1
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Hamilton MP, Craig E, Gentille Sanchez C, Mina A, Tamaresis J, Kirmani N, Ehlinger Z, Syal S, Good Z, Sworder B, Schroers-Martin J, Lu Y, Muffly L, Negrin RS, Arai S, Lowsky R, Meyer E, Rezvani AR, Shizuru JA, Weng WK, Shiraz P, Sidana S, Bharadwaj S, Smith M, Dahiya S, Sahaf B, Kurtz DM, Mackall CL, Tibshirani R, Alizadeh AA, Frank MJ, Miklos DB. CAR19 monitoring by peripheral blood immunophenotyping reveals histology-specific expansion and toxicity. Blood Adv 2024:bloodadvances.2024012637. [PMID: 38498731 DOI: 10.1182/bloodadvances.2024012637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024] Open
Abstract
Chimeric antigen receptor (CAR) T cells directed against CD19 (CAR19) are a revolutionary treatment for B-cell lymphomas. CAR19 cell expansion is necessary for CAR19 function but is also associated with toxicity. To define the impact of CAR19 expansion on patient outcomes, we prospectively followed a cohort of 236 patients treated with CAR19 (brexucabtagene autoleucel or axicabtagene ciloleucel) for mantle cell (MCL), follicular (FL), and large B-cell lymphoma (LBCL) over the course of five years and obtained CAR19 expansion data using peripheral blood immunophenotyping for 188 of these patients. CAR19 expansion was higher in patients with MCL compared to other lymphoma histologic subtypes. Notably, patients with MCL had increased toxicity and required four-fold higher cumulative steroid doses than patients with LBCL. CAR19 expansion was associated with the development of cytokine release syndrome (CRS), immune effector cell associated neurotoxicity syndrome (ICANS), and the requirement for granulocyte colony stimulating factor (GCSF) after day 14 post-infusion. Younger patients and those with elevated lactate dehydrogenase (LDH) had significantly higher CAR19 expansion. In general, no association between CAR19 expansion and LBCL treatment response was observed. However, when controlling for tumor burden, we found that lower CAR19 expansion in conjunction with low LDH was associated with improved outcomes in LBCL. In sum, this study finds CAR19 expansion principally associates with CAR-related toxicity. Additionally, CAR19 expansion as measured by peripheral blood immunophenotyping may be dispensable to favorable outcomes in LBCL.
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Affiliation(s)
| | - Erin Craig
- Stanford University, Stanford, California, United States
| | | | - Alain Mina
- Stanford University School of Medicine, United States
| | - John Tamaresis
- Stanford University, Stanford, California, United States
| | - Nadia Kirmani
- Stanford University, Stanford, California, United States
| | | | - Shriya Syal
- Stanford University, Palo Alto, California, United States
| | - Zinaida Good
- Stanford University, Stanford, California, United States
| | - Brian Sworder
- Stanford University School of Medicine, Palo Alto, California, United States
| | | | - Ying Lu
- Stanford University, Stanford, California, United States
| | - Lori Muffly
- Stanford University, Stanford, California, United States
| | - Robert S Negrin
- Stanford University Medical Center, Stanford, California, United States
| | - Sally Arai
- Stanford University, Stanford, California, United States
| | - Robert Lowsky
- Stanford University School of Medicine, Stanford (CA), Stanford, California, United States
| | - Everett Meyer
- Stanford University, Stanford, California, United States
| | | | - Judith A Shizuru
- Stanford University Medical Center, Stanford, California, United States
| | - Wen-Kai Weng
- Stanford University School of Medicine, Palo Alto, California, United States
| | - Parveen Shiraz
- Stanford University, Stanford, California, United States
| | - Surbhi Sidana
- Stanford University, Stanford, California, United States
| | - Sushma Bharadwaj
- Stanford University School of Medicine, Palo Alto, California, United States
| | - Melody Smith
- Stanford University, Stanford, California, United States
| | - Saurabh Dahiya
- Stanford University, Stanford, California, United States
| | - Bita Sahaf
- Stanford University School of Medicine, United States
| | - David M Kurtz
- Stanford University, Palo Alto, California, United States
| | | | | | - Ash A Alizadeh
- Stanford University School of Medicine, Stanford, California, United States
| | | | - David B Miklos
- Stanford University Medical School, Stanford, California, United States
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2
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Kastenschmidt JM, Schroers-Martin JG, Sworder BJ, Sureshchandra S, Khodadoust MS, Liu CL, Olsen M, Kurtz DM, Diehn M, Wagar LE, Alizadeh AA. A human lymphoma organoid model for evaluating and targeting the follicular lymphoma tumor immune microenvironment. Cell Stem Cell 2024; 31:410-420.e4. [PMID: 38402619 PMCID: PMC10960522 DOI: 10.1016/j.stem.2024.01.012] [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: 09/01/2023] [Revised: 12/11/2023] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Heterogeneity in the tumor microenvironment (TME) of follicular lymphomas (FLs) can affect clinical outcomes. Current immunotherapeutic strategies, including antibody- and cell-based therapies, variably overcome pro-tumorigenic mechanisms for sustained disease control. Modeling the intact FL TME, with its native, syngeneic tumor-infiltrating leukocytes, is a major challenge. Here, we describe an organoid culture method for cultivating patient-derived lymphoma organoids (PDLOs), which include cells from the native FL TME. We define the robustness of this method by successfully culturing cryopreserved FL specimens from diverse patients and demonstrate the stability of TME cellular composition, tumor somatic mutations, gene expression profiles, and B/T cell receptor dynamics over 3 weeks. PDLOs treated with CD3:CD19 and CD3:CD20 therapeutic bispecific antibodies showed B cell killing and T cell activation. This stable system offers a robust platform for advancing precision medicine efforts in FL through patient-specific modeling, high-throughput screening, TME signature identification, and treatment response evaluation.
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Affiliation(s)
- Jenna M Kastenschmidt
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California, Irvine, Irvine, CA 92617, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, USA; Cancer Research Institute, University of California, Irvine, Irvine, CA 92617, USA
| | | | - Brian J Sworder
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Suhas Sureshchandra
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California, Irvine, Irvine, CA 92617, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, USA; Cancer Research Institute, University of California, Irvine, Irvine, CA 92617, USA
| | - Michael S Khodadoust
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mari Olsen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lisa E Wagar
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92617, USA; Institute for Immunology, University of California, Irvine, Irvine, CA 92617, USA; Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92617, USA; Cancer Research Institute, University of California, Irvine, Irvine, CA 92617, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
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3
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Shukla ND, Schroers-Martin JG, Sworder BJ, Kathuria KR, Alig SK, Frank MJ, Miklos DB, Coutre S, Diehn M, Khodadoust MS, Roschewski M, Kurtz DM, Alizadeh AA. Specificity of immunoglobulin high-throughput sequencing minimal residual disease monitoring in non-Hodgkin lymphomas. Blood Adv 2024; 8:780-784. [PMID: 38147627 PMCID: PMC10847740 DOI: 10.1182/bloodadvances.2023011997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/07/2023] [Indexed: 12/28/2023] Open
Affiliation(s)
- Navika D. Shukla
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | | | - Brian J. Sworder
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Karan Raj Kathuria
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Stefan K. Alig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University, Stanford, CA
| | - David B. Miklos
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford University, Stanford, CA
| | - Steven Coutre
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, CA
| | | | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - David M. Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Ash A. Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
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4
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Tabari E, Lovejoy AF, Lin H, Bolen CR, Lor Saelee S, Lefkowitz JP, Kurtz DM, Bottos A, Nielsen TG, Parreira JM, Luong KT. NGS-determined molecular markers and disease burden metrics from ctDNA correlate with PFS in previously untreated DLBCL. Leuk Lymphoma 2024:1-11. [PMID: 38337191 DOI: 10.1080/10428194.2024.2301924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/02/2024] [Indexed: 02/12/2024]
Abstract
Personalized risk stratification and treatment may help improve outcomes among patients with diffuse large B-cell lymphoma (DLBCL). We developed a next-generation sequencing (NGS)-based method to assess a range of potential prognostic indicators, and evaluated it using pretreatment plasma samples from 310 patients with previously untreated DLBCL from the GOYA trial (NCT01287741). Variant calls and DLBCL subtyping with the plasma-based method were concordant with corresponding tissue-based methods. Patients with a tumor burden greater than the median (p = .003) and non-germinal center B-cell-like (non-GCB) DLBCL (p = .049) had worse progression-free survival than patients with a tumor burden less than the median or GCB DLBCL. Multi-factor assessment combining orthogonal features from a single pretreatment plasma sample has promise as a prognostic indicator in this setting (p = .085). This minimally invasive plasma-based NGS assay could enable comprehensive prognostic assessment of patients in a clinical setting, with greater accessibility than current methods.
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Affiliation(s)
| | | | - Hai Lin
- Roche Sequencing Solutions, Pleasanton, CA, USA
| | | | | | | | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
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5
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Alig SK, Shahrokh Esfahani M, Garofalo A, Li MY, Rossi C, Flerlage T, Flerlage JE, Adams R, Binkley MS, Shukla N, Jin MC, Olsen M, Telenius A, Mutter JA, Schroers-Martin JG, Sworder BJ, Rai S, King DA, Schultz A, Bögeholz J, Su S, Kathuria KR, Liu CL, Kang X, Strohband MJ, Langfitt D, Pobre-Piza KF, Surman S, Tian F, Spina V, Tousseyn T, Buedts L, Hoppe R, Natkunam Y, Fornecker LM, Castellino SM, Advani R, Rossi D, Lynch R, Ghesquières H, Casasnovas O, Kurtz DM, Marks LJ, Link MP, André M, Vandenberghe P, Steidl C, Diehn M, Alizadeh AA. Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling. Nature 2024; 625:778-787. [PMID: 38081297 DOI: 10.1038/s41586-023-06903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
The scarcity of malignant Hodgkin and Reed-Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profiling of cHL due to relatively high circulating tumour DNA (ctDNA) levels1-4. Here we show that the plasma representation of mutations exceeds the bulk tumour representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumours, we demonstrate Hodgkin and Reed-Sternberg ctDNA shedding to be shaped by DNASE1L3, whose increased tumour microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R mutations that are dependent on IL-13 signalling and therapeutically targetable with IL-4Rα-blocking antibodies. Finally, using PhasED-seq5, we demonstrate the clinical value of pretreatment and on-treatment ctDNA levels for longitudinally refining cHL risk prediction and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL, as well as capturing molecularly distinct subtypes with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Stefan K Alig
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | | | - Andrea Garofalo
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Michael Yu Li
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Cédric Rossi
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
- Hematology Department, University Hospital F. Mitterrand and Inserm UMR 1231, Dijon, France
| | - Tim Flerlage
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jamie E Flerlage
- Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Ragini Adams
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Stanford University, Stanford, CA, USA
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA
| | - Navika Shukla
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Mari Olsen
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Jurik A Mutter
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Joseph G Schroers-Martin
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Brian J Sworder
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Shinya Rai
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Daniel A King
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Andre Schultz
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Jan Bögeholz
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Shengqin Su
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA
| | - Karan R Kathuria
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Xiaoman Kang
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Maya J Strohband
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Deanna Langfitt
- Department of Bone Marrow Transplant and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Sherri Surman
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Feng Tian
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Valeria Spina
- Laboratory of Molecular Diagnostics, Department of Medical Genetics EOLAB, Bellinzona, Switzerland
| | - Thomas Tousseyn
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | | | - Richard Hoppe
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA
| | | | - Luc-Matthieu Fornecker
- Institut de Cancérologie Strasbourg Europe (ICANS) and University of Strasbourg, Strasbourg, France
| | - Sharon M Castellino
- Department of Pediatrics, Emory University, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Ranjana Advani
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Davide Rossi
- Clinic of Hematology, Oncology Institute of Southern Switzerland, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Laboratory of Experimental Hematology, Institute of Oncology Research, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Ryan Lynch
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hervé Ghesquières
- Department of Hematology, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Benite, France
| | - Olivier Casasnovas
- Hematology Department, University Hospital F. Mitterrand and Inserm UMR 1231, Dijon, France
| | - David M Kurtz
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA
| | - Lianna J Marks
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Stanford University, Stanford, CA, USA
| | - Michael P Link
- Department of Pediatrics, Division of Pediatric Hematology and Oncology, Stanford University, Stanford, CA, USA
| | - Marc André
- Department of Haematology, Université Catholique de Louvain, CHU UCL Namur, Yvoir, Belgium
| | - Peter Vandenberghe
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Hematology, University Hospitals Leuven, Leuven, Belgium
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA, USA.
| | - Ash A Alizadeh
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA, USA.
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6
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Affiliation(s)
- Adam C Palmer
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - David M Kurtz
- Stanford University School of Medicine, Stanford, CA
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7
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Sworder BJ, Kurtz DM. Cell-free DNA in large B-cell lymphoma: MRD and beyond. Semin Hematol 2023; 60:142-149. [PMID: 37474409 PMCID: PMC10528139 DOI: 10.1053/j.seminhematol.2023.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/31/2023] [Accepted: 06/24/2023] [Indexed: 07/22/2023]
Abstract
Large B-cell lymphomas (LBCLs) are a strikingly diverse set of diseases, including clinical, biological, and molecular heterogeneity. Despite a wealth of information resolving this heterogeneity in the research setting, applying molecular features routinely in the clinic remains challenging. The advent of circulating tumor DNA (ctDNA) liquid biopsies promises to unlock additional molecular information in the clinic, including mutational genotyping, molecular classification, and minimal residual disease detection. Here, we examine the technologies, applications, and studies exploring the utility of ctDNA in LBCLs.
