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Li X, Eastham J, Giltnane JM, Zou W, Zijlstra A, Tabatsky E, Banchereau R, Chang CW, Nabet BY, Patil NS, Molinero L, Chui S, Harryman M, Lau S, Rangell L, Waumans Y, Kockx M, Orlova D, Koeppen H. Automated tumor immunophenotyping predicts clinical benefit from anti-PD-L1 immunotherapy. J Pathol 2024; 263:190-202. [PMID: 38525811 DOI: 10.1002/path.6274] [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: 07/01/2023] [Revised: 12/22/2023] [Accepted: 02/14/2024] [Indexed: 03/26/2024]
Abstract
Cancer immunotherapy has transformed the clinical approach to patients with malignancies, as profound benefits can be seen in a subset of patients. To identify this subset, biomarker analyses increasingly focus on phenotypic and functional evaluation of the tumor microenvironment to determine if density, spatial distribution, and cellular composition of immune cell infiltrates can provide prognostic and/or predictive information. Attempts have been made to develop standardized methods to evaluate immune infiltrates in the routine assessment of certain tumor types; however, broad adoption of this approach in clinical decision-making is still missing. We developed approaches to categorize solid tumors into 'desert', 'excluded', and 'inflamed' types according to the spatial distribution of CD8+ immune effector cells to determine the prognostic and/or predictive implications of such labels. To overcome the limitations of this subjective approach, we incrementally developed four automated analysis pipelines of increasing granularity and complexity for density and pattern assessment of immune effector cells. We show that categorization based on 'manual' observation is predictive for clinical benefit from anti-programmed death ligand 1 therapy in two large cohorts of patients with non-small cell lung cancer or triple-negative breast cancer. For the automated analysis we demonstrate that a combined approach outperforms individual pipelines and successfully relates spatial features to pathologist-based readouts and the patient's response to therapy. Our findings suggest that tumor immunophenotype generated by automated analysis pipelines should be evaluated further as potential predictive biomarkers for cancer immunotherapy. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Xiao Li
- Genentech, South San Francisco, CA, USA
| | | | | | - Wei Zou
- Genentech, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Shari Lau
- Genentech, South San Francisco, CA, USA
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2
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Guan X, Hu R, Choi Y, Srivats S, Nabet BY, Silva J, McGinnis L, Hendricks R, Nutsch K, Banta KL, Duong E, Dunkle A, Chang PS, Han CJ, Mittman S, Molden N, Daggumati P, Connolly W, Johnson M, Abreu DR, Cho BC, Italiano A, Gil-Bazo I, Felip E, Mellman I, Mariathasan S, Shames DS, Meng R, Chiang EY, Johnston RJ, Patil NS. Publisher Correction: Anti-TIGIT antibody improves PD-L1 blockade through myeloid and T reg cells. Nature 2024:10.1038/s41586-024-07280-9. [PMID: 38480897 DOI: 10.1038/s41586-024-07280-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Affiliation(s)
| | - Ruozhen Hu
- Genentech Inc., South San Francisco, CA, USA
| | - Yoonha Choi
- Genentech Inc., South San Francisco, CA, USA
| | | | | | - John Silva
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | - Ellen Duong
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Melissa Johnson
- Sarah Cannon Research Institute/Tennessee Oncology, PLLC, Nashville, TN, USA
| | | | - Byoung Chul Cho
- Yonsei Cancer Centre, Yonsei University College of Medicine, Seoul, South Korea
| | - Antoine Italiano
- Institut Bergonie CLCC Bordeaux, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Ignacio Gil-Bazo
- Clínica Universidad de Navarra, CIMA Universidad de Navarra Pamplona, Pamplona, Spain
| | - Enriqueta Felip
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ira Mellman
- Genentech Inc., South San Francisco, CA, USA
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3
