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Nichakawade TD, Ge J, Mog BJ, Lee BS, Pearlman AH, Hwang MS, DiNapoli SR, Wyhs N, Marcou N, Glavaris S, Konig MF, Gabelli SB, Watson E, Sterling C, Wagner-Johnston N, Rozati S, Swinnen L, Fuchs E, Pardoll DM, Gabrielson K, Papadopoulos N, Bettegowda C, Kinzler KW, Zhou S, Sur S, Vogelstein B, Paul S. TRBC1-targeting antibody-drug conjugates for the treatment of T cell cancers. Nature 2024; 628:416-423. [PMID: 38538786 DOI: 10.1038/s41586-024-07233-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/16/2024] [Indexed: 04/06/2024]
Abstract
Antibody and chimeric antigen receptor (CAR) T cell-mediated targeted therapies have improved survival in patients with solid and haematologic malignancies1-9. Adults with T cell leukaemias and lymphomas, collectively called T cell cancers, have short survival10,11 and lack such targeted therapies. Thus, T cell cancers particularly warrant the development of CAR T cells and antibodies to improve patient outcomes. Preclinical studies showed that targeting T cell receptor β-chain constant region 1 (TRBC1) can kill cancerous T cells while preserving sufficient healthy T cells to maintain immunity12, making TRBC1 an attractive target to treat T cell cancers. However, the first-in-human clinical trial of anti-TRBC1 CAR T cells reported a low response rate and unexplained loss of anti-TRBC1 CAR T cells13,14. Here we demonstrate that CAR T cells are lost due to killing by the patient's normal T cells, reducing their efficacy. To circumvent this issue, we developed an antibody-drug conjugate that could kill TRBC1+ cancer cells in vitro and cure human T cell cancers in mouse models. The anti-TRBC1 antibody-drug conjugate may provide an optimal format for TRBC1 targeting and produce superior responses in patients with T cell cancers.
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Affiliation(s)
- Tushar D Nichakawade
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Jiaxin Ge
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Brian J Mog
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Bum Seok Lee
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Alexander H Pearlman
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael S Hwang
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Genentech, San Francisco, CA, USA
| | - Sarah R DiNapoli
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nicolas Wyhs
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Nikita Marcou
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Stephanie Glavaris
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Maximilian F Konig
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sandra B Gabelli
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Discovery Chemistry, Merck Research Laboratory, Merck and Co, West Point, PA, USA
| | - Evangeline Watson
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Cole Sterling
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nina Wagner-Johnston
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sima Rozati
- Department of Dermatology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lode Swinnen
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ephraim Fuchs
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathy Gabrielson
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Nickolas Papadopoulos
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Shibin Zhou
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Surojit Sur
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Suman Paul
- Ludwig Center and Lustgarten Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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Douville C, Lahouel K, Kuo A, Grant H, Avigdor BE, Curtis SD, Summers M, Cohen JD, Wang Y, Mattox A, Dudley J, Dobbyn L, Popoli M, Ptak J, Nehme N, Silliman N, Blair C, Romans K, Thoburn C, Gizzi J, Schoen RE, Tie J, Gibbs P, Ho-Pham LT, Tran BNH, Tran TS, Nguyen TV, Goggins M, Wolfgang CL, Wang TL, Shih IM, Lennon AM, Hruban RH, Bettegowda C, Kinzler KW, Papadopoulos N, Vogelstein B, Tomasetti C. Machine learning to detect the SINEs of cancer. Sci Transl Med 2024; 16:eadi3883. [PMID: 38266106 DOI: 10.1126/scitranslmed.adi3883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
We previously described an approach called RealSeqS to evaluate aneuploidy in plasma cell-free DNA through the amplification of ~350,000 repeated elements with a single primer. We hypothesized that an unbiased evaluation of the large amount of sequencing data obtained with RealSeqS might reveal other differences between plasma samples from patients with and without cancer. This hypothesis was tested through the development of a machine learning approach called Alu Profile Learning Using Sequencing (A-PLUS) and its application to 7615 samples from 5178 individuals, 2073 with solid cancer and the remainder without cancer. Samples from patients with cancer and controls were prespecified into four cohorts used for model training, analyte integration, and threshold determination, validation, and reproducibility. A-PLUS alone provided a sensitivity of 40.5% across 11 different cancer types in the validation cohort, at a specificity of 98.5%. Combining A-PLUS with aneuploidy and eight common protein biomarkers detected 51% of the cancers at 98.9% specificity. We found that part of the power of A-PLUS could be ascribed to a single feature-the global reduction of AluS subfamily elements in the circulating DNA of patients with solid cancer. We confirmed this reduction through the analysis of another independent dataset obtained with a different approach (whole-genome sequencing). The evaluation of Alu elements may therefore have the potential to enhance the performance of several methods designed for the earlier detection of cancer.
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Affiliation(s)
- Christopher Douville
- Division of Quantitative Sciences, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kamel Lahouel
- Center for Cancer Prevention and Early Detection, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Prevention and Early Detection, City of Hope, Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Albert Kuo
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Haley Grant
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
| | - Bracha Erlanger Avigdor
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Samuel D Curtis
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mahmoud Summers
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joshua D Cohen
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yuxuan Wang
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Austin Mattox
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan Dudley
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Lisa Dobbyn
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Popoli
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Janine Ptak
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Nadine Nehme
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Natalie Silliman
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Cherie Blair
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Katharine Romans
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Christopher Thoburn
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Jennifer Gizzi
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Robert E Schoen
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
- Department of Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Jeanne Tie
- Division of Personalized Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Oncology, Melbourne, VIC 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3011, Australia
| | - Peter Gibbs
- Division of Personalized Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Oncology, Melbourne, VIC 3000, Australia
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Lan T Ho-Pham
- BioMedical Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City 72510, Vietnam
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
| | - Bich N H Tran
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
| | - Thach S Tran
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
- School of Biomedical Engineering, University of Technology Sydney, NSW 2007, Australia
| | - Tuan V Nguyen
- Saigon Precision Medicine Research Center, Ho Chi Minh City 72512, Vietnam
- School of Biomedical Engineering, University of Technology Sydney, NSW 2007, Australia
- Tâm Anh Research Institute, Ho Chi Minh City, Vietnam
- Centre for Health Technologies, University of Technology, NSW 2007, Australia
- School of Population Health, University of New South Wales, NSW 2003, Australia
| | - Michael Goggins
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Medicine, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Tian-Li Wang
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Ie-Ming Shih
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Gynecology and Obstetrics, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Anne Marie Lennon
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Surgery, Johns Hopkins Medical Institutes, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Ralph H Hruban
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nickolas Papadopoulos
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Center for Cancer Prevention and Early Detection, City of Hope, Duarte, CA 91010, USA
- Center for Cancer Prevention and Early Detection, City of Hope, Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA 91010, USA
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD 21205, USA
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3
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Cook AL, Sur S, Dobbyn L, Watson E, Cohen JD, Ptak B, Lee BS, Paul S, Hsiue E, Popoli M, Vogelstein B, Papadopoulos N, Bettegowda C, Gabrielson K, Zhou S, Kinzler KW, Wyhs N. Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape. bioRxiv 2023:2023.12.28.573594. [PMID: 38234817 PMCID: PMC10793421 DOI: 10.1101/2023.12.28.573594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense- mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen revealed disruption of kinase SMG1's phosphorylation of UPF1 as a potent disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro . Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases. One Sentence Summary Disruption of the nonsense-mediated decay pathway with a newly developed SMG1 inhibitor with in-vivo activity increases the expression of T-cell targetable cancer neoantigens resulting from truncating mutations.
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Chu LC, Ahmed T, Blanco A, Javed A, Weisberg EM, Kawamoto S, Hruban RH, Kinzler KW, Vogelstein B, Fishman EK. Radiologists' Expectations of Artificial Intelligence in Pancreatic Cancer Imaging: How Good Is Good Enough? J Comput Assist Tomogr 2023; 47:845-849. [PMID: 37948357 PMCID: PMC10823576 DOI: 10.1097/rct.0000000000001503] [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] [Indexed: 07/29/2023]
Abstract
BACKGROUND Existing (artificial intelligence [AI]) tools in radiology are modeled without necessarily considering the expectations and experience of the end user-the radiologist. The literature is scarce on the tangible parameters that AI capabilities need to meet for radiologists to consider them useful tools. OBJECTIVE The purpose of this study is to explore radiologists' attitudes toward AI tools in pancreatic cancer imaging and to quantitatively assess their expectations of these tools. METHODS A link to the survey was posted on the www.ctisus.com website, advertised in the www.ctisus.com email newsletter, and publicized on LinkedIn, Facebook, and Twitter accounts. This survey asked participants about their demographics, practice, and current attitudes toward AI. They were also asked about their expectations of what constitutes a clinically useful AI tool. The survey consisted of 17 questions, which included 9 multiple choice questions, 2 Likert scale questions, 4 binary (yes/no) questions, 1 rank order question, and 1 free text question. RESULTS A total of 161 respondents completed the survey, yielding a response rate of 46.3% of the total 348 clicks on the survey link. The minimum acceptable sensitivity of an AI program for the detection of pancreatic cancer chosen by most respondents was either 90% or 95% at a specificity of 95%. The minimum size of pancreatic cancer that most respondents would find an AI useful at detecting was 5 mm. Respondents preferred AI tools that demonstrated greater sensitivity over those with greater specificity. Over half of respondents anticipated incorporating AI tools into their clinical practice within the next 5 years. CONCLUSION Radiologists are open to the idea of integrating AI-based tools and have high expectations regarding the performance of these tools. Consideration of radiologists' input is important to contextualize expectations and optimize clinical adoption of existing and future AI tools.
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Affiliation(s)
- Linda C. Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
| | - Taha Ahmed
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
| | - Alejandra Blanco
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
| | - Ammar Javed
- Department of Surgery, New York University Grossman School of Medicine, New York, NY
| | - Edmund M. Weisberg
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
| | - Satomi Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
| | - Ralph H. Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kenneth W. Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bert Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Elliot K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, Baltimore, Maryland
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5
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Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023; 13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Cell-free DNA (cfDNA) concentrations from patients with cancer are often elevated compared with those of healthy controls, but the sources of this extra cfDNA have never been determined. To address this issue, we assessed cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary and 64 patients without cancer. Eighty-three of these individuals had cfDNA concentrations much greater than those generally observed in healthy subjects. The major contributor of cfDNA in all samples was leukocytes, accounting for ∼76% of cfDNA, with neutrophils predominating. This was true regardless of whether the samples were derived from patients with cancer or the total plasma cfDNA concentration. High levels of cfDNA observed in patients with cancer did not come from either neoplastic cells or surrounding normal epithelial cells from the tumor's tissue of origin. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. SIGNIFICANCE The origin of excess cfDNA in patients with cancer is unknown. Using cfDNA methylation patterns, we determined that neither the tumor nor the surrounding normal tissue contributes this excess cfDNA-rather it comes from leukocytes. This finding suggests that cancers have a systemic impact on cell turnover or DNA clearance. See related commentary by Thierry and Pisareva, p. 2122. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Austin K. Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Steve Lu
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H. Pearlman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kamel Lahouel
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Cristian Tomasetti
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Peiyong Jiang
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K.C. Allen Chan
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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6
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Chan TA, Hermeking H, Lengauer C, Kinzler KW, Vogelstein B. Author Correction: 14-3-3σ is required to prevent mitotic catastrophe after DNA damage. Nature 2023; 621:E28-E29. [PMID: 37626188 DOI: 10.1038/s41586-023-06446-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Affiliation(s)
- Timothy A Chan
- The Johns Hopkins Oncology Center, Program in Human Genetics, and The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424 N. Bond Street, Baltimore, 21231, Maryland, USA
| | - Heiko Hermeking
- The Johns Hopkins Oncology Center, Program in Human Genetics, and The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424 N. Bond Street, Baltimore, 21231, Maryland, USA
| | - Christoph Lengauer
- The Johns Hopkins Oncology Center, Program in Human Genetics, and The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424 N. Bond Street, Baltimore, 21231, Maryland, USA
| | - Kenneth W Kinzler
- The Johns Hopkins Oncology Center, Program in Human Genetics, and The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424 N. Bond Street, Baltimore, 21231, Maryland, USA
| | - Bert Vogelstein
- The Johns Hopkins Oncology Center, Program in Human Genetics, and The Howard Hughes Medical Institute, The Johns Hopkins University School of Medicine, 424 N. Bond Street, Baltimore, 21231, Maryland, USA.
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7
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Wright KM, DiNapoli SR, Miller MS, Aitana Azurmendi P, Zhao X, Yu Z, Chakrabarti M, Shi W, Douglass J, Hwang MS, Hsiue EHC, Mog BJ, Pearlman AH, Paul S, Konig MF, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. Hydrophobic interactions dominate the recognition of a KRAS G12V neoantigen. Nat Commun 2023; 14:5063. [PMID: 37604828 PMCID: PMC10442379 DOI: 10.1038/s41467-023-40821-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 08/10/2023] [Indexed: 08/23/2023] Open
Abstract
Specificity remains a major challenge to current therapeutic strategies for cancer. Mutation associated neoantigens (MANAs) are products of genetic alterations, making them highly specific therapeutic targets. MANAs are HLA-presented (pHLA) peptides derived from intracellular mutant proteins that are otherwise inaccessible to antibody-based therapeutics. Here, we describe the cryo-EM structure of an antibody-MANA pHLA complex. Specifically, we determine a TCR mimic (TCRm) antibody bound to its MANA target, the KRASG12V peptide presented by HLA-A*03:01. Hydrophobic residues appear to account for the specificity of the mutant G12V residue. We also determine the structure of the wild-type G12 peptide bound to HLA-A*03:01, using X-ray crystallography. Based on these structures, we perform screens to validate the key residues required for peptide specificity. These experiments led us to a model for discrimination between the mutant and the wild-type peptides presented on HLA-A*03:01 based exclusively on hydrophobic interactions.
