Doumbo
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | - Samba Sow
- Center for Vaccine Development, Bamako, Mali
| | - Sian Floyd
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jörg M. Pönnighaus
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - David K. Warndorff
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Amelia C. Crampin
- Malawi Epidemiology and Intervention Research Unit (formerly Karonga Prevention Study), Chilumba, Malawi
| | - Paul E. M. Fine
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Benjamin P. Fairfax
- MRC–Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Jenner Institute, University of Oxford, Oxford, United Kingdom
- * E-mail: (JJG); (AVSH)
| |
Collapse
|
19
|
Voutouri C, Hardin CC, Naranbhai V, Khandekar MJ, Gainor JF, Stylianopoulos T, Munn LL, Jain RK. Abstract LB226: Requirement for booster doses in healthy, cancer and immunosuppressed patients infected with the ancestral or variant SARS-CoV-2. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-lb226] [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
Introduction: Current SARS-CoV-2 vaccines are effective at preventing COVID-19 or limiting disease severity in healthy individuals, but effectiveness is lower among patients with cancer or immunosuppression. Vaccine effectiveness wanes with time and varies by vaccine type. Moreover, current vaccines are based on the ancestral SARS-CoV-2 spike protein sequence, and emerging viral variants evade vaccine induced immunity. Booster doses partially overcome these issues, but there are limited clinical data on the durability of protection afforded by boosters - especially against SARS-CoV-2 variants.
Methods: Here we describe a mechanistic mathematical model for vaccination-induced immunity in patients with cancer and use it to predict vaccine effectiveness taking into account current and possible future viral, host and vaccine characteristics. Crucially, this allows predictions over time frames currently not reported in the clinical literature. The model incorporates the infection of lung epithelium by SARS-CoV-2, the response of innate and adaptive immune cells to infection, the production of pro-and anti-inflammatory cytokines, the activation of the coagulation cascade. The model further accounts for the interactions between the virus, immune cells and tumor cells as well as for vaccination-induced immunity and anti-cancer therapies.
Results: Model predictions were validated with available clinical data. The model predicts that for healthy individuals vaccinated and boosted with mRNA-1273, BNT-162b2a, and Ad26.COV2.S, robust immunogenicity against the ancestral and delta variant extends beyond a year. Immunogenicity is enhanced following booster vaccination in patients with cancer on various anti-cancer therapies and for patients without cancer on immunosuppressive agents. However, our model predicts that more than one booster dose will be required for patients with cancer, or on immunosuppression, to maintain protective immunity against current and hypothetical future variants. SARS-CoV2 variants with enhanced binding to target cells, reduced affinity for vaccine-generated antibodies or reduced immunogenicity resulted in lower antibody levels and more severe disease compared with variants with enhanced viral replication or internalization rates.
Conclusion: For patients with cancer and immunosuppressed individuals, SARS-CoV2 variants with enhanced ability to bind to target cells, altered antibody affinity or reduced immunogenicity could lead to breakthrough infections even after a single booster dose. Our mathematical model is useful for anticipating and planning future vaccinations in patients with cancer.
Citation Format: Chrysovalantis Voutouri, C. Corey Hardin, Vivek Naranbhai, Melin J. Khandekar, Justin F Gainor, Triantafyllos Stylianopoulos, Lance L. Munn, Rakesh K. Jain. Requirement for booster doses in healthy, cancer and immunosuppressed patients infected with the ancestral or variant SARS-CoV-2 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB226.
Collapse
Affiliation(s)
- Chrysovalantis Voutouri
- 1Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - C. Corey Hardin
- 2Department of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Vivek Naranbhai
- 3Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, MA
| | - Melin J. Khandekar
- 4Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Justin F Gainor
- 5Department of Medicine, Massachusetts General Hospital, Boston, USA, Boston, Massachusetts, MA
| | - Triantafyllos Stylianopoulos
- 6Cancer Biophysics Laboratory, Department of Mechanical and Manufacturing Engineering, University of Cyprus, Nicosia, Cyprus
| | - Lance L. Munn
- 1Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Rakesh K. Jain
- 1Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| |
Collapse
|
20
|
Barmettler S, DiGiacomo DV, Yang NJ, Lam T, Naranbhai V, Dighe AS, Burke KE, Blumenthal KG, Ling M, Hesterberg PE, Saff RR, MacLean J, Ofoman O, Berrios C, St Denis KJ, Lam EC, Gregory D, Iafrate AJ, Poznansky M, Lee H, Balazs A, Pillai S, Farmer JR. Response to Severe Acute Respiratory Syndrome Coronavirus 2 Initial Series and Additional Dose Vaccine in Patients With Predominant Antibody Deficiency. J Allergy Clin Immunol Pract 2022; 10:1622-1634.e4. [PMID: 35381395 PMCID: PMC8976568 DOI: 10.1016/j.jaip.2022.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/09/2022] [Accepted: 03/06/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with predominant antibody deficiency (PAD) is associated with high morbidity, yet data regarding the response to SARS-CoV-2 immunization in PAD patients, including additional dose vaccine, are limited. OBJECTIVE To characterize antibody response to SARS-CoV-2 vaccine in PAD patients and define correlates of vaccine response. METHODS We assessed the levels and function of anti-SARS-CoV-2 antibodies in 62 PAD patients compared with matched healthy controls at baseline, at 4 to 6 weeks after the initial series of immunization (a single dose of Ad26.COV2.S [Janssen] or two doses of BNT162b2 [Pfizer-BioNTech] or mRNA-1273 [Moderna]), and at 4 to 6 weeks after an additional dose immunization, if received. RESULTS After the initial series of SARS-CoV-2 vaccination, PAD patients had lower mean anti-spike antibody levels compared with matched healthy controls (140.1 vs 547.3 U/mL; P = .02). Patients with secondary PAD (eg, B-cell depletion therapy was used) and those with severe primary PAD (eg, common variable immunodeficiency with autoinflammatory complications) had the lowest mean anti-spike antibody levels. Immune correlates of a low anti-spike antibody response included low CD4+ T helper cells, low CD19+ total B cells, and low class-switched memory (CD27+IgD/M-) B cells. In addition, a low (<100 U/mL) anti-spike antibody response was associated with prior exposure to B-cell depletion therapy, both at any time in the past (odds ratio = 5.5; confidence interval, 1.5-20.4; P = .01) and proximal to vaccination (odds ratio = 36.4; confidence interval, 1.7-791.9; P = .02). Additional dose immunization with an mRNA vaccine in a subset of 31 PAD patients increased mean anti-spike antibody levels (76.3 U/mL before to 1065 U/mL after the additional dose; P < .0001). CONCLUSIONS Patients with secondary and severe primary PAD, characterized by low T helper cells, low B cells, and/or low class-switched memory B cells, were at risk for low antibody response to SARS-CoV-2 immunization, which improved after an additional dose vaccination in most patients.
Collapse
Affiliation(s)
- Sara Barmettler
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass.
| | - Daniel V DiGiacomo
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass
| | - Nancy J Yang
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass
| | - Tiffany Lam
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass
| | - Vivek Naranbhai
- Harvard Medical School, Boston, Mass; Dana-Farber Cancer Institute, Boston, Mass
| | - Anand S Dighe
- Harvard Medical School, Boston, Mass; Department of Pathology, Massachusetts General Hospital, Boston, Mass
| | - Kristin E Burke
- Gastroenterology Unit, Department of Medicine, Massachusetts General Hospital, Boston, Mass; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Mass
| | - Kimberly G Blumenthal
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Morris Ling
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, Mass
| | - Paul E Hesterberg
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass
| | - Rebecca R Saff
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass
| | | | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, Mass
| | - Cristhian Berrios
- Department of Pathology, Massachusetts General Hospital, Boston, Mass
| | - Kerri J St Denis
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, Mass
| | - Evan C Lam
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, Mass
| | - David Gregory
- Division of Infectious Diseases Medicine, Department of Medicine, Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, Mass; Pediatric Infectious Disease Unit, Department of Pediatrics, Massachusetts General Hospital, Boston, Mass
| | | | - Mark Poznansky
- Division of Infectious Diseases Medicine, Department of Medicine, Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, Mass
| | - Hang Lee
- Harvard Medical School, Boston, Mass
| | - Alejandro Balazs
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, Mass
| | - Shiv Pillai
- Harvard Medical School, Boston, Mass; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, Mass
| | - Jocelyn R Farmer
- Division of Rheumatology, Department of Medicine, Allergy, and Immunology, Massachusetts General Hospital, Boston, Mass; Harvard Medical School, Boston, Mass; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Department of Medicine, Harvard University, Cambridge, Mass
| |
Collapse
|
21
|
Naranbhai V, Garcia-Beltran WF, Chang CC, Berrios Mairena C, Thierauf JC, Kirkpatrick G, Onozato ML, Cheng J, St Denis KJ, Lam EC, Kaseke C, Tano-Menka R, Yang D, Pavlovic M, Yang W, Kui A, Miller TE, Astudillo MG, Cahill JE, Dighe AS, Gregory DJ, Poznansky MC, Gaiha GD, Balazs AB, Iafrate AJ. Comparative Immunogenicity and Effectiveness of mRNA-1273, BNT162b2, and Ad26.COV2.S COVID-19 Vaccines. J Infect Dis 2022; 225:1141-1150. [PMID: 34888672 PMCID: PMC8689763 DOI: 10.1093/infdis/jiab593] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [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: 10/15/2021] [Accepted: 12/08/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Understanding immunogenicity and effectiveness of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines is critical to guide rational use. METHODS We compared the immunogenicity of mRNA-1273, BNT-162b2, and Ad26.COV2.S in healthy ambulatory adults. We performed an inverse-variance meta-analysis of population-level effectiveness from public health reports in > 40 million individuals. RESULTS A single dose of either mRNA vaccine yielded comparable antibody and neutralization titers to convalescent individuals. Ad26.COV2.S yielded lower antibody concentrations and frequently undetectable neutralization titers. Bulk and cytotoxic T-cell responses were higher in mRNA1273 and BNT162b2 than Ad26.COV2.S recipients. Regardless of vaccine, <50% of vaccinees demonstrated CD8+ T-cell responses. Antibody concentrations and neutralization titers increased comparably after the first dose of either vaccine, and further in recipients of a second dose. Prior infection was associated with high antibody concentrations and neutralization even after a single dose and regardless of vaccine. Neutralization of Beta, Gamma, and Delta strains were poorer regardless of vaccine. In meta-analysis, relative to mRNA1273 the effectiveness of BNT162b2 was lower against infection and hospitalization, and Ad26COV2.S was lower against infection, hospitalization, and death. CONCLUSIONS Variation in the immunogenicity correlates with variable effectiveness of the 3 vaccines deployed in the United States.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Christina C Chang
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
- University of New South Wales, Sydney, Australia
- Monash University, Melbourne, Australia
| | | | - Julia C Thierauf
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Grace Kirkpatrick
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maristela L Onozato
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Ju Cheng
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maia Pavlovic
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Wendy Yang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Alexander Kui
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jennifer E Cahill
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Anand S Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David J Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mark C Poznansky
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
22
|
Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Zhao Z, St Denis KJ, Lam EC, Carrington M, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 2022; 185:1259. [PMID: 35364034 PMCID: PMC8969090 DOI: 10.1016/j.cell.2022.03.022] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
23
|
Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Zhao Z, St Denis KJ, Lam EC, Carrington M, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all individuals. Cell 2022; 185:1041-1051.e6. [PMID: 35202566 PMCID: PMC8810349 DOI: 10.1016/j.cell.2022.01.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/04/2022] [Accepted: 01/28/2022] [Indexed: 01/11/2023]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. In this study, we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike. Evaluation of functional CD4+ and CD8+ memory T cell responses confirmed these findings and revealed that reduced recognition to Omicron spike is primarily observed within the CD8+ T cell compartment potentially due to escape from HLA binding. Booster vaccination enhanced T cell responses to Omicron spike. In contrast to neutralizing immunity, these findings suggest preservation of T cell responses to the Omicron variant, although with reduced reactivity in some individuals.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa.
| | - Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School, Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Cristhian Berrios
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Shawn Choi
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew A Getz
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alton Gayton
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zezhou Zhao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School, Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Bruce D Walker
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Institute for Medical Engineering and Science, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
| |
Collapse
|
24
|
Denault E, Nakajima E, Naranbhai V, Balazs A, Mortensen L, Niehoff E, Barabell C, Hutchinson JA, Wander SA, Rosenstock AS, Ellisen LW, Moy B, Isakoff SJ, Gainor JF, Iafrate AJ, Bardia A, Spring LM. Abstract P3-23-02: Immunogenicity of SARS-CoV-2 vaccines in patients with breast cancer receiving CDK 4/6 inhibitors. Cancer Res 2022. [DOI: 10.1158/1538-7445.sabcs21-p3-23-02] [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: CDK 4/6 inhibitors have transformed the landscape of breast oncology. A CDK 4/6 inhibitor in combination with endocrine therapy is recommended as 1st line therapy for patients with metastatic hormone receptor positive breast cancer. CDK 4/6 inhibitors have purported immunomodulatory effects and while effective, myelosuppression is a common adverse effect of CDK 4/6 inhibitor treatment of breast cancer. The impact of CDK 4/6 inhibitor therapy on immunogenicity of vaccines is not known. In this study, we evaluated the spike antibody response to SARS-CoV-2 vaccines among patients with breast cancer receiving endocrine therapy with or without CDK 4/6 inhibitors.Methods: In the Cancer COVID and Vaccine (CANVAX) study eligible patients included patients with breast cancer who had completed all scheduled doses of SARS-CoV-2 vaccines. Chart review was conducted to identify patients who had received endocrine therapy with or without CDK 4/6 inhibitor. We used validated assays to measure anti-SARS-CoV-2 total IgA/M/G spike antibodies and virus neutralization. We evaluated the magnitude of antibody response based on geometric mean concentrations (GMCs) as well as the % of patients with inadequate seroconversion (defined as levels <100 U/ml). Independent T-test based on log-transformed antibody values was utilized to compare the spike antibody levels and p value of ≤ 0.05 was considered statistically significant.Results: Between April 2021 and June 2021, 203 patients with breast cancer were enrolled. As of the cut-off date (2nd July 2021), results were available for 73 patients treated with endocrine therapy alone (N = 23), or with CDK 4/6 inhibitor-based therapy (N = 50). Most were females (98.6%), white (83.6%), and had metastatic breast cancer (68.5%). 49.3% had received BNT162b2 (Pfizer), 37% mRNA1273 (Moderna), and 13.7% Ad26.COV2.S (Johnson and Johnson/Janssen) vaccines. Overall, the mean spike antibody levels were similar between patients treated with endocrine therapy alone vs CDK 4/6 inhibitor-based therapy (GMC: 326 vs. 719 U/mL; p=0.704). Mean spike antibody levels were higher in patients with early breast cancer vs. metastatic breast cancer (GMC: 555 vs. 465 U/mL; p=0.031). However, patients who received Ad26.COV2.S had lower levels of mean spike antibody levels (GMC 47 U/ml), compared with patients treated with BNT162b2 (GMC 400 U/ml) or mRNA1273 (GMC 2203 U/mL; P<0.01 for both comparisons). Comparison of neutralization titers in 66 individuals supported the above results. 11 (15.1%) patients had low antibody titers (<100U/ml) of seroconversion and 3 received a booster vaccine, with 1 having available repeat titer results thus far demonstrating a significant improvement.Conclusions: The majority of patients receiving CDK 4/6 inhibitor have adequate antibody response to SARS-CoV-2 vaccines, particularly mRNA vaccines. However, a minority of patients may require booster vaccine to augment immunity. Monitoring spike antibody levels could be helpful to identify patients with inadequate seroconversion and guide mitigation strategies for patients with breast cancer.
Citation Format: Elyssa Denault, Erika Nakajima, Vivek Naranbhai, Alejandro Balazs, Lindsey Mortensen, Elizabeth Niehoff, Caroline Barabell, Jennifer A. Hutchinson, Seth A. Wander, Aron S. Rosenstock, Leif W. Ellisen, Beverly Moy, Steven J. Isakoff, Justin F. Gainor, A. John Iafrate, Aditya Bardia, Laura M. Spring. Immunogenicity of SARS-CoV-2 vaccines in patients with breast cancer receiving CDK 4/6 inhibitors [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-23-02.
Collapse
|
25
|
Garcia-Beltran WF, St Denis KJ, Hoelzemer A, Lam EC, Nitido AD, Sheehan ML, Berrios C, Ofoman O, Chang CC, Hauser BM, Feldman J, Roederer AL, Gregory DJ, Poznansky MC, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. Cell 2022; 185:457-466.e4. [PMID: 34995482 PMCID: PMC8733787 DOI: 10.1016/j.cell.2021.12.033] [Citation(s) in RCA: 687] [Impact Index Per Article: 343.5] [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: 12/14/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 02/09/2023]
Abstract
Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured the neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild-type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that received their primary series recently (<3 months), distantly (6-12 months), or an additional "booster" dose, while accounting for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinees. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron, only 4-6-fold lower than wild type, suggesting enhanced cross-reactivity of neutralizing antibody responses. In addition, we find that Omicron pseudovirus infects more efficiently than other variants tested. Overall, this study highlights the importance of additional mRNA doses to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Wilfredo F Garcia-Beltran
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
| | - Kerri J St Denis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Angelique Hoelzemer
- First Department of Internal Medicine, Division of Infectious Diseases, University Medical Centre Eppendorf, Hamburg, Germany; German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany; Research Department Virus Immunology, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Evan C Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Adam D Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Maegan L Sheehan
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Cristhian Berrios
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christina C Chang
- Alfred Hospital, Central Clinical School, Monash University, Victoria 3181, Australia; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Alex L Roederer
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - David J Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA 02129, USA; Pediatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA 02129, USA; Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vivek Naranbhai
- Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Massachusetts General Hospital Cancer Center, Boston, MA 02114, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | |
Collapse
|
26
|
Tang K, Seo J, Tiu BC, Le TK, Pahalyants V, Raval NS, Ugwu-Dike PO, Zubiri L, Naranbhai V, Carrington M, Gusev A, Reynolds KL, LeBoeuf NR, Asgari MM, Kwatra SG, Semenov YR. Association of Cutaneous Immune-Related Adverse Events With Increased Survival in Patients Treated With Anti-Programmed Cell Death 1 and Anti-Programmed Cell Death Ligand 1 Therapy. JAMA Dermatol 2022; 158:189-193. [PMID: 35019948 PMCID: PMC8756357 DOI: 10.1001/jamadermatol.2021.5476] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
IMPORTANCE Despite the efficacy of immune checkpoint inhibitors (ICIs), cutaneous immune-related adverse events (cirAEs) occur in 20% to 40% of all treated patients. To our knowledge, little is known about the predictive value of these cutaneous eruptions and their subtypes regarding cancer survival. OBJECTIVE To determine the association of developing cirAEs following treatment with anti-programmed cell death 1 (PD-1) or anti-programmed cell death ligand 1 (PD-L1) therapy with patient survival. DESIGN, SETTING, AND PARTICIPANTS This retrospective cohort study used data from the TriNetX Diamond Network, a database of health records and claims data from more than 200 million US and European patients, to conduct a population-level cohort analysis. The study included 7008 eligible patients who developed cirAEs after treatment with anti-PD-1 or anti-PD-L1 therapy for malignant neoplasms of digestive organs, bronchus or lung, melanoma of skin, and urinary tract who were identified through the TriNetX Diamond Network along with 7008 matched controls. EXPOSURES Development of cirAEs within 6 months following anti-PD-1 or anti-PD-L1 therapy. MAIN OUTCOMES AND MEASURES A 6-month analysis using a Cox proportional hazards model was performed to determine the association of cirAEs with overall survival after adjusting for demographic characteristics, cancer type, and cancer stage. RESULTS A total of 7008 patients (3036 women [43.3%]; mean [SD] age, 68.2 [11.2] years) were matched to 7008 (3044 women [43.4%]; mean [SD] age, 68.3 [11.1] years) controls. Pruritus (hazard ratio [HR], 0.695; 95% CI, 0.602-0.803; P < .001), drug eruption (HR, 0.755; 95% CI, 0.635-0.897; P = .001), xerosis (HR, 0.626; 95% CI, 0.469-0.834; P = .001), nonspecific rashes (HR, 0.704; 95% CI, 0.634-0.781; P < .001), and appearance of any cirAE (HR, 0.778; 95% CI, 0.726-0.834; P < .001) were significantly protective of mortality using a Benjamini-Hochberg correction with a significance level of .05. Additionally, psoriasis (HR, 0.703; 95% CI, 0.497-0.994; P = .045) and lichen planus/lichenoid dermatitis (HR, 0.511; 95% CI, 0.279-0.939; P = .03) were significant. Eczematous dermatitis (HR, 0.612; 95% CI, 0.314-1.195), vitiligo (HR, 0.534; 95% CI, 0.254-1.123), bullous pemphigoid (HR, 0.524; 95% CI, 0.140-1.956), and Grover disease (HR, 0.468; 95% CI, 0.115-1.898) were all associated with strong protective clinical effects. CONCLUSIONS AND RELEVANCE The results of this cohort study suggest that the development of cirAEs is strongly associated with response to ICI therapy and patient survival.
