1
|
Memon D, Schoenfeld AJ, Ye D, Fromm G, Rizvi H, Zhang X, Keddar MR, Mathew D, Yoo KJ, Qiu J, Lihm J, Miriyala J, Sauter JL, Luo J, Chow A, Bhanot UK, McCarthy C, Vanderbilt CM, Liu C, Abu-Akeel M, Plodkowski AJ, McGranahan N, Łuksza M, Greenbaum BD, Merghoub T, Achour I, Barrett JC, Stewart R, Beltrao P, Schreiber TH, Minn AJ, Miller ML, Hellmann MD. Clinical and molecular features of acquired resistance to immunotherapy in non-small cell lung cancer. Cancer Cell 2024; 42:209-224.e9. [PMID: 38215748 DOI: 10.1016/j.ccell.2023.12.013] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 09/13/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Although immunotherapy with PD-(L)1 blockade is routine for lung cancer, little is known about acquired resistance. Among 1,201 patients with non-small cell lung cancer (NSCLC) treated with PD-(L)1 blockade, acquired resistance is common, occurring in >60% of initial responders. Acquired resistance shows differential expression of inflammation and interferon (IFN) signaling. Relapsed tumors can be separated by upregulated or stable expression of IFNγ response genes. Upregulation of IFNγ response genes is associated with putative routes of resistance characterized by signatures of persistent IFN signaling, immune dysfunction, and mutations in antigen presentation genes which can be recapitulated in multiple murine models of acquired resistance to PD-(L)1 blockade after in vitro IFNγ treatment. Acquired resistance to PD-(L)1 blockade in NSCLC is associated with an ongoing, but altered IFN response. The persistently inflamed, rather than excluded or deserted, tumor microenvironment of acquired resistance may inform therapeutic strategies to effectively reprogram and reverse acquired resistance.
Collapse
Affiliation(s)
- Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK; M:M Bio Limited, 99 Park Drive, Milton, Abingdon, UK
| | - Adam J Schoenfeld
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Darwin Ye
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Early Clinical Development, Oncology R&D, AstraZeneca, New York, NY, USA
| | - Xiang Zhang
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | | | - Divij Mathew
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology and Immune Health, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA; Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Jingya Qiu
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayon Lihm
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jia Luo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Umesh K Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline McCarthy
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chad M Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cailian Liu
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA
| | - Mohsen Abu-Akeel
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
| | - Marta Łuksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center (MSK), New York, NY, USA; Parker Institute for Cancer Immunotherapy, MSK, New York, NY, USA; Human Oncology and Pathogenesis Program, MSK, New York, NY, USA
| | - Ikbel Achour
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - J Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Ross Stewart
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Institute of Molecular Systems Biology, ETH Zürich, Zurich, Switzerland
| | | | - Andy J Minn
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Mark Foundation Center for Immunotherapy, Immune Signaling, and Radiation, University of Pennsylvania, Philadelphia, PA, USA.
| | - Martin L Miller
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK; Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK.
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Early Clinical Development, Oncology R&D, AstraZeneca, New York, NY, USA; Parker Institute for Cancer Immunotherapy, MSK, New York, NY, USA.
| |
Collapse
|
2
|
Meijers M, Ruchnewitz D, Eberhardt J, Łuksza M, Lässig M. Population immunity predicts evolutionary trajectories of SARS-CoV-2. Cell 2023; 186:5151-5164.e13. [PMID: 37875109 PMCID: PMC10964984 DOI: 10.1016/j.cell.2023.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 08/26/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023]
Abstract
The large-scale evolution of the SARS-CoV-2 virus has been marked by rapid turnover of genetic clades. New variants show intrinsic changes, notably increased transmissibility, and antigenic changes that reduce cross-immunity induced by previous infections or vaccinations. How this functional variation shapes global evolution has remained unclear. Here, we establish a predictive fitness model for SARS-CoV-2 that integrates antigenic and intrinsic selection. The model is informed by tracking of time-resolved sequence data, epidemiological records, and cross-neutralization data of viral variants. Our inference shows that immune pressure, including contributions of vaccinations and previous infections, has become the dominant force driving the recent evolution of SARS-CoV-2. The fitness model can serve continued surveillance in two ways. First, it successfully predicts the short-term evolution of circulating strains and flags emerging variants likely to displace the previously predominant variant. Second, it predicts likely antigenic profiles of successful escape variants prior to their emergence.