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Affiliation(s)
- Katharine M Wright
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Discovery Chemistry, Protein and Structural Chemistry, Merck & Co, Inc, West Point, PA, 19846, USA
| | - Sarah R DiNapoli
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michelle S Miller
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
| | - P Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
| | - Xiaowei Zhao
- Janelia Research Campus, HHMI,19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Zhiheng Yu
- Janelia Research Campus, HHMI,19700 Helix Drive, Ashburn, VA, 20147, USA
| | - Mayukh Chakrabarti
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - WuXian Shi
- Energy & Photon Sciences Directorate, Brookhaven National Laboratory, Upton, NY, 11973, USA
- Case Center for Synchrotron Biosciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jacqueline Douglass
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Michael S Hwang
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Emily Han-Chung Hsiue
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Novartis Institutes for BioMedical Research, 250 Massachusetts Ave, Cambridge, MA, 02139, USA
| | - Brian J Mog
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander H Pearlman
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Division of Hematologic Malignancies and Bone Marrow Transplantation, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maximilian F Konig
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21224, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Kenneth W Kinzler
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Bert Vogelstein
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shibin Zhou
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Discovery Chemistry, Protein and Structural Chemistry, Merck & Co, Inc, West Point, PA, 19846, USA.
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8
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Douville C, Curtis S, Summers M, Azad TD, Rincon-Torroella J, Wang Y, Mattox A, Avigdor B, Dudley J, Materi J, Raj D, Nair S, Bhanja D, Tuohy K, Dobbyn L, Popoli M, Ptak J, Nehme N, Silliman N, Blair C, Judge K, Gallia GL, Groves M, Jackson CM, Jackson EM, Laterra J, Lim M, Mukherjee D, Weingart J, Naidoo J, Koschmann C, Smith N, Schreck KC, Pardo CA, Glantz M, Holdhoff M, Kinzler KW, Papadopoulos N, Vogelstein B, Bettegowda C. Seq-ing the SINEs of central nervous system tumors in cerebrospinal fluid. Cell Rep Med 2023; 4:101148. [PMID: 37552989 PMCID: PMC10439243 DOI: 10.1016/j.xcrm.2023.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 08/10/2023]
Abstract
It is often challenging to distinguish cancerous from non-cancerous lesions in the brain using conventional diagnostic approaches. We introduce an analytic technique called Real-CSF (repetitive element aneuploidy sequencing in CSF) to detect cancers of the central nervous system from evaluation of DNA in the cerebrospinal fluid (CSF). Short interspersed nuclear elements (SINEs) are PCR amplified with a single primer pair, and the PCR products are evaluated by next-generation sequencing. Real-CSF assesses genome-wide copy-number alterations as well as focal amplifications of selected oncogenes. Real-CSF was applied to 280 CSF samples and correctly identified 67% of 184 cancerous and 96% of 96 non-cancerous brain lesions. CSF analysis was considerably more sensitive than standard-of-care cytology and plasma cell-free DNA analysis in the same patients. Real-CSF therefore has the capacity to be used in combination with other clinical, radiologic, and laboratory-based data to inform the diagnosis and management of patients with suspected cancers of the brain.
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Affiliation(s)
- Christopher Douville
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Samuel Curtis
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mahmoud Summers
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tej D Azad
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Jordina Rincon-Torroella
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Yuxuan Wang
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Austin Mattox
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bracha Avigdor
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jonathan Dudley
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Joshua Materi
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Divyaansh Raj
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Sumil Nair
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Debarati Bhanja
- Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA
| | - Kyle Tuohy
- Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA
| | - Lisa Dobbyn
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maria Popoli
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Janine Ptak
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nadine Nehme
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Natalie Silliman
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Cherie Blair
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kathy Judge
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Gary L Gallia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Mari Groves
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Christopher M Jackson
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Eric M Jackson
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - John Laterra
- Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael Lim
- Department of Neurosurgery, Stanford University, Palo Alto, CA, USA
| | - Debraj Mukherjee
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Jon Weingart
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Carl Koschmann
- Division of Pediatric Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Natalya Smith
- Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA
| | - Karisa C Schreck
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Carlos A Pardo
- Department of Neurology, Johns Hopkins Medical Institutions, Baltimore, MD, USA
| | - Michael Glantz
- Department of Neurosurgery, Pennsylvania State University, Hershey, PA, USA
| | - Matthias Holdhoff
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nickolas Papadopoulos
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
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9
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Rincon-Torroella J, Molin MD, Mog B, Han G, Watson E, Wyhs N, Ishiyama S, Ahmedna T, Minn I, Azad NS, Bettegowda C, Papadopoulos N, Kinzler KW, Zhou S, Vogelstein B, Gabrielson K, Sur S. ME3BP-7 is a targeted cytotoxic agent that rapidly kills pancreatic cancer cells expressing high levels of monocarboxylate transporter MCT1. bioRxiv 2023:2023.07.23.550207. [PMID: 37546808 PMCID: PMC10401962 DOI: 10.1101/2023.07.23.550207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Nearly 30% of Pancreatic ductal adenocarcinoma (PDAC)s exhibit a marked overexpression of Monocarboxylate Transporter 1 (MCT1) offering a unique opportunity for therapy. However, biochemical inhibitors of MCT1 have proven unsuccessful in clinical trials. In this study we present an alternative approach using 3-Bromopyruvate (3BP) to target MCT1 overexpressing PDACs. 3BP is a cytotoxic agent that is known to be transported into cells via MCT1, but its clinical usefulness has been hampered by difficulties in delivering the drug systemically. We describe here a novel microencapsulated formulation of 3BP (ME3BP-7), that is effective against a variety of PDAC cells in vitro and remains stable in serum. Furthermore, systemically administered ME3BP-7 significantly reduces pancreatic cancer growth and metastatic spread in multiple orthotopic models of pancreatic cancer with manageable toxicity. ME3BP-7 is, therefore, a prototype of a promising new drug, in which the targeting moiety and the cytotoxic moiety are both contained within the same single small molecule. One Sentence Summary ME3BP-7 is a novel formulation of 3BP that resists serum degradation and rapidly kills pancreatic cancer cells expressing high levels of MCT1 with tolerable toxicity in mice.
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10
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Wang Y, Douville C, Cohen JD, Mattox A, Curtis S, Silliman N, Popoli M, Ptak J, Dobbyn L, Nehme N, Dudley JC, Summers M, Zhang M, Ho-Pham LT, Tran BNH, Tran TS, Nguyen TV, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B. Detection of rare mutations, copy number alterations, and methylation in the same template DNA molecules. Proc Natl Acad Sci U S A 2023; 120:e2220704120. [PMID: 37014860 PMCID: PMC10104560 DOI: 10.1073/pnas.2220704120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/28/2023] [Indexed: 04/05/2023] Open
Abstract
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To further increase the sensitivity of such assays with limited amounts of sample, it would be useful to be able to evaluate the same template molecules for all these changes. Here, we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The epigenetic and genetic alterations present in the DNA molecules can then be obtained from the original and copied strands, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung, and colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics.
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Affiliation(s)
- Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD21218
| | - Austin Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sam Curtis
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pharmacology and Molecular Science, Johns Hopkins School of Medicine, Baltimore, MD21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Nadine Nehme
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Jonathan C. Dudley
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Mahmoud Summers
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ming Zhang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Lan T. Ho-Pham
- BioMedical Research Center, Pham Ngoc Thach University of Medicine, Ho Chi Minh City72510, Vietnam
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Bich N. H. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
| | - Thach S. Tran
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- School of Biomedical Engineering, University of Technology, NSW2007, Australia
| | - Tuan V. Nguyen
- Clinical Genetics Research Group, Saigon Precision Medicine Research Center, Ho Chi Minh City72512, Vietnam
- Centre for Health Technologies, University of Technology, NSW2007, Australia
- School of Population Health, University of New South Wales, NSW2003, Australia
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD21298
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD21287
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
- HHMI, Baltimore, MD21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD21287
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11
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Wang Y, Douville C, Cohen J, Bettegowda C, Papadopoulos N, Kinzler K, Vogelstein B. Abstract 6609: Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-6609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The analysis of cell-free DNA (cfDNA) from plasma offers great promise for the earlier detection of cancer. At present, changes in DNA sequence, methylation, or copy number are the most sensitive ways to detect the presence of cancer. To increase the sensitivity of such assays, it would be useful to be able evaluate the same template molecules for all these changes. Here we report an approach, called MethylSaferSeqS, that achieves this goal, and can be applied to any standard library preparation method suitable for massively parallel sequencing. The innovative step was to copy both strands of each DNA-barcoded molecule with a primer that allows the subsequent separation of the original strands (retaining their 5-methylcytosine residues) from the copied strands (in which the 5-methylcytosine residues are replaced with unmodified cytosine residues). The original and copied strands are queried for epigenetic and genetic alterations, respectively. We applied this approach to plasma from 265 individuals, including 198 with cancers of the pancreas, ovary, lung or colon, and found the expected patterns of mutations, copy number alterations, and methylation. Furthermore, we could determine which original template DNA molecules were methylated and/or mutated. MethylSaferSeqS should be useful for addressing a variety of questions relating genetics and epigenetics in the future.
Citation Format: Yuxuan Wang, Christopher Douville, Joshua Cohen, Chetan Bettegowda, Nick Papadopoulos, Ken Kinzler, Bert Vogelstein. Detection of rare mutations, copy number variation, and DNA methylation in the same template DNA molecules. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6609.
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12
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Lu S, Mattox AK, Aitana Azurmendi P, Christodoulou I, Wright KM, Popoli M, Chen Z, Sur S, Li Y, Bonifant CL, Bettegowda C, Papadopoulos N, Zhou S, Gabelli SB, Vogelstein B, Kinzler KW. The rapid and highly parallel identification of antibodies with defined biological activities by SLISY. Nat Commun 2023; 14:17. [PMID: 36596784 PMCID: PMC9808734 DOI: 10.1038/s41467-022-35668-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/15/2022] [Indexed: 01/04/2023] Open
Abstract
The therapeutic applications of antibodies are manifold and the emergence of SARS-CoV-2 provides a cogent example of the value of rapidly identifying biologically active antibodies. We describe an approach called SLISY (Sequencing-Linked ImmunoSorbent assaY) that in a single experiment can assess the binding specificity of millions of clones, be applied to any screen that links DNA sequence to a potential binding moiety, and requires only a single round of biopanning. We demonstrate this approach using an scFv library applied to cellular and protein targets to identify specific or broadly reacting antibodies. For a cellular target, we use paired HLA knockout cell lines to identify a panel of antibodies specific to HLA-A3. For a protein target, SLISY identifies 1279 clones that bound to the Receptor Binding Domain of the SARS-CoV-2 spike protein, with >40% of tested clones also neutralizing its interaction with ACE2 in in vitro assays. Using a multi-comparison SLISY against the Beta, Gamma, and Delta variants, we recovered clones that exhibited broad-spectrum neutralizing potential in vitro. By evaluating millions of scFvs simultaneously against multiple targets, SLISY allows the rapid identification of candidate scFvs with defined binding profiles facilitating the identification of antibodies with the desired biological activity.
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Affiliation(s)
- Steve Lu
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Austin K Mattox
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - P Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Ilias Christodoulou
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Katharine M Wright
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Maria Popoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Zan Chen
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Surojit Sur
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Challice L Bonifant
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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13
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Chu LC, Park S, Soleimani S, Fouladi DF, Shayesteh S, He J, Javed AA, Wolfgang CL, Vogelstein B, Kinzler KW, Hruban RH, Afghani E, Lennon AM, Fishman EK, Kawamoto S. Classification of pancreatic cystic neoplasms using radiomic feature analysis is equivalent to an experienced academic radiologist: a step toward computer-augmented diagnostics for radiologists. Abdom Radiol (NY) 2022; 47:4139-4150. [PMID: 36098760 PMCID: PMC10548448 DOI: 10.1007/s00261-022-03663-6] [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: 04/14/2022] [Revised: 08/21/2022] [Accepted: 08/23/2022] [Indexed: 01/18/2023]
Abstract
PURPOSE A wide array of benign and malignant lesions of the pancreas can be cystic and these cystic lesions can have overlapping imaging appearances. The purpose of this study is to compare the diagnostic accuracy of a radiomics-based pancreatic cyst classifier to an experienced academic radiologist. METHODS In this IRB-approved retrospective single-institution study, patients with surgically resected pancreatic cysts who underwent preoperative abdominal CT from 2003 to 2016 were identified. Pancreatic cyst(s) and background pancreas were manually segmented, and 488 radiomics features were extracted. Random forest classification based on radiomics features, age, and gender was evaluated with fourfold cross-validation. An academic radiologist blinded to the final pathologic diagnosis reviewed each case and provided the most likely diagnosis. RESULTS 214 patients were included (64 intraductal papillary mucinous neoplasms, 33 mucinous cystic neoplasms, 60 serous cystadenomas, 24 solid pseudopapillary neoplasms, and 33 cystic neuroendocrine tumors). The radiomics-based machine learning approach showed AUC of 0.940 in pancreatic cyst classification, compared with AUC of 0.895 for the radiologist. CONCLUSION Radiomics-based machine learning achieved equivalent performance as an experienced academic radiologist in the classification of pancreatic cysts. The high diagnostic accuracy can potentially maximize the efficiency of healthcare utilization by maximizing detection of high-risk lesions.