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Affiliation(s)
- Brian J Sworder
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA; Stanford Cancer Institute, Stanford University, Stanford, CA.
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8
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Schroers-Martin JG, Soo J, Brisou G, Scherer F, Kurtz DM, Sworder BJ, Khodadoust MS, Jin MC, Bru A, Liu CL, Stehr H, Vineis P, Natkunam Y, Teras LR, Song JY, Nadel B, Diehn M, Roulland S, Alizadeh AA. Tracing Founder Mutations in Circulating and Tissue-Resident Follicular Lymphoma Precursors. Cancer Discov 2023; 13:1310-1323. [PMID: 36939219 PMCID: PMC10239329 DOI: 10.1158/2159-8290.cd-23-0111] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/11/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023]
Abstract
Follicular lymphomas (FL) are characterized by BCL2 translocations, often detectable in blood years before FL diagnosis, but also observed in aging healthy individuals, suggesting additional lesions are required for lymphomagenesis. We directly characterized early cooperating mutations by ultradeep sequencing of prediagnostic blood and tissue specimens from 48 subjects who ultimately developed FL. Strikingly, CREBBP lysine acetyltransferase (KAT) domain mutations were the most commonly observed precursor lesions, and largely distinguished patients developing FL (14/48, 29%) from healthy adults with or without detected BCL2 rearrangements (0/13, P = 0.03 and 0/20, P = 0.007, respectively). CREBBP variants were detectable a median of 5.8 years before FL diagnosis, were clonally selected in FL tumors, and appeared restricted to the committed B-cell lineage. These results suggest that mutations affecting the CREBBP KAT domain are common lesions in FL cancer precursor cells (CPC), with the potential for discriminating subjects at risk of developing FL or monitoring residual disease. SIGNIFICANCE Our study provides direct evidence for recurrent genetic aberrations preceding FL diagnosis, revealing the combination of BCL2 translocation with CREBBP KAT domain mutations as characteristic committed lesions of FL CPCs. Such prediagnostic mutations are detectable years before clinical diagnosis and may help discriminate individuals at risk for lymphoma development. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Joseph G. Schroers-Martin
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Joanne Soo
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Gabriel Brisou
- Aix-Marseille University, CNRS, INSERM, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Florian Scherer
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - David M. Kurtz
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Brian J. Sworder
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Michael S. Khodadoust
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Michael C. Jin
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Agnès Bru
- Aix-Marseille University, CNRS, INSERM, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Chih Long Liu
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Henning Stehr
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK
| | - Yasodha Natkunam
- Department of Pathology, Stanford University Medical Center, Stanford, CA
| | | | - Joo Y. Song
- City of Hope Cancer Research Hospital, Duarte, CA
| | - Bertrand Nadel
- Aix-Marseille University, CNRS, INSERM, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Sandrine Roulland
- Aix-Marseille University, CNRS, INSERM, Centre d’Immunologie de Marseille-Luminy, Marseille, France
| | - Ash A. Alizadeh
- Department of Medicine, Divisions of Hematology & Oncology, Stanford University Medical Center, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
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9
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Cherng HJJ, Alig SK, Oki Y, Nastoupil LJ, Fayad L, Neelapu SS, Turturro F, Hagemeister F, Craig AFM, Macaulay CW, Rodriguez MA, Lee HJ, McDonnell TJ, Flowers CR, Vega F, Green MR, Feng L, Kurtz DM, Alizadeh AA, Davis RE, Westin JR. A phase 1/2 study of lenalidomide and obinutuzumab with CHOP for newly diagnosed DLBCL. Blood Adv 2023; 7:1137-1145. [PMID: 36375046 PMCID: PMC10111343 DOI: 10.1182/bloodadvances.2022008174] [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: 06/01/2022] [Revised: 09/19/2022] [Accepted: 10/02/2022] [Indexed: 11/16/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) can be cured with rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP); however, one-third of patients experience refractory or relapsed disease. Studies comparing R-CHOP with modified regimens replacing R with obinutuzumab (O) or adding lenalidomide (L) did not result in improved outcomes; however, L and O together may enhance natural killer-cell mediated antibody-dependent cellular toxicity when paired with CHOP. Here, we report on a phase 1b/2 study of 53 patients with newly diagnosed DLBCL who received 6 cycles of LO-CHOP. The end of treatment overall and complete response rates of the 50 evaluable patients were 98% and 90%, respectively. After a median follow-up of 4.5 years, the 4-year progression free and overall survival rates were 87.4% and 91.3%, respectively. Grade 3 to 4 adverse events were experienced by 70% of patients, including neutropenia (38%), thrombocytopenia (17%), fatigue (13%), and neutropenic fever (13%). Of the 33 patients profiled with circulating tumor DNA (ctDNA) sequencing, 31 (94%) had detectable pretreatment ctDNA with cancer personalized profiling by deep sequencing, 24 (73%) were classifiable by the LymphGen classifier, and 15/20 (75%) and 12/17 (71%) patients achieved early and major molecular responses after 1 and 2 cycles, respectively. Using phased variant enrichment and detection sequencing, 16/18 evaluable patients (89%) showed no detectable ctDNA after at least 5 cycles of LO-CHOP. LO-CHOP demonstrates high efficacy and tolerability in newly diagnosed DLBCL, leading to a high rate of undetectable minimal residual disease by ctDNA. This trial has been registered at www.clinicaltrials.gov as NCT02529852.
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Affiliation(s)
- Hua-Jay J. Cherng
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Hematology and Oncology, Columbia University Irving Medical Center, New York, NY
| | - Stefan K. Alig
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Yasuhiro Oki
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Loretta J. Nastoupil
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis Fayad
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sattva S. Neelapu
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Francesco Turturro
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fredrick Hagemeister
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexander F. M. Craig
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Charles W. Macaulay
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Maria Alma Rodriguez
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hun Ju Lee
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy J. McDonnell
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher R. Flowers
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael R. Green
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David M. Kurtz
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Ash A. Alizadeh
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - R. Eric Davis
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason R. Westin
- Department of Lymphoma & Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Isbell JM, Li BT, Razavi P, Reis-Filo J, Liu SY, Selenica P, Adusumilli P, Bott M, Jones DR, Rusch VW, Sihag S, Buonocore DJ, Jee J, Lebow E, Gomez D, Rimner A, Santini FC, Rudin CM, Eichholz JE, Martinez A, Alerte D, Hogan GJ, Schultz A, Schuyler RP, Roff A, Hite D, Chabon JJ, Kurtz DM, Alizadeh AA, Diehn M. Abstract 3375: Ultrasensitive ctDNA minimal residual disease monitoring in early NSCLC with PhasED-Seq. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3375] [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
Background: Circulating tumor DNA (ctDNA) minimal residual disease (MRD) detection is a promising approach for personalization of adjuvant therapy in non-small cell lung cancer (NSCLC). First generation ctDNA MRD assays that employ tumor-informed approaches to track single nucleotide variants (SNVs) have limits of detection (LOD95) of ~1E-4 and have high positive predictive values for recurrence. However, they have suboptimal clinical sensitivity, with false negative results at the completion of therapy in most patients who will ultimately recur. PhasED-Seq is a novel ctDNA MRD method that tracks multiple “phased” variants (PVs) within individual DNA fragments with a LOD95 ~100-fold better than first generation assays. Here we report PhasED-Seq ctDNA MRD results for the first prospective cohort of early stage NSCLC patients.
Methods: Tumor tissues (n=46), PBMCs (n=46) and plasma samples (n=169) from 46 Stage I-III NSCLC patients treated with curative intent were prospectively collected at Memorial Sloan Kettering Cancer Center. All patients underwent resection and received neoadjuvant +/- adjuvant therapy (n=14), adjuvant therapy only (n=17), or neither (n=15). Samples were analyzed in Foresight Diagnostics' CLIA laboratory (Aurora, CO) using personalized PhasED-Seq. Briefly, PVs were identified via whole genome sequencing of tumors and matched blood germline DNA. Custom capture panels targeting PVs were synthesized and used to assess MRD status in pre-, on- and post-treatment plasma samples. Detection of ctDNA MRD was assessed at a post-treatment landmark, defined as the first post-therapy sample or when not available the last post-surgical sample taken during therapy. To enable comparisons, the same plasma samples were analyzed using an SNV-based ctDNA MRD approach.
Results: PVs were identified in tumor tissue from all 46 patients. Across all plasma samples PhasED-Seq achieved a median LOD95 of 1.3E-6 and as low as 2.5E-7. Of 74 plasma samples with detectable ctDNA, 38 (51%) contained concentrations below 1E-4 and the lowest level of ctDNA MRD detected was 1.7E-7. For post-treatment landmark samples (n=45), the median time from end of therapy was 2 months. Cancer recurred in all patients (n=10) with detectable MRD at the landmark. Furthermore, PhasED-Seq better stratified freedom from recurrence (log-rank p=3E-8, Cox HR=10.8) than the SNV-based approach (log-rank p=0.08, Cox HR=2.5) and detected MRD at the landmark in more patients who ultimately recurred (56% vs 28%). PhasED-Seq also achieved longer lead times, including detecting MRD in 66% of samples collected 12 to 24 months prior to recurrence versus only 33% using SNV-based monitoring.
Conclusion: PhasED-Seq achieves ctDNA detection below 1 part per million and appears to be significantly more sensitive than SNV-based MRD monitoring. These results suggest that PhasED-Seq is a promising approach for use in risk adapted trials in early stage NSCLC.
Citation Format: James M. Isbell, Bob T. Li, Pedram Razavi, Jorge Reis-Filo, Si-Yang Liu, Pier Selenica, Prasad Adusumilli, Matthew Bott, David R. Jones, Valerie W. Rusch, Smita Sihag, Darren J. Buonocore, Justin Jee, Emily Lebow, Daniel Gomez, Andreas Rimner, Fernando C. Santini, Charles M. Rudin, Jordan E. Eichholz, Andres Martinez, Daphne Alerte, Gregory J. Hogan, Andre Schultz, Ronald P. Schuyler, Alanna Roff, Dustin Hite, Jacob J. Chabon, David M. Kurtz, Ash A. Alizadeh, Maximilian Diehn. Ultrasensitive ctDNA minimal residual disease monitoring in early NSCLC with PhasED-Seq [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 3375.
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Affiliation(s)
| | - Bob T. Li
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Si-Yang Liu
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pier Selenica
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Matthew Bott
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | - Smita Sihag
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Justin Jee
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Emily Lebow
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Gomez
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | - Daphne Alerte
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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11
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Mutter JA, Alig SK, Esfahani MS, Lauer EM, Mitschke J, Kurtz DM, Kühn J, Bleul S, Olsen M, Liu CL, Jin MC, Macaulay CW, Neidert N, Volk T, Eisenblaetter M, Rauer S, Heiland DH, Finke J, Duyster J, Wehrle J, Prinz M, Illerhaus G, Reinacher PC, Schorb E, Diehn M, Alizadeh AA, Scherer F. Circulating Tumor DNA Profiling for Detection, Risk Stratification, and Classification of Brain Lymphomas. J Clin Oncol 2023; 41:1684-1694. [PMID: 36542815 PMCID: PMC10419411 DOI: 10.1200/jco.22.00826] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 09/26/2022] [Accepted: 11/08/2022] [Indexed: 12/24/2022] Open
Abstract
PURPOSE Clinical outcomes of patients with CNS lymphomas (CNSLs) are remarkably heterogeneous, yet identification of patients at high risk for treatment failure is challenging. Furthermore, CNSL diagnosis often remains unconfirmed because of contraindications for invasive stereotactic biopsies. Therefore, improved biomarkers are needed to better stratify patients into risk groups, predict treatment response, and noninvasively identify CNSL. PATIENTS AND METHODS We explored the value of circulating tumor DNA (ctDNA) for early outcome prediction, measurable residual disease monitoring, and surgery-free CNSL identification by applying ultrasensitive targeted next-generation sequencing to a total of 306 tumor, plasma, and CSF specimens from 136 patients with brain cancers, including 92 patients with CNSL. RESULTS Before therapy, ctDNA was detectable in 78% of plasma and 100% of CSF samples. Patients with positive ctDNA in pretreatment plasma had significantly shorter progression-free survival (PFS, P < .0001, log-rank test) and overall survival (OS, P = .0001, log-rank test). In multivariate analyses including established clinical and radiographic risk factors, pretreatment plasma ctDNA concentrations were independently prognostic of clinical outcomes (PFS HR, 1.4; 95% CI, 1.0 to 1.9; P = .03; OS HR, 1.6; 95% CI, 1.1 to 2.2; P = .006). Moreover, measurable residual disease detection by plasma ctDNA monitoring during treatment identified patients with particularly poor prognosis following curative-intent immunochemotherapy (PFS, P = .0002; OS, P = .004, log-rank test). Finally, we developed a proof-of-principle machine learning approach for biopsy-free CNSL identification from ctDNA, showing sensitivities of 59% (CSF) and 25% (plasma) with high positive predictive value. CONCLUSION We demonstrate robust and ultrasensitive detection of ctDNA at various disease milestones in CNSL. Our findings highlight the role of ctDNA as a noninvasive biomarker and its potential value for personalized risk stratification and treatment guidance in patients with CNSL. [Media: see text].