Collapse
Affiliation(s)
- Matthijs Meijers
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Jan Eberhardt
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Departments of Oncological Sciences and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Zülpicherstr. 77, 50937 Köln, Germany.
| |
Collapse
|
3
|
Rojas LA, Sethna Z, Soares KC, Olcese C, Pang N, Patterson E, Lihm J, Ceglia N, Guasp P, Chu A, Yu R, Chandra AK, Waters T, Ruan J, Amisaki M, Zebboudj A, Odgerel Z, Payne G, Derhovanessian E, Müller F, Rhee I, Yadav M, Dobrin A, Sadelain M, Łuksza M, Cohen N, Tang L, Basturk O, Gönen M, Katz S, Do RK, Epstein AS, Momtaz P, Park W, Sugarman R, Varghese AM, Won E, Desai A, Wei AC, D'Angelica MI, Kingham TP, Mellman I, Merghoub T, Wolchok JD, Sahin U, Türeci Ö, Greenbaum BD, Jarnagin WR, Drebin J, O'Reilly EM, Balachandran VP. Personalized RNA neoantigen vaccines stimulate T cells in pancreatic cancer. Nature 2023; 618:144-150. [PMID: 37165196 PMCID: PMC10171177 DOI: 10.1038/s41586-023-06063-y] [Citation(s) in RCA: 172] [Impact Index Per Article: 172.0] [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: 01/10/2023] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is lethal in 88% of patients1, yet harbours mutation-derived T cell neoantigens that are suitable for vaccines 2,3. Here in a phase I trial of adjuvant autogene cevumeran, an individualized neoantigen vaccine based on uridine mRNA-lipoplex nanoparticles, we synthesized mRNA neoantigen vaccines in real time from surgically resected PDAC tumours. After surgery, we sequentially administered atezolizumab (an anti-PD-L1 immunotherapy), autogene cevumeran (a maximum of 20 neoantigens per patient) and a modified version of a four-drug chemotherapy regimen (mFOLFIRINOX, comprising folinic acid, fluorouracil, irinotecan and oxaliplatin). The end points included vaccine-induced neoantigen-specific T cells by high-threshold assays, 18-month recurrence-free survival and oncologic feasibility. We treated 16 patients with atezolizumab and autogene cevumeran, then 15 patients with mFOLFIRINOX. Autogene cevumeran was administered within 3 days of benchmarked times, was tolerable and induced de novo high-magnitude neoantigen-specific T cells in 8 out of 16 patients, with half targeting more than one vaccine neoantigen. Using a new mathematical strategy to track T cell clones (CloneTrack) and functional assays, we found that vaccine-expanded T cells comprised up to 10% of all blood T cells, re-expanded with a vaccine booster and included long-lived polyfunctional neoantigen-specific effector CD8+ T cells. At 18-month median follow-up, patients with vaccine-expanded T cells (responders) had a longer median recurrence-free survival (not reached) compared with patients without vaccine-expanded T cells (non-responders; 13.4 months, P = 0.003). Differences in the immune fitness of the patients did not confound this correlation, as responders and non-responders mounted equivalent immunity to a concurrent unrelated mRNA vaccine against SARS-CoV-2. Thus, adjuvant atezolizumab, autogene cevumeran and mFOLFIRINOX induces substantial T cell activity that may correlate with delayed PDAC recurrence.
Collapse
Affiliation(s)
- Luis A Rojas
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin C Soares
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cristina Olcese
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nan Pang
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Erin Patterson
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jayon Lihm
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Ceglia
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pablo Guasp
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander Chu
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca Yu
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adrienne Kaya Chandra
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Theresa Waters
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Ruan
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Masataka Amisaki
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abderezak Zebboudj
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zagaa Odgerel
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - George Payne
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Ina Rhee
- Genentech, San Francisco, CA, USA
| | | | - Anton Dobrin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noah Cohen
- Department of Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Tang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Olca Basturk
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seth Katz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard Kinh Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew S Epstein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parisa Momtaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Wungki Park
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Sugarman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna M Varghese
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth Won
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Avni Desai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alice C Wei
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael I D'Angelica
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - T Peter Kingham
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Taha Merghoub
- Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jedd D Wolchok
- Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Özlem Türeci
- BioNTech, Mainz, Germany
- HI-TRON, Helmholtz Institute for Translational Oncology, Mainz, Germany
| | - Benjamin D Greenbaum
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - William R Jarnagin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeffrey Drebin
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eileen M O'Reilly
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vinod P Balachandran
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
4
|
Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Author Correction: Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature 2022; 606:E5. [PMID: 35641605 PMCID: PMC9200628 DOI: 10.1038/s41586-022-04879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta Zappasodi
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
| | - Isabell Schulze
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelvin César de Andrade
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Dean F Bajorin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret K Callahan
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sine R Hadrup
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jeppe S Holm
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan E Rosenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology & 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
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vinod P Balachandran
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Medicine, Weill Cornell Medical College, New York, NY, USA. .,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & 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.