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Nabet BY, Hamidi H, Lee MC, Banchereau R, Morris S, Adler L, Gayevskiy V, Elhossiny AM, Srivastava MK, Patil NS, Smith KA, Jesudason R, Chan C, Chang PS, Fernandez M, Rost S, McGinnis LM, Koeppen H, Gay CM, Minna JD, Heymach JV, Chan JM, Rudin CM, Byers LA, Liu SV, Reck M, Shames DS. Immune heterogeneity in small-cell lung cancer and vulnerability to immune checkpoint blockade. Cancer Cell 2024; 42:429-443.e4. [PMID: 38366589 DOI: 10.1016/j.ccell.2024.01.010] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 12/02/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024]
Abstract
Atezolizumab (anti-PD-L1), combined with carboplatin and etoposide (CE), is now a standard of care for extensive-stage small-cell lung cancer (ES-SCLC). A clearer understanding of therapeutically relevant SCLC subsets could identify rational combination strategies and improve outcomes. We conduct transcriptomic analyses and non-negative matrix factorization on 271 pre-treatment patient tumor samples from IMpower133 and identify four subsets with general concordance to previously reported SCLC subtypes (SCLC-A, -N, -P, and -I). Deeper investigation into the immune heterogeneity uncovers two subsets with differing neuroendocrine (NE) versus non-neuroendocrine (non-NE) phenotypes, demonstrating immune cell infiltration hallmarks. The NE tumors with low tumor-associated macrophage (TAM) but high T-effector signals demonstrate longer overall survival with PD-L1 blockade and CE versus CE alone than non-NE tumors with high TAM and high T-effector signal. Our study offers a clinically relevant approach to discriminate SCLC patients likely benefitting most from immunotherapies and highlights the complex mechanisms underlying immunotherapy responses.
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Affiliation(s)
| | | | | | | | | | - Leah Adler
- F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Velimir Gayevskiy
- Genentech Inc., South San Francisco CA, USA; Rancho Biosciences, San Diego, CA, USA
| | | | | | | | | | | | - Caleb Chan
- Genentech Inc., South San Francisco CA, USA
| | | | | | | | | | | | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390-8593, USA; Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA; Departments of Internal Medicine and Pharmacology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph M Chan
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA
| | - Charles M Rudin
- Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program for Computational and Systems Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10016, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen V Liu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
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4
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Guan X, Hu R, Choi Y, Srivats S, Nabet BY, Silva J, McGinnis L, Hendricks R, Nutsch K, Banta KL, Duong E, Dunkle A, Chang PS, Han CJ, Mittman S, Molden N, Daggumati P, Connolly W, Johnson M, Abreu DR, Cho BC, Italiano A, Gil-Bazo I, Felip E, Mellman I, Mariathasan S, Shames DS, Meng R, Chiang EY, Johnston RJ, Patil NS. Anti-TIGIT antibody improves PD-L1 blockade through myeloid and T reg cells. Nature 2024; 627:646-655. [PMID: 38418879 DOI: 10.1038/s41586-024-07121-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 01/26/2024] [Indexed: 03/02/2024]
Abstract
Tiragolumab, an anti-TIGIT antibody with an active IgG1κ Fc, demonstrated improved outcomes in the phase 2 CITYSCAPE trial (ClinicalTrials.gov: NCT03563716 ) when combined with atezolizumab (anti-PD-L1) versus atezolizumab alone1. However, there remains little consensus on the mechanism(s) of response with this combination2. Here we find that a high baseline of intratumoural macrophages and regulatory T cells is associated with better outcomes in patients treated with atezolizumab plus tiragolumab but not with atezolizumab alone. Serum sample analysis revealed that macrophage activation is associated with a clinical benefit in patients who received the combination treatment. In mouse tumour models, tiragolumab surrogate antibodies inflamed tumour-associated macrophages, monocytes and dendritic cells through Fcγ receptors (FcγR), in turn driving anti-tumour CD8+ T cells from an exhausted effector-like state to a more memory-like state. These results reveal a mechanism of action through which TIGIT checkpoint inhibitors can remodel immunosuppressive tumour microenvironments, and suggest that FcγR engagement is an important consideration in anti-TIGIT antibody development.