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Affiliation(s)
- Jurik A. Mutter
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- University of Freiburg, Faculty of Biology, Freiburg, Germany
| | - Stefan K. Alig
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Mohammad S. Esfahani
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Eliza M. Lauer
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jan Mitschke
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - David M. Kurtz
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Julia Kühn
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sabine Bleul
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Mari Olsen
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Chih Long Liu
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Michael C. Jin
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Charles W. Macaulay
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Nicolas Neidert
- Department of Neurosurgery, Medical Center—University of Freiburg, Freiburg, Germany
- Berta-Ottenstein-Programme for Clinician Scientists Medical Center, University of Freiburg, Freiburg, Germany
| | - Timo Volk
- Department of Neurology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Michel Eisenblaetter
- Department of Radiology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Sebastian Rauer
- Department of Neurology, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dieter H. Heiland
- Department of Neurosurgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jürgen Finke
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Justus Duyster
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Julius Wehrle
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marco Prinz
- Institute of Neuropathology, Medical Faculty, University of Freiburg, Freiburg, Germany
- Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Gerald Illerhaus
- Department of Hematology/Oncology and Palliative Care, Klinikum Stuttgart, Stuttgart, Germany
| | - Peter C. Reinacher
- Department of Stereotactic and Functional Neurosurgery, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Fraunhofer Institute for Laser Technology (ILT), Aachen, Germany
| | - Elisabeth Schorb
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA
| | - Ash A. Alizadeh
- Divisions of Oncology and Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - Florian Scherer
- Department of Medicine I, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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12
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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13
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Sworder BJ, Kurtz DM, Alig SK, Frank MJ, Shukla N, Garofalo A, Macaulay CW, Shahrokh Esfahani M, Olsen MN, Hamilton J, Hosoya H, Hamilton M, Spiegel JY, Baird JH, Sugio T, Carleton M, Craig AFM, Younes SF, Sahaf B, Sheybani ND, Schroers-Martin JG, Liu CL, Oak JS, Jin MC, Beygi S, Hüttmann A, Hanoun C, Dührsen U, Westin JR, Khodadoust MS, Natkunam Y, Majzner RG, Mackall CL, Diehn M, Miklos DB, Alizadeh AA. Determinants of resistance to engineered T cell therapies targeting CD19 in large B cell lymphomas. Cancer Cell 2023; 41:210-225.e5. [PMID: 36584673 PMCID: PMC10010070 DOI: 10.1016/j.ccell.2022.12.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 10/17/2022] [Accepted: 12/06/2022] [Indexed: 12/31/2022]
Abstract
Most relapsed/refractory large B cell lymphoma (r/rLBCL) patients receiving anti-CD19 chimeric antigen receptor (CAR19) T cells relapse. To characterize determinants of resistance, we profiled over 700 longitudinal specimens from two independent cohorts (n = 65 and n = 73) of r/rLBCL patients treated with axicabtagene ciloleucel. A method for simultaneous profiling of circulating tumor DNA (ctDNA), cell-free CAR19 (cfCAR19) retroviral fragments, and cell-free T cell receptor rearrangements (cfTCR) enabled integration of tumor and both engineered and non-engineered T cell effector-mediated factors for assessing treatment failure and predicting outcomes. Alterations in multiple classes of genes are associated with resistance, including B cell identity (PAX5 and IRF8), immune checkpoints (CD274), and those affecting the microenvironment (TMEM30A). Somatic tumor alterations affect CAR19 therapy at multiple levels, including CAR19 T cell expansion, persistence, and tumor microenvironment. Further, CAR19 T cells play a reciprocal role in shaping tumor genotype and phenotype. We envision these findings will facilitate improved chimeric antigen receptor (CAR) T cells and personalized therapeutic approaches.
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Affiliation(s)
- Brian J Sworder
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Stefan K Alig
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Matthew J Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Navika Shukla
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Andrea Garofalo
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Charles W Macaulay
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Mohammad Shahrokh Esfahani
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Mari N Olsen
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - James Hamilton
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Hitomi Hosoya
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark Hamilton
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA; Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jay Y Spiegel
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA
| | - John H Baird
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Takeshi Sugio
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Mia Carleton
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Sheren F Younes
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Bita Sahaf
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Natasha D Sheybani
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Joseph G Schroers-Martin
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Jean S Oak
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Sara Beygi
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA
| | - Andreas Hüttmann
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Christine Hanoun
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Ulrich Dührsen
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Jason R Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael S Khodadoust
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robbie G Majzner
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA; Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA; Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Parker Institute for Cancer Immunotherapy, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - David B Miklos
- Division of Blood and Marrow Transplantation and Cellular Therapy, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, 265 Campus Drive, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
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14
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Randall TA, Kurtz DM. Assembly of a Draft Genome for the Mouse Ectoparasite Myocoptes musculinus. J Am Assoc Lab Anim Sci 2023; 62:55-63. [PMID: 36755207 PMCID: PMC9936850 DOI: 10.30802/aalas-jaalas-22-000066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Myocoptes musculinus is a common ectoparasite of wild mice and is occasionally found on research mice. Infestations of research mice are often subclinical but can cause severe dermatitis. Perhaps more importantly, infestations can cause immunologic reactions that may alter research outcomes, and most animal research facilities strive to prevent or eliminate mites from their mouse colonies. M. musculinus infestations are currently detected by using microscopic evaluation of the fur and skin and PCR assays of pelt swabs targeting the rRNA genes of this mite. In our facility, we encountered multiple, false-positive 18S rRNA PCR results from a closed mouse colony. We could not identify the source of the false positives even after performing PCR analysis of other Myocoptes gene targets using assays developed from the few other target genomic sequences available for M. musculinus or Myocoptes japonensis in public databases. This situation highlighted the limited genetic resources available for development of diagnostic tests specific for this ectoparasite. To expand the available genetic resources, we generated a metagenome of M. musculinus derived by sequencing from fur plucks of an infected mouse. We also determined the completeness of this metagenome and compared it with those of related mites.
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Affiliation(s)
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina,Corresponding author.
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15
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Adsit FG, Randall TA, Locklear J, Kurtz DM. The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome. Microbiologyopen 2022; 11:e1333. [PMID: 36479628 PMCID: PMC9638481 DOI: 10.1002/mbo3.1333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the E. coli genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of E. coli to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of E. coli, EcoFA807-17, possessing a tetrathionate reductase (ttr) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The ttr operon is a potent virulence factor for several enteric pathogens, most prominently Salmonella enterica. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type E. coli or Shigella. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in E. coli and Shigella and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of Salmonella enterica.
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Affiliation(s)
- Floyd G. Adsit
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Thomas A. Randall
- Integrative BioinformaticsNational Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Jacqueline Locklear
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - David M. Kurtz
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
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16
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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18
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Shree T, Shankar V, Lohmeyer JJ, Czerwinski DK, Schroers-Martin JG, Rodriguez GM, Beygi S, Kanegai AM, Corbelli KS, Gabriel E, Kurtz DM, Khodadoust MS, Gupta NK, Maeda LS, Advani RH, Alizadeh AA, Levy R. CD20-Targeted Therapy Ablates De Novo Antibody Response to Vaccination but Spares Preestablished Immunity. Blood Cancer Discov 2022; 3:95-102. [PMID: 35015688 PMCID: PMC9610898 DOI: 10.1158/2643-3230.bcd-21-0222] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 11/16/2022] Open
Abstract
To obtain a deeper understanding of poor responses to COVID-19 vaccination in patients with lymphoma, we assessed blocking antibodies, total anti-spike IgG, and spike-specific memory B cells in the peripheral blood of 126 patients with lymphoma and 20 age-matched healthy controls 1 and 4 months after COVID-19 vaccination. Fifty-five percent of patients developed blocking antibodies postvaccination, compared with 100% of controls. When evaluating patients last treated from days to nearly 18 years prior to vaccination, time since last anti-CD20 was a significant independent predictor of vaccine response. None of 31 patients who had received anti-CD20 treatment within 6 months prior to vaccination developed blocking antibodies. In contrast, patients who initiated anti-CD20 treatment shortly after achieving a vaccine-induced antibody response tended to retain that response during treatment, suggesting a policy of immunizing prior to treatment whenever possible. SIGNIFICANCE In a large cohort of patients with B-cell lymphoma, time since anti-CD20 treatment was an independent predictor of neutralizing antibody response to COVID-19 vaccination. Comparing patients who received anti-CD20 treatment before or after vaccination, we demonstrate that vaccinating first can generate an antibody response that endures through anti-CD20-containing treatment. This article is highlighted in the In This Issue feature, p. 85.
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Affiliation(s)
- Tanaya Shree
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Vishnu Shankar
- Program in Immunology, Stanford University School of Medicine, Stanford, California
| | - Julian J.K. Lohmeyer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Debra K. Czerwinski
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | | | - Gladys M. Rodriguez
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Sara Beygi
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Alyssa M. Kanegai
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Karen S. Corbelli
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Etelka Gabriel
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - David M. Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Michael S. Khodadoust
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Neel K. Gupta
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Lauren S. Maeda
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ranjana H. Advani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ash A. Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ronald Levy
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California.,Corresponding Author: Ronald Levy, Division of Oncology, Stanford University Hospital and Clinics, 269 Campus Drive, Stanford, CA 94305. Phone: 650-725-6452; Fax: 650-736-1454; E-mail:
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Johnston MD, Whiteside TE, Allen ME, Kurtz DM. Toxigenic Profile of Clostridium perfringens Strains Isolated from Natural Ingredient Laboratory Animal Diets. Comp Med 2022; 72:50-58. [PMID: 35148812 DOI: 10.30802/aalas-cm-22-000013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Clostridium perfringens is an anaerobic, gram-positive, spore-forming bacterium that ubiquitously inhabits a wide varietyof natural environments including the gastrointestinal tract of humans and animals. C. perfringens is an opportunistic enteropathogen capable of producing at least 20 different toxins in various combinations. Strains of C. perfringens are currentlycategorized into 7 toxinotypes (A, B, C, D, E, F, and G) based on the presence or absence of 6 typing-toxins (α, β, epsilon, iota, enterotoxin, and netB). Each toxinotype is associated with specific histotoxic and enteric diseases. Spontaneous enteritis due to C. perfringens has been reported in laboratory animals; however, the source of the bacteria was unknown. The Quality Assurance Laboratory (QAL) at the National Institute of Environmental Health Sciences (NIEHS) routinely screens incoming animal feeds for aerobic, enteric pathogens, such as Salmonella spp. and E. coli. Recently, QAL incorporated anaerobic screening of incoming animal feeds. To date, the lab has isolated numerous Clostridium species, including C. perfringens, from 23 lots ofnatural ingredient laboratory animal diets. Published reports of C. perfringens isolation from laboratory animal feeds couldnot be found in the literature. Therefore, we performed a toxin profile screen of our isolated strains of C. perfringens usingPCR to determine which toxinotypes were present in the laboratory animal diets. Our results showed that most C. perfringens strains we isolated from the laboratory animal feed were toxinotype A with most strains also possessing the theta toxin. Two of the C. perfringens strains also possessed the β toxin. Our results demonstrated the presence of C. perfringens in nonsterile, natural ingredient feeds for laboratory animals which could serve as a source of this opportunistic pathogen.
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20
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Johnston MD, Whiteside TE, Allen ME, Kurtz DM. Toxigenic Profile of Clostridium perfringens Strains Isolated from Natural Ingredient Laboratory Animal Diets. J Am Assoc Lab Anim Sci 2022. [PMID: 35074042 DOI: 10.30802/aalas-jaalas-21-000066] [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: 06/14/2023]
Abstract
Clostridium perfringens is an anaerobic, gram-positive, spore-forming bacterium that ubiquitously inhabits a wide varietyof natural environments including the gastrointestinal tract of humans and animals. C. perfringens is an opportunistic enteropathogen capable of producing at least 20 different toxins in various combinations. Strains of C. perfringens are currentlycategorized into 7 toxinotypes (A, B, C, D, E, F, and G) based on the presence or absence of 6 typing-toxins (α, β, epsilon, iota, enterotoxin, and netB). Each toxinotype is associated with specific histotoxic and enteric diseases. Spontaneous enteritis due to C. perfringens has been reported in laboratory animals; however, the source of the bacteria was unknown. The Quality Assurance Laboratory (QAL) at the National Institute of Environmental Health Sciences (NIEHS) routinely screens incoming animal feeds for aerobic, enteric pathogens, such as Salmonella spp. and E. coli. Recently, QAL incorporated anaerobic screening of incoming animal feeds. To date, the lab has isolated numerous Clostridium species, including C. perfringens, from 23 lots ofnatural ingredient laboratory animal diets. Published reports of C. perfringens isolation from laboratory animal feeds couldnot be found in the literature. Therefore, we performed a toxin profile screen of our isolated strains of C. perfringens usingPCR to determine which toxinotypes were present in the laboratory animal diets. Our results showed that most C. perfringens strains we isolated from the laboratory animal feed were toxinotype A with most strains also possessing the theta toxin. Two of the C. perfringens strains also possessed the β toxin. Our results demonstrated the presence of C. perfringens in nonsterile, natural ingredient feeds for laboratory animals which could serve as a source of this opportunistic pathogen.