| |
Collapse
|
5
|
Hoyos D, Zappasodi R, Schulze I, Sethna Z, de Andrade KC, Bajorin DF, Bandlamudi C, Callahan MK, Funt SA, Hadrup SR, Holm JS, Rosenberg JE, Shah SP, Vázquez-García I, Weigelt B, Wu M, Zamarin D, Campitelli LF, Osborne EJ, Klinger M, Robins HS, Khincha PP, Savage SA, Balachandran VP, Wolchok JD, Hellmann MD, Merghoub T, Levine AJ, Łuksza M, Greenbaum BD. Fundamental immune-oncogenicity trade-offs define driver mutation fitness. Nature 2022; 606:172-179. [PMID: 35545680 PMCID: PMC9159948 DOI: 10.1038/s41586-022-04696-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/28/2022] [Indexed: 12/29/2022]
Abstract
Missense driver mutations in cancer are concentrated in a few hotspots1. Various mechanisms have been proposed to explain this skew, including biased mutational processes2, phenotypic differences3-6 and immunoediting of neoantigens7,8; however, to our knowledge, no existing model weighs the relative contribution of these features to tumour evolution. We propose a unified theoretical 'free fitness' framework that parsimoniously integrates multimodal genomic, epigenetic, transcriptomic and proteomic data into a biophysical model of the rate-limiting processes underlying the fitness advantage conferred on cancer cells by driver gene mutations. Focusing on TP53, the most mutated gene in cancer1, we present an inference of mutant p53 concentration and demonstrate that TP53 hotspot mutations optimally solve an evolutionary trade-off between oncogenic potential and neoantigen immunogenicity. Our model anticipates patient survival in The Cancer Genome Atlas and patients with lung cancer treated with immunotherapy as well as the age of tumour onset in germline carriers of TP53 variants. The predicted differential immunogenicity between hotspot mutations was validated experimentally in patients with cancer and in a unique large dataset of healthy individuals. Our data indicate that immune selective pressure on TP53 mutations has a smaller role in non-cancerous lesions than in tumours, suggesting that targeted immunotherapy may offer an early prophylactic opportunity for the former. Determining the relative contribution of immunogenicity and oncogenic function to the selective advantage of hotspot mutations thus has important implications for both precision immunotherapies and our understanding of tumour evolution.
Collapse
Affiliation(s)
- David Hoyos
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta Zappasodi
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
| | - Isabell Schulze
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kelvin César de Andrade
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Dean F Bajorin
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaitanya Bandlamudi
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Margaret K Callahan
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel A Funt
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sine R Hadrup
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jeppe S Holm
- Experimental and Translational Immunology, Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jonathan E Rosenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology & 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
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michelle Wu
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | | | | | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics, Clinical Genetics Branch, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Vinod P Balachandran
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Swim Across America Laboratory and Ludwig Collaborative, Immunology Program, Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Marta Łuksza
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin D Greenbaum
- Computational Oncology, Department of Epidemiology & 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.
| |
Collapse
|
6
|
Vanshylla K, Fan C, Wunsch M, Poopalasingam N, Meijers M, Kreer C, Kleipass F, Ruchnewitz D, Ercanoglu MS, Gruell H, Münn F, Pohl K, Janicki H, Nolden T, Bartl S, Stein SC, Augustin M, Dewald F, Gieselmann L, Schommers P, Schulz TF, Sander LE, Koch M, Łuksza M, Lässig M, Bjorkman PJ, Klein F. Discovery of ultrapotent broadly neutralizing antibodies from SARS-CoV-2 elite neutralizers. Cell Host Microbe 2022; 30:69-82.e10. [PMID: 34973165 PMCID: PMC8683262 DOI: 10.1016/j.chom.2021.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [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: 09/28/2021] [Revised: 11/08/2021] [Accepted: 12/10/2021] [Indexed: 01/14/2023]
Abstract
A fraction of COVID-19 convalescent individuals mount a potent antibody response to SARS-CoV-2 with cross-reactivity to SARS-CoV-1. To uncover their humoral response in detail, we performed single B cell analysis from 10 SARS-CoV-2 elite neutralizers. We isolated and analyzed 126 monoclonal antibodies, many of which were sarbecovirus cross-reactive, with some displaying merbecovirus- and embecovirus-reactivity. Several isolated broadly neutralizing antibodies were effective against B.1.1.7, B.1.351, B.1.429, B.1.617, and B.1.617.2 variants and 19 prominent potential escape sites. Furthermore, assembly of 716,806 SARS-CoV-2 sequences predicted emerging escape variants, which were also effectively neutralized. One of these broadly neutralizing potent antibodies, R40-1G8, is a IGHV3-53 RBD-class-1 antibody. Remarkably, cryo-EM analysis revealed that R40-1G8 has a flexible binding mode, targeting both "up" and "down" conformations of the RBD. Given the threat of emerging SARS-CoV-2 variants, we demonstrate that elite neutralizers are a valuable source for isolating ultrapotent antibody candidates to prevent and treat SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Kanika Vanshylla
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Chengcheng Fan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie Wunsch
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nareshkumar Poopalasingam
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Matthijs Meijers
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Christoph Kreer
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Franziska Kleipass
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Meryem S. Ercanoglu
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Henning Gruell
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Friederike Münn
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Kai Pohl