Collapse
Affiliation(s)
- Kimberly Tang
- Massachusetts General Hospital, Department of Dermatology, Boston
| | - Jayhyun Seo
- Massachusetts General Hospital, Department of Dermatology, Boston
| | - Bruce C. Tiu
- Massachusetts General Hospital, Department of Dermatology, Boston,Harvard Medical School, Department of Dermatology, Boston, Massachusetts
| | - Thomas K. Le
- Johns Hopkins University, Department of Dermatology, Baltimore, Maryland
| | - Vartan Pahalyants
- Massachusetts General Hospital, Department of Dermatology, Boston,Harvard Medical School, Department of Dermatology, Boston, Massachusetts
| | - Neel S. Raval
- Massachusetts General Hospital, Department of Dermatology, Boston,Harvard Medical School, Department of Dermatology, Boston, Massachusetts,Washington University School of Medicine, St Louis, Missouri
| | | | - Leyre Zubiri
- Massachusetts General Hospital, Department of Medicine, Division of Oncology, Boston
| | - Vivek Naranbhai
- Massachusetts General Hospital, Department of Medicine, Division of Oncology, Boston
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, Maryland,Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge,Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Alexander Gusev
- Dana Farber Cancer Institute, Department of Medicine, Boston, Massachusetts
| | - Kerry L. Reynolds
- Massachusetts General Hospital, Department of Medicine, Division of Oncology, Boston
| | - Nicole R. LeBoeuf
- Dana Farber Cancer Institute, Department of Dermatology, Boston, Massachusetts
| | - Maryam M. Asgari
- Massachusetts General Hospital, Department of Dermatology, Boston,Harvard Medical School, Department of Dermatology, Boston, Massachusetts,Department of Population Medicine, Harvard Medical School, Boston, Massachusetts
| | - Shawn G. Kwatra
- Johns Hopkins University, Department of Dermatology, Baltimore, Maryland
| | - Yevgeniy R. Semenov
- Massachusetts General Hospital, Department of Dermatology, Boston,Harvard Medical School, Department of Dermatology, Boston, Massachusetts
| |
Collapse
|
27
|
Naranbhai V, St Denis KJ, Lam EC, Ofoman O, Garcia-Beltran WF, Mairena CB, Bhan AK, Gainor JF, Balazs AB, Iafrate AJ. Neutralization breadth of SARS-CoV-2 viral variants following primary series and booster SARS-CoV-2 vaccines in patients with cancer. Cancer Cell 2022; 40:103-108.e2. [PMID: 34990570 PMCID: PMC8730528 DOI: 10.1016/j.ccell.2021.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 01/12/2023]
Abstract
Patients with cancer are more likely to have impaired immune responses to SARS-CoV-2 vaccines. We study the breadth of responses against SARS-CoV-2 variants after primary vaccination in 178 patients with a variety of tumor types and after booster doses in a subset. Neutralization of alpha, beta, gamma, and delta SARS-CoV-2 variants is impaired relative to wildtype, regardless of vaccine type. Regardless of viral variant, mRNA1273 is the most immunogenic, followed by BNT162b2, and then Ad26.COV2.S. Neutralization of more variants (breadth) is associated with a greater magnitude of wildtype neutralization, and increases with time since vaccination; advancing age associates with a lower breadth. The concentrations of anti-spike protein antibody are a good surrogate for breadth (positive predictive value of =90% at >1,000 U/mL). Booster SARS-CoV-2 vaccines confer enhanced breadth. These data suggest that achieving a high antibody titer is desirable to achieve broad neutralization; a single booster dose with the current vaccines increases the breadth of responses against variants.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA
| | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Atul K Bhan
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | | | - A John Iafrate
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
| | | |
Collapse
|
28
|
Naranbhai V, Nathan A, Kaseke C, Berrios C, Khatri A, Choi S, Getz MA, Tano-Menka R, Ofoman O, Gayton A, Senjobe F, Denis KJS, Lam EC, Garcia-Beltran WF, Balazs AB, Walker BD, Iafrate AJ, Gaiha GD. T cell reactivity to the SARS-CoV-2 Omicron variant is preserved in most but not all prior infected and vaccinated individuals. medRxiv 2022:2022.01.04.21268586. [PMID: 35018386 PMCID: PMC8750712 DOI: 10.1101/2022.01.04.21268586] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The SARS-CoV-2 Omicron variant (B.1.1.529) contains mutations that mediate escape from infection and vaccine-induced antibody responses, although the extent to which these substitutions in spike and non-spike proteins affect T cell recognition is unknown. Here we show that T cell responses in individuals with prior infection, vaccination, both prior infection and vaccination, and boosted vaccination are largely preserved to Omicron spike and non-spike proteins. However, we also identify a subset of individuals (∼21%) with a >50% reduction in T cell reactivity to the Omicron spike. Evaluation of functional CD4 + and CD8 + memory T cell responses confirmed these findings and reveal that reduced recognition to Omicron spike is primarily observed within the CD8 + T cell compartment. Booster vaccination substantially enhanced T cell responses to Omicron spike. In contrast to neutralizing immunity, these findings suggest preservation of T cell responses to the Omicron variant, although with reduced reactivity in some individuals.
Collapse
|
29
|
Naranbhai V, Viard M, Dean M, Groha S, Braun DA, Labaki C, Shukla SA, Yuki Y, Shah P, Chin K, Wind-Rotolo M, Mu XJ, Robbins PB, Gusev A, Choueiri TK, Gulley JL, Carrington M. HLA-A*03 and response to immune checkpoint blockade in cancer: an epidemiological biomarker study. Lancet Oncol 2022; 23:172-184. [PMID: 34895481 PMCID: PMC8742225 DOI: 10.1016/s1470-2045(21)00582-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [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: 06/01/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Predictive biomarkers could allow more precise use of immune checkpoint inhibitors (ICIs) in treating advanced cancers. Given the central role of HLA molecules in immunity, variation at the HLA loci could differentially affect the response to ICIs. The aim of this epidemiological study was to determine the effect of HLA-A*03 as a biomarker for predicting response to immunotherapy. METHODS In this epidemiological study, we investigated the clinical outcomes (overall survival, progression free survival, and objective response rate) after treatment for advanced cancer in eight cohorts of patients: three observational cohorts of patients with various types of advanced tumours (the Memorial Sloan Kettering Integrated Mutation Profiling of Actionable Cancer Targets [MSK-IMPACT] cohort, the Dana-Farber Cancer Institute [DFCI] Profile cohort, and The Cancer Genome Atlas) and five clinical trials of patients with advanced bladder cancer (JAVELIN Solid Tumour) or renal cell carcinoma (CheckMate-009, CheckMate-010, CheckMate-025, and JAVELIN Renal 101). In total, these cohorts included 3335 patients treated with various ICI agents (anti-PD-1, anti-PD-L1, and anti-CTLA-4 inhibitors) and 10 917 patients treated with non-ICI cancer-directed therapeutic approaches. We initially modelled the association of HLA amino-acid variation with overall survival in the MSK-IMPACT discovery cohort, followed by a detailed analysis of the association between HLA-A*03 and clinical outcomes in MSK-IMPACT, with replication in the additional cohorts (two further observational cohorts and five clinical trials). FINDINGS HLA-A*03 was associated in an additive manner with reduced overall survival after ICI treatment in the MSK-IMPACT cohort (HR 1·48 per HLA-A*03 allele [95% CI 1·20-1·82], p=0·00022), the validation DFCI Profile cohort (HR 1·22 per HLA-A*03 allele, 1·05-1·42; p=0·0097), and in the JAVELIN Solid Tumour clinical trial for bladder cancer (HR 1·36 per HLA-A*03 allele, 1·01-1·85; p=0·047). The HLA-A*03 effect was observed across ICI agents and tumour types, but not in patients treated with alternative therapies. Patients with HLA-A*03 had shorter progression-free survival in the pooled patient population from the three CheckMate clinical trials of nivolumab for renal cell carcinoma (HR 1·31, 1·01-1·71; p=0·044), but not in those receiving control (everolimus) therapies. Objective responses were observed in none of eight HLA-A*03 homozygotes in the ICI group (compared with 59 [26·6%] of 222 HLA-A*03 non-carriers and 13 (17·1%) of 76 HLA-A*03 heterozygotes). HLA-A*03 was associated with shorter progression-free survival in patients receiving ICI in the JAVELIN Renal 101 randomised clinical trial for renal cell carcinoma (avelumab plus axitinib; HR 1·59 per HLA-A*03 allele, 1·16-2·16; p=0·0036), but not in those receiving control (sunitinib) therapy. Objective responses were recorded in one (12·5%) of eight HLA-A*03 homozygotes in the ICI group (compared with 162 [63·8%] of 254 HLA-A*03 non-carriers and 40 [55·6%] of 72 HLA-A*03 heterozygotes). HLA-A*03 was associated with impaired outcome in meta-analysis of all 3335 patients treated with ICI at genome-wide significance (p=2·01 × 10-8) with no evidence of heterogeneity in effect (I2 0%, 95% CI 0-0·76) INTERPRETATION: HLA-A*03 is a predictive biomarker of poor response to ICI. Further evaluation of HLA-A*03 is warranted in randomised trials. HLA-A*03 carriage could be considered in decisions to initiate ICI in patients with cancer. FUNDING National Institutes of Health, Merck KGaA, and Pfizer.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital, Boston, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA; Centre for the AIDS Programme of Research In South Africa, Durban, South Africa
| | - Mathias Viard
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Yuko Yuki
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA
| | - Parantu Shah
- Bioinformatics, Department of Translational Medicine and Global Clinical Development, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | - Kevin Chin
- Immunooncology, EMD Serono Research and Development Institute, Merck KGaA, Darmstadt, Germany
| | | | | | | | | | | | - James L Gulley
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mary Carrington
- Basic Science Programme, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| |
Collapse
|
30
|
Naranbhai V, Pernat CA, Gavralidis A, St Denis KJ, Lam EC, Spring LM, Isakoff SJ, Farmer JR, Zubiri L, Hobbs GS, How J, Brunner AM, Fathi AT, Peterson JL, Sakhi M, Hambelton G, Denault EN, Mortensen LJ, Perriello LA, Bruno MN, Bertaux BY, Lawless AR, Jackson MA, Niehoff E, Barabell C, Nambu CN, Nakajima E, Reinicke T, Bowes C, Berrios-Mairena CJ, Ofoman O, Kirkpatrick GE, Thierauf JC, Reynolds K, Willers H, Beltran WG, Dighe AS, Saff R, Blumenthal K, Sullivan RJ, Chen YB, Kim A, Bardia A, Balazs AB, Iafrate AJ, Gainor JF. Immunogenicity and Reactogenicity of SARS-CoV-2 Vaccines in Patients With Cancer: The CANVAX Cohort Study. J Clin Oncol 2022; 40:12-23. [PMID: 34752147 PMCID: PMC8683230 DOI: 10.1200/jco.21.01891] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/24/2021] [Accepted: 10/13/2021] [Indexed: 01/03/2023] Open
Abstract
PURPOSE The immunogenicity and reactogenicity of SARS-CoV-2 vaccines in patients with cancer are poorly understood. METHODS We performed a prospective cohort study of adults with solid-organ or hematologic cancers to evaluate anti-SARS-CoV-2 immunoglobulin A/M/G spike antibodies, neutralization, and reactogenicity ≥ 7 days following two doses of mRNA-1273, BNT162b2, or one dose of Ad26.COV2.S. We analyzed responses by multivariate regression and included data from 1,638 healthy controls, previously reported, for comparison. RESULTS Between April and July 2021, we enrolled 1,001 patients; 762 were eligible for analysis (656 had neutralization measured). mRNA-1273 was the most immunogenic (log10 geometric mean concentration [GMC] 2.9, log10 geometric mean neutralization titer [GMT] 2.3), followed by BNT162b2 (GMC 2.4; GMT 1.9) and Ad26.COV2.S (GMC 1.5; GMT 1.4; P < .001). The proportion of low neutralization (< 20% of convalescent titers) among Ad26.COV2.S recipients was 69.9%. Prior COVID-19 infection (in 7.1% of the cohort) was associated with higher responses (P < .001). Antibody titers and neutralization were quantitatively lower in patients with cancer than in comparable healthy controls, regardless of vaccine type (P < .001). Receipt of chemotherapy in the prior year or current steroids were associated with lower antibody levels and immune checkpoint blockade with higher neutralization. Systemic reactogenicity varied by vaccine and correlated with immune responses (P = .002 for concentration, P = .016 for neutralization). In 32 patients who received an additional vaccine dose, side effects were similar to prior doses, and 30 of 32 demonstrated increased antibody titers (GMC 1.05 before additional dose, 3.17 after dose). CONCLUSION Immune responses to SARS-CoV-2 vaccines are modestly impaired in patients with cancer. These data suggest utility of antibody testing to identify patients for whom additional vaccine doses may be effective and appropriate, although larger prospective studies are needed.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Claire A. Pernat