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21
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Roschewski M, Rossi D, Kurtz DM, Alizadeh AA, Wilson WH. Circulating Tumor DNA in Lymphoma: Principles and Future Directions. Blood Cancer Discov 2022; 3:5-15. [PMID: 35015693 PMCID: PMC9245363 DOI: 10.1158/2643-3230.bcd-21-0029] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/26/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphomas are heterogeneous tumors with striking genetic diversity and variable outcomes even within pathologic diagnoses. Treatment response assessment relies on radiologic and nuclear scans, which cannot detect disease at the molecular level. Molecular tumor analyses require invasive tissue biopsies that cannot accurately capture spatial tumor heterogeneity within each patient. Circulating tumor DNA (ctDNA) is a minimally invasive and highly versatile biomarker that overcomes fundamental limitations of imaging scans and tissue biopsies and may aid clinical decision-making in lymphoma. In this review, we highlight the key established principles regarding ctDNA in lymphoma and emphasize the important research questions and future directions. SIGNIFICANCE: ctDNA is an emerging biomarker for lymphomas that noninvasively provides genotypic information and can measure the effectiveness of treatment by detecting the presence of minimal residual disease. Key principles have emerged related to ctDNA for lymphoma, but further studies are needed to standardize its use and establish clinical utility.
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Affiliation(s)
- Mark Roschewski
- Lymphoid Malignancies Branch, National Cancer Institute, Bethesda, Maryland.
| | - Davide Rossi
- Experimental Hematology, Institute of Oncology Research, Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine; Division of Hematology, Department of Medicine, Institute for Stem Cell Biology and Regenerative Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, National Cancer Institute, Bethesda, Maryland
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22
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Ascher J, Cohen J, Huerkamp MJ, Kurtz DM, Newsome JT, Skinner B. Rapid Response by Laboratory Animal Research Institutions During the COVID-19 Pandemic: Key Lessons Learned From a 2021 National Academies of Sciences, Engineering, and Medicine Workshop. ILAR J 2021; 62:332-336. [PMID: 36410003 PMCID: PMC9803960 DOI: 10.1093/ilar/ilac009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Jill Ascher
- Division of Veterinary Resources, National Institutes of Health (NIH), Bethesda, Maryland, USA
| | - Joyce Cohen
- Division of Animal Resources, Emory National Primate Research Center and Emory University School of Medicine, Division of Psychiatry and Behavioral Sciences, Atlanta, Georgia, USA
| | - Michael J Huerkamp
- Division of Animal Resources, School of Medicine and Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
| | - David M Kurtz
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Joseph T Newsome
- Division of Laboratory Animal Resources and School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Brianna Skinner
- Office of the Commissioner, Office of Counterterrorism and Emerging Threats, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
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23
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Kurtz DM, Soo J, Co Ting Keh L, Alig S, Chabon JJ, Sworder BJ, Schultz A, Jin MC, Scherer F, Garofalo A, Macaulay CW, Hamilton EG, Chen B, Olsen M, Schroers-Martin JG, Craig AFM, Moding EJ, Esfahani MS, Liu CL, Dührsen U, Hüttmann A, Casasnovas RO, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA. Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. Nat Biotechnol 2021; 39:1537-1547. [PMID: 34294911 PMCID: PMC8678141 DOI: 10.1038/s41587-021-00981-w] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 06/11/2021] [Indexed: 12/11/2022]
Abstract
Circulating tumor-derived DNA (ctDNA) is an emerging biomarker for many cancers, but the limited sensitivity of current detection methods reduces its utility for diagnosing minimal residual disease. Here we describe phased variant enrichment and detection sequencing (PhasED-seq), a method that uses multiple somatic mutations in individual DNA fragments to improve the sensitivity of ctDNA detection. Leveraging whole-genome sequences from 2,538 tumors, we identify phased variants and their associations with mutational signatures. We show that even without molecular barcodes, the limits of detection of PhasED-seq outperform prior methods, including duplex barcoding, allowing ctDNA detection in the ppm range in participant samples. We profiled 678 specimens from 213 participants with B cell lymphomas, including serial cell-free DNA samples before and during therapy for diffuse large B cell lymphoma. In participants with undetectable ctDNA after two cycles of therapy using a next-generation sequencing-based approach termed cancer personalized profiling by deep sequencing, an additional 25% have ctDNA detectable by PhasED-seq and have worse outcomes. Finally, we demonstrate the application of PhasED-seq to solid tumors.
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Joanne Soo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Lyron Co Ting Keh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Stefan Alig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Foresight Diagnostics, Aurora, CO, USA
| | - Brian J Sworder
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Scherer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Andrea Garofalo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Charles W Macaulay
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Binbin Chen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mari Olsen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Joseph G Schroers-Martin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ulrich Dührsen
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center Essen, University Hospital Essen, Essen, Germany
| | - Andreas Hüttmann
- Department of Hematology and Stem Cell Transplantation, West German Cancer Center Essen, University Hospital Essen, Essen, Germany
| | | | - Jason R Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA.
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24
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Steen CB, Luca BA, Esfahani MS, Azizi A, Sworder BJ, Nabet BY, Kurtz DM, Liu CL, Khameneh F, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles AJ, Newman AM, Alizadeh AA. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell 2021; 39:1422-1437.e10. [PMID: 34597589 PMCID: PMC9205168 DOI: 10.1016/j.ccell.2021.08.011] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/24/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022]
Abstract
Biological heterogeneity in diffuse large B cell lymphoma (DLBCL) is partly driven by cell-of-origin subtypes and associated genomic lesions, but also by diverse cell types and cell states in the tumor microenvironment (TME). However, dissecting these cell states and their clinical relevance at scale remains challenging. Here, we implemented EcoTyper, a machine-learning framework integrating transcriptome deconvolution and single-cell RNA sequencing, to characterize clinically relevant DLBCL cell states and ecosystems. Using this approach, we identified five cell states of malignant B cells that vary in prognostic associations and differentiation status. We also identified striking variation in cell states for 12 other lineages comprising the TME and forming cell state interactions in stereotyped ecosystems. While cell-of-origin subtypes have distinct TME composition, DLBCL ecosystems capture clinical heterogeneity within existing subtypes and extend beyond cell-of-origin and genotypic classes. These results resolve the DLBCL microenvironment at systems-level resolution and identify opportunities for therapeutic targeting (https://ecotyper.stanford.edu/lymphoma).
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Affiliation(s)
- Chloé B Steen
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Bogdan A Luca
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mohammad S Esfahani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Armon Azizi
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - David M Kurtz
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Farnaz Khameneh
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Yasodha Natkunam
- Department of Pathology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - June H Myklebust
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; KG Jebsen Centre for B-cell malignancies, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA 94305, USA
| | - Andrew J Gentles
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Stanford Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.
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25
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Shah AT, Azad TD, Breese MR, Chabon JJ, Hamilton EG, Straessler K, Kurtz DM, Leung SG, Spillinger A, Liu HY, Behroozfard IH, Wittber FM, Hazard FK, Cho SJ, Daldrup-Link HE, Vo KT, Rangaswami A, Pribnow A, Spunt SL, Lacayo NJ, Diehn M, Alizadeh AA, Sweet-Cordero EA. A Comprehensive Circulating Tumor DNA Assay for Detection of Translocation and Copy-Number Changes in Pediatric Sarcomas. Mol Cancer Ther 2021; 20:2016-2025. [PMID: 34353895 PMCID: PMC9307079 DOI: 10.1158/1535-7163.mct-20-0987] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/09/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Most circulating tumor DNA (ctDNA) assays are designed to detect recurrent mutations. Pediatric sarcomas share few recurrent mutations but rather are characterized by translocations and copy-number changes. We applied Cancer Personalized Profiling by deep Sequencing (CAPP-Seq) for detection of translocations found in the most common pediatric sarcomas. We also applied ichorCNA to the combined off-target reads from our hybrid capture to simultaneously detect copy-number alterations (CNA). We analyzed 64 prospectively collected plasma samples from 17 patients with pediatric sarcoma. Translocations were detected in the pretreatment plasma of 13 patients and were confirmed by tumor sequencing in 12 patients. Two of these patients had evidence of complex chromosomal rearrangements in their ctDNA. We also detected copy-number changes in the pretreatment plasma of 7 patients. We found that ctDNA levels correlated with metastatic status and clinical response. Furthermore, we detected rising ctDNA levels before relapse was clinically apparent, demonstrating the high sensitivity of our assay. This assay can be utilized for simultaneous detection of translocations and CNAs in the plasma of patients with pediatric sarcoma. While we describe our experience in pediatric sarcomas, this approach can be applied to other tumors that are driven by structural variants.
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Affiliation(s)
- Avanthi Tayi Shah
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Tej D Azad
- Stanford University School of Medicine, Stanford University, Stanford, California
| | - Marcus R Breese
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Emily G Hamilton
- Cancer Biology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Krystal Straessler
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
- University of Utah School of Medicine, Salt Lake City, Utah
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Stanley G Leung
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Aviv Spillinger
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Heng-Yi Liu
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Inge H Behroozfard
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Frederick M Wittber
- Department of Radiology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Florette K Hazard
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Soo-Jin Cho
- Departments of Pathology and Laboratory Medicine, University of California San Francisco, San Francisco, California
| | - Heike E Daldrup-Link
- Department of Radiology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Kieuhoa T Vo
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Arun Rangaswami
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California
| | - Allison Pribnow
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Sheri L Spunt
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford University, Stanford, California
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Norman J Lacayo
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford University, Stanford, California
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Maximilian Diehn
- Division of Radiation Therapy, Department of Radiation Oncology, Stanford University School of Medicine, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford University, Stanford, California
| | - E Alejandro Sweet-Cordero
- Division of Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Fransisco, California.
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26
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Alig S, Macaulay CW, Kurtz DM, Dührsen U, Hüttmann A, Schmitz C, Jin MC, Sworder BJ, Garofalo A, Shahrokh Esfahani M, Nabet BY, Soo J, Scherer F, Craig AFM, Casasnovas O, Westin JR, Gaidano G, Rossi D, Roschewski M, Wilson WH, Meignan M, Diehn M, Alizadeh AA. Short Diagnosis-to-Treatment Interval Is Associated With Higher Circulating Tumor DNA Levels in Diffuse Large B-Cell Lymphoma. J Clin Oncol 2021; 39:2605-2616. [PMID: 33909455 DOI: 10.1200/jco.20.02573] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE Patients with Diffuse Large B-cell Lymphoma (DLBCL) in need of immediate therapy are largely under-represented in clinical trials. The diagnosis-to-treatment interval (DTI) has recently been described as a metric to quantify such patient selection bias, with short DTI being associated with adverse risk factors and inferior outcomes. Here, we characterized the relationships between DTI, circulating tumor DNA (ctDNA), conventional risk factors, and clinical outcomes, with the goal of defining objective disease metrics contributing to selection bias. PATIENTS AND METHODS We evaluated pretreatment ctDNA levels in 267 patients with DLBCL treated across multiple centers in Europe and the United States using Cancer Personalized Profiling by Deep Sequencing. Pretreatment ctDNA levels were correlated with DTI, total metabolic tumor volumes (TMTVs), the International Prognostic Index (IPI), and outcome. RESULTS Short DTI was associated with advanced-stage disease (P < .001) and higher IPI (P < .001). We also found an inverse correlation between DTI and TMTV (RS = -0.37; P < .001). Similarly, pretreatment ctDNA levels were significantly associated with stage, IPI, and TMTV (all P < .001), demonstrating that both DTI and ctDNA reflect disease burden. Notably, patients with shorter DTI had higher pretreatment ctDNA levels (P < .001). Pretreatment ctDNA levels predicted short DTI independent of the IPI (P < .001). Although each risk factor was significantly associated with event-free survival in univariable analysis, ctDNA level was prognostic of event-free survival independent of DTI and IPI in multivariable Cox regression (ctDNA: hazard ratio, 1.5; 95% CI [1.2 to 2.0]; IPI: 1.1 [0.9 to 1.3]; -DTI: 1.1 [1.0 to 1.2]). CONCLUSION Short DTI largely reflects baseline tumor burden, which can be objectively measured using pretreatment ctDNA levels. Pretreatment ctDNA levels therefore have utility for quantifying and guarding against selection biases in prospective DLBCL clinical trials.