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Affiliation(s)
- Linda C Chu
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Seyoun Park
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sahar Soleimani
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel F Fouladi
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shahab Shayesteh
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ammar A Javed
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Christopher L Wolfgang
- Department of Surgery, New York University Grossman School of Medicine, New York, NY, USA
| | - Bert Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ralph H Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elham Afghani
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anne Marie Lennon
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elliot K Fishman
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Satomi Kawamoto
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Sur S, Rincon-Toroella J, Molin MD, Gabrielson K, Bettegowda C, Zhou S, Kinzler K, Vogelstein B. Abstract B004: sCD-3BP: An MCT-1-“gated” therapeutic for pancreatic adenocarcinoma. Cancer Res 2022. [DOI: 10.1158/1538-7445.panca22-b004] [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: 11/17/2022]
Abstract
Abstract
Metabolic reprogramming is a hallmark of Pancreatic Ductal Adenocarcinomas (PDAC) and offers unique opportunities for therapeutic development. TCGA datasets and pancreatic tissue microarrays reveal that nearly 30% of PDACs exhibit a marked overexpression of Monocarboxylate Transporter 1 (MCT-1), a known lactate/pyruvate transporter. In addition, several clinical studies have correlated MCT-1 expression to poor patient prognosis in other cancers and potential resistance to therapies in PDAC, making MCT-1 an intriguing therapeutic target for pancreatic cancer. In this study, we leverage 3-Bromopyruvate (3BP), a cytotoxic pyruvate analog, to target MCT-1 overexpressing PDACs and optimize it for systemic delivery. First, we establish that the sensitivity of PDAC cells to 3BP correlates to MCT-1 expression. In vitro studies with a panel of pancreatic cancer cell lines highlight that the cytotoxicity of 3BP is limited to PDAC cells with elevated MCT-1 and the mode of action of 3BP is distinctly different from AZD-3965, an MCT-1 inhibitor under clinical investigation. We demonstrate that 3BP exerts its effect on PDAC cells using MCT-1 as gate to enter a cell and then induce cytotoxicity. While 3BP is considered promising, poor serum stability, pharmacokinetics, and excessive in vivo toxicity have hampered its clinical development. We show here, a novel formulation where 3BP is entrapped inside a cyclodextrin cage (sCD-3BP) stabilizes 3BP in vivo, retains its MCT-1 specific activity, and delivers significantly more drug to the tumor with a single dose. Additionally, we show that even short exposures of sCD-3BP are adequate for induction of cell death when compared to current standard-of-care therapeutics such as gemcitabine and components of FOLFIRINOX. Finally, we test our MCT-1 gated approach in multiple in vivo models of pancreatic cancer: an orthotopic pancreatic cancer cell line model and two patient-derived orthotopic xenografts (PDoX) models originating from a primary pancreatic and a metastatic site. Arguably more clinically relevant, the PDoX models used in our study closely mimic clinical features of donor disease, causing significant metastasis to lung and liver, marked invasion into the pancreas, and development of duct-like structures within the tumor. In these models, sCD-3BP significantly reduces pancreatic cancer growth and metastatic spread. In summary, we show that intravenous administration of sCD-3BP is safe, causes no damage to normal tissue and effectively suppresses PDAC tumor growth and reduces metastatic burden. In addition, elucidating the mechanism of action of 3BP allows us to identify potential candidates for this therapy. Our study demonstrates that sCD-3BP can be a powerful therapeutic tool against MCT-1 overexpressed PDACs and present a strong rationale for future human clinical trials.
Citation Format: Surojit Sur, Jordina Rincon-Toroella, Marco Dal Molin, Kathleen Gabrielson, Chetan Bettegowda, Shibin Zhou, Ken Kinzler, Bert Vogelstein. sCD-3BP: An MCT-1-“gated” therapeutic for pancreatic adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B004.
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Affiliation(s)
- Surojit Sur
- 1Johns Hopkins School of Medicine, Baltimore, MD,
| | | | - Marco Dal Molin
- 2University of Maryland School of Medicine, Baltimore, MD
- 1Johns Hopkins School of Medicine, Baltimore, MD,
| | | | | | - Shibin Zhou
- 1Johns Hopkins School of Medicine, Baltimore, MD,
| | - Ken Kinzler
- 1Johns Hopkins School of Medicine, Baltimore, MD,
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Tie J, Cohen J, Lahouel K, Lo S, Wang Y, Wong R, Shapiro J, Harris S, Khattak A, Burge M, Horvath L, Karapetis C, Shannon J, Singh M, Yip D, Papadopoulos N, Tomasetti C, Kinzler K, Vogelstein B, Gibbs P. 318MO Circulating tumour DNA (ctDNA) dynamics, CEA and sites of recurrence for the randomised DYNAMIC study: Adjuvant chemotherapy (ACT) guided by ctDNA analysis in stage II colon cancer (CC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Cook AL, Wyhs N, Sur S, Ptak B, Popoli M, Dobbyn L, Papadopoulos T, Bettegowda C, Papadopoulos N, Vogelstein B, Zhou S, Kinzler KW. An isogenic cell line panel for sequence-based screening of targeted anticancer drugs. iScience 2022; 25:104437. [PMID: 35692635 PMCID: PMC9184558 DOI: 10.1016/j.isci.2022.104437] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/11/2022] [Accepted: 05/18/2022] [Indexed: 12/05/2022] Open
Abstract
We describe the creation of an isogenic cell line panel representing common cancer pathways, with features optimized for high-throughput screening. More than 1,800 cell lines from three normal human cell lines were generated using CRISPR technologies. Surprisingly, most of these lines did not result in complete gene inactivation despite integration of sgRNA at the desired genomic site. A subset of the lines harbored biallelic disruptions of the targeted tumor suppressor gene, yielding a final panel of 100 well-characterized lines covering 19 frequently lost cancer pathways. This panel included genetic markers optimized for sequence-based ratiometric assays for drug-based screening assays. To illustrate the potential utility of this panel, we developed a high-throughput screen that identified Wee1 inhibitor MK-1775 as a selective growth inhibitor of cells with inactivation of TP53. These cell lines and screening approach should prove useful for researchers studying a variety of cellular and biochemical phenomena. Creation of an isogenic cell line panel representing the loss of 19 cancer pathways HTS confirmed MK-1775 as a selective inhibitor of cells with loss of TP53 These cell lines are useful for studying a variety of cellular biochemical phenomena
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Affiliation(s)
- Ashley L. Cook
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Wyhs
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Surojit Sur
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Blair Ptak
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Laura Dobbyn
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
| | - Tasos Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
- Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Corresponding author
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Tie J, Cohen JD, Lahouel K, Lo SN, Wang Y, Kosmider S, Wong R, Shapiro J, Lee M, Harris S, Khattak A, Burge M, Harris M, Lynam J, Nott L, Day F, Hayes T, McLachlan SA, Lee B, Ptak J, Silliman N, Dobbyn L, Popoli M, Hruban R, Lennon AM, Papadopoulos N, Kinzler KW, Vogelstein B, Tomasetti C, Gibbs P. Circulating Tumor DNA Analysis Guiding Adjuvant Therapy in Stage II Colon Cancer. N Engl J Med 2022; 386:2261-2272. [PMID: 35657320 PMCID: PMC9701133 DOI: 10.1056/nejmoa2200075] [Citation(s) in RCA: 279] [Impact Index Per Article: 139.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND The role of adjuvant chemotherapy in stage II colon cancer continues to be debated. The presence of circulating tumor DNA (ctDNA) after surgery predicts very poor recurrence-free survival, whereas its absence predicts a low risk of recurrence. The benefit of adjuvant chemotherapy for ctDNA-positive patients is not well understood. METHODS We conducted a trial to assess whether a ctDNA-guided approach could reduce the use of adjuvant chemotherapy without compromising recurrence risk. Patients with stage II colon cancer were randomly assigned in a 2:1 ratio to have treatment decisions guided by either ctDNA results or standard clinicopathological features. For ctDNA-guided management, a ctDNA-positive result at 4 or 7 weeks after surgery prompted oxaliplatin-based or fluoropyrimidine chemotherapy. Patients who were ctDNA-negative were not treated. The primary efficacy end point was recurrence-free survival at 2 years. A key secondary end point was adjuvant chemotherapy use. RESULTS Of the 455 patients who underwent randomization, 302 were assigned to ctDNA-guided management and 153 to standard management. The median follow-up was 37 months. A lower percentage of patients in the ctDNA-guided group than in the standard-management group received adjuvant chemotherapy (15% vs. 28%; relative risk, 1.82; 95% confidence interval [CI], 1.25 to 2.65). In the evaluation of 2-year recurrence-free survival, ctDNA-guided management was noninferior to standard management (93.5% and 92.4%, respectively; absolute difference, 1.1 percentage points; 95% CI, -4.1 to 6.2 [noninferiority margin, -8.5 percentage points]). Three-year recurrence-free survival was 86.4% among ctDNA-positive patients who received adjuvant chemotherapy and 92.5% among ctDNA-negative patients who did not. CONCLUSIONS A ctDNA-guided approach to the treatment of stage II colon cancer reduced adjuvant chemotherapy use without compromising recurrence-free survival. (Supported by the Australian National Health and Medical Research Council and others; DYNAMIC Australian New Zealand Clinical Trials Registry number, ACTRN12615000381583.).
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Affiliation(s)
- Jeanne Tie
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Joshua D Cohen
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Kamel Lahouel
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Serigne N Lo
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Yuxuan Wang
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Suzanne Kosmider
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Rachel Wong
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Jeremy Shapiro
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Margaret Lee
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Sam Harris
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Adnan Khattak
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Matthew Burge
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Marion Harris
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - James Lynam
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Louise Nott
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Fiona Day
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Theresa Hayes
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Sue-Anne McLachlan
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Belinda Lee
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Janine Ptak
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Natalie Silliman
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Lisa Dobbyn
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Maria Popoli
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Ralph Hruban
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Anne Marie Lennon
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Nicholas Papadopoulos
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Kenneth W Kinzler
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Bert Vogelstein
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Cristian Tomasetti
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
| | - Peter Gibbs
- From the Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research (J.T., R.W., M.L., B.L., P.G.), the Department of Medical Oncology, Peter MacCallum Cancer Centre (J.T., B.L.), the Department of Medical Oncology, Western Health (J.T., S.K., M.L., P.G.), the Faculty of Medicine, Dentistry, and Health Sciences, University of Melbourne (J.T., P.G.), the Department of Medical Oncology, Eastern Health (R.W., M.L.), the Eastern Health Clinical School, Faculty of Medicine, Nursing, and Health Sciences, Monash University (R.W., M.L.), the Department of Medical Oncology, Cabrini Health (J.S.), the Department of Medical Oncology, Monash Health (M.H.), the Department of Medical Oncology, St. Vincent's Hospital (S.-A.M.), and the Department of Medical Oncology, Northern Health (B.L.), Melbourne, VIC, the Research and Biostatistics Group, Melanoma Institute Australia, and the Faculty of Medicine and Health, University of Sydney, Sydney (S.N.L.), the Department of Medical Oncology, Bendigo Health, Bendigo, VIC (S.H.), the Department of Medical Oncology, Fiona Stanley Hospital, and Edith Cowan University, Perth, WA (A.K.), the Department of Medical Oncology, Royal Brisbane and Women's Hospital, and the University of Queensland, Brisbane, QLD (M.B.), Newcastle Private Hospital (J.L.), and the Department of Medical Oncology, Calvary Mater Newcastle Hospital (F.D.), Newcastle, NSW, the Department of Medical Oncology, Royal Hobart Hospital, Hobart, TAS (L.N.), and South West Healthcare, Warrnambool, VIC (T.H.) - all in Australia; the Ludwig Center for Cancer Genetics and Therapeutics (J.D.C., Y.W., J.P., N.S., L.D., M.P., N.P., K.W.K., B.V.), the Division of Biostatistics and Bioinformatics (K.L., C.T.), Department of Oncology, Sidney Kimmel Comprehensive Cancer Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), the Sol Goldman Pancreatic Cancer Research Center (J.D.C., Y.W., J.P., N.S., L.D., M.P., R.H., A.M.L., N.P., K.W.K., B.V.), and the Departments of Pathology (R.H.) and Medicine (A.M.L.), Johns Hopkins University School of Medicine, the Howard Hughes Medical Institute (J.P., N.S., B.V.), the Department of Biomedical Engineering, Johns Hopkins University (J.D.C.), and the Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health (C.T.) - all in Baltimore; and the Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia (S.N.L.)