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Affiliation(s)
| | - Ruozhen Hu
- Genentech Inc., South San Francisco, CA, USA
| | - Yoonha Choi
- Genentech Inc., South San Francisco, CA, USA
| | | | | | - John Silva
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | - Ellen Duong
- Genentech Inc., South San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Melissa Johnson
- Sarah Cannon Research Institute/Tennessee Oncology, PLLC, Nashville, TN, USA
| | | | - Byoung Chul Cho
- Yonsei Cancer Centre, Yonsei University College of Medicine, Seoul, South Korea
| | - Antoine Italiano
- Institut Bergonie CLCC Bordeaux, Bordeaux, France
- Faculty of Medicine, University of Bordeaux, Bordeaux, France
| | - Ignacio Gil-Bazo
- Clínica Universidad de Navarra, CIMA Universidad de Navarra Pamplona, Pamplona, Spain
| | - Enriqueta Felip
- Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Ira Mellman
- Genentech Inc., South San Francisco, CA, USA
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5
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Liu SV, Mok TSK, Nabet BY, Mansfield AS, De Boer R, Losonczy G, Sugawara S, Dziadziuszko R, Krzakowski M, Smolin A, Hochmair MJ, Garassino MC, Gay CM, Heymach JV, Byers LA, Lam S, Cardona A, Morris S, Adler L, Shames DS, Reck M. Clinical and molecular characterization of long-term survivors with extensive-stage small cell lung cancer treated with first-line atezolizumab plus carboplatin and etoposide. Lung Cancer 2023; 186:107418. [PMID: 37931445 DOI: 10.1016/j.lungcan.2023.107418] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/06/2023] [Accepted: 10/29/2023] [Indexed: 11/08/2023]
Abstract
OBJECTIVES In the Phase I/III IMpower133 study, first-line atezolizumab plus carboplatin and etoposide (CP/ET) treatment for extensive-stage small cell lung cancer (ES-SCLC) significantly improved overall survival (OS) and progression-free survival versus placebo plus CP/ET. We explored patient and disease characteristics associated with long-term survival in IMpower133, and associations of differential gene expression and SCLC-A (ASCL1-driven), SCLC-N (NEUROD1-driven), SCLC-P (POU2F3-driven), and SCLC-inflamed (SCLC-I) transcriptional subtypes with long-term survival. MATERIALS AND METHODS Patients with previously untreated ES-SCLC were randomized 1:1 to four 21-day cycles of CP/ET with atezolizumab or placebo. Long-term survivors (LTS) were defined as patients who lived ≥ 18 months post randomization. A generalized linear model was used to evaluate the odds of living ≥ 18 months. Differential gene expression was analyzed using RNA-sequencing data in LTS and non-LTS. OS was assessed by T-effector and B-cell gene signature expression. Distribution of SCLC transcriptional subtypes was assessed in LTS and non-LTS. RESULTS More LTS were in the atezolizumab arm (34%) than in the placebo arm (20%). The odds ratio for living ≥ 18 months in the atezolizumab arm versus the placebo arm was 2.1 (P < 0.03). Enhanced immune-related signaling was seen in LTS in both arms. Exploratory OS analyses showed atezolizumab treatment benefit versus placebo across T-effector and B-cell gene signature expression subgroups. A higher proportion of LTS than non-LTS in both arms had the SCLC-I subtype; this difference was particularly pronounced in the atezolizumab arm. CONCLUSION These exploratory analyses suggest that long-term survival is more likely with atezolizumab than placebo in ES-SCLC, confirming the treatment benefit of the IMpower133 regimen. CLINICALTRIAL gov Identifier: NCT02763579.