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Alexander Gavralidis
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Salem Hospital, Salem, MA
| | | | - Evan C. Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
| | - Laura M. Spring
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Steven J. Isakoff
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Jocelyn R. Farmer
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Leyre Zubiri
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Gabriela S. Hobbs
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Joan How
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Division of Hematology, Brigham and Women's Hospital, Boston, MA
| | - Andrew M. Brunner
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Amir T. Fathi
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Jennifer L. Peterson
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Mustafa Sakhi
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Grace Hambelton
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Elyssa N. Denault
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Lindsey J. Mortensen
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Lailoo A. Perriello
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Marissa N. Bruno
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Brittany Y. Bertaux
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Aleigha R. Lawless
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Monica A. Jackson
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Elizabeth Niehoff
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Caroline Barabell
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Christian N. Nambu
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Erika Nakajima
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Trenton Reinicke
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Cynthia Bowes
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA
| | | | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | | | | | - Kerry Reynolds
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA
| | - Wilfredo-Garcia Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Anand S. Dighe
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Rebecca Saff
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Kimberly Blumenthal
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Ryan J. Sullivan
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Yi-Bin Chen
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Arthur Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| | | | - A. John Iafrate
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Justin F. Gainor
- Massachusetts General Hospital Cancer Center, Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA
| |
Collapse
|
31
|
Bowes CL, Naranbhai V, St Denis KJ, Lam EC, Bertaux B, Keane FK, Khandekar MJ, Balazs AB, Iafrate JA, Gainor JF, Willers H. Heterogeneous immunogenicity of SARS-CoV-2 vaccines in cancer patients receiving radiotherapy. Radiother Oncol 2022; 166:88-91. [PMID: 34838892 PMCID: PMC8613981 DOI: 10.1016/j.radonc.2021.11.012] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/14/2021] [Accepted: 11/15/2021] [Indexed: 01/11/2023]
Abstract
The immunogenicity of SARS-CoV-2 vaccines in cancer patients receiving radiotherapy is unknown. This prospective cohort study demonstrates that anti-SARS-CoV-2 spike antibody and neutralization titers are reduced in a subset of thoracic radiotherapy patients, possibly due to immunosuppressive conditions. Antibody testing may be useful to identify candidates for additional vaccine doses.
Collapse
Affiliation(s)
- Cynthia L Bowes
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Evan C Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Brittany Bertaux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Florence K Keane
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Melin J Khandekar
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA
| | | | - John A Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Justin F Gainor
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Henning Willers
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA, USA.
| |
Collapse
|
32
|
Garcia-Beltran WF, St. Denis KJ, Hoelzemer A, Lam EC, Nitido AD, Sheehan ML, Berrios C, Ofoman O, Chang CC, Hauser BM, Feldman J, Gregory DJ, Poznansky MC, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant. medRxiv 2021:2021.12.14.21267755. [PMID: 34931201 PMCID: PMC8687472 DOI: 10.1101/2021.12.14.21267755] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of vaccine-induced neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that were vaccinated recently (<3 months), distantly (6-12 months), or recently boosted, and accounted for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinated individuals. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron only 4-6-fold lower than wild type, suggesting that boosters enhance the cross-reactivity of neutralizing antibody responses. In addition, we find Omicron pseudovirus is more infectious than any other variant tested. Overall, this study highlights the importance of boosters to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Wilfredo F. Garcia-Beltran
- These authors contributed equally
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Kerri J. St. Denis
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Angelique Hoelzemer
- First Department of Internal Medicine, Division of Infectious Diseases, University Medical Centre Eppendorf, Hamburg, Germany
- German Center for Infection Research (DZIF), Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Evan C. Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | | | - Cristhian Berrios
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Onosereme Ofoman
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Christina C. Chang
- Center for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Pediatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Vivek Naranbhai
- Center for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
- Massachusetts General Hospital Cancer Center, Boston, MA, 02114, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | | |
Collapse
|
33
|
Semenov Y, Tang K, Seo J, Reynolds K, Tiu B, Le T, Pahalyants V, Raval N, Ugwu-Dike P, Zubiri L, Naranbhai V, Gusev A, LeBoeuf N, Asgari M, Kwatra S. 814 Cutaneous immune-related adverse events are protective of mortality in patients treated with anti-PD1 and anti-PDL1 therapy in a multi-institutional cohort study. J Immunother Cancer 2021. [DOI: 10.1136/jitc-2021-sitc2021.814] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BackgroundImmune checkpoint inhibitors (ICIs) have revolutionized cancer therapy over the last decade. Despite the efficacy of ICIs, immune-related adverse events (irAEs) occur in over a third of treated patients and can cause lasting morbidity and mortality.1–3 Cutaneous irAEs (cirAEs) are the most frequently reported toxicities, occurring in 20–40% of treated patients. Though recent reports have investigated the prognostic significance of irAEs on cancer outcomes, little is known about the specific impact of cirAEs and their subtypes on cancer survival.4 In this landmark analysis, we present the first population-level study examining the influence of cirAE development following ICI therapy on the mortality of cancer patients.Methods7,008 patients who developed cirAEs after treatment with anti-programmed cell death receptor/ligand 1 (PD-1/PD-L1) therapy for malignant neoplasms of digestive organs, bronchus or lung, melanoma of skin, and urinary tract were identified through the TriNetX Diamond network along with 7,008 matched controls (table 1). The malignant neoplasms and cutaneous diagnoses for this study were identified from published literature and expert opinion.5 6 Looking at cutaneous eruptions within 6 months of the first instance of ICI administration, a 6-month landmark analysis using a Cox proportional hazards model was performed to determine the impact of cirAE on overall survival.ResultsPresence of any cirAE (HR=0.695, p<0.0001), nonspecific rashes (HR=0.704 , p<0.0001), pruritus (HR=0.695, p<0.0001), drug eruption (HR=0.755, p=0.0013), and xerosis (HR=0.626, p=0.0013) were significantly protective of mortality using a Benjamini-Hochberg (BH) correction for multiple comparisons (table 2). Psoriasis (HR=0.703, p=0.0451) and lichen planus/lichenoid dermatitis (HR=0.511, p=0.0274) were nominally significant. Notably, though not reaching statistical significance, eczematous dermatitis (HR=0.0.612), vitiligo (HR=0.534), bullous pemphigoid (HR=0.524), and Grover's disease (HR=0.468) were associated with strong protective clinical effects. To explore the impact of landmark time on mortality, a sensitivity analysis was performed for cirAE onset within 3 months (HR=0.759, p<0.0001) and 9 months (HR=0.84, p<0.0001) of ICI initiation. A separate sensitivity analysis expanded to include all cancer types treated with ICI yielded similar results, with additional statistical significance reached for ICI-induced psoriasis (table 3).ConclusionsThis is the first population-level study and largest analysis to date of the impact of cirAEs on mortality among patients with advanced cancer. With the exception of mucositis and hyperhidrosis, there was a strong clinically protective effect of cirAEs across all individual morphologies investigated. Our results demonstrate that cirAE development after ICI initiation is an important positive prognostic indicator of response to ICI therapy and patient survival.Abstract 814 Table 1Propensity score-matched baseline characteristics for patients treated with PD-1 or PL-L1 therapyAbstract 814 Table 2Association between cutaneous eruptions and surviv‡Cutaneous diagnoses were identified based on published literature and expert opinion.*Benjamini-Hochberg p-value of significance = 0.0013.Abstract 814 Table 3Association between cutaneous eruptions and surviva‡Cutaneous diagnoses were identified based on published literature and expert opinion.*Benjamini-Hochberg p-value of significance = 0.0025.ReferencesPuzanov I, Diab A, Abdallah K, et al. Managing toxicities associated with immune checkpoint inhibitors: consensus recommendations from the Society for Immunotherapy of Cancer (SITC) Toxicity Management Working Group. J Immunother Cancer 2017;5(1):1–28. doi:10.1186/s40425-017-0300-z.Brahmer JR, Lacchetti C, Schneider BJ, et al. Management of immune-related adverse events in patients treated with immune checkpoint inhibitor therapy: American society of clinical oncology clinical practice guideline. J Clin Oncol 2018;36(17):1714–1768. doi:10.1200/JCO.2017.77.6385.Phillips GS, Wu J, Hellmann MD, et al. Treatment outcomes of immune-related cutaneous adverse events. J Clin Oncol 2019;37(30):2746–2758. doi:10.1200/JCO.18.02141.Petrelli F, Grizzi G, Ghidini M, et al. Immune-related adverse events and survival in solid tumors treated with immune checkpoint inhibitors: a systematic review and meta-analysis. J Immunother. 2020;43(1):1–7. doi:10.1097/CJI.0000000000000300.Wongvibulsin S, Pahalyants V, Kalinich M, et al. Epidemiology and risk factors for the development of cutaneous toxicities in patients treated with immune checkpoint inhibitors: A United States population-level analysis. J Am Acad Dermatol. Published online 2021:1–10. doi:10.1016/j.jaad.2021.03.094.Kalinich M, Murphy W, Wongvibulsin S, Pahalyants V, et al. Prediction of severe immune-related adverse events requiring hospital admission in patients on immune checkpoint inhibitors: study of a population level insurance claims database from the USA. J Immunother Cancer. 2021;9(3):e001935. doi: 10.1136/jitc-2020-001935. PMID: 33789879; PMCID: PMC8016099.Ethics ApprovalStudy utilized de-identified data from a multi-institutional registry and is exempt from IRB approval.