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18
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Tie J, Cohen J, Lahouel K, Lo SN, Wang Y, Wong R, Shapiro JD, Harris SJ, Khattak MA, Burge ME, Harris M, Lynam JF, Nott LM, Day F, Hayes T, Papadopoulos N, Tomasetti C, Kinzler KW, Vogelstein B, Gibbs P. Adjuvant chemotherapy guided by circulating tumor DNA analysis in stage II colon cancer: The randomized DYNAMIC trial. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.17_suppl.lba100] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
LBA100 Background: The role of adjuvant chemotherapy (CT) in stage II colon cancer continues to be debated. The presence of circulating tumor DNA (ctDNA) after surgery predicts very poor recurrence-free survival (RFS), while its absence predicts a low recurrence risk. For ctDNA-positive cases the benefit of adjuvant CT is unknown. DYNAMIC was designed to assess if a ctDNA-guided approach could reduce the use of adjuvant CT without compromising recurrence risk. Methods: DYNAMIC is a multi-center randomized controlled phase II trial. Eligible patients had resected stage II colon cancer and were suitable for adjuvant CT. Patients were randomly assigned 2:1 to ctDNA-guided management or standard management (clinician-guided based on conventional criteria), after stratification for T stage and participating center location. Criteria for clinical low versus high risk were predefined. The Safe-SeqS tumor-informed personalized ctDNA assay was used. For ctDNA-guided management, a ctDNA-positive result at 4 or 7 weeks after surgery prompted oxaliplatin-based or fluoropyrimidine CT; ctDNA-negative patients were not treated. The primary efficacy endpoint was non-inferiority in RFS rate at 2 years. A key secondary endpoint was adjuvant CT use. The target sample size of 450 provided 80% power with 95% confidence to confirm non-inferiority between the two arms with a margin of 8.5%. Results: Of 455 patients randomized between Aug 2015 and Aug 2019, 302 were assigned to ctDNA-guided and 153 to standard management. Median follow-up was 37 months. In the ctDNA-guided arm, ctDNA analysis was successful in all but three patients; only two patients did not receive ctDNA-guided management. In the intention to treat population, fewer patients overall in the ctDNA-guided arm received adjuvant CT compared to standard management (15.3% vs 27.9%, odds ratio 2.14; P = 0.002), with the largest difference seen in patients with T4 or poorly differentiated tumors (odds ratios 6.22 and 6.31, respectively). Of those who received treatment, oxaliplatin-based doublet was more frequently administered than fluoropyrimidine alone for ctDNA-guided compared to standard management patients (62.2% vs. 9.8%; P < 0.001). ctDNA-guided management was non-inferior to standard management for 2-year RFS (93.5% vs 92.4%, difference 1.1%, 95% confidence interval, -4.1% to 6.2%). Following adjuvant CT, 3-year RFS for ctDNA-positive patients was 86.4%. Without adjuvant CT, 3-year RFS for ctDNA-negative patients was 92.5%, with a 3-year RFS of 96.7% in the clinical low risk subgroup. Conclusions: A ctDNA-guided approach to stage II colon cancer reduced adjuvant chemotherapy use without compromising recurrence-free survival. The low recurrence rate in ctDNA-positive patients who received chemotherapy suggests a survival benefit from adjuvant therapy. ctDNA-negative patients are unlikely to benefit from chemotherapy. Clinical trial information: ACTRN12615000381583.
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Affiliation(s)
- Jeanne Tie
- Peter MacCallum Cancer Centre, University of Melbourne, Walter and Eliza Hall Institute, Melbourne, Australia
| | - Joshua Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Kamel Lahouel
- Division of Biostatistics & Bioinformatics, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore
| | - Serigne N. Lo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Rachel Wong
- Eastern Health & Epworth Healthcare & Eastern Health Clinical School, Monash University, Melbourne, Australia
| | | | | | | | | | | | | | | | - Fiona Day
- Calvary Mater Hospital, Newcastle, Australia
| | | | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine; Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD
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19
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Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EHC, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. TCR-mimic bispecific antibodies to target the HIV-1 reservoir. Proc Natl Acad Sci U S A 2022; 119:e2123406119. [PMID: 35394875 PMCID: PMC9169739 DOI: 10.1073/pnas.2123406119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
HIV-1 infection is incurable due to the persistence of the virus in a latent reservoir of resting memory CD4+ T cells. “Shock-and-kill” approaches that seek to induce HIV-1 gene expression, protein production, and subsequent targeting by the host immune system have been unsuccessful due to a lack of effective latency-reversing agents (LRAs) and kill strategies. In an effort to develop reagents that could be used to promote killing of infected cells, we constructed T cell receptor (TCR)-mimic antibodies to HIV-1 peptide-major histocompatibility complexes (pMHC). Using phage display, we panned for phages expressing antibody-like variable sequences that bound HIV-1 pMHC generated using the common HLA-A*02:01 allele. We targeted three epitopes in Gag and reverse transcriptase identified and quantified via Poisson detection mass spectrometry from cells infected in vitro with a pseudotyped HIV-1 reporter virus (NL4.3 dEnv). Sequences isolated from phages that bound these pMHC were cloned into a single-chain diabody backbone (scDb) sequence, such that one fragment is specific for an HIV-1 pMHC and the other fragment binds to CD3ε, an essential signal transduction subunit of the TCR. Thus, these antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and as agents to promote killing of infected cells. Notably, these scDbs are exquisitely sensitive and specific for the peptide portion of the pMHC. Most importantly, one scDb caused killing of infected cells presenting a naturally processed target pMHC. This work lays the foundation for a novel therapeutic killing strategy toward elimination of the HIV-1 reservoir.
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Affiliation(s)
- Srona Sengupta
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Nathan L. Board
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Fengting Wu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Milica Moskovljevic
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Josephine Zhang
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bruce R. Reinhold
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jonathan Duke-Cohan
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Jeanna Yu
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Madison C. Reed
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Yasmine Tabdili
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Emily J. Fray
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Hao Zhang
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Katharine Jenike
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ya-Chi Ho
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06519
| | - Sandra B. Gabelli
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Janet D. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | - Ellis L. Reinherz
- Laboratory of Immunobiology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Robert F. Siliciano
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
- HHMI, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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20
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Rodriguez Pena MDC, Springer SU, Taheri D, Li L, Tregnago AC, Eich ML, Eltoum IEA, VandenBussche CJ, Papadopoulos N, Kinzler KW, Vogelstein B, Netto GJ. Correction to: Performance of novel non-invasive urine assay UroSEEK in cohorts of equivocal urine cytology. Virchows Arch 2022; 480:719. [PMID: 35178604 DOI: 10.1007/s00428-022-03292-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Maria Del Carmen Rodriguez Pena
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, 21231, USA
| | - Simeon U Springer
- The Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD, 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21231, USA
| | - Diana Taheri
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, 21231, USA.,Department of Pathology, Isfahan Kidney Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Lu Li
- The Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD, 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21231, USA
| | - Aline C Tregnago
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, 21231, USA
| | - Marie-Lisa Eich
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA.,Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, 21231, USA
| | - Isam-Eldin A Eltoum
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | | | - Nickolas Papadopoulos
- The Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD, 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21231, USA
| | - Kenneth W Kinzler
- The Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD, 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21231, USA
| | - Bert Vogelstein
- The Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD, 21231, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, 21231, USA
| | - George J Netto
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA. .,Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD, 21231, USA.
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21
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Hwang MS, Miller MS, Thirawatananond P, Douglass J, Wright KM, Hsiue EHC, Mog BJ, Aytenfisu TY, Murphy MB, Aitana Azurmendi P, Skora AD, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Bettegowda C, Pardoll DM, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. Structural engineering of chimeric antigen receptors targeting HLA-restricted neoantigens. Nat Commun 2021; 12:5271. [PMID: 34489470 PMCID: PMC8421441 DOI: 10.1038/s41467-021-25605-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 08/16/2021] [Indexed: 01/17/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cells have emerged as a promising class of therapeutic agents, generating remarkable responses in the clinic for a subset of human cancers. One major challenge precluding the wider implementation of CAR therapy is the paucity of tumor-specific antigens. Here, we describe the development of a CAR targeting the tumor-specific isocitrate dehydrogenase 2 (IDH2) with R140Q mutation presented on the cell surface in complex with a common human leukocyte antigen allele, HLA-B*07:02. Engineering of the hinge domain of the CAR, as well as crystal structure-guided optimization of the IDH2R140Q-HLA-B*07:02-targeting moiety, enhances the sensitivity and specificity of CARs to enable targeting of this HLA-restricted neoantigen. This approach thus holds promise for the development and optimization of immunotherapies specific to other cancer driver mutations that are difficult to target by conventional means. Chimeric antigen receptor T cells in the clinic currently target cell-type-specific extracellular antigens on malignant cells. Here, authors engineer tumor-specific chimeric antigen receptor T cells that target human leukocyte antigen-presented neoantigens derived from mutant intracellular proteins.
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Affiliation(s)
- Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Genentech, Inc., South San Francisco, CA, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.,Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Puchong Thirawatananond
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Tihitina Y Aytenfisu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - P Aitana Azurmendi
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lilly Biotechnology Center, Eli Lilly and Co, San Diego, CA, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD, USA. .,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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22
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Koenecke A, Powell M, Xiong R, Shen Z, Fischer N, Huq S, Khalafallah AM, Trevisan M, Sparen P, Carrero JJ, Nishimura A, Caffo B, Stuart EA, Bai R, Staedtke V, Thomas DL, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Bettegowda C, Konig MF, Mensh B, Vogelstein JT, Athey S. Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection. ArXiv 2021:arXiv:2004.10117v8. [PMID: 32550250 PMCID: PMC7280904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Revised: 08/02/2021] [Indexed: 06/11/2023]
Abstract
In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor ($\alpha_1$-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n=18,547) and three cohorts with pneumonia (n=400,907). Federated across two ARD cohorts, we find that patients exposed to $\alpha_1$-AR antagonists, as compared to unexposed patients, had a 34% relative risk reduction for mechanical ventilation and death (OR=0.70, p=0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of $\alpha_1$-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.
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23
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Pearlman AH, Hwang MS, Konig MF, Hsiue EHC, Douglass J, DiNapoli SR, Mog BJ, Bettegowda C, Pardoll DM, Gabelli SB, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Author Correction: Targeting public neoantigens for cancer immunotherapy. Nat Cancer 2021; 2:865-867. [PMID: 35122030 PMCID: PMC11003703 DOI: 10.1038/s43018-021-00246-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Genentech, Inc., South San Francisco, CA, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Drew M Pardoll
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Sandra B Gabelli
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
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24
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Tie J, Cohen JD, Wang Y, Christie M, Simons K, Lee M, Wong R, Kosmider S, Ananda S, McKendrick J, Lee B, Cho JH, Faragher I, Jones IT, Ptak J, Schaeffer MJ, Silliman N, Dobbyn L, Li L, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating Tumor DNA Analyses as Markers of Recurrence Risk and Benefit of Adjuvant Therapy for Stage III Colon Cancer. JAMA Oncol 2021; 5:1710-1717. [PMID: 31621801 DOI: 10.1001/jamaoncol.2019.3616] [Citation(s) in RCA: 329] [Impact Index Per Article: 109.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Importance Adjuvant chemotherapy in patients with stage III colon cancer prevents recurrence by eradicating minimal residual disease. However, which patients remain at high risk of recurrence after completing standard adjuvant treatment cannot currently be determined. Postsurgical circulating tumor DNA (ctDNA) analysis can detect minimal residual disease and is associated with recurrence in colorectal cancers. Objective To determine whether serial postsurgical and postchemotherapy ctDNA analysis could provide a real-time indication of adjuvant therapy efficacy in stage III colon cancer. Design, Setting, and Participants This multicenter, Australian, population-based cohort biomarker study recruited 100 consecutive patients with newly diagnosed stage III colon cancer planned for 24 weeks of adjuvant chemotherapy from November 1, 2014, through May 31, 2017. Patients with another malignant neoplasm diagnosed within the last 3 years were excluded. Median duration of follow-up was 28.9 months (range, 11.6-46.4 months). Physicians were blinded to ctDNA results. Data were analyzed from December 10, 2018, through June 23, 2019. Exposures Serial plasma samples were collected after surgery and after chemotherapy. Somatic mutations in individual patients' tumors were identified via massively parallel sequencing of 15 genes commonly mutated in colorectal cancer. Personalized assays were designed to quantify ctDNA. Main Outcomes and Measures Detection of ctDNA and recurrence-free interval (RFI). Results After 4 exclusions, 96 eligible patients were eligible; median patient age was 64 years (range, 26-82 years); 49 (51%) were men. At least 1 somatic mutation was identified in the tumor tissue of all 96 evaluable patients. Circulating tumor DNA was detectable in 20 of 96 (21%) postsurgical samples and was associated with inferior recurrence-free survival (hazard ratio [HR], 3.8; 95% CI, 2.4-21.0; P < .001). Circulating tumor DNA was detectable in 15 of 88 (17%) postchemotherapy samples. The estimated 3-year RFI was 30% when ctDNA was detectable after chemotherapy and 77% when ctDNA was undetectable (HR, 6.8; 95% CI, 11.0-157.0; P < .001). Postsurgical ctDNA status remained independently associated with RFI after adjusting for known clinicopathologic risk factors (HR, 7.5; 95% CI, 3.5-16.1; P < .001). Conclusions and Relevance Results suggest that ctDNA analysis after surgery is a promising prognostic marker in stage III colon cancer. Postchemotherapy ctDNA analysis may define a patient subset that remains at high risk of recurrence despite completing standard adjuvant treatment. This high-risk population presents a unique opportunity to explore additional therapeutic approaches.