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Affiliation(s)
- Stefan Alig
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Charles W Macaulay
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - David M Kurtz
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Ulrich Dührsen
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Andreas Hüttmann
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Christine Schmitz
- Department of Hematology, University Hospital of Essen, Essen, Germany
| | - Michael C Jin
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Brian J Sworder
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Andrea Garofalo
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | | | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA
| | - Joanne Soo
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Florian Scherer
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA.,Department Medicine I, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander F M Craig
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA
| | - Olivier Casasnovas
- Hematology Department, University Hospital F. Mitterrand and Inserm UMR 1231, Dijon, France
| | - Jason R Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Piemonte Orientale Amedeo Avogadro, Novara, Italy
| | - Davide Rossi
- Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Mark Roschewski
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Wyndham H Wilson
- National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, CA.,Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford, CA
| | - Ash A Alizadeh
- Department of Medicine, Divisions of Oncology and Hematology, Stanford University, Stanford, CA.,Stanford Cancer Institute, Institute for Stem Cell Biology & Regenerative Medicine, Stanford, CA
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27
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Binkley MS, Jeon YJ, Nesselbush M, Moding EJ, Nabet B, Almanza D, Yoo C, Kurtz DM, Owen SG, Backhus LM, Berry MF, Shrager JB, Ramchandran KJ, Padda SK, Das M, Neal JW, Wakelee HA, Alizadeh AA, Loo BW, Diehn M. Abstract PO-059: Investigating gene expression profiles associated with clinical radiation resistance in KEAP1/NFE2L2 wildtype lung cancer. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.radsci21-po-059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: We previously reported that approximately half of local recurrences (LR) after radiotherapy for localized NSCLC harbor mutations in KEAP1 or NFE2L2. Here we sought to explore factors associated with LR after radiotherapy in KEAP1/NFE2L2 wildtype NSCLC. Methods: We identified consecutive patients with stage IA1-IIIC NSCLC treated at our institution with chemoradiotherapy (CRT) or stereotactic ablative radiotherapy (SABR) from 2009-2018 and who had genotyping performed on tumor tissue with full coverage of common recurrent lung cancer driver genes including TP53, KRAS, KEAP1, and NFE2L2. We defined LR as tumor regrowth within the prescription dose radiotherapy volume. Our primary objective was to identify factors associated with LR in KEAP1/NFE2L2WT tumors. We performed RNA-seq on a subset of cases with available tissue using the SMARTer Stranded total RNA-seq Kit v2 (Takara Bio USA, Inc.). Statistical analysis was performed using R (version 3.6) with differential gene expression performed using ‘DESeq2’. All P-values were two-sided and considered significant at P<0.05 with adjustment for multiple hypothesis testing when appropriate. Results: We identified 139 consecutive patients with localized NSCLC who received tumor genotyping and were treated with CRT for stage IIB-IIIC NSCLC (n=58) or SABR for stage I-IIB NSCLC (n=81). 26 (18.7%) of these patients harbored KEAP1/NFE2L2WT tumors. Clinical factors such as tumor volume (P=0.18), histology (P=0.87), and radiation dose (P=0.3) were not associated with LR in this subset. Similarly, somatic mutation analysis did not reveal association of any recurrent driver mutations with LR in these KEAP1/NFE2L2WT tumors, including in TP53 (n=19; P=0.73) or KRAS (n=9; P=0.98). Tissue was available for RNA-seq analysis of 38 KEAP1/NFE2L2WT tumors, of which the majority were adenocarcinomas (n=25, 65.8%) and approximately half each received CRT (n=20, 52.6%) and SABR (n=18, 47.4%). Gene set enrichment analysis revealed a trend for association of LR with expression of hypoxia genes (P=0.07, Q=0.28). Similarly, a previously reported 10-gene radiation sensitivity index (RSI) was not associated with LR (P=0.34). Individual gene analysis identified KRT14 as being significantly less expressed in cases with LR (adjusted P=2.2e-9). In a validation cohort of 24 stage I-IIA KEAP1/NFE2L2WT patients from the TCGA who were treated with radiotherapy, those who died had lower expression of KRT14 than those who did not (P=0.0003). Conclusions: In summary, we identify low expression of KRT14, a squamous cell carcinoma differentiation gene, as a potential biomarker for increased risk of LR after definitive radiotherapy of KEAP1/NFE2L2WT NSCLC. Validation in larger cohorts and biological characterization will be required to determine if this biomarker could be useful for guiding precision radiotherapy approaches.
Citation Format: Michael S. Binkley, Young-Jun Jeon, Monica Nesselbush, Everett J. Moding, Barzin Nabet, Diego Almanza, Christopher Yoo, David M. Kurtz, Susie Grant Owen, Leah M. Backhus, Mark F. Berry, Joseph B. Shrager, Kavitha J. Ramchandran, Sukhmani K. Padda, Millie Das, Joel W. Neal, Heather A. Wakelee, Ash A. Alizadeh, Billy W. Loo, Maximilian Diehn. Investigating gene expression profiles associated with clinical radiation resistance in KEAP1/NFE2L2 wildtype lung cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr PO-059.
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Affiliation(s)
| | | | | | | | - Barzin Nabet
- 3Department of Oncology Biomarker Development, Genentech, South San Francisco, CA
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28
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA.
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29
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Sills RC, Johnson GA, Anderson RJ, Johnson CL, Staup M, Brown DL, Churchill SR, Kurtz DM, Cushman JD, Waidyanatha S, Robinson VG, Cesta MF, Andrews DMK, Behl M, Shockley KR, Little PB. Qualitative and Quantitative Neuropathology Approaches Using Magnetic Resonance Microscopy (Diffusion Tensor Imaging) and Stereology in a Hexachlorophene Model of Myelinopathy in Sprague-Dawley Rats. Toxicol Pathol 2020; 48:965-980. [PMID: 33334257 PMCID: PMC7755100 DOI: 10.1177/0192623320968210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
It is well established that hexachlorophene, which is used as an antibacterial agent, causes intramyelinic edema in humans and animal models. The hexachlorophene myelinopathy model, in which male Sprague-Dawley rats received 25 to 30 mg/kg hexachlorophene by gavage for up to 5 days, provided an opportunity to compare traditional neuropathology evaluations with magnetic resonance microscopy (MRM) findings. In addition, stereology assessments of 3 neuroanatomical sites were compared to quantitative measurements of similar structures by MRM. There were positive correlations between hematoxylin and eosin and luxol fast blue stains and MRM for identifying intramyelinic edema in the cingulum of corpus callosum, optic chiasm, anterior commissure (aca), lateral olfactory tracts, pyramidal tracts (py), and white matter tracts in the cerebellum. Stereology assessments were focused on the aca, longitudinal fasciculus of the pons, and py and demonstrated differences between control and treated rats, as was observed using MRM. The added value of MRM assessments was the ability to acquire qualitative 3-dimensional (3-D) images and obtain quantitative measurements of intramyelinic edema in 26 neuroanatomical sites in the intact brain. Also, diffusion tensor imaging (fractional anisotropy [FA]) indicated that there were changes in the cytoarchitecture of the white matter as detected by decreases in the FA in the treated compared to the control rats. This study demonstrates creative strategies that are possible using qualitative and quantitative assessments of potential white matter neurotoxicants in nonclinical toxicity studies. Our results lead us to the conclusion that volumetric analysis by MRM and stereology adds significant value to the standard 2-D microscopic evaluations.
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Affiliation(s)
- Robert C Sills
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - G Allan Johnson
- Duke Center for In Vivo Microscopy, 3065Duke University School of Medicine, Durham, NC, USA
| | - Robert J Anderson
- Duke Center for In Vivo Microscopy, 3065Duke University School of Medicine, Durham, NC, USA
| | | | - Michael Staup
- 25913Charles River Laboratories Inc, Durham, NC, USA
| | | | | | - David M Kurtz
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jesse D Cushman
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Suramya Waidyanatha
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Veronica Godfrey Robinson
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Mark F Cesta
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Danica M K Andrews
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Mamta Behl
- Division of the National Toxicology Program, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Keith R Shockley
- Division of Intramural Research, 6857National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Peter B Little
- Experimental Pathology Laboratories, Inc, Research Triangle Park, NC, USA
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30
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Cirillo M, Craig AFM, Borchmann S, Kurtz DM. Liquid biopsy in lymphoma: Molecular methods and clinical applications. Cancer Treat Rev 2020; 91:102106. [PMID: 33049623 PMCID: PMC8043056 DOI: 10.1016/j.ctrv.2020.102106] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/31/2020] [Accepted: 09/15/2020] [Indexed: 02/07/2023]
Abstract
In this article, we broadly review the application of cfDNA analysis to the diagnosis and management of lymphoma. We introduce the advantages of cfDNA measurement over conventional tissue biopsy and describe how cfDNA may be utilized for both genotyping and detection of minimal residual disease. First, we discuss genotyping, beginning with differences in identifying mutations from the blood plasma vs. from circulating cells. We review the technical distinctions between PCR- and NGS-based assays and describe two important applications of NGS-based cfDNA tests, namely the identification of resistance mutations and classification of disease subtype. We discuss difficulties in genotyping diseases with low burden of tumor cells and the application of cfDNA assays in these contexts. Second, we describe the utility of ctDNA measurement in assessing MRD. We cover recent advances in the assessment of pre-treatment disease burden as a prognostic biomarker, detection of molecular response to therapy, and early detection of relapsing disease. Third, we explore select emerging areas of research in ctDNA technologies that show promise in boosting the performance of existing ctDNA-based assays. These include cell-free DNA fragment structure analysis or 'fragmentomics', epigenetic modifications, and novel circulating analytes such as tumor-educated platelets and extracellular vesicular DNA. We also discuss alternative analytes to blood plasma for tumor detection, such as urine, saliva, and stool. Finally, we present a case that highlights potential applications of ctDNA approaches to the management of patients with lymphoma, while also defining important prerequisite advances before this can be fully realized. We close with a look to the future of cfDNA applications, outlining one potential timeline and path forward towards routine clinical application.
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Affiliation(s)
- Melita Cirillo
- Royal Perth Hospital, Perth, Australia; University of Western Australia, Perth, Australia
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; University of California, San Francisco School of Medicine, San Francisco, CA, USA
| | - Sven Borchmann
- University of Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologne Duesseldorf, German Hodgkin Study Group, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital of Cologne, Center for Molecular Medicine, Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital of Cologne, Else Kröner Forschungskolleg Clonal Evolution in Cancer, Cologne, Germany.
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
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31
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Binkley MS, Jeon YJ, Nesselbush M, Moding EJ, Nabet BY, Almanza D, Kunder C, Stehr H, Yoo CH, Rhee S, Xiang M, Chabon JJ, Hamilton E, Kurtz DM, Gojenola L, Owen SG, Ko RB, Shin JH, Maxim PG, Lui NS, Backhus LM, Berry MF, Shrager JB, Ramchandran KJ, Padda SK, Das M, Neal JW, Wakelee HA, Alizadeh AA, Loo BW, Diehn M. KEAP1/NFE2L2 Mutations Predict Lung Cancer Radiation Resistance That Can Be Targeted by Glutaminase Inhibition. Cancer Discov 2020; 10:1826-1841. [PMID: 33071215 PMCID: PMC7710558 DOI: 10.1158/2159-8290.cd-20-0282] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [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: 03/08/2020] [Revised: 08/12/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022]
Abstract
Tumor genotyping is not routinely performed in localized non-small cell lung cancer (NSCLC) due to lack of associations of mutations with outcome. Here, we analyze 232 consecutive patients with localized NSCLC and demonstrate that KEAP1 and NFE2L2 mutations are predictive of high rates of local recurrence (LR) after radiotherapy but not surgery. Half of LRs occurred in tumors with KEAP1/NFE2L2 mutations, indicating that they are major molecular drivers of clinical radioresistance. Next, we functionally evaluate KEAP1/NFE2L2 mutations in our radiotherapy cohort and demonstrate that only pathogenic mutations are associated with radioresistance. Furthermore, expression of NFE2L2 target genes does not predict LR, underscoring the utility of tumor genotyping. Finally, we show that glutaminase inhibition preferentially radiosensitizes KEAP1-mutant cells via depletion of glutathione and increased radiation-induced DNA damage. Our findings suggest that genotyping for KEAP1/NFE2L2 mutations could facilitate treatment personalization and provide a potential strategy for overcoming radioresistance conferred by these mutations. SIGNIFICANCE: This study shows that mutations in KEAP1 and NFE2L2 predict for LR after radiotherapy but not surgery in patients with NSCLC. Approximately half of all LRs are associated with these mutations and glutaminase inhibition may allow personalized radiosensitization of KEAP1/NFE2L2-mutant tumors.This article is highlighted in the In This Issue feature, p. 1775.
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Affiliation(s)
- Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford, California
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | | | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, California
- Stanford Cancer Institute, Stanford, California
| | - Diego Almanza
- Cancer Biology Program, Stanford University, Stanford, California
| | - Christian Kunder
- Department of Pathology, Stanford University, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, California
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Siyeon Rhee
- Department of Biology, Stanford University, Stanford, California
| | - Michael Xiang
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, California
| | | | - Emily Hamilton
- Cancer Biology Program, Stanford University, Stanford, California
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, California
| | - Susie Grant Owen
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, California
| | | | - Peter G Maxim
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Natalie S Lui
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Leah M Backhus
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Mark F Berry
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Kavitha J Ramchandran
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Millie Das
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Joel W Neal
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, California
- Stanford Cancer Institute, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California.
- Stanford Cancer Institute, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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Avanzini S, Kurtz DM, Chabon JJ, Moding EJ, Hori SS, Gambhir SS, Alizadeh AA, Diehn M, Reiter JG. A mathematical model of ctDNA shedding predicts tumor detection size. Sci Adv 2020; 6:eabc4308. [PMID: 33310847 PMCID: PMC7732186 DOI: 10.1126/sciadv.abc4308] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/29/2020] [Indexed: 05/12/2023]
Abstract
Early cancer detection aims to find tumors before they progress to an incurable stage. To determine the potential of circulating tumor DNA (ctDNA) for cancer detection, we developed a mathematical model of tumor evolution and ctDNA shedding to predict the size at which tumors become detectable. From 176 patients with stage I to III lung cancer, we inferred that, on average, 0.014% of a tumor cell's DNA is shed into the bloodstream per cell death. For annual screening, the model predicts median detection sizes of 2.0 to 2.3 cm representing a ~40% decrease from the current median detection size of 3.5 cm. For informed monthly cancer relapse testing, the model predicts a median detection size of 0.83 cm and suggests that treatment failure can be detected 140 days earlier than with imaging-based approaches. This mechanistic framework can help accelerate clinical trials by precomputing the most promising cancer early detection strategies.