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Hanna Janicki
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | | | - Simone Bartl
- Vira Therapeutics GmbH, 6063 Rum, Austria,Boehringer Ingelheim International GmbH, Ingelheim, Germany
| | - Saskia C. Stein
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Max Augustin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
| | - Felix Dewald
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Lutz Gieselmann
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität Berlin, 13353 Berlin, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology and Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Marta Łuksza
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, 50937 Cologne, Germany
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Florian Klein
- Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany,German Center for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany,Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany,Corresponding author
| |
Collapse
|
7
|
Robilotti EV, Whiting K, Lucca A, Poon C, Guest R, McMillen T, Jani K, Solovyov A, Kelson S, Browne K, Freeswick S, Hohl TM, Korenstein D, Ruchnewitz D, Lässig M, Łuksza M, Greenbaum B, Seshan VE, Esther Babady N, Kamboj M. Clinical and Genomic Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Infections in mRNA Vaccinated Health Care Personnel in New York City. Clin Infect Dis 2021; 75:e774-e782. [PMID: 34644393 PMCID: PMC9612794 DOI: 10.1093/cid/ciab886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 07/17/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Vaccine-induced clinical protection against severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) variants is an evolving target. There are limited genomic level data on SARS CoV-2 breakthrough infections and vaccine effectiveness (VE) since the global spread of the B.1.617.2 (Delta) variant. METHODS In a retrospective study from 1 November 2020 to 31 August 2021, divided as pre-Delta and Delta-dominant periods, laboratory-confirmed SARS CoV-2 infections among healthcare personnel (HCP) at a large tertiary cancer center in New York City were examined to compare the weekly infection rate-ratio in vaccinated, partially vaccinated, and unvaccinated HCP. We describe the clinical and genomic epidemiologic features of post-vaccine infections to assess for selection of variants of concern (VOC)/variants of interest (VOI) in the early post-vaccine period and impact of B.1.617.2 (Delta) variant domination on VE. RESULTS Among 13658 HCP in our cohort, 12379 received at least 1 dose of a messenger RNA (mRNA) vaccine. In the pre-Delta period overall VE was 94.5%. Whole genome sequencing (WGS) of 369 isolates in the pre-Delta period did not reveal a clade bias for VOC/VOI specific to post-vaccine infections. VE in the Delta dominant phase was 75.6%. No hospitalizations occurred among vaccinated HCP in the entire study period, compared to 17 hospitalizations and 1 death among unvaccinated HCP. CONCLUSIONS Findings show high VE among HCP in New York City in the pre-Delta phase, with moderate decline in VE post-Delta emergence. SARS CoV-2 clades were similarly distributed among vaccinated and unvaccinated infected HCP without apparent clustering during the pre-Delta period of diverse clade circulation. Strong vaccine protection against hospitalization was maintained through the entire study period.
Collapse
Affiliation(s)
| | | | - Anabella Lucca
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Chester Poon
- Division of Digital Informatics and Technology Solutions, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rebecca Guest
- Employee Health Service, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tracy McMillen
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Krupa Jani
- Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexander Solovyov
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Suzanne Kelson
- Division of Digital Products and Informatics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kevin Browne
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Scott Freeswick
- Division of Pharmacy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Tobias M Hohl
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA
| | - Deborah Korenstein
- Department of Medicine, Joan and Sanford Weill Medical College of Cornell University, New York, New York, USA,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Denis Ruchnewitz
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Michael Lässig
- Institute for Biological Physics, University of Cologne, Cologne, Germany
| | - Marta Łuksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin Greenbaum
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Department of Physiology, Biophysics and Systems Biology, Weill Cornell Medicine, New York, New York, USA
| | - Venkatraman E Seshan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - N Esther Babady
- Infectious Diseases, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA,Clinical Microbiology Service, Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Mini Kamboj
- Correspondence: M. Kamboj, 1275 York Ave, New York, NY 10065 ()
| |
Collapse
|
8
|
Luo J, Rizvi H, Preeshagul IR, Egger JV, Hoyos D, Bandlamudi C, Donoghue MT, Łuksza M, Greenbaum BD, Wolchok JD, Kris MG, Hellmann MD. Abstract IA04: COVID-19 in patients with lung cancers in New York City. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.covid-19-ia04] [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: Patients with lung cancers may have distinct vulnerability to severe COVID-19. Understanding the patient-specific and cancer-specific features that impact severity of COVID-19 may inform optimal cancer care during this pandemic. A key question is whether PD-1 blockade therapy impacts COVID-19 severity.
Methods: We identified consecutive patients with lung cancer and a positive SARS-CoV-2 RT-PCR test seen at a single cancer center in New York City. We performed detailed manual review of the disease course, medical and oncologic history. COVID-19 severity outcomes were predefined, including need for hospitalization, ICU/intubation/transition to DNI-status, or death. We examined clinical features associated with severity using single and multivariable analyses. Regarding the impact of PD-1 blockade, we prespecified several bio-plausible comparisons of PD-1 exposure. HLA alleles were inferred from NGS and compared to controls with lung cancer and no known COVID-19.