Collapse
|
34
|
Naranbhai V, Garcia-Beltran WF, Chang CC, Mairena CB, Thierauf JC, Kirkpatrick G, Onozato ML, Cheng J, St. Denis KJ, Lam EC, Kaseke C, Tano-Menka R, Yang D, Pavlovic M, Yang W, Kui A, Miller TE, Astudillo MG, Cahill JE, Dighe AS, Gregory DJ, Poznansky MC, Gaiha GD, Balazs AB, Iafrate AJ. Comparative immunogenicity and effectiveness of mRNA-1273, BNT162b2 and Ad26.COV2.S COVID-19 vaccines. medRxiv 2021:2021.07.18.21260732. [PMID: 34671780 PMCID: PMC8528089 DOI: 10.1101/2021.07.18.21260732] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Understanding immunogenicity and effectiveness of SARS-CoV-2 vaccines is critical to guide rational use. METHODS We compared the immunogenicity of mRNA-1273, BNT-162b2 or Ad26.COV2.S in ambulatory adults in Massachusetts, USA. To correlate immunogenicity with effectiveness of the three vaccines, we performed an inverse-variance meta-analysis of population level effectiveness from public health reports in >40 million individuals. RESULTS A single dose of either mRNA vaccine yielded comparable antibody and neutralization titers to convalescent individuals. Ad26.COV2.S yielded lower antibody concentrations and frequently negative neutralization titers. Bulk and cytotoxic T-cell responses were higher in mRNA1273 and BNT162b2 than Ad26.COV2.S recipients, and <50% of vaccinees demonstrate CD8+ T-cell responses to spike peptides. Antibody concentrations and neutralization titers increased comparably after the first dose of either vaccine, and further in recipients of a second dose. Prior infection was associated with high antibody concentrations and neutralization even after a single dose and regardless of vaccine. Neutralization of beta, gamma and delta strains were poorer regardless of vaccine. Relative to mRNA1273, the effectiveness of BNT162b2 was lower against infection and hospitalization; and Ad26COV2.S was lower against infection, hospitalization and death. CONCLUSIONS Variation in the immunogenicity correlates with variable effectiveness of the three FDA EUA vaccines deployed in the USA.
Collapse
|
35
|
Nathan A, Rossin EJ, Kaseke C, Park RJ, Khatri A, Koundakjian D, Urbach JM, Singh NK, Bashirova A, Tano-Menka R, Senjobe F, Waring MT, Piechocka-Trocha A, Garcia-Beltran WF, Iafrate AJ, Naranbhai V, Carrington M, Walker BD, Gaiha GD. Structure-guided T cell vaccine design for SARS-CoV-2 variants and sarbecoviruses. Cell 2021; 184:4401-4413.e10. [PMID: 34265281 PMCID: PMC8241654 DOI: 10.1016/j.cell.2021.06.029] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/02/2021] [Accepted: 06/24/2021] [Indexed: 12/05/2022]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape convalescent and vaccine-induced antibody responses has renewed focus on the development of broadly protective T-cell-based vaccines. Here, we apply structure-based network analysis and assessments of HLA class I peptide stability to define mutationally constrained CD8+ T cell epitopes across the SARS-CoV-2 proteome. Highly networked residues are conserved temporally among circulating variants and sarbecoviruses and disproportionately impair spike pseudotyped lentivirus infectivity when mutated. Evaluation of HLA class I stabilizing activity for 18 globally prevalent alleles identifies CD8+ T cell epitopes within highly networked regions with limited mutational frequencies in circulating SARS-CoV-2 variants and deep-sequenced primary isolates. Moreover, these epitopes elicit demonstrable CD8+ T cell reactivity in convalescent individuals but reduced recognition in recipients of mRNA-based vaccines. These data thereby elucidate key mutationally constrained regions and immunogenic epitopes in the SARS-CoV-2 proteome for a global T-cell-based vaccine against emerging variants and SARS-like coronaviruses.
Collapse
Affiliation(s)
- Anusha Nathan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Health Sciences & Technology, Harvard Medical School & Massachusetts Institute of Technology, Boston, MA 02115, USA
| | - Elizabeth J Rossin
- The Broad Institute, Cambridge, MA 02142, USA; Harvard Medical School Department of Ophthalmology, Massachusetts Eye and Ear, Boston, MA 02114, USA
| | - Clarety Kaseke
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Ryan J Park
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Harvard Radiation Oncology Program, Boston, MA 02114, USA
| | - Ashok Khatri
- Massachusetts General Hospital Endocrine Division and Department of Medicine, Harvard Medical School, Boston, MA 02114, USA
| | | | | | - Nishant K Singh
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02142, USA
| | - Arman Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Rhoda Tano-Menka
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Fernando Senjobe
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Program in Virology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael T Waring
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Wilfredo F Garcia-Beltran
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital, MA 02115, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, MA 02115, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | - Mary Carrington
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD 20892, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; The Broad Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa; Institute for Medical Engineering and Science and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gaurav D Gaiha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.
| |
Collapse
|
36
|
Singh R, Ramsuran V, Naranbhai V, Yende-Zuma N, Garrett N, Mlisana K, Dong KL, Walker BD, Abdool Karim SS, Carrington M, Ndung'u T. Epigenetic Regulation of BST-2 Expression Levels and the Effect on HIV-1 Pathogenesis. Front Immunol 2021; 12:669241. [PMID: 34025670 PMCID: PMC8131512 DOI: 10.3389/fimmu.2021.669241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
HIV-1 must overcome host antiviral restriction factors for efficient replication. We hypothesized that elevated levels of bone marrow stromal cell antigen 2 (BST-2), a potent host restriction factor that interferes with HIV-1 particle release in some human cells and is antagonized by the viral protein Vpu, may associate with viral control. Using cryopreserved samples, from HIV-1 seronegative and seropositive Black women, we measured in vitro expression levels of BST-2 mRNA using a real-time PCR assay and protein levels were validated by Western blotting. The expression level of BST-2 showed an association with viral control within two independent cohorts of Black HIV infected females (r=-0.53, p=0.015, [n =21]; and r=-0.62, p=0.0006, [n=28]). DNA methylation was identified as a mechanism regulating BST-2 levels, where increased BST-2 methylation results in lower expression levels and associates with worse HIV disease outcome. We further demonstrate the ability to regulate BST-2 levels using a DNA hypomethylation drug. Our results suggest BST-2 as a factor for potential therapeutic intervention against HIV and other diseases known to involve BST-2.
Collapse
Affiliation(s)
- Ravesh Singh
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Veron Ramsuran
- School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Vivek Naranbhai
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nigel Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban, South Africa
| | - Krista L Dong
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Bruce D Walker
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Mary Carrington
- The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, Bethesda, MD, United States
| | - Thumbi Ndung'u
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.,Africa Health Research Institute (AHRI), Durban, South Africa.,The Ragon Institute of MGH, MIT and Harvard University, Cambridge, MA, United States.,Max Planck Institute for Infection Biology, Chariteplatz, Berlin, Germany.,Division of Infection and Immunity, University College London, London, United Kingdom
| |
Collapse
|
37
|
Garcia-Beltran WF, Lam EC, St Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC, Sigal A, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 2021; 184:2372-2383.e9. [PMID: 33743213 PMCID: PMC7953441 DOI: 10.1016/j.cell.2021.03.013] [Citation(s) in RCA: 851] [Impact Index Per Article: 283.7] [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: 02/12/2021] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 01/11/2023]
Abstract
Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we evaluated the neutralization potency of 99 individuals that received one or two doses of either BNT162b2 or mRNA-1273 vaccines against pseudoviruses representing 10 globally circulating strains of SARS-CoV-2. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Cross-neutralization of B.1.351 variants was comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.