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Affiliation(s)
- Jeanne Tie
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Western Health, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Joshua D Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael Christie
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Australia
| | - Koen Simons
- Western Centre for Health, Research and Education, Western Health, Melbourne, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Australia
| | - Margaret Lee
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Western Health, Melbourne, Australia.,Department of Medical Oncology, Eastern Health, Melbourne, Australia
| | - Rachel Wong
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Eastern Health, Melbourne, Australia.,Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Australia
| | - Suzanne Kosmider
- Department of Medical Oncology, Western Health, Melbourne, Australia
| | - Sumitra Ananda
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Western Health, Melbourne, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Joseph McKendrick
- Department of Medical Oncology, Eastern Health, Melbourne, Australia
| | - Belinda Lee
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Jin Hee Cho
- Department of Medical Oncology, Western Health, Melbourne, Australia
| | - Ian Faragher
- Department of Medical Oncology, Western Health, Melbourne, Australia
| | - Ian T Jones
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Mary J Schaeffer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lu Li
- Division of Biostatistics & Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cristian Tomasetti
- Division of Biostatistics & Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Nicholas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kenneth W Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter Gibbs
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia.,Department of Medical Oncology, Western Health, Melbourne, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
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25
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Douville C, Moinova HR, Thota PN, Shaheen NJ, Iyer PG, Canto MI, Wang JS, Dumot JA, Faulx A, Kinzler KW, Papadopoulos N, Vogelstein B, Markowitz SD, Bettegowda C, Willis JE, Chak A. Massively Parallel Sequencing of Esophageal Brushings Enables an Aneuploidy-Based Classification of Patients With Barrett's Esophagus. Gastroenterology 2021; 160:2043-2054.e2. [PMID: 33493502 PMCID: PMC8141353 DOI: 10.1053/j.gastro.2021.01.209] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 10/12/2020] [Revised: 01/04/2021] [Accepted: 01/13/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Aneuploidy has been proposed as a tool to assess progression in patients with Barrett's esophagus (BE), but has heretofore required multiple biopsies. We assessed whether a single esophageal brushing that widely sampled the esophagus could be combined with massively parallel sequencing to characterize aneuploidy and identify patients with disease progression to dysplasia or cancer. METHODS Esophageal brushings were obtained from patients without BE, with non-dysplastic BE (NDBE), low-grade dysplasia (LGD), high-grade dysplasia (HGD), or adenocarcinoma (EAC). To assess aneuploidy, we used RealSeqS, a technique that uses a single primer pair to interrogate ∼350,000 genome-spanning regions and identify specific chromosome arm alterations. A classifier to distinguish NDBE from EAC was trained on results from 79 patients. An independent validation cohort of 268 subjects was used to test the classifier at distinguishing patients at successive phases of BE progression. RESULTS Aneuploidy progression was associated with gains of 1q, 12p, and 20q and losses on 9p and 17p. The entire chromosome 8q was often gained in NDBE, whereas focal gain of 8q24 was identified only when there was dysplasia. Among validation subjects, a classifier incorporating these features with a global measure of aneuploidy scored positive in 96% of EAC, 68% of HGD, but only 7% of NDBE. CONCLUSIONS RealSeqS analysis of esophageal brushings provides a practical and sensitive method to determine aneuploidy in BE patients. It identifies specific chromosome changes that occur early in NDBE and others that occur late and mark progression to dysplasia. The clinical implications of this approach can now be tested in prospective trials.
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Affiliation(s)
- Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Helen R Moinova
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Prashanthi N Thota
- Department of Gastroenterology and Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Department of Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Marcia Irene Canto
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jean S Wang
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - John A Dumot
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Ashley Faulx
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio
| | - Kenneth W Kinzler
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bert Vogelstein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sanford D Markowitz
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.
| | - Chetan Bettegowda
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph E Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio; Department of Pathology, Case Western Reserve University, Cleveland, Ohio
| | - Amitabh Chak
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio; Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio; Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio.
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26
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Rose L, Graham L, Koenecke A, Powell M, Xiong R, Shen Z, Mench B, Kinzler KW, Bettegowda C, Vogelstein B, Athey S, Vogelstein JT, Konig MF, Wagner TH. The Association Between Alpha-1 Adrenergic Receptor Antagonists and In-Hospital Mortality From COVID-19. Front Med (Lausanne) 2021; 8:637647. [PMID: 33869251 PMCID: PMC8048524 DOI: 10.3389/fmed.2021.637647] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
Effective therapies for coronavirus disease 2019 (COVID-19) are urgently needed, and pre-clinical data suggest alpha-1 adrenergic receptor antagonists (α1-AR antagonists) may be effective in reducing mortality related to hyperinflammation independent of etiology. Using a retrospective cohort design with patients in the Department of Veterans Affairs healthcare system, we use doubly robust regression and matching to estimate the association between baseline use of α1-AR antagonists and likelihood of death due to COVID-19 during hospitalization. Having an active prescription for any α1-AR antagonist (tamsulosin, silodosin, prazosin, terazosin, doxazosin, or alfuzosin) at the time of admission had a significant negative association with in-hospital mortality (relative risk reduction 18%; odds ratio 0.73; 95% CI 0.63–0.85; p ≤ 0.001) and death within 28 days of admission (relative risk reduction 17%; odds ratio 0.74; 95% CI 0.65–0.84; p ≤ 0.001). In a subset of patients on doxazosin specifically, an inhibitor of all three alpha-1 adrenergic receptors, we observed a relative risk reduction for death of 74% (odds ratio 0.23; 95% CI 0.03–0.94; p = 0.028) compared to matched controls not on any α1-AR antagonist at the time of admission. These findings suggest that use of α1-AR antagonists may reduce mortality in COVID-19, supporting the need for randomized, placebo-controlled clinical trials in patients with early symptomatic infection.
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Affiliation(s)
- Liam Rose
- Department of Veterans Affairs Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, United States
| | - Laura Graham
- Department of Veterans Affairs Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, United States
| | - Allison Koenecke
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, United States
| | - Michael Powell
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, United States
| | - Ruoxuan Xiong
- Department of Management Science and Engineering, Stanford University, Stanford, CA, United States
| | - Zhu Shen
- Department of Statistics, Stanford University, Stanford, CA, United States
| | - Brett Mench
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, United States
| | - Kenneth W Kinzler
- Lustgarten Laboratory, Ludwig Center, Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, United States
| | - Chetan Bettegowda
- Lustgarten Laboratory, Ludwig Center, Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, United States.,Department of Neurosurgery and Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Bert Vogelstein
- Lustgarten Laboratory, Ludwig Center, Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, United States
| | - Susan Athey
- Stanford Graduate School of Business, Stanford University, Stanford, CA, United States
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, United States.,Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health at The Johns Hopkins University, Baltimore, MD, United States
| | - Maximilian F Konig
- Lustgarten Laboratory, Ludwig Center, Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, United States.,Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Todd H Wagner
- Department of Veterans Affairs Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, United States.,Department of Surgery, Stanford University, Stanford, CA, United States
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27
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Hwang MS, Mog BJ, Douglass J, Pearlman AH, Hsiue EHC, Paul S, DiNapoli SR, Konig MF, Pardoll DM, Gabelli SB, Bettegowda C, Papadopoulos N, Vogelstein B, Zhou S, Kinzler KW. Targeting loss of heterozygosity for cancer-specific immunotherapy. Proc Natl Acad Sci U S A 2021; 118:e2022410118. [PMID: 33731480 PMCID: PMC8000272 DOI: 10.1073/pnas.2022410118] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Developing therapeutic agents with potent antitumor activity that spare normal tissues remains a significant challenge. Clonal loss of heterozygosity (LOH) is a widespread and irreversible genetic alteration that is exquisitely specific to cancer cells. We hypothesized that LOH events can be therapeutically targeted by "inverting" the loss of an allele in cancer cells into an activating signal. Here we describe a proof-of-concept approach utilizing engineered T cells approximating NOT-gate Boolean logic to target counterexpressed antigens resulting from LOH events in cancer. The NOT gate comprises a chimeric antigen receptor (CAR) targeting the allele of human leukocyte antigen (HLA) that is retained in the cancer cells and an inhibitory CAR (iCAR) targeting the HLA allele that is lost in the cancer cells. We demonstrate that engineered T cells incorporating such NOT-gate logic can be activated in a genetically predictable manner in vitro and in mice to kill relevant cancer cells. This therapeutic approach, termed NASCAR (Neoplasm-targeting Allele-Sensing CAR), could, in theory, be extended to LOH of other polymorphic genes that result in altered cell surface antigens in cancers.
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Affiliation(s)
- Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- HHMI, Chevy Chase, MD 20815
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287;
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287;
- Lustgarten Laboratory for Pancreatic Cancer Research, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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28
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Paul S, Pearlman AH, Douglass J, Mog BJ, Hsiue EHC, Hwang MS, DiNapoli SR, Konig MF, Brown PA, Wright KM, Sur S, Gabelli SB, Li Y, Ghiaur G, Pardoll DM, Papadopoulos N, Bettegowda C, Kinzler KW, Zhou S, Vogelstein B. TCR β chain-directed bispecific antibodies for the treatment of T cell cancers. Sci Transl Med 2021; 13:eabd3595. [PMID: 33649188 PMCID: PMC8236299 DOI: 10.1126/scitranslmed.abd3595] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 12/27/2022]
Abstract
Immunotherapies such as chimeric antigen receptor (CAR) T cells and bispecific antibodies redirect healthy T cells to kill cancer cells expressing the target antigen. The pan-B cell antigen-targeting immunotherapies have been remarkably successful in treating B cell malignancies. Such therapies also result in the near-complete loss of healthy B cells, but this depletion is well tolerated by patients. Although analogous targeting of pan-T cell markers could, in theory, help control T cell cancers, the concomitant healthy T cell depletion would result in severe and unacceptable immunosuppression. Thus, therapies directed against T cell cancers require more selective targeting. Here, we describe an approach to target T cell cancers through T cell receptor (TCR) antigens. Each T cell, normal or malignant, expresses a unique TCR β chain generated from 1 of 30 TCR β chain variable gene families (TRBV1 to TRBV30). We hypothesized that bispecific antibodies targeting a single TRBV family member expressed in malignant T cells could promote killing of these cancer cells, while preserving healthy T cells that express any of the other 29 possible TRBV family members. We addressed this hypothesis by demonstrating that bispecific antibodies targeting TRBV5-5 (α-V5) or TRBV12 (α-V12) specifically lyse relevant malignant T cell lines and patient-derived T cell leukemias in vitro. Treatment with these antibodies also resulted in major tumor regressions in mouse models of human T cell cancers. This approach provides an off-the-shelf, T cell cancer selective targeting approach that preserves enough healthy T cells to maintain cellular immunity.
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Affiliation(s)
- Suman Paul
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Alexander H Pearlman
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Brian J Mog
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Emily Han-Chung Hsiue
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Michael S Hwang
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Patrick A Brown
- Division of Pediatric Oncology, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Surojit Sur
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Gabriel Ghiaur
- Hematologic Malignancies and Bone Marrow Transplantation Program, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Nickolas Papadopoulos
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Chetan Bettegowda
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Kenneth W Kinzler
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Shibin Zhou
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA.
- Howard Hughes Medical Institute, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Ludwig Center and Lustgarten Laboratory, at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
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29
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Hsiue EHC, Wright KM, Douglass J, Hwang MS, Mog BJ, Pearlman AH, Paul S, DiNapoli SR, Konig MF, Wang Q, Schaefer A, Miller MS, Skora AD, Azurmendi PA, Murphy MB, Liu Q, Watson E, Li Y, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Gabelli SB, Zhou S. Targeting a neoantigen derived from a common TP53 mutation. Science 2021; 371:eabc8697. [PMID: 33649166 PMCID: PMC8208645 DOI: 10.1126/science.abc8697] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/30/2020] [Accepted: 02/05/2021] [Indexed: 12/12/2022]
Abstract
TP53 (tumor protein p53) is the most commonly mutated cancer driver gene, but drugs that target mutant tumor suppressor genes, such as TP53, are not yet available. Here, we describe the identification of an antibody highly specific to the most common TP53 mutation (R175H, in which arginine at position 175 is replaced with histidine) in complex with a common human leukocyte antigen-A (HLA-A) allele on the cell surface. We describe the structural basis of this specificity and its conversion into an immunotherapeutic agent: a bispecific single-chain diabody. Despite the extremely low p53 peptide-HLA complex density on the cancer cell surface, the bispecific antibody effectively activated T cells to lyse cancer cells that presented the neoantigen in vitro and in mice. This approach could in theory be used to target cancers containing mutations that are difficult to target in conventional ways.
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Affiliation(s)
- Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Qing Wang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Complete Omics, Baltimore, MD 21227, USA
| | - Annika Schaefer
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - P Aitana Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | | | - Qiang Liu
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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30
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Douglass J, Hsiue EHC, Mog BJ, Hwang MS, DiNapoli SR, Pearlman AH, Miller MS, Wright KM, Azurmendi PA, Wang Q, Paul S, Schaefer A, Skora AD, Molin MD, Konig MF, Liu Q, Watson E, Li Y, Murphy MB, Pardoll DM, Bettegowda C, Papadopoulos N, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S. Bispecific antibodies targeting mutant RAS neoantigens. Sci Immunol 2021; 6:6/57/eabd5515. [PMID: 33649101 DOI: 10.1126/sciimmunol.abd5515] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
Mutations in the RAS oncogenes occur in multiple cancers, and ways to target these mutations has been the subject of intense research for decades. Most of these efforts are focused on conventional small-molecule drugs rather than antibody-based therapies because the RAS proteins are intracellular. Peptides derived from recurrent RAS mutations, G12V and Q61H/L/R, are presented on cancer cells in the context of two common human leukocyte antigen (HLA) alleles, HLA-A3 and HLA-A1, respectively. Using phage display, we isolated single-chain variable fragments (scFvs) specific for each of these mutant peptide-HLA complexes. The scFvs did not recognize the peptides derived from the wild-type form of RAS proteins or other related peptides. We then sought to develop an immunotherapeutic agent that was capable of killing cells presenting very low levels of these RAS-derived peptide-HLA complexes. Among many variations of bispecific antibodies tested, one particular format, the single-chain diabody (scDb), exhibited superior reactivity to cells expressing low levels of neoantigens. We converted the scFvs to this scDb format and demonstrated that they were capable of inducing T cell activation and killing of target cancer cells expressing endogenous levels of the mutant RAS proteins and cognate HLA alleles. CRISPR-mediated alterations of the HLA and RAS genes provided strong genetic evidence for the specificity of the scDbs. Thus, this approach could be applied to other common oncogenic mutations that are difficult to target by conventional means, allowing for more specific anticancer therapeutics.