Results: We identified 102 patients with lung cancers and a SARS-CoV-2 positive swab between March 12, 2020 and May 6, 2020. Patients were followed until May 11, 2020. COVID-19 was severe in patients with lung cancers (62% hospitalized, 25% died), but accounted for only 11% of deaths among patients with lung cancer during the pandemic. Determinants of COVID-19 severity were largely patient specific, including smoking status and chronic obstructive pulmonary disease. Cancer-specific features, including prior thoracic surgery/radiation and recent systemic therapies, did not impact severity. Likelihood of severe COVID-19 was generally similar across HLA class I supertypes. We found no significant differences in the impact of PD-1 blockade on COVID-19 severity. Modest numerical increases in severity of COVID-19 associated with prior PD-1 blockade were diminished (Odds ratio 0.86-1.01) after adjusting for expected imbalances in prior smoking history. Most patients recovered from COVID-19, including 25% of patients initially requiring intubation.
Conclusion: COVID-19 is associated with a high burden of severity in patients with lung cancers. Patient-specific features, rather than cancer-specific features or treatments, were the greatest determinants of severity. In particular, PD-1 blockade did not appear to impact severity of COVID-19 in patients with lung cancers.
Citation Format: Jia Luo, Hira Rizvi, Isabel R. Preeshagul, Jacklynn V. Egger, David Hoyos, Chaitanya Bandlamudi, Mark T.A. Donoghue, Marta Łuksza, Benjamin D. Greenbaum, Jedd D. Wolchok, Mark G. Kris, Matthew D. Hellmann. COVID-19 in patients with lung cancers in New York City [abstract]. In: Proceedings of the AACR Virtual Meeting: COVID-19 and Cancer; 2020 Jul 20-22. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(18_Suppl):Abstract nr IA04.
Collapse
Affiliation(s)
- Jia Luo
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | - Hira Rizvi
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - David Hoyos
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | | | | - Marta Łuksza
- 2Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Mark G. Kris
- 1Memorial Sloan Kettering Cancer Center, New York, NY,
| | | |
Collapse
|
9
|
Ho JSY, Angel M, Ma Y, Sloan E, Wang G, Martinez-Romero C, Alenquer M, Roudko V, Chung L, Zheng S, Chang M, Fstkchyan Y, Clohisey S, Dinan AM, Gibbs J, Gifford R, Shen R, Gu Q, Irigoyen N, Campisi L, Huang C, Zhao N, Jones JD, van Knippenberg I, Zhu Z, Moshkina N, Meyer L, Noel J, Peralta Z, Rezelj V, Kaake R, Rosenberg B, Wang B, Wei J, Paessler S, Wise HM, Johnson J, Vannini A, Amorim MJ, Baillie JK, Miraldi ER, Benner C, Brierley I, Digard P, Łuksza M, Firth AE, Krogan N, Greenbaum BD, MacLeod MK, van Bakel H, Garcìa-Sastre A, Yewdell JW, Hutchinson E, Marazzi I. Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection. Cell 2020; 181:1502-1517.e23. [PMID: 32559462 PMCID: PMC7323901 DOI: 10.1016/j.cell.2020.05.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 03/29/2019] [Revised: 02/26/2020] [Accepted: 05/18/2020] [Indexed: 01/12/2023]
Abstract
RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host transcripts to prime viral mRNA synthesis ("cap-snatching"). We hypothesized that start codons within cap-snatched host transcripts could generate chimeric human-viral mRNAs with coding potential. We report the existence of this mechanism of gene origination, which we named "start-snatching." Depending on the reading frame, start-snatching allows the translation of host and viral "untranslated regions" (UTRs) to create N-terminally extended viral proteins or entirely novel polypeptides by genetic overprinting. We show that both types of chimeric proteins are made in IAV-infected cells, generate T cell responses, and contribute to virulence. Our results indicate that during infection with IAV, and likely a multitude of other human, animal and plant viruses, a host-dependent mechanism allows the genesis of hybrid genes.
Collapse
Affiliation(s)
- Jessica Sook Yuin Ho
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew Angel
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yixuan Ma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elizabeth Sloan
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Guojun Wang
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carles Martinez-Romero
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marta Alenquer
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Vladimir Roudko
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Liliane Chung
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Simin Zheng
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Max Chang
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Yesai Fstkchyan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sara Clohisey
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Adam M Dinan
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - James Gibbs
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Robert Gifford
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Rong Shen
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Laura Campisi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cheng Huang
- Department of Pathology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nan Zhao
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | | | - Zeyu Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Natasha Moshkina
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Léa Meyer
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Justine Noel
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zuleyma Peralta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Veronica Rezelj
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
| | - Robyn Kaake
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Brad Rosenberg
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Wang
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Jiajie Wei
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Slobodan Paessler
- Department of Pathology, the University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Helen M Wise
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Jeffrey Johnson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alessandro Vannini
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK; Fondazione Human Technopole, Structural Biology Research Centre, 20157 Milan, Italy
| | | | - J Kenneth Baillie
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Emily R Miraldi
- Divisions of Immunobiology and Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45257, USA
| | - Christopher Benner
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Paul Digard
- The Roslin Institute, University of Edinburgh, Edinburgh EH25 9PS, UK
| | - Marta Łuksza
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 0SP, UK
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Megan K MacLeod
- Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8QQ, UK
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adolfo Garcìa-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Edward Hutchinson
- MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK.