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Affiliation(s)
- Stefano Avanzini
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - David M Kurtz
- Division of Oncology, Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jacob J Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Everett J Moding
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sharon Seiko Hori
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sanjiv Sam Gambhir
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Molecular Imaging Program at Stanford, Department of Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Bio-X Program, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering and Department of Materials Science and Engineering, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Division of Hematology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johannes G Reiter
- Canary Center for Cancer Early Detection, Department of Radiology, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Bio-X Program, Stanford University, Stanford, CA 94305, USA
- Department of Biomedical Data Science, Biophysics Program, Stanford University, Stanford, CA 94305, USA
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Kurtz DM. Abstract IA41: Approaches for personalized medicine in lymphoma through liquid biopsies. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-ia41] [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] Open
Abstract
Abstract
Over the last decade, circulating tumor DNA (ctDNA) has emerged as an important biomarker across a range of cancers, including lymphomas. The potential clinical applications of ctDNA technologies are broad, including tumor mutational genotyping, detection of molecular responses and minimal residual disease, as well as early detection of relapsing disease with specific attention to mechanisms of resistance. Numerous opportunities therefore exist to apply ctDNA methodologies to tailor therapy for individual patients. By applying targeted next-generation sequencing of ctDNA via Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) in patients with lymphoma, these opportunities for precision oncology largely fall into two groups—identification of specific targetable molecular features and quantitative assessment of disease burden and risk. Here we explore these approaches in patients with diffuse large B-cell lymphoma (DLBCL) undergoing first-line or salvage therapy. Utilizing CAPP-Seq from pretreatment plasma, mutational genotyping of diverse somatic alterations is possible, including single-nucleotide variants (SNVs), translocations, and copy number alterations. By combining these mutations through an integrated Bayesian framework, identification of specific disease subtypes is possible, including activated and germinal center B-cell molecular cell-of-origin subtypes. In addition, detection of emergent mutations during and after treatment can provide insights into mechanisms of therapeutic resistance, many of which are potentially targetable. In addition to these insights into disease biology, ctDNA can serve as a quantitative handle on disease burden. By measuring ctDNA disease burden in DLBCL patients from six centers throughout North America and Europe, we demonstrate the prognostic value of ctDNA levels prior to treatment. Additionally, we found that a molecular response to treatment, as detected by the change in ctDNA after one or two cycles of therapy, is highly prognostic for patient outcomes in both front-line and later lines of therapy. Moreover, these molecular response features can be combined with additional outcome predictors, such as the IPI and interim PET/CT scans, to build a dynamic risk model termed the Continuous Individualized Risk Index (CIRI). CIRI provides a personalized probability of likely patient outcomes that updates over time as more information becomes available. Outcome prediction with CIRI significantly improved on predictions using ctDNA molecular response, interim PET/CT scans, or the IPI alone. In summary, liquid biopsies through ctDNA afford numerous opportunities for personalized medicine, ranging from mutational profiling and molecular subtyping to disease quantification and response prediction. Further studies of novel clinical approaches are likely to change treatment paradigms in the near future.
Citation Format: David M. Kurtz. Approaches for personalized medicine in lymphoma through liquid biopsies [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr IA41.
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Kurtz DM, Feeney WP. The Influence of Feed and Drinking Water on Terrestrial Animal Research and Study Replicability. ILAR J 2020; 60:175-196. [PMID: 32706372 DOI: 10.1093/ilar/ilaa012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 12/29/2022] Open
Abstract
For more than 50 years, the research community has made strides to better determine the nutrient requirements for many common laboratory animal species. This work has resulted in high-quality animal feeds that can optimize growth, maintenance, and reproduction in most species. We have a much better understanding of the role that individual nutrients play in physiological responses. Today, diet is often considered as an independent variable in experimental design, and specialized diet formulations for experimental purposes are widely used. In contrast, drinking water provided to laboratory animals has rarely been a consideration in experimental design except in studies of specific water-borne microbial or chemical contaminants. As we advance in the precision of scientific measurements, we are constantly discovering previously unrecognized sources of experimental variability. This is the nature of science. However, science is suffering from a lack of experimental reproducibility or replicability that undermines public trust. The issue of reproducibility/replicability is especially sensitive when laboratory animals are involved since we have the ethical responsibility to assure that laboratory animals are used wisely. One way to reduce problems with reproducibility/replicability is to have a strong understanding of potential sources of inherent variability in the system under study and to provide "…a clear, specific, and complete description of how the reported results were reached [1]." A primary intent of this review is to provide the reader with a high-level overview of some basic elements of laboratory animal nutrition, methods used in the manufacturing of feeds, sources of drinking water, and general methods of water purification. The goal is to provide background on contemporary issues regarding how diet and drinking water might serve as a source of extrinsic variability that can impact animal health, study design, and experimental outcomes and provide suggestions on how to mitigate these effects.
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Affiliation(s)
- David M Kurtz
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - William P Feeney
- Global Comparative and Translational Sciences, Integrated Biological Platform Sciences Department, GlaxoSmithKline, Collegeville, Pennsylvania
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Avanzini S, Kurtz DM, Chabon JJ, Hori SS, Alizadeh AA, Diehn M, Reiter JG. Abstract PR01: ctDNA shedding dynamics dictate early lung cancer detection potential. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-pr01] [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
Early cancer detection aims to find tumors before they progress to an incurable stage. Prospective studies with tens of thousands of healthy participants are ongoing to determine whether asymptomatic cancers can be accurately detected by analyzing circulating tumor DNA (ctDNA) from blood samples. We developed a stochastic mathematical model of tumor evolution and ctDNA shedding to investigate the potential and the limitations of ctDNA-based cancer early detection tests. We inferred ctDNA shedding rates of early-stage lung cancers and calculated that a 15-mL blood sample contains on average only 1.5 genome equivalents (GE) of ctDNA for lung tumors with 1 billion cells (concentration of 0.19 GE per plasma mL; tumor fraction of 0.02%). This low level of ctDNA can be explained by the relatively low turnover rate of lung cancer cells. Similarly, fast-growing tumors led to lower levels of ctDNA because a lower number of cell death events decreases the amount of released ctDNA. We designed a detection test of virtual tumors that accounts for the varying plasma DNA concentrations in cancer and cancer-free patients and that incorporates various sources for technical and biologic errors. Two important considerations for disease detection are the expected number of mutations per tumor covered by the sequencing panel and the underlying error rate of the sequencing assay. To determine the potential performance of mutation-based ctDNA detection tests, we computed receiver operating characteristic (ROC) curves and calculated area under the curve (AUC) values. In the case of early relapse detection, we assumed that the sequencing panel covers 20 known clonal mutations per primary tumor with a background error-rate of 1.5 × 10−5 per base pair. For monthly relapse testing with a specificity of 99.5%, we found a median detection size of 0.19 cm3. Moreover, we observed a lead time of 180 days compared to monthly imaging-based relapse detection. While tracking fewer than 20 mutations drastically decreased the expected lead time, tracking more than 20 mutations only minimally increased the expected lead time. Similarly, the increases in lead time gained slowed down for more frequent testing than one month for relapsing tumors with a growth rate of 1%. In the case of cancer screening, we assumed that the sequencing panel has the same error rate as above and covers 2,000 base pairs, resulting in approximately one detectable mutation per lung cancer, which is similar to the CancerSEEK panel. For an annual screening test with a specificity of 99.5%, we found a median lung cancer detection size of 4.4 cm3. This detection size constitutes a more than 80% reduction from the current median detection size of 22.5 cm3 for lung cancers and suggests a potential lead time of 410 days. This mathematical framework provides a mechanistic interpretation of ctDNA-based test results and informs the design of future screening and relapse detection initiatives across cancer types and subpopulations with varying risks.
This abstract is also being presented as Poster A01.
Citation Format: Stefano Avanzini, David M. Kurtz, Jacob J. Chabon, Sharon S. Hori, Ash A. Alizadeh, Maximilian Diehn, Johannes G. Reiter. ctDNA shedding dynamics dictate early lung cancer detection potential [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 PR01.
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Chabon JJ, Hamilton EG, Kurtz DM, Esfahani MS, Moding EJ, Stehr H, Schroers-Martin J, Nabet BY, Chen B, Chaudhuri AA, Liu CL, Hui AB, Jin MC, Azad TD, Almanza D, Jeon YJ, Nesselbush MC, Co Ting Keh L, Bonilla RF, Yoo CH, Ko RB, Chen EL, Merriott DJ, Massion PP, Mansfield AS, Jen J, Ren HZ, Lin SH, Costantino CL, Burr R, Tibshirani R, Gambhir SS, Berry GJ, Jensen KC, West RB, Neal JW, Wakelee HA, Loo BW, Kunder CA, Leung AN, Lui NS, Berry MF, Shrager JB, Nair VS, Haber DA, Sequist LV, Alizadeh AA, Diehn M. Integrating genomic features for non-invasive early lung cancer detection. Nature 2020; 580:245-251. [PMID: 32269342 PMCID: PMC8230734 DOI: 10.1038/s41586-020-2140-0] [Citation(s) in RCA: 324] [Impact Index Per Article: 81.0] [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: 07/30/2019] [Accepted: 02/13/2020] [Indexed: 11/08/2022]
Abstract
Radiologic screening of high-risk adults reduces lung-cancer-related mortality1,2; however, a small minority of eligible individuals undergo such screening in the United States3,4. The availability of blood-based tests could increase screening uptake. Here we introduce improvements to cancer personalized profiling by deep sequencing (CAPP-Seq)5, a method for the analysis of circulating tumour DNA (ctDNA), to better facilitate screening applications. We show that, although levels are very low in early-stage lung cancers, ctDNA is present prior to treatment in most patients and its presence is strongly prognostic. We also find that the majority of somatic mutations in the cell-free DNA (cfDNA) of patients with lung cancer and of risk-matched controls reflect clonal haematopoiesis and are non-recurrent. Compared with tumour-derived mutations, clonal haematopoiesis mutations occur on longer cfDNA fragments and lack mutational signatures that are associated with tobacco smoking. Integrating these findings with other molecular features, we develop and prospectively validate a machine-learning method termed 'lung cancer likelihood in plasma' (Lung-CLiP), which can robustly discriminate early-stage lung cancer patients from risk-matched controls. This approach achieves performance similar to that of tumour-informed ctDNA detection and enables tuning of assay specificity in order to facilitate distinct clinical applications. Our findings establish the potential of cfDNA for lung cancer screening and highlight the importance of risk-matching cases and controls in cfDNA-based screening studies.
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Affiliation(s)
- Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joseph Schroers-Martin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Barzin Y Nabet
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Binbin Chen
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Tej D Azad
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Diego Almanza
- Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | | | | | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily L Chen
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - David J Merriott
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Pierre P Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Veterans Affairs, Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Aaron S Mansfield
- Department of Oncology, Division of Medical Oncology, Mayo Clinic, Rochester, MN, USA
| | - Jin Jen
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hong Z Ren
- Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Steven H Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christina L Costantino
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Risa Burr
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Robert Tibshirani
- Department of Statistics, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Sanjiv S Gambhir
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kristin C Jensen
- Department of Pathology, Stanford University, Stanford, CA, USA
- VA Palo Alto Healthcare System, Palo Alto, Stanford, CA, USA
| | - Robert B West
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | | | - Ann N Leung
- Department of Radiology, Stanford University, Stanford, CA, USA
| | - Natalie S Lui
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Mark F Berry
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Joseph B Shrager
- VA Palo Alto Healthcare System, Palo Alto, Stanford, CA, USA
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford University, Stanford, CA, USA
| | - Viswam S Nair
- Department of Radiology, Stanford University, Stanford, CA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, USA
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
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Whiteside TE, Qu W, DeVito MJ, Brar SS, Bradham KD, Nelson CM, Travlos GS, Kissling GE, Kurtz DM. Elevated Arsenic and Lead Concentrations in Natural Healing Clay Applied Topically as a Treatment for Ulcerative Dermatitis in Mice. J Am Assoc Lab Anim Sci 2020; 59:212-220. [PMID: 32059757 PMCID: PMC7073401 DOI: 10.30802/aalas-jaalas-19-000068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/10/2019] [Accepted: 08/22/2019] [Indexed: 11/05/2022]
Abstract
Ulcerative dermatitis in laboratory mice remains an ongoing clinical problem and animal welfare issue. Many products have been used to treat dermatitis in mice, with varying success. Recently, the topical administration of healing clays, such as bentonite and green clays, has been explored as a viable, natural treatment. We found high concentrations of arsenic and lead in experimental samples of therapeutic clay. Given the known toxic effects of these environmental heavy metals, we sought to determine whether the topical administration of a clay product containing bioavailable arsenic and lead exerted a biologic effect in mice that potentially could introduce unwanted research variability. Two cohorts of 20 singly housed, shaved, dermatitis free, adult male CD1 mice were dosed daily for 2 wk by topical application of saline or green clay paste. Samples of liver, kidney and whole blood were collected and analyzed for total arsenic and lead concentrations. Hepatic and renal concentrations of arsenic were not different between treated and control mice in either cohort; however, hepatic and renal concentrations of lead were elevated in clay treated mice compared to controls in both cohorts. In addition, in both cohorts, the activity of δ-aminolevulinate acid dehydratase, an enzyme involved with heme biosynthesis and a marker of lead toxicity, did not differ significantly between the clay-treated mice and controls. We have demonstrated that these clay products contain high concentrations of arsenic and lead and that topical application can result in the accumulation of lead in the liver and kidneys; however, these concentrations did not result in measurable biologic effects. These products should be used with caution, especially in studies of lead toxicity, heme biosynthesis, and renal α2 microglobulin function.