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Affiliation(s)
- Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - P Aitana Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Qing Wang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Complete Omics Inc., Baltimore, MD 21227, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Annika Schaefer
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Marco Dal Molin
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Surgery, University of Maryland Medical Center, Baltimore, MD 21201, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Qiang Liu
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yana Li
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Drew M Pardoll
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sandra B Gabelli
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. .,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA. .,Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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Rose L, Graham L, Koenecke A, Powell M, Xiong R, Shen Z, Kinzler KW, Bettegowda C, Vogelstein B, Athey S, Vogelstein JT, Konig MF, Wagner TH. The Association Between Alpha-1 Adrenergic Receptor Antagonists and In-Hospital Mortality from COVID-19. medRxiv 2021. [PMID: 33398294 PMCID: PMC7781337 DOI: 10.1101/2020.12.18.20248346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Effective therapies for coronavirus disease 2019 (COVID-19) are urgently needed, and preclinical data suggest alpha-1 adrenergic receptor antagonists (α1-AR antagonists) may be effective in reducing mortality related to hyperinflammation independent of etiology. Using a retrospective cohort design with patients in the Department of Veterans Affairs healthcare system, we use doubly robust regression and matching to estimate the association between baseline use of α1-AR antagonists and likelihood of death due to COVID-19 during hospitalization. Having an active prescription for any α1-AR antagonist (tamsulosin, silodosin, prazosin, terazosin, doxazosin, or alfuzosin) at the time of admission had a significant negative association with in-hospital mortality (relative risk reduction 18%; odds ratio 0.73; 95% CI 0.63 to 0.85; p ≤ 0.001) and death within 28 days of admission (relative risk reduction 17%; odds ratio 0.74; 95% CI 0.65 to 0.84; p ≤ 0.001). In a subset of patients on doxazosin specifically, an inhibitor of all three alpha-1 adrenergic receptors, we observed a relative risk reduction for death of 74% (odds ratio 0.23; 95% CI 0.03 to 0.94; p = 0.028) compared to matched controls not on any α1-AR antagonist at the time of admission. These findings suggest that use of α1-AR antagonists may reduce mortality in COVID-19, supporting the need for randomized, placebo-controlled clinical trials in patients with early symptomatic infection.
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Affiliation(s)
- Liam Rose
- VA Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, USA
| | - Laura Graham
- VA Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, USA
| | - Allison Koenecke
- Institute for Computational & Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Michael Powell
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA
| | - Ruoxuan Xiong
- Management Science & Engineering, Stanford University, Stanford, CA, USA
| | - Zhu Shen
- Department of Statistics, Stanford University, Stanford, CA, USA
| | - Kenneth W Kinzler
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA
| | - Chetan Bettegowda
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA.,The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bert Vogelstein
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA
| | - Susan Athey
- Stanford Graduate School of Business, Stanford University, Stanford, CA, USA
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, MD, USA.,Department of Biostatistics, The Johns Hopkins Bloomberg School of Public Health at The Johns Hopkins University, Baltimore, MD, USA
| | - Maximilian F Konig
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer Center, Baltimore, MD, USA.,Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, US
| | - Todd H Wagner
- VA Health Economics Resource Center, Palo Alto VA, Menlo Park, CA, USA.,Department of Surgery, Stanford University, Stanford, CA, USA
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32
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Thomsen RW, Christiansen CF, Heide-Jørgensen U, Vogelstein JT, Vogelstein B, Bettegowda C, Tamang S, Athey S, Sørensen HT. Association of α1-Blocker Receipt With 30-Day Mortality and Risk of Intensive Care Unit Admission Among Adults Hospitalized With Influenza or Pneumonia in Denmark. JAMA Netw Open 2021; 4:e2037053. [PMID: 33566109 PMCID: PMC7876591 DOI: 10.1001/jamanetworkopen.2020.37053] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
IMPORTANCE Alpha 1-adrenergic receptor blocking agents (α1-blockers) have been reported to have protective benefits against hyperinflammation and cytokine storm syndrome, conditions that are associated with mortality in patients with coronavirus disease 2019 and other severe respiratory tract infections. However, studies of the association of α1-blockers with outcomes among human participants with respiratory tract infections are scarce. OBJECTIVE To examine the association between the receipt of α1-blockers and outcomes among adult patients hospitalized with influenza or pneumonia. DESIGN, SETTING, AND PARTICIPANTS This population-based cohort study used data from Danish national registries to identify individuals 40 years and older who were hospitalized with influenza or pneumonia between January 1, 2005, and November 30, 2018, with follow-up through December 31, 2018. In the main analyses, patients currently receiving α1-blockers were compared with those not receiving α1-blockers (defined as patients with no prescription for an α1-blocker filled within 365 days before the index date) and those currently receiving 5α-reductase inhibitors. Propensity scores were used to address confounding factors and to compute weighted risks, absolute risk differences, and risk ratios. Data were analyzed from April 21 to December 21, 2020. EXPOSURES Current receipt of α1-blockers compared with nonreceipt of α1-blockers and with current receipt of 5α-reductase inhibitors. MAIN OUTCOMES AND MEASURES Death within 30 days of hospital admission and risk of intensive care unit (ICU) admission. RESULTS A total of 528 467 adult patients (median age, 75.0 years; interquartile range, 64.4-83.6 years; 273 005 men [51.7%]) were hospitalized with influenza or pneumonia in Denmark between 2005 and 2018. Of those, 21 772 patients (4.1%) were currently receiving α1-blockers compared with a population of 22 117 patients not receiving α1-blockers who were weighted to the propensity score distribution of those receiving α1-blockers. In the propensity score-weighted analyses, patients receiving α1-blockers had lower 30-day mortality (15.9%) compared with patients not receiving α1-blockers (18.5%), with a corresponding risk difference of -2.7% (95% CI, -3.2% to -2.2%) and a risk ratio (RR) of 0.85 (95% CI, 0.83-0.88). The risk of ICU admission was 7.3% among patients receiving α1-blockers and 7.7% among those not receiving α1-blockers (risk difference, -0.4% [95% CI, -0.8% to 0%]; RR, 0.95 [95% CI, 0.90-1.00]). A comparison between 18 280 male patients currently receiving α1-blockers and 18 228 propensity score-weighted male patients currently receiving 5α-reductase inhibitors indicated that those receiving α1-blockers had lower 30-day mortality (risk difference, -2.0% [95% CI, -3.4% to -0.6%]; RR, 0.89 [95% CI, 0.82-0.96]) and a similar risk of ICU admission (risk difference, -0.3% [95% CI, -1.4% to 0.7%]; RR, 0.96 [95% CI, 0.83-1.10]). CONCLUSIONS AND RELEVANCE This cohort study's findings suggest that the receipt of α1-blockers is associated with protective benefits among adult patients hospitalized with influenza or pneumonia.
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Affiliation(s)
- Reimar W. Thomsen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Uffe Heide-Jørgensen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
| | - Joshua T. Vogelstein
- Department of Biomedical Engineering, Institute of Computational Medicine, Johns Hopkins University, Baltimore, Maryland
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Bert Vogelstein
- Ludwig Center, Lustgarten Laboratory, Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Chetan Bettegowda
- Ludwig Center, Lustgarten Laboratory, Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Suzanne Tamang
- Center for Population Health and Sciences, Stanford University, Stanford, California
| | - Susan Athey
- Stanford Graduate School of Business, Stanford University, Stanford, California
| | - Henrik Toft Sørensen
- Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, Denmark
- Center for Population Health and Sciences, Stanford University, Stanford, California
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33
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Afsari B, Kuo A, Zhang Y, Li L, Lahouel K, Danilova L, Favorov A, Rosenquist TA, Grollman AP, Kinzler KW, Cope L, Vogelstein B, Tomasetti C. Supervised mutational signatures for obesity and other tissue-specific etiological factors in cancer. eLife 2021; 10:61082. [PMID: 33491650 PMCID: PMC7872524 DOI: 10.7554/elife.61082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Determining the etiologic basis of the mutations that are responsible for cancer is one of the fundamental challenges in modern cancer research. Different mutational processes induce different types of DNA mutations, providing 'mutational signatures' that have led to key insights into cancer etiology. The most widely used signatures for assessing genomic data are based on unsupervised patterns that are then retrospectively correlated with certain features of cancer. We show here that supervised machine-learning techniques can identify signatures, called SuperSigs, that are more predictive than those currently available. Surprisingly, we found that aging yields different SuperSigs in different tissues, and the same is true for environmental exposures. We were able to discover SuperSigs associated with obesity, the most important lifestyle factor contributing to cancer in Western populations.
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Affiliation(s)
- Bahman Afsari
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Albert Kuo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - YiFan Zhang
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Lu Li
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Kamel Lahouel
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Ludmila Danilova
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | - Alexander Favorov
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russian Federation
| | | | - Arthur P Grollman
- State University of New York at Stony Brook, Stony Brook, United States
| | - Ken W Kinzler
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Leslie Cope
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Bert Vogelstein
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, United States
| | - Cristian Tomasetti
- Division of Biostatistics and Bioinformatics, Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
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Koenecke A, Powell M, Xiong R, Shen Z, Fischer N, Huq S, Khalafallah AM, Trevisan M, Sparen P, Carrero JJ, Nishimura A, Caffo B, Stuart EA, Bai R, Staedtke V, Thomas DL, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Bettegowda C, Konig MF, Mensh BD, Vogelstein JT, Athey S. Alpha-1 adrenergic receptor antagonists to prevent hyperinflammation and death from lower respiratory tract infection. eLife 2021; 10:61700. [PMID: 34114951 PMCID: PMC8195605 DOI: 10.7554/elife.61700] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 05/11/2021] [Indexed: 01/16/2023] Open
Abstract
In severe viral pneumonia, including Coronavirus disease 2019 (COVID-19), the viral replication phase is often followed by hyperinflammation, which can lead to acute respiratory distress syndrome, multi-organ failure, and death. We previously demonstrated that alpha-1 adrenergic receptor (⍺1-AR) antagonists can prevent hyperinflammation and death in mice. Here, we conducted retrospective analyses in two cohorts of patients with acute respiratory distress (ARD, n = 18,547) and three cohorts with pneumonia (n = 400,907). Federated across two ARD cohorts, we find that patients exposed to ⍺1-AR antagonists, as compared to unexposed patients, had a 34% relative risk reduction for mechanical ventilation and death (OR = 0.70, p = 0.021). We replicated these methods on three pneumonia cohorts, all with similar effects on both outcomes. All results were robust to sensitivity analyses. These results highlight the urgent need for prospective trials testing whether prophylactic use of ⍺1-AR antagonists ameliorates lower respiratory tract infection-associated hyperinflammation and death, as observed in COVID-19.
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Affiliation(s)
- Allison Koenecke
- Institute for Computational & Mathematical Engineering, Stanford UniversityStanfordUnited States
| | - Michael Powell
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins UniversityBaltimoreUnited States
| | - Ruoxuan Xiong
- Management Science & Engineering, Stanford UniversityStanfordUnited States
| | - Zhu Shen
- Department of Statistics, Stanford UniversityStanfordUnited States
| | - Nicole Fischer
- The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Sakibul Huq
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Adham M Khalafallah
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Marco Trevisan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Pär Sparen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Juan J Carrero
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, SwedenSolnaSweden
| | - Akihiko Nishimura
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Brian Caffo
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Elizabeth A Stuart
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Renyuan Bai
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Verena Staedtke
- Department of Neurosurgery and Neurology, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - David L Thomas
- The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Nickolas Papadopoulos
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Ken W Kinzler
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Bert Vogelstein
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Shibin Zhou
- Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Chetan Bettegowda
- The Johns Hopkins University School of MedicineBaltimoreUnited States,Ludwig Center, Lustgarten Laboratory, and the Howard Hughes Medical Institute at The Johns Hopkins Kimmel Cancer CenterBaltimoreUnited States
| | - Maximilian F Konig
- Division of Rheumatology, Department of Medicine, The Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Joshua T Vogelstein
- Department of Biomedical Engineering, Institute for Computational Medicine, The Johns Hopkins UniversityBaltimoreUnited States,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health at Johns Hopkins UniversityBaltimoreUnited States
| | - Susan Athey
- Stanford Graduate School of Business, Stanford UniversityStanfordUnited States
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Tie J, Cohen JD, Lo SN, Wang Y, Li L, Christie M, Lee M, Wong R, Kosmider S, Skinner I, Wong HL, Lee B, Burge ME, Yip D, Karapetis CS, Price TJ, Tebbutt NC, Haydon AM, Ptak J, Schaeffer MJ, Silliman N, Dobbyn L, Popoli M, Tomasetti C, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Prognostic significance of postsurgery circulating tumor DNA in nonmetastatic colorectal cancer: Individual patient pooled analysis of three cohort studies. Int J Cancer 2020; 148:1014-1026. [PMID: 32984952 DOI: 10.1002/ijc.33312] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 06/18/2020] [Revised: 08/15/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023]
Abstract
Studies in multiple solid tumor types have demonstrated the prognostic significance of ctDNA analysis after curative intent surgery. A combined analysis of data across completed studies could further our understanding of circulating tumor DNA (ctDNA) as a prognostic marker and inform future trial design. We combined individual patient data from three independent cohort studies of nonmetastatic colorectal cancer (CRC). Plasma samples were collected 4 to 10 weeks after surgery. Mutations in ctDNA were assayed using a massively parallel sequencing technique called SafeSeqS. We analyzed 485 CRC patients (230 Stage II colon, 96 Stage III colon, and 159 locally advanced rectum). ctDNA was detected after surgery in 59 (12%) patients overall (11.0%, 12.5% and 13.8% for samples taken at 4-6, 6-8 and 8-10 weeks; P = .740). ctDNA detection was associated with poorer 5-year recurrence-free (38.6% vs 85.5%; P < .001) and overall survival (64.6% vs 89.4%; P < .001). The predictive accuracy of postsurgery ctDNA for recurrence was higher than that of individual clinicopathologic risk features. Recurrence risk increased exponentially with increasing ctDNA mutant allele frequency (MAF) (hazard ratio, 1.2, 2.5 and 5.8 for MAF of 0.1%, 0.5% and 1%). Postsurgery ctDNA was detected in 3 of 20 (15%) patients with locoregional and 27 of 60 (45%) with distant recurrence (P = .018). This analysis demonstrates a consistent long-term impact of ctDNA as a prognostic marker across nonmetastatic CRC, where ctDNA outperforms other clinicopathologic risk factors and MAF further stratifies recurrence risk. ctDNA is a better predictor of distant vs locoregional recurrence.