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Affiliation(s)
- Stephen V Liu
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA.
| | - Tony S K Mok
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong, China
| | | | | | | | - György Losonczy
- Department of Pulmonology, Semmelweis University, Budapest, Hungary
| | | | - Rafal Dziadziuszko
- Department of Oncology and Radiotherapy and Early Phase Clinical Trials Center, Medical University of Gdańsk, Gdańsk, Poland
| | - Maciej Krzakowski
- Maria Sklodowska Curie National Research Institute of Oncology, Warsaw, Poland
| | - Alexey Smolin
- Burdenko Main Military Clinical Hospital, Moscow, Russia
| | - Maximilian J Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Vienna North Hospital Klinik Floridsdorf, Vienna, Austria
| | - Marina C Garassino
- The University of Chicago Department of Hematology/Oncology, Chicago, IL, USA
| | - Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren A Byers
- Department of Thoracic/Head & Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | | | | | - Leah Adler
- F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | | | - Martin Reck
- Lung Clinic Grosshansdorf, Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany
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6
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Chow A, Uddin FZ, Liu M, Dobrin A, Nabet BY, Mangarin L, Lavin Y, Rizvi H, Tischfield SE, Quintanal-Villalonga A, Chan JM, Shah N, Allaj V, Manoj P, Mattar M, Meneses M, Landau R, Ward M, Kulick A, Kwong C, Wierzbicki M, Yavner J, Egger J, Chavan SS, Farillas A, Holland A, Sridhar H, Ciampricotti M, Hirschhorn D, Guan X, Richards AL, Heller G, Mansilla-Soto J, Sadelain M, Klebanoff CA, Hellmann MD, Sen T, de Stanchina E, Wolchok JD, Merghoub T, Rudin CM. The ectonucleotidase CD39 identifies tumor-reactive CD8 + T cells predictive of immune checkpoint blockade efficacy in human lung cancer. Immunity 2023; 56:93-106.e6. [PMID: 36574773 PMCID: PMC9887636 DOI: 10.1016/j.immuni.2022.12.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
Improved identification of anti-tumor T cells is needed to advance cancer immunotherapies. CD39 expression is a promising surrogate of tumor-reactive CD8+ T cells. Here, we comprehensively profiled CD39 expression in human lung cancer. CD39 expression enriched for CD8+ T cells with features of exhaustion, tumor reactivity, and clonal expansion. Flow cytometry of 440 lung cancer biospecimens revealed weak association between CD39+ CD8+ T cells and tumoral features, such as programmed death-ligand 1 (PD-L1), tumor mutation burden, and driver mutations. Immune checkpoint blockade (ICB), but not cytotoxic chemotherapy, increased intratumoral CD39+ CD8+ T cells. Higher baseline frequency of CD39+ CD8+ T cells conferred improved clinical outcomes from ICB therapy. Furthermore, a gene signature of CD39+ CD8+ T cells predicted benefit from ICB, but not chemotherapy, in a phase III clinical trial of non-small cell lung cancer. These findings highlight CD39 as a proxy of tumor-reactive CD8+ T cells in human lung cancer.
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Affiliation(s)
- Andrew Chow
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Fathema Z Uddin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Liu
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Dobrin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barzin Y Nabet
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Levi Mangarin
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yonit Lavin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira Rizvi
- Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sam E Tischfield
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alvaro Quintanal-Villalonga
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph M Chan
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nisargbhai Shah
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viola Allaj
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximiliano Meneses
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca Landau
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariana Ward
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Kulick
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlene Kwong
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Wierzbicki
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Yavner
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklynn Egger
- Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abigail Farillas
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliya Holland
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harsha Sridhar
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Metamia Ciampricotti
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Hirschhorn
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangnan Guan
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Glenn Heller
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triparna Sen
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Charles M Rudin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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7