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Affiliation(s)
- Tanya E Whiteside
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Wei Qu
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Michael J DeVito
- National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Sukhdev S Brar
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Karen D Bradham
- Office of Research and Development, Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Clay M Nelson
- Office of Research and Development, Environmental Protection Agency, Research Triangle Park, North Carolina
| | - Gregory S Travlos
- Cellular and Molecular Pathology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Grace E Kissling
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina;,
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Azad TD, Chaudhuri AA, Fang P, Qiao Y, Esfahani MS, Chabon JJ, Hamilton EG, Yang YD, Lovejoy A, Newman AM, Kurtz DM, Jin M, Schroers-Martin J, Stehr H, Liu CL, Hui ABY, Patel V, Maru D, Lin SH, Alizadeh AA, Diehn M. Circulating Tumor DNA Analysis for Detection of Minimal Residual Disease After Chemoradiotherapy for Localized Esophageal Cancer. Gastroenterology 2020; 158:494-505.e6. [PMID: 31711920 PMCID: PMC7010551 DOI: 10.1053/j.gastro.2019.10.039] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Biomarkers are needed to risk stratify after chemoradiotherapy for localized esophageal cancer. These could improve identification of patients at risk for cancer progression and selection of additional therapy. METHODS We performed deep sequencing (CAncer Personalized Profiling by deep Sequencing, [CAPP-Seq]) analyses of plasma cell-free DNA collected from 45 patients before and after chemoradiotherapy for esophageal cancer, as well as DNA from leukocytes and fixed esophageal tumor biopsy samples collected during esophagogastroduodenoscopy. Patients were treated from May 2010 through October 2015; 23 patients subsequently underwent esophagectomy, and 22 did not undergo surgery. We also sequenced DNA from blood samples from 40 healthy control individuals. We analyzed 802 regions of 607 genes for single-nucleotide variants previously associated with esophageal adenocarcinoma or squamous cell carcinoma. Patients underwent imaging analyses 6-8 weeks after chemoradiotherapy and were followed for 5 years. Our primary aim was to determine whether detection of circulating tumor DNA (ctDNA) after chemoradiotherapy is associated with risk of tumor progression (growth of local, regional, or distant tumors, detected by imaging or biopsy). RESULTS The median proportion of tumor-derived DNA in total cell-free DNA before treatment was 0.07%, indicating that ultrasensitive assays are needed for quantification and analysis of ctDNA from localized esophageal tumors. Detection of ctDNA after chemoradiotherapy was associated with tumor progression (hazard ratio, 18.7; P < .0001), formation of distant metastases (hazard ratio, 32.1; P < .0001), and shorter disease-specific survival times (hazard ratio, 23.1; P < .0001). A higher proportion of patients with tumor progression had new mutations detected in plasma samples collected after chemoradiotherapy than patients without progression (P = .03). Detection of ctDNA after chemoradiotherapy preceded radiographic evidence of tumor progression by an average of 2.8 months. Among patients who received chemoradiotherapy without surgery, combined ctDNA and metabolic imaging analysis predicted progression in 100% of patients with tumor progression, compared with 71% for only ctDNA detection and 57% for only metabolic imaging analysis (P < .001 for comparison of either technique to combined analysis). CONCLUSIONS In an analysis of cell-free DNA in blood samples from patients who underwent chemoradiotherapy for esophageal cancer, detection of ctDNA was associated with tumor progression, metastasis, and disease-specific survival. Analysis of ctDNA might be used to identify patients at highest risk for tumor progression.
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Affiliation(s)
- Tej D. Azad
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Aadel A. Chaudhuri
- Department of Radiation Oncology, Washington University in St. Louis, St. Louis, MO, USA
| | - Penny Fang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yawei Qiao
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mohammad S. Esfahani
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Emily G. Hamilton
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Yi D. Yang
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Alex Lovejoy
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Aaron M. Newman
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - David M. Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Michael Jin
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Joseph Schroers-Martin
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Henning Stehr
- Department of Radiation Oncology, Stanford University, Stanford, California, USA,Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Viren Patel
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dipen Maru
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Steven H. Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, California, USA,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California; Stanford Cancer Institute, Stanford University, Stanford, California; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.
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39
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Rossi D, Kurtz DM, Roschewski M, Cavalli F, Zucca E, Wilson WH. The development of liquid biopsy for research and clinical practice in lymphomas: Report of the 15‐ICML workshop on ctDNA. Hematol Oncol 2019; 38:34-37. [DOI: 10.1002/hon.2704] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Davide Rossi
- Institute of Oncology ResearchUniversità della Svizzera Italiana Bellinzona Switzerland
- HematologyOncology Institute of Southern Switzerland Bellinzona Switzerland
| | - David M. Kurtz
- Division of Oncology, Department of MedicineStanford University Stanford California
| | - Mark Roschewski
- National Cancer InstituteNational Institutes of Health Bethesda Maryland
| | - Franco Cavalli
- Institute of Oncology ResearchUniversità della Svizzera Italiana Bellinzona Switzerland
| | - Emanuele Zucca
- Institute of Oncology ResearchUniversità della Svizzera Italiana Bellinzona Switzerland
- HematologyOncology Institute of Southern Switzerland Bellinzona Switzerland
| | - Wyndham H. Wilson
- National Cancer InstituteNational Institutes of Health Bethesda Maryland
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40
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Abstract
Emerging methods to detect tumor-derived DNA in the blood plasma of patients with lymphomas-so-called "circulating tumor DNA" (ctDNA)-have the potential to change the way in which lymphoma is diagnosed and managed in the clinic. The possible applications for ctDNA are numerous, including mutation genotyping, response monitoring, and detection of minimal residual disease during a time of radiographic remission. This article discusses the methodology for detecting ctDNA in aggressive B-cell lymphomas, including digital polymerase chain reaction, targeted sequencing of immunoglobulin receptors, and targeted next-generation sequencing. The advantages of each of these methods are also compared, with a focus on promising clinical applications. These include identification of molecular subtypes (eg, cell-of-origin and double-hit lymphomas) from pretreatment plasma, molecular response prediction after an initial course of therapy, and early detection of relapsing disease prior to clinical relapse. Finally, this article discusses the challenges in implementing ctDNA assays in the clinic today, including possible solutions to these challenges.
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
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41
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Kurtz DM, Esfahani MS, Scherer F, Soo J, Jin MC, Liu CL, Newman AM, Dührsen U, Hüttmann A, Casasnovas O, Westin JR, Ritgen M, Böttcher S, Langerak AW, Roschewski M, Wilson WH, Gaidano G, Rossi D, Bahlo J, Hallek M, Tibshirani R, Diehn M, Alizadeh AA. Dynamic Risk Profiling Using Serial Tumor Biomarkers for Personalized Outcome Prediction. Cell 2019; 178:699-713.e19. [PMID: 31280963 DOI: 10.1016/j.cell.2019.06.011] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/19/2019] [Accepted: 06/04/2019] [Indexed: 12/18/2022]
Abstract
Accurate prediction of long-term outcomes remains a challenge in the care of cancer patients. Due to the difficulty of serial tumor sampling, previous prediction tools have focused on pretreatment factors. However, emerging non-invasive diagnostics have increased opportunities for serial tumor assessments. We describe the Continuous Individualized Risk Index (CIRI), a method to dynamically determine outcome probabilities for individual patients utilizing risk predictors acquired over time. Similar to "win probability" models in other fields, CIRI provides a real-time probability by integrating risk assessments throughout a patient's course. Applying CIRI to patients with diffuse large B cell lymphoma, we demonstrate improved outcome prediction compared to conventional risk models. We demonstrate CIRI's broader utility in analogous models of chronic lymphocytic leukemia and breast adenocarcinoma and perform a proof-of-concept analysis demonstrating how CIRI could be used to develop predictive biomarkers for therapy selection. We envision that dynamic risk assessment will facilitate personalized medicine and enable innovative therapeutic paradigms.
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Affiliation(s)
- David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Florian Scherer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Joanne Soo
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ulrich Dührsen
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Andreas Hüttmann
- Department of Hematology, University Hospital Essen, Essen, Germany
| | - Olivier Casasnovas
- Department of Hematology, Hopital F. Mitterrand, CHU Dijon and INSERM 1231, Dijon, France
| | - Jason R Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthais Ritgen
- Department II of Internal Medicine, Campus Kiel, University of Schleswig-Holstein, Kiel, Germany
| | - Sebastian Böttcher
- Department III of Internal Medicine, University Hospital Rostock, Rostock, Germany
| | - Anton W Langerak
- Department of Immunology, Laboratory Medical Immunology, Erasmus MC, Rotterdam, the Netherlands
| | - Mark Roschewski
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Hematology, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jasmin Bahlo
- German CLL Study Group, Department I of Internal Medicine and Center of Integrated Oncology Cologne Bonn, University Hospital of Cologne, Cologne, Germany
| | - Michael Hallek
- German CLL Study Group, Department I of Internal Medicine and Center of Integrated Oncology Cologne Bonn, University Hospital of Cologne, Cologne, Germany; Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Related Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Robert Tibshirani
- Department Statistics, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Radiation Oncology, Stanford University, Stanford, CA, USA.
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
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42
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Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas O, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA. Reply to J. Wang et al. J Clin Oncol 2019; 37:755-757. [PMID: 30753108 DOI: 10.1200/jco.18.01907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- David M Kurtz
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Florian Scherer
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michael C Jin
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Joanne Soo
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Alexander F M Craig
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Mohammad S Esfahani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Jacob J Chabon
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Henning Stehr
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Chih Long Liu
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Robert Tibshirani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Lauren S Maeda
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Neel K Gupta
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michael S Khodadoust
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ranjana H Advani
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Aaron M Newman
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ulrich Dührsen
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Andreas Hüttmann
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Michel Meignan
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Olivier Casasnovas
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Jason R Westin
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Mark Roschewski
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Wyndham H Wilson
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Gianluca Gaidano
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Davide Rossi
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Maximilian Diehn
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
| | - Ash A Alizadeh
- David M. Kurtz, MD, PhD; Florian Scherer, MD; Michael C. Jin; Joanne Soo; Alexander F.M. Craig, MPhil; Mohammad S. Esfahani, PhD; Jacob J. Chabon, PhD; Henning Stehr, PhD; Chih Long Liu, PhD; Robert Tibshirani, PhD; Lauren S. Maeda, MD; Neel K. Gupta, MD; Michael S. Khodadoust, MD, PhD; Ranjana H. Advani, MD; and Aaron M. Newman, PhD, Stanford University, Stanford, CA; Ulrich Dührsen, MD; and Andreas Hüttmann, MD, University Hospital Essen, Essen, Germany; Michel Meignan, MD, PhD, Hôpitaux Universitaires Henri Mondor, Creteil, France; Olivier Casasnovas, MD, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, MD, The University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski, MD; and Wyndham H. Wilson, MD, PhD, National Institutes of Health, Bethesda, MD; Gianluca Gaidano, MD, PhD; and Davide Rossi, MD, PhD, University of Eastern Piedmont, Novara, Italy, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland; and Maximilian Diehn, MD, PhD; and Ash A. Alizadeh, MD, PhD, Stanford University, Stanford, CA
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Kurtz DM, Glascoe R, Caviness G, Locklear J, Whiteside T, Ward T, Adsit F, Lih F, Deterding LJ, Churchwell MI, Doerge DR, Kissling GE. Acrylamide Production in Autoclaved Rodent Feed. J Am Assoc Lab Anim Sci 2018; 57. [PMID: 30360773 PMCID: PMC6241378 DOI: 10.30802/aalas-jaalas-18-000011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/05/2018] [Accepted: 04/09/2018] [Indexed: 11/05/2022]
Abstract
Sterilization of rodent feed by steam autoclaving is a common practice in many research institutions. Often we only considerthe beneficial effects of this process-the reduction of microbial contamination-and forget that the high temperatures andpressures can have negative effects on diet quality. The purpose of our study was to assess both the physical and chemicalchanges to a standard rodent feed autoclaved at multiple sterilization temperatures and the effects of the treated diets on mice. Pelleted NIH31 rodent feed was autoclaved at 4 sterilization temperatures (230, 250, 260, and 270 °F). Feed pellet hardness and the acrylamide concentrations of the diets were tested and compared with irradiated NIH31 feed. Study diets were fed to mice for 28 d, after which tissue samples were collected for analysis of acrylamide, glycidamide (the active metabolite of acrylamide), and genotoxicity. Both feed pellet hardness and acrylamide concentration increased with increasing sterilization temperatures; however, neither affected feed intake or body weight gain. Plasma acrylamide and glycidamide weresignificantly elevated only in mice fed NIH31 diet autoclaved at 270 °F compared with the irradiated feed, whereas urineacrylamide and glycidamide metabolites were significantly elevated in most autoclaved diets. Liver DNA adducts, whichcorrelate with genotoxicity, were significantly elevated in all autoclaved diets compared with the irradiated diet. Institutionsthat autoclave their animal diets should carefully consider the temperatures necessary to achieve feed sterilization and thetype of studies in which these autoclaved diets are used.