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Affiliation(s)
- Jeanne Tie
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua D Cohen
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Serigne N Lo
- Melanoma Institute Australia, The University of Sydney, North Sydney, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - Yuxuan Wang
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Lu Li
- Division of Biostatistics & Bioinformatics, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Michael Christie
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia.,Department of Pathology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Margaret Lee
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia.,Department of Medical Oncology, Eastern Health, Melbourne, Victoria, Australia.,Eastern Health Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Rachel Wong
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Eastern Health, Melbourne, Victoria, Australia.,Eastern Health Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, Victoria, Australia
| | - Suzanne Kosmider
- Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia
| | - Iain Skinner
- Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia
| | - Hui Li Wong
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Belinda Lee
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Matthew E Burge
- Department of Medical Oncology, Royal Brisbane and Women's Hospital, Brisbane, Queensland, Australia
| | - Desmond Yip
- Department of Medical Oncology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Christos S Karapetis
- Department of Medical Oncology, Flinders Medical Centre, Flinders University, Adelaide, South Australia, Australia
| | - Timothy J Price
- Department of Medical Oncology, Queen Elizabeth Hospital, University of Adelaide, Adelaide, South Australia, Australia
| | - Niall C Tebbutt
- Department of Medical Oncology, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Victoria, Australia
| | - Andrew M Haydon
- Department of Medical Oncology, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Janine Ptak
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Mary J Schaeffer
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Natalie Silliman
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Lisa Dobbyn
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Maria Popoli
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Cristian Tomasetti
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nickolas Papadopoulos
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Kenneth W Kinzler
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Bert Vogelstein
- Ludwig Center and Howard Hughes Medical Institute, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medicine, Baltimore, Maryland, USA
| | - Peter Gibbs
- Division of Personalised Oncology, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
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36
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Chu LC, Park S, Kawamoto S, Wang Y, Zhou Y, Shen W, Zhu Z, Xia Y, Xie L, Liu F, Yu Q, Fouladi DF, Shayesteh S, Zinreich E, Graves JS, Horton KM, Yuille AL, Hruban RH, Kinzler KW, Vogelstein B, Fishman EK. Application of Deep Learning to Pancreatic Cancer Detection: Lessons Learned From Our Initial Experience. J Am Coll Radiol 2020; 16:1338-1342. [PMID: 31492412 DOI: 10.1016/j.jacr.2019.05.034] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 05/18/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Linda C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Seyoun Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Satomi Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yan Wang
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Yuyin Zhou
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Wei Shen
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Zhuotun Zhu
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Yingda Xia
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Lingxi Xie
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Fengze Liu
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Qihang Yu
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Daniel F Fouladi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Shahab Shayesteh
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eva Zinreich
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jefferson S Graves
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karen M Horton
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan L Yuille
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland
| | - Ralph H Hruban
- Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kenneth W Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bert Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Elliot K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, Maryland
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37
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Wright K, Hsiue EHC, Douglass J, Hwang MS, Mog BJ, Pearlman AH, Paul S, DiNapoli S, Azurmendi PA, Pardoll DM, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Gabelli S, Zhou S. Dissecting the specificity of a TCR-mimic antibody targeting TP53 R175H mutation-derived neoantigen. Acta Crystallogr A Found Adv 2020. [DOI: 10.1107/s0108767320099420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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38
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Springer S, Masica DL, Dal Molin M, Douville C, Thoburn CJ, Afsari B, Li L, Cohen JD, Thompson E, Allen PJ, Klimstra DS, Schattner MA, Schmidt CM, Yip-Schneider M, Simpson RE, Fernandez-Del Castillo C, Mino-Kenudson M, Brugge W, Brand RE, Singhi AD, Scarpa A, Lawlor R, Salvia R, Zamboni G, Hong SM, Hwang DW, Jang JY, Kwon W, Swan N, Geoghegan J, Falconi M, Crippa S, Doglioni C, Paulino J, Schulick RD, Edil BH, Park W, Yachida S, Hijioka S, van Hooft J, He J, Weiss MJ, Burkhart R, Makary M, Canto MI, Goggins MG, Ptak J, Dobbyn L, Schaefer J, Sillman N, Popoli M, Klein AP, Tomasetti C, Karchin R, Papadopoulos N, Kinzler KW, Vogelstein B, Wolfgang CL, Hruban RH, Lennon AM. A multimodality test to guide the management of patients with a pancreatic cyst. Sci Transl Med 2020; 11:11/501/eaav4772. [PMID: 31316009 DOI: 10.1126/scitranslmed.aav4772] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/07/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022]
Abstract
Pancreatic cysts are common and often pose a management dilemma, because some cysts are precancerous, whereas others have little risk of developing into invasive cancers. We used supervised machine learning techniques to develop a comprehensive test, CompCyst, to guide the management of patients with pancreatic cysts. The test is based on selected clinical features, imaging characteristics, and cyst fluid genetic and biochemical markers. Using data from 436 patients with pancreatic cysts, we trained CompCyst to classify patients as those who required surgery, those who should be routinely monitored, and those who did not require further surveillance. We then tested CompCyst in an independent cohort of 426 patients, with histopathology used as the gold standard. We found that clinical management informed by the CompCyst test was more accurate than the management dictated by conventional clinical and imaging criteria alone. Application of the CompCyst test would have spared surgery in more than half of the patients who underwent unnecessary resection of their cysts. CompCyst therefore has the potential to reduce the patient morbidity and economic costs associated with current standard-of-care pancreatic cyst management practices.
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Affiliation(s)
- Simeon Springer
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - David L Masica
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21287, USA.,Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Marco Dal Molin
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher Douville
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21287, USA.,Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher J Thoburn
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Bahman Afsari
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Lu Li
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Joshua D Cohen
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Biomedical Engineering, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Elizabeth Thompson
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Peter J Allen
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - David S Klimstra
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Mark A Schattner
- Department of Gastroenterology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - C Max Schmidt
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Michele Yip-Schneider
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Rachel E Simpson
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - Mari Mino-Kenudson
- Department of Histopathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - William Brugge
- Department of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Randall E Brand
- Department of Medicine, University of Pittsburgh, Pittsburgh PA 15213, USA
| | - Aatur D Singhi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Aldo Scarpa
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona 37134, Italy.,Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Rita Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona 37134, Italy.,Department of Pathology and Diagnostics, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Roberto Salvia
- General and Pancreatic Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Giuseppe Zamboni
- Department of Pathology, Ospedale Sacro Cuore-Don Calabria, Negrar 37024, Italy
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, South Korea
| | - Dae Wook Hwang
- Hepatobiliary and Pancreas Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, South Korea
| | - Jin-Young Jang
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Wooil Kwon
- Department of Surgery and Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, South Korea
| | - Niall Swan
- Department of Histopathology, St. Vincent's University Hospital, Dublin D04 T6F4, Ireland
| | - Justin Geoghegan
- Department of Surgery, St. Vincent's University Hospital, Dublin D04 T6F4, Ireland
| | - Massimo Falconi
- Division of Pancreatic Surgery, Department of Surgery, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Stefano Crippa
- Division of Pancreatic Surgery, Department of Surgery, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Claudio Doglioni
- Department of Pathology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Jorge Paulino
- Department of Surgery, Centro Hepatobiliopancreático e Transplantação, Hospital Curry Cabral, Lisbon 1050-099, Portugal
| | | | - Barish H Edil
- Department of Surgery, University of Colorado, Aurora, CO 80045, USA
| | - Walter Park
- Department of Medicine, Stanford University Medical Center, Palo Alto, CA 94304, USA
| | - Shinichi Yachida
- Department of Hepatobiliary and Pancreatic Surgery, Pathology and Cancer Genomics, National Cancer Center Hospital and National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Susumu Hijioka
- Department of Gastroenterology, Aichi Cancer Center Hospital, Nagoya 464-8681, Japan
| | - Jeanin van Hooft
- Department of Gastroenterology and Hepatology, Amsterdam Medical Center, Amsterdam 1017 ZX, Netherlands
| | - Jin He
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Matthew J Weiss
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Richard Burkhart
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Martin Makary
- Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Marcia I Canto
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Michael G Goggins
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Janine Ptak
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Lisa Dobbyn
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Joy Schaefer
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Natalie Sillman
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Maria Popoli
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Alison P Klein
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Cristian Tomasetti
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA. .,Department of Biostatistics and Bioinformatics, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Rachel Karchin
- Department of Biomedical Engineering, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21287, USA.,Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.
| | - Nickolas Papadopoulos
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Kenneth W Kinzler
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA. .,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Christopher L Wolfgang
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA. .,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Ralph H Hruban
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA.,Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA.
| | - Anne Marie Lennon
- Ludwig Center and Howard Hughes Medical Institute at the Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, MD 21287, USA. .,Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Surgery, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA.,Department of Radiology, Johns Hopkins University, Baltimore, MD 21287, USA
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39
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Mattox AK, Bettegowda C, Zhou S, Papadopoulos N, Kinzler KW, Vogelstein B. Applications of liquid biopsies for cancer. Sci Transl Med 2020; 11:11/507/eaay1984. [PMID: 31462507 DOI: 10.1126/scitranslmed.aay1984] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022]
Abstract
Liquid biopsies have the potential to detect, characterize, and monitor cancers earlier than is possible with conventional approaches.
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Affiliation(s)
- Austin K Mattox
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA
| | - Chetan Bettegowda
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA
| | - Shibin Zhou
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA
| | - Nickolas Papadopoulos
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA
| | - Kenneth W Kinzler
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA
| | - Bert Vogelstein
- Ludwig Center and the Howard Hughes Medical Institute at the Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, 1650 Orleans St., CRB1, Room 520, Baltimore, MD 21128, USA.
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40
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Affiliation(s)
- Suzanne J Baker
- St Jude Children's Research Hospital, Department of Developmental Neurobiology, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Bert Vogelstein
- Ludwig Center & Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, 1650 Orleans Street St, Baltimore, MD 21205, USA
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41
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Lennon AM, Buchanan AH, Kinde I, Warren A, Honushefsky A, Cohain AT, Ledbetter DH, Sanfilippo F, Sheridan K, Rosica D, Adonizio CS, Hwang HJ, Lahouel K, Cohen JD, Douville C, Patel AA, Hagmann LN, Rolston DD, Malani N, Zhou S, Bettegowda C, Diehl DL, Urban B, Still CD, Kann L, Woods JI, Salvati ZM, Vadakara J, Leeming R, Bhattacharya P, Walter C, Parker A, Lengauer C, Klein A, Tomasetti C, Fishman EK, Hruban RH, Kinzler KW, Vogelstein B, Papadopoulos N. Feasibility of blood testing combined with PET-CT to screen for cancer and guide intervention. Science 2020; 369:eabb9601. [PMID: 32345712 PMCID: PMC7509949 DOI: 10.1126/science.abb9601] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 04/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer treatments are often more successful when the disease is detected early. We evaluated the feasibility and safety of multicancer blood testing coupled with positron emission tomography-computed tomography (PET-CT) imaging to detect cancer in a prospective, interventional study of 10,006 women not previously known to have cancer. Positive blood tests were independently confirmed by a diagnostic PET-CT, which also localized the cancer. Twenty-six cancers were detected by blood testing. Of these, 15 underwent PET-CT imaging and nine (60%) were surgically excised. Twenty-four additional cancers were detected by standard-of-care screening and 46 by neither approach. One percent of participants underwent PET-CT imaging based on false-positive blood tests, and 0.22% underwent a futile invasive diagnostic procedure. These data demonstrate that multicancer blood testing combined with PET-CT can be safely incorporated into routine clinical care, in some cases leading to surgery with intent to cure.