| | - Ivan Marazzi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
10
|
Luo J, Rizvi H, Preeshagul IR, Egger JV, Hoyos D, Bandlamudi C, McCarthy CG, Falcon CJ, Schoenfeld AJ, Arbour KC, Chaft JE, Daly RM, Drilon A, Eng J, Iqbal A, Lai WV, Li BT, Lito P, Namakydoust A, Ng K, Offin M, Paik PK, Riely GJ, Rudin CM, Yu HA, Zauderer MG, Donoghue MTA, Łuksza M, Greenbaum BD, Kris MG, Hellmann MD. COVID-19 in patients with lung cancer. Ann Oncol 2020; 31:1386-1396. [PMID: 32561401 PMCID: PMC7297689 DOI: 10.1016/j.annonc.2020.06.007] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 06/05/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Patients with lung cancers may have disproportionately severe coronavirus disease 2019 (COVID-19) outcomes. Understanding the patient-specific and cancer-specific features that impact the severity of COVID-19 may inform optimal cancer care during this pandemic. PATIENTS AND METHODS We examined consecutive patients with lung cancer and confirmed diagnosis of COVID-19 (n = 102) at a single center from 12 March 2020 to 6 May 2020. Thresholds of severity were defined a priori as hospitalization, intensive care unit/intubation/do not intubate ([ICU/intubation/DNI] a composite metric of severe disease), or death. Recovery was defined as >14 days from COVID-19 test and >3 days since symptom resolution. Human leukocyte antigen (HLA) alleles were inferred from MSK-IMPACT (n = 46) and compared with controls with lung cancer and no known non-COVID-19 (n = 5166). RESULTS COVID-19 was severe in patients with lung cancer (62% hospitalized, 25% died). Although severe, COVID-19 accounted for a minority of overall lung cancer deaths during the pandemic (11% overall). Determinants of COVID-19 severity were largely patient-specific features, including smoking status and chronic obstructive pulmonary disease [odds ratio for severe COVID-19 2.9, 95% confidence interval 1.07-9.44 comparing the median (23.5 pack-years) to never-smoker and 3.87, 95% confidence interval 1.35-9.68, respectively]. Cancer-specific features, including prior thoracic surgery/radiation and recent systemic therapies did not impact severity. Human leukocyte antigen supertypes were generally similar in mild or severe cases of COVID-19 compared with non-COVID-19 controls. Most patients recovered from COVID-19, including 25% patients initially requiring intubation. Among hospitalized patients, hydroxychloroquine did not improve COVID-19 outcomes. CONCLUSION COVID-19 is associated with high burden of severity in patients with lung cancer. Patient-specific features, rather than cancer-specific features or treatments, are the greatest determinants of severity.
Collapse
Affiliation(s)
- J Luo
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - H Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, USA
| | - I R Preeshagul
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - J V Egger
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, USA
| | - D Hoyos
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C Bandlamudi
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C G McCarthy
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C J Falcon
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, USA
| | - A J Schoenfeld
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - K C Arbour
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - J E Chaft
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - R M Daly
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - A Drilon
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - J Eng
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - A Iqbal
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - W V Lai
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - B T Li
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - P Lito
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - A Namakydoust
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - K Ng
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - M Offin
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - P K Paik
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - G J Riely
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - C M Rudin
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - H A Yu
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - M G Zauderer
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - M T A Donoghue
- Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - M Łuksza
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - B D Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, USA
| | - M G Kris
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA
| | - M D Hellmann
- Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA; Department of Medicine, Weill Cornell Medical Center, New York, USA; Parker Institute for Cancer Immunotherapy at Memorial Sloan Kettering Cancer Center, New York, USA.
| |
Collapse
|
11
|
Abstract
During chronic infection, HIV-1 engages in a rapid coevolutionary arms race with the host's adaptive immune system. While it is clear that HIV exerts strong selection on the adaptive immune system, the characteristics of the somatic evolution that shape the immune response are still unknown. Traditional population genetics methods fail to distinguish chronic immune response from healthy repertoire evolution. Here, we infer the evolutionary modes of B-cell repertoires and identify complex dynamics with a constant production of better B-cell receptor (BCR) mutants that compete, maintaining large clonal diversity and potentially slowing down adaptation. A substantial fraction of mutations that rise to high frequencies in pathogen-engaging CDRs of BCRs are beneficial, in contrast to many such changes in structurally relevant frameworks that are deleterious and circulate by hitchhiking. We identify a pattern where BCRs in patients who experience larger viral expansions undergo stronger selection with a rapid turnover of beneficial mutations due to clonal interference in their CDR3 regions. Using population genetics modeling, we show that the extinction of these beneficial mutations can be attributed to the rise of competing beneficial alleles and clonal interference. The picture is of a dynamic repertoire, where better clones may be outcompeted by new mutants before they fix.