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Affiliation(s)
- David M Kurtz
- Quality Assurance Laboratory, Comparative Medicine Branch
| | - Rallene Glascoe
- Food Safety and Inspection Service, USDA, Alameda, California; and
| | | | | | | | - Toni Ward
- Quality Assurance Laboratory, Comparative Medicine Branch
| | - Floyd Adsit
- Quality Assurance Laboratory, Comparative Medicine Branch
| | - Fred Lih
- Mass Spectrometry Research and Support, Epigenetics and Stem Cell Biology Laboratory
| | - Leesa J Deterding
- Mass Spectrometry Research and Support, Epigenetics and Stem Cell Biology Laboratory
| | - Mona I Churchwell
- Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Daniel R Doerge
- Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas
| | - Grace E Kissling
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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44
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Kurtz DM, Scherer F, Jin MC, Soo J, Craig AFM, Esfahani MS, Chabon JJ, Stehr H, Liu CL, Tibshirani R, Maeda LS, Gupta NK, Khodadoust MS, Advani RH, Levy R, Newman AM, Dührsen U, Hüttmann A, Meignan M, Casasnovas RO, Westin JR, Roschewski M, Wilson WH, Gaidano G, Rossi D, Diehn M, Alizadeh AA. Circulating Tumor DNA Measurements As Early Outcome Predictors in Diffuse Large B-Cell Lymphoma. J Clin Oncol 2018; 36:2845-2853. [PMID: 30125215 DOI: 10.1200/jco.2018.78.5246] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Outcomes for patients with diffuse large B-cell lymphoma remain heterogeneous, with existing methods failing to consistently predict treatment failure. We examined the additional prognostic value of circulating tumor DNA (ctDNA) before and during therapy for predicting patient outcomes. PATIENTS AND METHODS We studied the dynamics of ctDNA from 217 patients treated at six centers, using a training and validation framework. We densely characterized early ctDNA dynamics during therapy using cancer personalized profiling by deep sequencing to define response-associated thresholds within a discovery set. These thresholds were assessed in two independent validation sets. Finally, we assessed the prognostic value of ctDNA in the context of established risk factors, including the International Prognostic Index and interim positron emission tomography/computed tomography scans. RESULTS Before therapy, ctDNA was detectable in 98% of patients; pretreatment levels were prognostic in both front-line and salvage settings. In the discovery set, ctDNA levels changed rapidly, with a 2-log decrease after one cycle (early molecular response [EMR]) and a 2.5-log decrease after two cycles (major molecular response [MMR]) stratifying outcomes. In the first validation set, patients receiving front-line therapy achieving EMR or MMR had superior outcomes at 24 months (EMR: EFS, 83% v 50%; P = .0015; MMR: EFS, 82% v 46%; P < .001). EMR also predicted superior 24-month outcomes in patients receiving salvage therapy in the first validation set (EFS, 100% v 13%; P = .011). The prognostic value of EMR and MMR was further confirmed in the second validation set. In multivariable analyses including International Prognostic Index and interim positron emission tomography/computed tomography scans across both cohorts, molecular response was independently prognostic of outcomes, including event-free and overall survival. CONCLUSION Pretreatment ctDNA levels and molecular responses are independently prognostic of outcomes in aggressive lymphomas. These risk factors could potentially guide future personalized risk-directed approaches.
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Affiliation(s)
- David M Kurtz
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Florian Scherer
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michael C Jin
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Joanne Soo
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Alexander F M Craig
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Mohammad Shahrokh Esfahani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jacob J Chabon
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Henning Stehr
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Chih Long Liu
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Robert Tibshirani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Lauren S Maeda
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Neel K Gupta
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michael S Khodadoust
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ranjana H Advani
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ronald Levy
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Aaron M Newman
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ulrich Dührsen
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Andreas Hüttmann
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Michel Meignan
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - René-Olivier Casasnovas
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Jason R Westin
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Mark Roschewski
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Wyndham H Wilson
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Gianluca Gaidano
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Davide Rossi
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Maximilian Diehn
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Ash A Alizadeh
- David M. Kurtz, Florian Scherer, Michael C. Jin, Joanne Soo, Alexander F.M. Craig, Mohammad Shahrokh Esfahani, Jacob J. Chabon, Henning Stehr, Chih Long Liu, Robert Tibshirani, Lauren S. Maeda, Neel K. Gupta, Michael S. Khodadoust, Ranjana H. Advani, Ronald Levy, Aaron M. Newman, Maximilian Diehn, and Ash A. Alizadeh, Stanford University, Stanford, CA; Florian Scherer, University Medical Center Freiburg, Freiburg; Ulrich Dührsen and Andreas Hüttmann, University Hospital Essen, Essen, Germany; Michel Meignan, Hôpitaux Universitaires Henri Mondor, Creteil; René-Olivier Casasnovas, Hôpital Le Bocage, Centre Hospitalier Universitaire, Dijon, France; Jason R. Westin, University of Texas MD Anderson Cancer Center, Houston, TX; Mark Roschewski and Wyndham H. Wilson, National Cancer Institute, National Institutes of Health, Bethesda, MD; Gianluca Gaidano and Davide Rossi, University of Eastern Piedmont, Novara, Italy; and Davide Rossi, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Khodadoust MS, Esfahani MS, Liu CL, Zhou L, Scherer F, Kurtz DM, Say C, Carter JN, Merriott DJ, Dudley JC, Binkley MS, Modlin L, Padda SK, Gensheimer MF, West RB, Shrager JB, Neal JW, Wakelee HA, Loo BW, Alizadeh AA, Diehn M. Early Detection of Molecular Residual Disease in Localized Lung Cancer by Circulating Tumor DNA Profiling. Cancer Discov 2017; 7:1394-1403. [PMID: 28899864 DOI: 10.1158/2159-8290.cd-17-0716] [Citation(s) in RCA: 606] [Impact Index Per Article: 86.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/07/2017] [Accepted: 08/31/2017] [Indexed: 12/15/2022]
Abstract
Identifying molecular residual disease (MRD) after treatment of localized lung cancer could facilitate early intervention and personalization of adjuvant therapies. Here, we apply cancer personalized profiling by deep sequencing (CAPP-seq) circulating tumor DNA (ctDNA) analysis to 255 samples from 40 patients treated with curative intent for stage I-III lung cancer and 54 healthy adults. In 94% of evaluable patients experiencing recurrence, ctDNA was detectable in the first posttreatment blood sample, indicating reliable identification of MRD. Posttreatment ctDNA detection preceded radiographic progression in 72% of patients by a median of 5.2 months, and 53% of patients harbored ctDNA mutation profiles associated with favorable responses to tyrosine kinase inhibitors or immune checkpoint blockade. Collectively, these results indicate that ctDNA MRD in patients with lung cancer can be accurately detected using CAPP-seq and may allow personalized adjuvant treatment while disease burden is lowest.Significance: This study shows that ctDNA analysis can robustly identify posttreatment MRD in patients with localized lung cancer, identifying residual/recurrent disease earlier than standard-of-care radiologic imaging, and thus could facilitate personalized adjuvant treatment at early time points when disease burden is lowest. Cancer Discov; 7(12); 1394-403. ©2017 AACR.See related commentary by Comino-Mendez and Turner, p. 1368This article is highlighted in the In This Issue feature, p. 1355.
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Affiliation(s)
- Aadel A Chaudhuri
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Alexander F Lovejoy
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Tej D Azad
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Michael S Khodadoust
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Florian Scherer
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - David M Kurtz
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Bioengineering, Stanford University, Stanford, California
| | - Carmen Say
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Justin N Carter
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - David J Merriott
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Jonathan C Dudley
- Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Pathology, Stanford University, Stanford, California
| | - Michael S Binkley
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Leslie Modlin
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Robert B West
- Department of Pathology, Stanford University, Stanford, California
| | - Joseph B Shrager
- Division of Thoracic Surgery, Department of Cardiothoracic Surgery, Stanford School of Medicine, Stanford University, Stanford, California
| | - Joel W Neal
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, California. .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford University, Stanford, California. .,Stanford Cancer Institute, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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46
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Chaudhuri AA, Chabon JJ, Lovejoy AF, Newman AM, Stehr H, Azad TD, Zhou L, Liu CL, Scherer F, Kurtz DM, Esfahani MS, Say C, Carter JN, Merriott D, Dudley J, Binkley MS, Modlin L, Padda SK, Gensheimer M, West RB, Shrager JB, Neal JW, Wakelee HA, Billy, Loo W, Alizadeh AA, Diehn M. (S012) Circulating Tumor DNA Detects Residual Disease and Anticipates Tumor Progression Earlier Than CT Imaging. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.02.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Scherer F, Kurtz DM, Newman AM, Stehr H, Craig AFM, Esfahani MS, Lovejoy AF, Chabon JJ, Klass DM, Liu CL, Zhou L, Glover C, Visser BC, Poultsides GA, Advani RH, Maeda LS, Gupta NK, Levy R, Ohgami RS, Kunder CA, Diehn M, Alizadeh AA. Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA. Sci Transl Med 2016; 8:364ra155. [PMID: 27831904 PMCID: PMC5490494 DOI: 10.1126/scitranslmed.aai8545] [Citation(s) in RCA: 318] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/19/2016] [Indexed: 12/11/2022]
Abstract
Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy.
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Affiliation(s)
- Florian Scherer
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - David M Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Aaron M Newman
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Alexander F M Craig
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Alexander F Lovejoy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Jacob J Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel M Klass
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Chih Long Liu
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Li Zhou
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Cynthia Glover
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Brendan C Visser
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - George A Poultsides
- Division of Surgical Oncology, Department of Surgery, Stanford University, Stanford, CA 94305, USA
| | - Ranjana H Advani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Lauren S Maeda
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Neel K Gupta
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Ronald Levy
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Robert S Ohgami
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Ash A Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
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48
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Chabon JJ, Simmons AD, Lovejoy AF, Esfahani MS, Newman AM, Haringsma HJ, Kurtz DM, Stehr H, Scherer F, Karlovich CA, Harding TC, Durkin KA, Otterson GA, Purcell WT, Camidge DR, Goldman JW, Sequist LV, Piotrowska Z, Wakelee HA, Neal JW, Alizadeh AA, Diehn M. Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients. Nat Commun 2016; 7:11815. [PMID: 27283993 PMCID: PMC4906406 DOI: 10.1038/ncomms11815] [Citation(s) in RCA: 452] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/03/2016] [Indexed: 12/20/2022] Open
Abstract
Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.
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Affiliation(s)
- Jacob J. Chabon
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | | | - Alexander F. Lovejoy
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Mohammad S. Esfahani
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | | | - David M. Kurtz
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | - Henning Stehr
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
| | - Florian Scherer
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | | | | | - Kathleen A. Durkin
- Molecular Graphics and Computation Facility, College of Chemistry, University of California, Berkeley, California 94720, USA
| | | | - W. Thomas Purcell
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - D. Ross Camidge
- Division of Medical Oncology, Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
| | - Jonathan W. Goldman
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Lecia V. Sequist
- Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Zofia Piotrowska
- Massachusetts General Hospital & Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Heather A. Wakelee
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Joel W. Neal
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Ash A. Alizadeh
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California 94305, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, California 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California 94305, USA
- Stanford Cancer Institute, Stanford University, Stanford, California 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, California 94305, USA
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49
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Karmakar S, Harcourt EM, Hewings DS, Scherer F, Lovejoy AF, Kurtz DM, Ehrenschwender T, Barandun LJ, Roost C, Alizadeh AA, Kool ET. Corrigendum: Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nat Chem 2015; 7:1033. [PMID: 26587722 DOI: 10.1038/nchem.2401] [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: 11/09/2022]
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50
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Abstract
While remission and cure rates for Hodgkin and non-Hodgkin lymphoma continue to improve, surveillance approaches remain controversial, especially in light of recent reports suggesting limited benefit for routine radiologic assessment. Routine cross-sectional imaging results in considerable patient expense and anxiety, and this approach does not clearly improve patient outcomes. Next-generation approaches including minimal residual disease detection may provide an opportunity to identify relapse early and intervene prior to progression of clinical disease. This review discusses the role of surveillance imaging in Hodgkin and non-Hodgkin lymphoma and provides an introduction to serologic assessment of minimal residual disease. Future studies will need to focus on the clinical application of minimal residual disease surveillance and its ability to predict relapse, treatment response and survival.
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Affiliation(s)
- Jonathon B Cohen
- Department of Hematology & Medical Oncology, Emory University, 1365 Clifton Road NE, Atlanta, GA 30322, USA
| | - David M Kurtz
- Division of Oncology, Stanford University, 450 Serra Mall, Stanford, CA 94305, USA
| | - Ashley D Staton
- Department of Hematology & Medical Oncology, Emory University, 1365 Clifton Road NE, Atlanta, GA 30322, USA
| | - Christopher R Flowers
- Department of Hematology & Medical Oncology, Emory University, 1365 Clifton Road NE, Atlanta, GA 30322, USA
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