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Affiliation(s)
- Anne Marie Lennon
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Medicine Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | | | - Isaac Kinde
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Andrew Warren
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | | | - Ariella T Cohain
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Fred Sanfilippo
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, 100 Woodruff Circle Atlanta, GA 30322, USA
| | | | | | - Christian S Adonizio
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
- Geisinger Cancer Institute, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Hee Jung Hwang
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Kamel Lahouel
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Joshua D Cohen
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Christopher Douville
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Aalpen A Patel
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Leonardo N Hagmann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Nirav Malani
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Shibin Zhou
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - David L Diehl
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Bobbi Urban
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | | | - Lisa Kann
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Julie I Woods
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | | | | | | | | | - Carroll Walter
- Geisinger, 100 N. Academy Avenue Danville, PA 17822, USA
| | - Alex Parker
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
| | - Christoph Lengauer
- Thrive Earlier Detection Corp., 38 Sidney Street Cambridge, MA 02139, USA
- Third Rock Ventures, LLC, 29 Newbury Street Boston, MA 02116, USA
| | - Alison Klein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Epidemiology, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Cristian Tomasetti
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Division of Biostatistics and Bioinformatics, Department of Oncology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Biostatistics, the Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street Baltimore, MD 21205, USA
| | - Elliot K Fishman
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Radiology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD, 21205, USA
| | - Ralph H Hruban
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Bert Vogelstein
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Department of Oncology, the Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, Baltimore, MD 21205, USA
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42
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Konig MF, Powell M, Staedtke V, Bai RY, Thomas DL, Fischer N, Huq S, Khalafallah AM, Koenecke A, Xiong R, Mensh B, Papadopoulos N, Kinzler KW, Vogelstein B, Vogelstein JT, Athey S, Zhou S, Bettegowda C. Preventing cytokine storm syndrome in COVID-19 using α-1 adrenergic receptor antagonists. J Clin Invest 2020; 130:3345-3347. [PMID: 32352407 PMCID: PMC7324164 DOI: 10.1172/jci139642] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Maximilian F. Konig
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
- Division of Rheumatology
- Johns Hopkins University (JHU) School of Medicine, Baltimore, Maryland, USA
| | - Mike Powell
- Department of Biomedical Engineering, Institute of Computational Medicine, JHU, Baltimore, Maryland, USA
| | | | | | - David L. Thomas
- Division of Infectious Diseases, JHU School of Medicine, Baltimore, Maryland, USA
| | - Nicole Fischer
- Johns Hopkins University (JHU) School of Medicine, Baltimore, Maryland, USA
| | | | | | | | - Ruoxuan Xiong
- Management Science and Engineering, Stanford University, Stanford, California, USA
| | - Brett Mensh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Nickolas Papadopoulos
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
| | - Kenneth W. Kinzler
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
| | - Bert Vogelstein
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
| | - Joshua T. Vogelstein
- Department of Biomedical Engineering, Institute of Computational Medicine, JHU, Baltimore, Maryland, USA
| | - Susan Athey
- Stanford Graduate School of Business, Stanford University, Stanford, California, USA
| | - Shibin Zhou
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
| | - Chetan Bettegowda
- Ludwig Center
- Lustgarten Laboratory, and
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland, USA
- Department of Neurosurgery, and
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43
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Tie J, Papadopoulos N, Kinzler K, Vogelstein B, Gibbs P. Abstract IA05: ctDNA and MRD in colorectal cancer: Time to reinvent adjuvant clinical trials. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-ia05] [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
The most substantial opportunity for improving cancer survival outcomes is in the setting of early-stage disease, where evidence indicates that adjuvant chemotherapy can reduce recurrence and prevent cancer-related death through the eradication of minimal residual disease. However, the current stage-based treatment approach lacks precision and has quite a modest survival impact. A powerful prognostic marker could revolutionize adjuvant therapy by (i) better defining the recurrence risk of individual patients and allowing delivery of a more personalized treatment approach and (ii) enriching studies of new therapies with high-risk patients, substantially reducing the size and cost of adjuvant therapy trials. Circulating tumor DNA (ctDNA) has emerged as a promising noninvasive biomarker, with the ability to detect minimal residual disease following curative intent treatment in early-stage colorectal cancer. I will discuss the potential clinical utilities of ctDNA in early-stage colorectal cancer, including ongoing biomarker-driven adjuvant randomized trials.
Citation Format: Jeanne Tie, Nickolas Papadopoulos, Kenneth Kinzler, Bert Vogelstein, Peter Gibbs. ctDNA and MRD in colorectal cancer: Time to reinvent adjuvant clinical trials [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr IA05.
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Affiliation(s)
- Jeanne Tie
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | | | | | | | - Peter Gibbs
- 3Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
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Tie J, Vogelstein B, Gibbs P. Circulating Tumor DNA as a Prognostic Marker in Stage III Colon Cancer-Reply. JAMA Oncol 2020; 6:932-933. [PMID: 32239186 DOI: 10.1001/jamaoncol.2020.0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jeanne Tie
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia.,Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Peter Gibbs
- Division of Personalised Oncology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Oncology, Western Health, Melbourne, Victoria, Australia.,Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Victoria, Australia
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45
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Park S, Chu LC, Fishman EK, Yuille AL, Vogelstein B, Kinzler KW, Horton KM, Hruban RH, Zinreich ES, Fouladi DF, Shayesteh S, Graves J, Kawamoto S. Erratum to "Annotated normal CT data of the abdomen for deep learning: Challenges and strategies for implementation" [Diagn. Interv. Imaging. 101 (2020) 35-44]. Diagn Interv Imaging 2020; 101:427. [PMID: 32446597 DOI: 10.1016/j.diii.2020.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- S Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - L C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - E K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - A L Yuille
- Department of Computer Science, Johns Hopkins University, School of Arts and Sciences, Baltimore, MD 21218, USA
| | - B Vogelstein
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K W Kinzler
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21287, USA; Johns Hopkins University, School of Medicine, Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, MD 21205, USA
| | - K M Horton
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - R H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - E S Zinreich
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - D F Fouladi
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Shayesteh
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - J Graves
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA
| | - S Kawamoto
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, School of Medicine, 601N. Caroline Street, Baltimore, MD 21287, USA.
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46
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Sengupta S, Douglass J, Wu F, Moskovljevic M, Reed M, Yu J, Tabdili Y, Hsiue EHC, Veenhuis R, Vogelstein B, Siliciano J, Siliciano R, Sadegh-Nasseri S. Use of TCR-mimic bispecific antibodies against pMHC-II for monitoring antigen processing and redirecting cytolytic effector cells. The Journal of Immunology 2020. [DOI: 10.4049/jimmunol.204.supp.86.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
HIV-1 infects CD4+ T cells and macrophages and is currently incurable due to a latent reservoir. Targeting infected cells using TCR-mimic antibodies to peptide-MHC (pMHC) would provide a specific, high-affinity platform for immune system activation and monitoring antigen processing. However, antibodies to pMHC are notoriously difficult to isolate. Using a phage display platform, we panned for phage expressing variable fragments against immunodominant HIV pMHC complexes. These Fab fragments were cloned into a bispecific antibody (bsAb) backbone, such that one Fab fragment is specific for an HIV pMHC and the other fragment binds to CD3. These antibodies utilize the sensitivity of T cell signaling as readouts for antigen processing and potentially as therapeutic formats. Using this approach, we have shown that bsAbs specific for the most conserved MHC-II HIV capsid epitope (Gag293) can recognize the processed epitope on human monocyte-derived dendritic cells (moDCs) fed with the whole Gag protein antigen. Recognition is exquisitely epitope-specific. Additionally, human monocyte-derived macrophages infected with HIV were able to present Gag293 using the endogenous MHC-II pathway, as read out by a Gag-specific bsAb. To our knowledge, this is the first description of endogenous class II presentation of HIV in a major cell type that supports viral replication. By developing bsAbs to detect HIV peptide presentation, we can begin to address the kinetics, pathways, and cell types contributing to the priming events in early HIV infection, which will inform improved vaccine therapies. Additionally, given the potential for therapeutic application, these bsAbs may be used to redirect cytolytic effector cells towards infected targets.
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47
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Miller MS, Douglass J, Hwang MS, Skora AD, Murphy M, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S, Gabelli SB. An engineered antibody fragment targeting mutant β-catenin via major histocompatibility complex I neoantigen presentation. J Biol Chem 2019; 294:19322-19334. [PMID: 31690625 PMCID: PMC6916501 DOI: 10.1074/jbc.ra119.010251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 07/17/2019] [Revised: 11/04/2019] [Indexed: 12/18/2022] Open
Abstract
Mutations in CTNNB1, the gene encoding β-catenin, are common in colon and liver cancers, the most frequent mutation affecting Ser-45 in β-catenin. Peptides derived from WT β-catenin have previously been shown to be presented on the cell surface as part of major histocompatibility complex (MHC) class I, suggesting an opportunity for targeting this common driver gene mutation with antibody-based therapies. Here, crystal structures of both the WT and S45F mutant peptide bound to HLA-A*03:01 at 2.20 and 2.45 Å resolutions, respectively, confirmed the accessibility of the phenylalanine residue for antibody recognition. Phage display was then used to identify single-chain variable fragment clones that selectively bind the S45F mutant peptide presented in HLA-A*03:01 and have minimal WT or other off-target binding. Following the initial characterization of five clones, we selected a single clone, E10, for further investigation. We developed a computational model of the binding of E10 to the mutant peptide-bound HLA-A3, incorporating data from affinity maturation as initial validation. In the future, our model may be used to design clones with maintained specificity and higher affinity. Such derivatives could be adapted into either cell-based (CAR-T) or protein-based (bispecific T-cell engagers) therapies to target cancer cells harboring the S45F mutation in CTNNB1.
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Affiliation(s)
- Michelle S Miller
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Andrew D Skora
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Michael Murphy
- GE Healthcare Life Sciences, Marlborough, Massachusetts 01752
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.,Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287 .,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205
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48
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Reiter JG, Baretti M, Gerold JM, Makohon-Moore AP, Daud A, Iacobuzio-Donahue CA, Azad NS, Kinzler KW, Nowak MA, Vogelstein B. An analysis of genetic heterogeneity in untreated cancers. Nat Rev Cancer 2019; 19:639-650. [PMID: 31455892 PMCID: PMC6816333 DOI: 10.1038/s41568-019-0185-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/23/2019] [Indexed: 12/12/2022]
Abstract
Genetic intratumoural heterogeneity is a natural consequence of imperfect DNA replication. Any two randomly selected cells, whether normal or cancerous, are therefore genetically different. Here, we review the different forms of genetic heterogeneity in cancer and re-analyse the extent of genetic heterogeneity within seven types of untreated epithelial cancers, with particular regard to its clinical relevance. We find that the homogeneity of predicted functional mutations in driver genes is the rule rather than the exception. In primary tumours with multiple samples, 97% of driver-gene mutations in 38 patients were homogeneous. Moreover, among metastases from the same primary tumour, 100% of the driver mutations in 17 patients were homogeneous. With a single biopsy of a primary tumour in 14 patients, the likelihood of missing a functional driver-gene mutation that was present in all metastases was 2.6%. Furthermore, all functional driver-gene mutations detected in these 14 primary tumours were present among all their metastases. Finally, we found that individual metastatic lesions responded concordantly to targeted therapies in 91% of 44 patients. These analyses indicate that the cells within the primary tumours that gave rise to metastases are genetically homogeneous with respect to functional driver-gene mutations, and we suggest that future efforts to develop combination therapies have the potential to be curative.
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Affiliation(s)
- Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA, USA.
| | - Marina Baretti
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeffrey M Gerold
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA
| | - Alvin P Makohon-Moore
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adil Daud
- University of California, San Francisco, San Francisco, CA, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nilofer S Azad
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth W Kinzler
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Martin A Nowak
- Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Mathematics, Harvard University, Cambridge, MA, USA.
| | - Bert Vogelstein
- The Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Ludwig Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- The Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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49
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Wang Q, Douglass J, Hwang MS, Hsiue EHC, Mog BJ, Zhang M, Papadopoulos N, Kinzler KW, Zhou S, Vogelstein B. Direct Detection and Quantification of Neoantigens. Cancer Immunol Res 2019; 7:1748-1754. [PMID: 31527070 PMCID: PMC6825591 DOI: 10.1158/2326-6066.cir-19-0107] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/15/2019] [Accepted: 09/04/2019] [Indexed: 12/30/2022]
Abstract
Many immunotherapeutic approaches under development rely on T-cell recognition of cancer-derived peptides bound to human leukocyte antigen molecules on the cell surface. Direct experimental demonstration that such peptides are processed and bound is currently challenging. Here, we describe a method that meets this challenge. The method entailed an optimized immunoprecipitation protocol coupled with two-dimensional chromatography and mass spectrometry. The ability to detect and quantify minute amounts of predefined antigens should be useful both for basic research in tumor immunology and for the development of rationally designed cancer vaccines.
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Affiliation(s)
- Qing Wang
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland.
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Jacqueline Douglass
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Michael S Hwang
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Emily Han-Chung Hsiue
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Brian J Mog
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Ming Zhang
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Nickolas Papadopoulos
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Kenneth W Kinzler
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Shibin Zhou
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland.
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Bert Vogelstein
- Ludwig Center, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland.
- Howard Hughes Medical Institute, Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
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50
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Weisberg EM, Chu LC, Park S, Yuille AL, Kinzler KW, Vogelstein B, Fishman EK. Deep lessons learned: Radiology, oncology, pathology, and computer science experts unite around artificial intelligence to strive for earlier pancreatic cancer diagnosis. Diagn Interv Imaging 2019; 101:111-115. [PMID: 31629672 DOI: 10.1016/j.diii.2019.09.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/03/2019] [Accepted: 09/17/2019] [Indexed: 10/25/2022]
Affiliation(s)
- E M Weisberg
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA.
| | - L C Chu
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
| | - S Park
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
| | - A L Yuille
- Department of Cognitive Science, The Johns Hopkins University, Baltimore, MD, USA
| | - K W Kinzler
- Department of Pharmacology and Molecular Science, Johns Hopkins Hospital, Baltimore, MD, USA
| | - B Vogelstein
- Department of Pathology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Hospital, Baltimore, MD, USA
| | - E K Fishman
- The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Hospital, 601 North Caroline Street, Baltimore, MD 21287, USA
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