Collapse
Affiliation(s)
- Wilfredo F Garcia-Beltran
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Kerri St Denis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Adam D Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Zeidy H Garcia
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Maia N Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA 02129, USA
| | - David J Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA 02129, USA; Pedriatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA 02129, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban 4001, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4041, South Africa; Max Planck Institute for Infection Biology, Berlin 10117, Germany
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for the AIDS Programme of Research in South Africa, Durban 4001, South Africa
| | | |
Collapse
|
38
|
Garcia-Beltran WF, Lam EC, St Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC, Sigal A, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. Cell 2021; 184:2523. [PMID: 33930298 PMCID: PMC8082941 DOI: 10.1016/j.cell.2021.04.006] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
39
|
Garcia-Beltran WF, Miller TE, Kirkpatrick G, Nixon A, Astudillo MG, Yang D, Mahanta LM, Murali M, Dighe AS, Lennerz J, Thierauf J, Naranbhai V, Iafrate AJ. Remote Fingerstick Blood Collection for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Testing. Arch Pathol Lab Med 2021; 145:415-418. [PMID: 33264390 DOI: 10.5858/arpa.2020-0713-sa] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2020] [Indexed: 11/06/2022]
Abstract
The rapid worldwide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has propelled the rapid development of serologic tests that can detect anti-SARS-CoV-2 antibodies. These have been used for studying the prevalence and spread of infection in different populations, and helping establish a recent diagnosis of coronavirus disease 2019 (COVID-19), and will likely be used to confirm humoral immunity after infection or vaccination. However, nearly all lab-based high-throughput SARS-CoV-2 serologic assays require a serum sample from venous blood draw, limiting their applications and scalability. Here, we present a method that enables large-scale SARS-CoV-2 serologic studies by combining self or office collection of fingerprick blood with a volumetric absorptive microsampling device (Mitra, Neoteryx LLC) with a high-throughput electrochemiluminescence-based SARS-CoV-2 total antibody assay (Roche Elecsys, Roche Diagnostics Inc) that is emergency use authorization approved for use on serum samples and widely used by clinical laboratories around the world. We found that the Roche Elecsys assay has a high dynamic range that allows for accurate detection of SARS-CoV-2 antibodies in serum samples diluted 1:20 as well as contrived dried blood extracts. Extracts of dried blood from Mitra devices acquired in a community seroprevalence study showed near identical sensitivity and specificity in detection of SARS-CoV-2 antibodies compared with neat sera using predefined thresholds for each specimen type. Overall, this study affirms the use of Mitra dried blood collection device with the Roche Elecsys SARS-CoV-2 total antibody assay for remote or at-home testing as well as large-scale community seroprevalence studies.
Collapse
Affiliation(s)
- Wilfredo F Garcia-Beltran
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston.,Garcia-Beltran and Miller contributed equally to this work
| | - Tyler E Miller
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston.,Garcia-Beltran and Miller contributed equally to this work
| | - Grace Kirkpatrick
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Andrea Nixon
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Michael G Astudillo
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Diane Yang
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Lisa M Mahanta
- Mass General Brigham Biobank, Boston, Massachusetts (Mahanta)
| | - Mandakolathur Murali
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston.,Medicine (Murali, Naranbhai), Massachusetts General Hospital, Boston
| | - Anand S Dighe
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Jochen Lennerz
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Julia Thierauf
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| | - Vivek Naranbhai
- Medicine (Murali, Naranbhai), Massachusetts General Hospital, Boston
| | - A John Iafrate
- From the Departments of Pathology (Garcia-Beltran, Miller, Kirkpatrick, Nixon, Astudillo, Yang, Murali, Dighe, Lennerz, Thierauf, Iafrate), Massachusetts General Hospital, Boston
| |
Collapse
|
40
|
Garcia-Beltran WF, Lam EC, St. Denis K, Nitido AD, Garcia ZH, Hauser BM, Feldman J, Pavlovic MN, Gregory DJ, Poznansky MC, Sigal A, Schmidt AG, Iafrate AJ, Naranbhai V, Balazs AB. Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity. medRxiv 2021:2021.02.14.21251704. [PMID: 33619506 PMCID: PMC7899476 DOI: 10.1101/2021.02.14.21251704] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we evaluated the neutralization potency of 99 individuals that received one or two doses of either BNT162b2 or mRNA-1273 vaccines against pseudoviruses representing 10 globally circulating strains of SARS-CoV-2. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Crossneutralization of B.1.351 variants was comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.
Collapse
Affiliation(s)
- Wilfredo F. Garcia-Beltran
- These authors contributed equally
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA, 02115, USA
| | - Evan C. Lam
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Kerri St. Denis
- These authors contributed equally
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Zeidy H. Garcia
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Blake M. Hauser
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Jared Feldman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - Maia N. Pavlovic
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
| | - David J. Gregory
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Pedriatric Infectious Disease, Massachusetts General Hospital for Children, Boston, MA 02114, USA
| | - Mark C. Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Alex Sigal
- Africa Health Research Institute, Durban, 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4041 South Africa
- Max Planck Institute for Infection Biology, Berlin, 10117, Germany
| | - Aaron G. Schmidt
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA
| | - A. John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Vivek Naranbhai
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Center for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
| | | |
Collapse
|
41
|
Kalinich M, Murphy W, Wongvibulsin S, Pahalyants V, Yu KH, Lu C, Wang F, Zubiri L, Naranbhai V, Gusev A, Kwatra SG, Reynolds KL, Semenov YR. Prediction of severe immune-related adverse events requiring hospital admission in patients on immune checkpoint inhibitors: study of a population level insurance claims database from the USA. J Immunother Cancer 2021; 9:e001935. [PMID: 33789879 PMCID: PMC8016099 DOI: 10.1136/jitc-2020-001935] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Immune-related adverse events (irAEs) are a serious side effect of immune checkpoint inhibitor (ICI) therapy for patients with advanced cancer. Currently, predisposing risk factors are undefined but understanding which patients are at increased risk for irAEs severe enough to require hospitalization would be beneficial to tailor treatment selection and monitoring. METHODS We performed a retrospective review of patients with cancer treated with ICIs using unidentifiable claims data from an Aetna nationwide US health insurance database from January 3, 2011 to December 31, 2019, including patients with an identified primary cancer and at least one administration of an ICI. Regression analyses were performed. Main outcomes were incidence of and factors associated with irAE requiring hospitalization in ICI therapy. RESULTS There were 68.8 million patients identified in the national database, and 14 378 patients with cancer identified with at least 1 administration of ICI in the study period. Patients were followed over 19 117 patient years and 504 (3.5%) developed an irAE requiring hospitalization. The incidence of irAEs requiring hospitalization per patient ICI treatment year was 2.6%, rising from 0% (0/71) in 2011 to 3.7% (93/2486) in 2016. Combination immunotherapy (OR: 2.44, p<0.001) was associated with increased odds of developing irAEs requiring hospitalization, whereas older patients (OR 0.98 per additional year, p<0.001) and those with non-lung cancer were associated with decreased odds of irAEs requiring hospitalization (melanoma OR: 0.70, p=0.01, renal cell carcinoma OR: 0.71, p=0.03, other cancers OR: 0.50, p<0.001). Sex, region, zip-code-imputed income, and zip-code unemployment were not associated with incidence of irAE requiring hospitalization. Prednisone (72%) and methylprednisolone (25%) were the most common immunosuppressive treatments identified in irAE hospitalizations. CONCLUSIONS We found that 3.5% of patients initiating ICI therapy experienced irAEs requiring hospitalization and immunosuppression. The odds of irAEs requiring hospitalization were higher with younger age, treatment with combination ICI therapy (cytotoxic T lymphocyte-associated 4 and programmed cell death protein 1 (PD-1) or programmed death-ligand 1 (PD-L1)), and lower for other cancers compared with patients on PD-1 or PD-L1 inhibitors with lung cancer. This evidence from the first nationwide study of irAEs requiring hospitalization in the USA identified the real-world epidemiology, risk factors, and treatment patterns of these irAEs which may guide treatment and management decisions.
Collapse
Affiliation(s)
| | - William Murphy
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard Business School, Boston, Massachusetts, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shannon Wongvibulsin
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vartan Pahalyants
- Harvard Medical School, Boston, Massachusetts, USA
- Harvard Business School, Boston, Massachusetts, USA
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kun-Hsing Yu
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Chenyue Lu
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Feicheng Wang
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Leyre Zubiri
- Department of Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Vivek Naranbhai
- Department of Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alexander Gusev
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Shawn G Kwatra
- Department of Dermatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Kerry L Reynolds
- Department of Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
| | - Yevgeniy R Semenov
- Department of Dermatology, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
42
|
Naranbhai V, Chang CC, Beltran WFG, Miller TE, Astudillo MG, Villalba JA, Yang D, Gelfand J, Bernstein BE, Feldman J, Hauser BM, Caradonna TM, Alter G, Murali MR, Jasrasaria R, Quinlan J, Xerras DC, Betancourt JR, Louis DN, Schmidt AG, Lennerz J, Poznansky MC, Iafrate AJ. High Seroprevalence of Anti-SARS-CoV-2 Antibodies in Chelsea, Massachusetts. J Infect Dis 2020; 222:1955-1959. [PMID: 32906151 PMCID: PMC7499676 DOI: 10.1093/infdis/jiaa579] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 06/13/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
SARS-CoV-2 antibody testing allows quantitative determination of disease prevalence, which is especially important in high-risk communities. We performed anonymized convenience sampling of 200 currently asymptomatic residents of Chelsea, the epicenter of COVID-19 illness in Massachusetts, by BioMedomics SARS-CoV-2 combined IgM-IgG point-of-care lateral flow immunoassay. The seroprevalence was 31.5% (17.5% IgM+IgG+, 9.0% IgM+IgG-, and 5.0% IgM-IgG+). Of the 200 participants, 50.5% reported no symptoms in the preceding 4 weeks, of which 24.8% (25/101) were seropositive, and 60% of these were IgM+IgG-. These data are the highest seroprevalence rates observed to date and highlight the significant burden of asymptomatic infection.