Collapse
Affiliation(s)
- Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-organization, Göttingen, Germany.,Department of Physics, University of Washington, Seattle, WA
| | - Jakub Otwinowski
- Max Planck Institute for Dynamics and Self-organization, Göttingen, Germany
| | - Marta Łuksza
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Thierry Mora
- Laboratoire de Physique Statistique, CNRS, Sorbonne University, Paris-Diderot University, École Normale Supérieure (PSL), Paris, France
| | - Aleksandra M Walczak
- Laboratoire de Physique Théorique, CNRS, Sorbonne University, École Normale Supérieure (PSL), Paris, France
| |
Collapse
|
12
|
Morris DH, Gostic KM, Pompei S, Bedford T, Łuksza M, Neher RA, Grenfell BT, Lässig M, McCauley JW. Predictive Modeling of Influenza Shows the Promise of Applied Evolutionary Biology. Trends Microbiol 2018; 26:102-118. [PMID: 29097090 PMCID: PMC5830126 DOI: 10.1016/j.tim.2017.09.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 01/16/2023]
Abstract
Seasonal influenza is controlled through vaccination campaigns. Evolution of influenza virus antigens means that vaccines must be updated to match novel strains, and vaccine effectiveness depends on the ability of scientists to predict nearly a year in advance which influenza variants will dominate in upcoming seasons. In this review, we highlight a promising new surveillance tool: predictive models. Based on data-sharing and close collaboration between the World Health Organization and academic scientists, these models use surveillance data to make quantitative predictions regarding influenza evolution. Predictive models demonstrate the potential of applied evolutionary biology to improve public health and disease control. We review the state of influenza predictive modeling and discuss next steps and recommendations to ensure that these models deliver upon their considerable biomedical promise.
Collapse
Affiliation(s)
- Dylan H Morris
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
| | - Katelyn M Gostic
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Simone Pompei
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Marta Łuksza
- Institute for Advanced Study, Princeton, NJ, USA
| | - Richard A Neher
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Bryan T Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Michael Lässig
- Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - John W McCauley
- Worldwide Influenza Centre, Francis Crick Institute, London, UK
| |
Collapse
|
13
|
Balachandran VP, Łuksza M, Zhao JN, Makarov V, Moral JA, Remark R, Herbst B, Askan G, Bhanot U, Senbabaoglu Y, Wells DK, Cary CIO, Grbovic-Huezo O, Attiyeh M, Medina B, Zhang J, Loo J, Saglimbeni J, Abu-Akeel M, Zappasodi R, Riaz N, Smoragiewicz M, Kelley ZL, Basturk O, Gönen M, Levine AJ, Allen PJ, Fearon DT, Merad M, Gnjatic S, Iacobuzio-Donahue CA, Wolchok JD, DeMatteo RP, Chan TA, Greenbaum BD, Merghoub T, Leach SD. Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer. Nature 2017; 551:512-516. [PMID: 29132146 PMCID: PMC6145146 DOI: 10.1038/nature24462] [Citation(s) in RCA: 744] [Impact Index Per Article: 106.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/02/2017] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival. Investigating the specific neoantigen qualities promoting T-cell activation in long-term survivors, we discovered that these individuals were enriched in neoantigen qualities defined by a fitness model, and neoantigens in the tumour antigen MUC16 (also known as CA125). A neoantigen quality fitness model conferring greater immunogenicity to neoantigens with differential presentation and homology to infectious disease-derived peptides identified long-term survivors in two independent datasets, whereas a neoantigen quantity model ascribing greater immunogenicity to increasing neoantigen number alone did not. We detected intratumoural and lasting circulating T-cell reactivity to both high-quality and MUC16 neoantigens in long-term survivors of pancreatic cancer, including clones with specificity to both high-quality neoantigens and predicted cross-reactive microbial epitopes, consistent with neoantigen molecular mimicry. Notably, we observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting. Our results identify neoantigens with unique qualities as T-cell targets in pancreatic ductal adenocarcinoma. More broadly, we identify neoantigen quality as a biomarker for immunogenic tumours that may guide the application of immunotherapies.