Collapse
Affiliation(s)
- Vivek Naranbhai
- Dana Farber Cancer Institute, Boston, Massachusetts, USA
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- Centre for the AIDS Programme of Research in South Africa, Durban, KwaZulu Natal, South Africa
| | - Christina C Chang
- Centre for the AIDS Programme of Research in South Africa, Durban, KwaZulu Natal, South Africa
- Department of Infectious Diseases, Alfred Hospital and Monash University, Melbourne, Victoria, Australia
- Therapeutic and Vaccine Research Programme, Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Julian A Villalba
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Diane Yang
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jeffrey Gelfand
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- Vaccine and Immunotherapy Center, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Jared Feldman
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
| | - Blake M Hauser
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
| | - Timothy M Caradonna
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
| | - Galit Alter
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
| | - Mandakolathur R Murali
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- Department of Allergy and Immunology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Rashmi Jasrasaria
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- MGH Chelsea HealthCare Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Joan Quinlan
- Centre for Community Health Improvement, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Dean C Xerras
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- MGH Chelsea HealthCare Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Joseph R Betancourt
- Centre for Community Health Improvement, Massachusetts General Hospital, Boston, Massachusetts, USA
- Center for Diversity and Inclusion, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - David N Louis
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Aaron G Schmidt
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
| | - Jochen Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mark C Poznansky
- Department of Medicine, Massachusetts General Hospital, Massachusetts, USA
- Vaccine and Immunotherapy Center, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts, USA
| |
Collapse
|
43
|
Bashirova AA, Viard M, Naranbhai V, Grifoni A, Garcia-Beltran W, Akdag M, Yuki Y, Gao X, O'hUigin C, Raghavan M, Wolinsky S, Bream JH, Duggal P, Martinson J, Michael NL, Kirk GD, Buchbinder SP, Haas D, Goedert JJ, Deeks SG, Fellay J, Walker B, Goulder P, Cresswell P, Elliott T, Sette A, Carlson J, Carrington M. HLA tapasin independence: broader peptide repertoire and HIV control. Proc Natl Acad Sci U S A 2020; 117:28232-28238. [PMID: 33097667 PMCID: PMC7668082 DOI: 10.1073/pnas.2013554117] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [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] [Indexed: 12/20/2022] Open
Abstract
Human leukocyte antigen (HLA) class I allotypes vary in their ability to present peptides in the absence of tapasin, an essential component of the peptide loading complex. We quantified tapasin dependence of all allotypes that are common in European and African Americans (n = 97), which revealed a broad continuum of values. Ex vivo examination of cytotoxic T cell responses to the entire HIV-1 proteome from infected subjects indicates that tapasin-dependent allotypes present a more limited set of distinct peptides than do tapasin-independent allotypes, data supported by computational predictions. This suggests that variation in tapasin dependence may impact the strength of the immune responses by altering peptide repertoire size. In support of this model, we observed that individuals carrying HLA class I genotypes characterized by greater tapasin independence progress more slowly to AIDS and maintain lower viral loads, presumably due to increased breadth of peptide presentation. Thus, tapasin dependence level, like HLA zygosity, may serve as a means to restrict or expand breadth of the HLA-I peptide repertoire across humans, ultimately influencing immune responses to pathogens and vaccines.
Collapse
Affiliation(s)
- Arman A Bashirova
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Vivek Naranbhai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Wilfredo Garcia-Beltran
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Marjan Akdag
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Xiaojiang Gao
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Colm O'hUigin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109
| | - Steven Wolinsky
- Division of Infectious Diseases, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Jay H Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Jeremy Martinson
- Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261
| | - Nelson L Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Susan P Buchbinder
- HIV Research Section, San Francisco Department of Public Health, San Francisco, CA 94102
| | - David Haas
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37204
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD 20850
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, CA 94110
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| | - Philip Goulder
- Department of Paediatrics, University of Oxford, Oxford, OX1 4AJ, United Kingdom
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Tim Elliott
- Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
- Centre for Cancer Immunology, University of Southampton, Southampton SO16 6YD, United Kingdom
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA 92037
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | | | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702;
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139
| |
Collapse
|
44
|
Müller J, Tanner R, Matsumiya M, Snowden MA, Landry B, Satti I, Harris SA, O’Shea MK, Stockdale L, Marsay L, Chomka A, Harrington-Kandt R, Thomas ZRM, Naranbhai V, Stylianou E, Mbandi SK, Hatherill M, Hussey G, Mahomed H, Tameris M, McClain JB, Evans TG, Hanekom WA, Scriba TJ, McShane H, Fletcher HA. Cytomegalovirus infection is a risk factor for tuberculosis disease in infants. JCI Insight 2019; 4:130090. [PMID: 31697647 PMCID: PMC6962026 DOI: 10.1172/jci.insight.130090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/23/2019] [Indexed: 02/05/2023] Open
Abstract
Immune activation is associated with increased risk of tuberculosis (TB) disease in infants. We performed a case-control analysis to identify drivers of immune activation and disease risk. Among 49 infants who developed TB disease over the first 2 years of life, and 129 healthy matched controls, we found the cytomegalovirus-stimulated (CMV-stimulated) IFN-γ response to be associated with CD8+ T cell activation (Spearman's rho, P = 6 × 10-8). A CMV-specific IFN-γ response was also associated with increased risk of developing TB disease (conditional logistic regression; P = 0.043; OR, 2.2; 95% CI, 1.02-4.83) and shorter time to TB diagnosis (Log Rank Mantel-Cox, P = 0.037). CMV+ infants who developed TB disease had lower expression of NK cell-associated gene signatures and a lower frequency of CD3-CD4-CD8- lymphocytes. We identified transcriptional signatures predictive of TB disease risk among CMV ELISpot-positive (area under the receiver operating characteristic [AUROC], 0.98, accuracy, 92.57%) and -negative (AUROC, 0.9; accuracy, 79.3%) infants; the CMV- signature was validated in an independent infant study (AUROC, 0.71; accuracy, 63.9%). A 16-gene signature that previously identified adolescents at risk of developing TB disease did not accurately classify case and control infants in this study. Understanding the microbial drivers of T cell activation, such as CMV, could guide new strategies for prevention of TB disease in infants.
Collapse
Affiliation(s)
- Julius Müller
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel Tanner
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Magali Matsumiya
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Iman Satti
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephanie A. Harris
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Matthew K. O’Shea
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Lisa Stockdale
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Leanne Marsay
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Agnieszka Chomka
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- The Kennedy Institute and
| | - Rachel Harrington-Kandt
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Zita-Rose Manjaly Thomas
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elena Stylianou
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Stanley Kimbung Mbandi
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Gregory Hussey
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Hassan Mahomed
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Michele Tameris
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | | | | | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine & Division of Immunology, Department of Pathology, University of Cape Town, South Africa
| | - Helen McShane
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Helen A. Fletcher
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- London School of Hygiene & Tropical Medicine, London, United Kingdom
| |
Collapse
|
45
|
Kulkarni S, Lied A, Kulkarni V, Rucevic M, Martin MP, Walker-Sperling V, Anderson SK, Ewy R, Singh S, Nguyen H, McLaren PJ, Viard M, Naranbhai V, Zou C, Lin Z, Gatanaga H, Oka S, Takiguchi M, Thio CL, Margolick J, Kirk GD, Goedert JJ, Hoots WK, Deeks SG, Haas DW, Michael N, Walker B, Le Gall S, Chowdhury FZ, Yu XG, Carrington M. Author Correction: CCR5AS lncRNA variation differentially regulates CCR5, influencing HIV disease outcome. Nat Immunol 2019; 20:1555. [PMID: 31548709 DOI: 10.1038/s41590-019-0516-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Collapse
Affiliation(s)
- Smita Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
| | - Alexandra Lied
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Viraj Kulkarni
- Texas Biomedical Research Institute, San Antonio, TX, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Marijana Rucevic
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Olink Proteomic, Watertown, MA, USA
| | - Maureen P Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Victoria Walker-Sperling
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rodger Ewy
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Hoang Nguyen
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Paul J McLaren
- J.C. Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Vivek Naranbhai
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Chengcheng Zou
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Zhansong Lin
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
| | - Hiroyuki Gatanaga
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | - Shinichi Oka
- Center for AIDS Research, Kumamoto University, Kumamoto, Japan
- AIDS Clinical Center, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Chloe L Thio
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Margolick
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory D Kirk
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - James J Goedert
- Epidemiology and Biostatistics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - W Keith Hoots
- Division of Blood Diseases and Resources, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven G Deeks
- San Francisco General Hospital Medical Center, San Francisco, CA, USA
| | - David W Haas
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Bruce Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sylvie Le Gall
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Fatema Z Chowdhury
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Mary Carrington
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| |
Collapse
|
46
|
Miyahara R, Piyaworawong S, Naranbhai V, Prachamat P, Kriengwatanapong P, Tsuchiya N, Wongyai J, Bupachat S, Yamada N, Summanapan S, Mahasirimongkol S, Yanai H. Predicting the risk of pulmonary tuberculosis based on the neutrophil-to-lymphocyte ratio at TB screening in HIV-infected individuals. BMC Infect Dis 2019; 19:667. [PMID: 31357936 PMCID: PMC6664723 DOI: 10.1186/s12879-019-4292-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 07/16/2019] [Indexed: 01/14/2023] Open
Abstract
Background The neutrophil to lymphocyte ratio (NL ratio) has been reported to be a predictive biomarker of tuberculosis (TB). We assessed the association between the NL ratio and the incidence of active TB cases within 1 year after TB screening among HIV-infected individuals in Thailand. Methods A day care center that supports HIV-infected individuals in northernmost Thailand performed TB screening and follow-up visits. We compared the baseline characteristics between the TB screening positive group and the TB screening negative group. The threshold value of NL ratio was determined by cubic-spline curves and NL ratios were categorized as high or low NL ratio. We assessed the association between NL ratio and progression to active TB within 1-year using the Cox-proportional hazard model. Results Of the 1064 HIV-infected individuals who screened negative for TB at baseline, 5.6% (N = 60) eventually developed TB and 26 died after TB diagnosis. A high NL ratio was associated with a higher risk of TB (adjusted hazard ratio (aHR) 2.19, 95% CI: 1.23–3.90), after adjusting for age, sex, ethnicity, CD4 counts, and other risk factors. A high NL ratio in HIV-infected individuals with normal chest X-ray predicted TB development risk. In particular, a high NL ratio with TB symptoms could predict the highest risk of TB development (aHR 2.58, 95%CI: 1.07–6.23). Conclusions Our results showed that high NL ratio increased the risk of TB. NL ratio combined with TB symptoms could increase the accuracy of TB screening among HIV-infected individuals. Electronic supplementary material The online version of this article (10.1186/s12879-019-4292-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Reiko Miyahara
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan. .,Genome Medical Science Project, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan.
| | | | - Vivek Naranbhai
- Massachusetts General Hospital, Boston, USA.,Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | | | - Naho Tsuchiya
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | | | - Norio Yamada
- Research Institute of Tuberculosis (RIT), Anti-Tuberculosis Association (JATA), Tokyo, Japan
| | | | | | - Hideki Yanai
- Research Institute of Tuberculosis (RIT), Anti-Tuberculosis Association (JATA), Tokyo, Japan.,JATA, Fukujuji Hospital, Tokyo, Japan
| |
Collapse
|
47
|
Stanaway IB, Hall TO, Rosenthal EA, Palmer M, Naranbhai V, Knevel R, Namjou-Khales B, Carroll RJ, Kiryluk K, Gordon AS, Linder J, Howell KM, Mapes BM, Lin FTJ, Joo YY, Hayes MG, Gharavi AG, Pendergrass SA, Ritchie MD, de Andrade M, Croteau-Chonka DC, Raychaudhuri S, Weiss ST, Lebo M, Amr SS, Carrell D, Larson EB, Chute CG, Rasmussen-Torvik LJ, Roy-Puckelwartz MJ, Sleiman P, Hakonarson H, Li R, Karlson EW, Peterson JF, Kullo IJ, Chisholm R, Denny JC, Jarvik GP, Crosslin DR. The eMERGE genotype set of 83,717 subjects imputed to ~40 million variants genome wide and association with the herpes zoster medical record phenotype. Genet Epidemiol 2018; 43:63-81. [PMID: 30298529 PMCID: PMC6375696 DOI: 10.1002/gepi.22167] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 08/10/2018] [Accepted: 08/28/2018] [Indexed: 12/30/2022]
Abstract
The Electronic Medical Records and Genomics (eMERGE) network is a network of medical centers with electronic medical records linked to existing biorepository samples for genomic discovery and genomic medicine research. The network sought to unify the genetic results from 78 Illumina and Affymetrix genotype array batches from 12 contributing medical centers for joint association analysis of 83,717 human participants. In this report, we describe the imputation of eMERGE results and methods to create the unified imputed merged set of genome‐wide variant genotype data. We imputed the data using the Michigan Imputation Server, which provides a missing single‐nucleotide variant genotype imputation service using the minimac3 imputation algorithm with the Haplotype Reference Consortium genotype reference set. We describe the quality control and filtering steps used in the generation of this data set and suggest generalizable quality thresholds for imputation and phenotype association studies. To test the merged imputed genotype set, we replicated a previously reported chromosome 6 HLA‐B herpes zoster (shingles) association and discovered a novel zoster‐associated loci in an epigenetic binding site near the terminus of chromosome 3 (3p29).
Collapse
Affiliation(s)
- Ian B Stanaway
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Taryn O Hall
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| | - Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Melody Palmer
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Vivek Naranbhai
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington.,Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Rachel Knevel
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Bahram Namjou-Khales
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Robert J Carroll
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | - Krzysztof Kiryluk
- Department of Medicine, Columbia University, New York City, New York
| | - Adam S Gordon
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | - Jodell Linder
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Kayla Marie Howell
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Brandy M Mapes
- Vanderbilt Institute for Clinical and Translational Research, School of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Frederick T J Lin
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | - M Geoffrey Hayes
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ali G Gharavi
- Department of Medicine, Columbia University, New York City, New York
| | | | - Marylyn D Ritchie
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | | | - Soumya Raychaudhuri
- Harvard Medical School, Harvard University, Cambridge, Massachusetts.,Program in Medical and Population Genetics, Broad Institute of Massachusetts Technical Institute and Harvard University, Cambridge, Massachusetts
| | - Scott T Weiss
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Matt Lebo
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - Sami S Amr
- Harvard Medical School, Harvard University, Cambridge, Massachusetts
| | - David Carrell
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington
| | - Eric B Larson
- Kaiser Permanente Washington Health Research Institute (Formerly Group Health Cooperative-Seattle), Kaiser Permanente, Seattle, Washington
| | - Christopher G Chute
- Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Patrick Sleiman
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Elizabeth W Karlson
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Josh F Peterson
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | | | - Rex Chisholm
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Joshua Charles Denny
- Departments of Biomedical Informatics and Medicine, Vanderbilt University, Nashville, Tennessee
| | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington
| | -
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David R Crosslin
- Department of Biomedical Informatics Medical Education, School of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
48
|
Martin MP, Naranbhai V, Shea PR, Qi Y, Ramsuran V, Vince N, Gao X, Thomas R, Brumme ZL, Carlson JM, Wolinsky SM, Goedert JJ, Walker BD, Segal FP, Deeks SG, Haas DW, Migueles SA, Connors M, Michael N, Fellay J, Gostick E, Llewellyn-Lacey S, Price DA, Lafont BA, Pymm P, Saunders PM, Widjaja J, Wong SC, Vivian JP, Rossjohn J, Brooks AG, Carrington M. Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1. J Clin Invest 2018; 128:1903-1912. [PMID: 29461980 DOI: 10.1172/jci98463] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/13/2018] [Indexed: 01/11/2023] Open
Abstract
HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.
Collapse
Affiliation(s)
- Maureen P Martin
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Patrick R Shea
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Ying Qi
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Veron Ramsuran
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa.,KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicolas Vince
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,ATIP-Avenir, Centre de Recherche en Transplantation et Immunologie, UMR 1064, INSERM, Université de Nantes, Nantes, France.,Institut de Transplantation Urologie Néphrologie (ITUN), Centre Hospitalier Universitaire (CHU) de Nantes, Nantes, France
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Zabrina L Brumme
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia, Canada.,British Columbia Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
| | | | - Steven M Wolinsky
- Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - James J Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| | | | - Steven G Deeks
- San Francisco General Hospital Medical Center, San Francisco, California, USA
| | - David W Haas
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Stephen A Migueles
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, Maryland, USA
| | - Nelson Michael
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Jacques Fellay
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Emma Gostick
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - Sian Llewellyn-Lacey
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA
| | - David A Price
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland, USA
| | - Bernard A Lafont
- Viral Immunology Section, Office of the Scientific Director, NIAID, NIH, Bethesda, Maryland, USA
| | - Phillip Pymm
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Philippa M Saunders
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Jacqueline Widjaja
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Shu Cheng Wong
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Julian P Vivian
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Cardiff University School of Medicine, Heath Park, University Hospital of Wales, Cardiff, United Kingdom.,Non-Human Primate Immunogenetics and Cellular Immunology Unit, NIAID, NIH, Bethesda, Maryland, USA.,Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, and Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Andrew G Brooks
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA.,Ragon Institute of MGH, MIT and Harvard, Boston, Massachusetts, USA
| |
Collapse
|
49
|
Gilchrist JJ, Rautanen A, Fairfax BP, Mills TC, Naranbhai V, Trochet H, Pirinen M, Muthumbi E, Mwarumba S, Njuguna P, Mturi N, Msefula CL, Gondwe EN, MacLennan JM, Chapman SJ, Molyneux ME, Knight JC, Spencer CCA, Williams TN, MacLennan CA, Scott JAG, Hill AVS. Risk of nontyphoidal Salmonella bacteraemia in African children is modified by STAT4. Nat Commun 2018. [PMID: 29523850 PMCID: PMC5844948 DOI: 10.1038/s41467-017-02398-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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] [Indexed: 12/17/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) is a major cause of bacteraemia in Africa. The disease typically affects HIV-infected individuals and young children, causing substantial morbidity and mortality. Here we present a genome-wide association study (180 cases, 2677 controls) and replication analysis of NTS bacteraemia in Kenyan and Malawian children. We identify a locus in STAT4, rs13390936, associated with NTS bacteraemia. rs13390936 is a context-specific expression quantitative trait locus for STAT4 RNA expression, and individuals carrying the NTS-risk genotype demonstrate decreased interferon-γ (IFNγ) production in stimulated natural killer cells, and decreased circulating IFNγ concentrations during acute NTS bacteraemia. The NTS-risk allele at rs13390936 is associated with protection against a range of autoimmune diseases. These data implicate interleukin-12-dependent IFNγ-mediated immunity as a determinant of invasive NTS disease in African children, and highlight the shared genetic architecture of infectious and autoimmune disease.
Collapse
Affiliation(s)
- James J Gilchrist
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,Department of Paediatrics, University of Oxford, Oxford, OX3 9DU, UK.
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Benjamin P Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Tara C Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Vivek Naranbhai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Holly Trochet
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Matti Pirinen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Institute for Molecular Medicine, Finland (FIMM) University of Helsinki, FI-00014, Helsinki, Finland
| | - Esther Muthumbi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Salim Mwarumba
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | | | - Neema Mturi
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,Pathology Department, College of Medicine, P.O. Box 360, Chichiri, Blantyre, Malawi
| | - Esther N Gondwe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi
| | - Jenny M MacLennan
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Stephen J Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.,Oxford Centre for Respiratory Medicine, Churchill Hospital Site, Oxford University Hospitals, Oxford, OX3 7LE, UK
| | - Malcolm E Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi
| | - Julian C Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Medicine, Imperial College, Norfolk Place, London, W2 1PG, UK
| | - Calman A MacLennan
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, P.O. Box 30096, Chichiri, Blantyre, Malawi.,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - J Anthony G Scott
- KEMRI-Wellcome Trust Research Programme, Kilifi, 80108, Kenya.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Adrian V S Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK. .,The Jenner Institute, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
| |
Collapse
|
50
|
Körner C, Simoneau CR, Schommers P, Granoff M, Ziegler M, Hölzemer A, Lunemann S, Chukwukelu J, Corleis B, Naranbhai V, Kwon DS, Scully EP, Jost S, Kirchhoff F, Carrington M, Altfeld M. HIV-1-Mediated Downmodulation of HLA-C Impacts Target Cell Recognition and Antiviral Activity of NK Cells. Cell Host Microbe 2018; 22:111-119.e4. [PMID: 28704647 DOI: 10.1016/j.chom.2017.06.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 01/17/2017] [Revised: 05/03/2017] [Accepted: 06/16/2017] [Indexed: 11/24/2022]
Abstract
It was widely accepted that HIV-1 downregulates HLA-A/B to avoid CTL recognition while leaving HLA-C unaltered in order to prevent NK cell activation by engaging inhibitory NK cell receptors, but it was recently observed that most primary isolates of HIV-1 can mediate HLA-C downmodulation. Now we report that HIV-1-mediated downmodulation of HLA-C was associated with reduced binding to its respective inhibitory receptors. Despite this, HLA-C-licensed NK cells displayed reduced antiviral activity compared to their unlicensed counterparts, potentially due to residual binding to the respective inhibitory receptors. Nevertheless, NK cells were able to sense alterations of HLA-C expression demonstrated by increased antiviral activity when exposed to viral strains with differential abilities to downmodulate HLA-C. These results suggest that the capability of HLA-C-licensed NK cells to control HIV-1 replication is determined by the strength of KIR/HLA-C interactions and is thus dependent on both host genetics and the extent of virus-mediated HLA-C downregulation.
Collapse
Affiliation(s)
- Christian Körner
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany.
| | | | - Philipp Schommers
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany; Department I of Internal Medicine, University Hospital Cologne, 50937 Cologne, Germany; German Center for Infection Research (DZIF), Cologne, Germany
| | - Mitchell Granoff
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Maja Ziegler
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany
| | - Angelique Hölzemer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany; German Center for Infection Research (DZIF), Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sebastian Lunemann
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany
| | - Janet Chukwukelu
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany; German Center for Infection Research (DZIF), Hamburg, Germany
| | - Björn Corleis
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Vivek Naranbhai
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eileen P Scully
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Stephanie Jost
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA; Cancer and Inflammation Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Marcus Altfeld
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Department of Virus Immunology, 20251 Hamburg, Germany
| |
Collapse
|