Collapse
Affiliation(s)
- Vinod P. Balachandran
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marta Łuksza
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Julia N. Zhao
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Alec Moral
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romain Remark
- Tisch Cancer Institute, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Herbst
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gokce Askan
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pathology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umesh Bhanot
- Pathology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yasin Senbabaoglu
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel K. Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | | | - Olivera Grbovic-Huezo
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Attiyeh
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin Medina
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Zhang
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer Loo
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph Saglimbeni
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mohsen Abu-Akeel
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roberta Zappasodi
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Radiation Oncology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martin Smoragiewicz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Z. Larkin Kelley
- Cold Spring Harbor Laboratory, New York, NY, USA. Department of Microbiology and Immunology, Weill Cornell Medical School, New York, NY, USA
| | - Olca Basturk
- Pathology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Mithat Gönen
- Biostatistics Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnold J. Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Peter J. Allen
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas T. Fearon
- Cold Spring Harbor Laboratory, New York, NY, USA. Department of Microbiology and Immunology, Weill Cornell Medical School, New York, NY, USA
| | - Miriam Merad
- Tisch Cancer Institute, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sacha Gnjatic
- Tisch Cancer Institute, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christine A. Iacobuzio-Donahue
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pathology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D. Wolchok
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, Cornell University, New York, NY, USA
- Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ronald P. DeMatteo
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A. Chan
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Radiation Oncology Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin D. Greenbaum
- Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Oncology, Oncological Sciences, and Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Taha Merghoub
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Ludwig Center for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven D. Leach
- Departments of Surgery Memorial Sloan Kettering Cancer Center, New York, NY, USA
- David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
14
|
Łuksza M, Riaz N, Makarov V, Balachandran VP, Hellmann MD, Solovyov A, Rizvi NA, Merghoub T, Levine AJ, Chan TA, Wolchok JD, Greenbaum BD. A neoantigen fitness model predicts tumour response to checkpoint blockade immunotherapy. Nature 2017; 551:517-520. [PMID: 29132144 DOI: 10.1038/nature24473] [Citation(s) in RCA: 449] [Impact Index Per Article: 64.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 10/09/2017] [Indexed: 12/12/2022]
Abstract
Checkpoint blockade immunotherapies enable the host immune system to recognize and destroy tumour cells. Their clinical activity has been correlated with activated T-cell recognition of neoantigens, which are tumour-specific, mutated peptides presented on the surface of cancer cells. Here we present a fitness model for tumours based on immune interactions of neoantigens that predicts response to immunotherapy. Two main factors determine neoantigen fitness: the likelihood of neoantigen presentation by the major histocompatibility complex (MHC) and subsequent recognition by T cells. We estimate these components using the relative MHC binding affinity of each neoantigen to its wild type and a nonlinear dependence on sequence similarity of neoantigens to known antigens. To describe the evolution of a heterogeneous tumour, we evaluate its fitness as a weighted effect of dominant neoantigens in the subclones of the tumour. Our model predicts survival in anti-CTLA-4-treated patients with melanoma and anti-PD-1-treated patients with lung cancer. Importantly, low-fitness neoantigens identified by our method may be leveraged for developing novel immunotherapies. By using an immune fitness model to study immunotherapy, we reveal broad similarities between the evolution of tumours and rapidly evolving pathogens.
Collapse
Affiliation(s)
- Marta Łuksza
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vladimir Makarov
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vinod P Balachandran
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Matthew D Hellmann
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York, USA
| | - Alexander Solovyov
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Naiyer A Rizvi
- Department of Medicine, Columbia University Medical Center, New York, New York, USA
| | - Taha Merghoub
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Arnold J Levine
- The Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, USA
| | - Timothy A Chan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jedd D Wolchok
- Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York, USA.,Melanoma and Immunotherapeutics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Benjamin D Greenbaum
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Medicine, Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
15
|
Lina B, Łuksza M. Is it possible to predict influenza antigenic variants? Virologie (Montrouge) 2017; 21:5-8. [PMID: 31967567 DOI: 10.1684/vir.2017.0678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Bruno Lina
- CNR des virus des infections respiratoires, Institut des agents Iinfectieux, Hôpital de la Croix-Rousse, Groupement hospitalier Nord des HCL, 69317 Lyon cedex 04, CIRI, Virpath, Inserm U1111, CNRS 5308, ENS, UCBL, Faculté de Médecine Lyon Est, 69372 Lyon cedex 08, France
| | - Marta Łuksza
- The Simons Center for Systems Biology, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA
| |
Collapse
|
16
|
Abstract
A new method uses genealogies based on sequence data to predict short-term evolutionary patterns.
Collapse
Affiliation(s)
- Michael Lässig
- Michael Lässig is in the Institute for Theoretical Physics, University of Cologne, Cologne, Germany
| | - Marta Łuksza
- Marta Łuksza is in the Institute for Advanced Study, Princeton University, Princeton, United States
| |
Collapse
|
17
|
Łuksza M, Lässig M, Berg J. Significance analysis and statistical mechanics: an application to clustering. Phys Rev Lett 2010; 105:220601. [PMID: 21231375 DOI: 10.1103/physrevlett.105.220601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2009] [Indexed: 05/30/2023]
Abstract
This Letter addresses the statistical significance of structures in random data: given a set of vectors and a measure of mutual similarity, how likely is it that a subset of these vectors forms a cluster with enhanced similarity among its elements? The computation of this cluster p value for randomly distributed vectors is mapped onto a well-defined problem of statistical mechanics. We solve this problem analytically, establishing a connection between the physics of quenched disorder and multiple-testing statistics in clustering and related problems. In an application to gene expression data, we find a remarkable link between the statistical significance of a cluster and the functional relationships between its genes.
Collapse
Affiliation(s)
- Marta Łuksza
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | | | | |
Collapse
|