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Nair VS, Hui ABY, Chabon JJ, Esfahani MS, Stehr H, Nabet BY, Zhou L, Chaudhuri AA, Benson J, Ayers K, Bedi H, Ramsey M, Van Wert R, Antic S, Lui N, Backhus L, Berry M, Sung AW, Massion PP, Shrager JB, Alizadeh AA, Diehn M. Genomic Profiling of Bronchoalveolar Lavage Fluid in Lung Cancer. Cancer Res 2022; 82:2838-2847. [PMID: 35748739 PMCID: PMC9379362 DOI: 10.1158/0008-5472.can-22-0554] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/24/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022]
Abstract
Genomic profiling of bronchoalveolar lavage (BAL) samples may be useful for tumor profiling and diagnosis in the clinic. Here, we compared tumor-derived mutations detected in BAL samples from subjects with non-small cell lung cancer (NSCLC) to those detected in matched plasma samples. Cancer Personalized Profiling by Deep Sequencing (CAPP-Seq) was used to genotype DNA purified from BAL, plasma, and tumor samples from patients with NSCLC. The characteristics of cell-free DNA (cfDNA) isolated from BAL fluid were first characterized to optimize the technical approach. Somatic mutations identified in tumor were then compared with those identified in BAL and plasma, and the potential of BAL cfDNA analysis to distinguish lung cancer patients from risk-matched controls was explored. In total, 200 biofluid and tumor samples from 38 cases and 21 controls undergoing BAL for lung cancer evaluation were profiled. More tumor variants were identified in BAL cfDNA than plasma cfDNA in all stages (P < 0.001) and in stage I to II disease only. Four of 21 controls harbored low levels of cancer-associated driver mutations in BAL cfDNA [mean variant allele frequency (VAF) = 0.5%], suggesting the presence of somatic mutations in nonmalignant airway cells. Finally, using a Random Forest model with leave-one-out cross-validation, an exploratory BAL genomic classifier identified lung cancer with 69% sensitivity and 100% specificity in this cohort and detected more cancers than BAL cytology. Detecting tumor-derived mutations by targeted sequencing of BAL cfDNA is technically feasible and appears to be more sensitive than plasma profiling. Further studies are required to define optimal diagnostic applications and clinical utility. SIGNIFICANCE Hybrid-capture, targeted deep sequencing of lung cancer mutational burden in cell-free BAL fluid identifies more tumor-derived mutations with increased allele frequencies compared with plasma cell-free DNA. See related commentary by Rolfo et al., p. 2826.
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Affiliation(s)
- Viswam S. Nair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Division of Pulmonary, Critical Care & Sleep Medicine, University of Washington School of Medicine, Seattle, Washington
- Department of Radiology, Stanford University School of Medicine, Stanford, California
| | - Angela Bik-Yu Hui
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Jacob J. Chabon
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Mohammad S. Esfahani
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Barzin Y. Nabet
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Li Zhou
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Aadel A. Chaudhuri
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
| | - Jalen Benson
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Kelsey Ayers
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Harmeet Bedi
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Meghan Ramsey
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Ryan Van Wert
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Sanja Antic
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Natalie Lui
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Leah Backhus
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Mark Berry
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Arthur W. Sung
- Division of Pulmonary, Allergy & Critical Care Medicine, Stanford University School of Medicine, Stanford, California
| | - Pierre P. Massion
- Division of Allergy, Pulmonary & Critical Care Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Joseph B. Shrager
- Division of Thoracic Surgery, Stanford University School of Medicine, Stanford, California
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, California
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California
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8
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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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9
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Patil NS, Nabet BY, Müller S, Koeppen H, Zou W, Giltnane J, Au-Yeung A, Srivats S, Cheng JH, Takahashi C, de Almeida PE, Chitre AS, Grogan JL, Rangell L, Jayakar S, Peterson M, Hsia AW, O'Gorman WE, Ballinger M, Banchereau R, Shames DS. Intratumoral plasma cells predict outcomes to PD-L1 blockade in non-small cell lung cancer. Cancer Cell 2022; 40:289-300.e4. [PMID: 35216676 DOI: 10.1016/j.ccell.2022.02.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 11/11/2021] [Accepted: 02/02/2022] [Indexed: 12/15/2022]
Abstract
Inhibitors of the programmed cell death-1 (PD-1/PD-L1) signaling axis are approved to treat non-small cell lung cancer (NSCLC) patients, based on their significant overall survival (OS) benefit. Using transcriptomic analysis of 891 NSCLC tumors from patients treated with either the PD-L1 inhibitor atezolizumab or chemotherapy from two large randomized clinical trials, we find a significant B cell association with extended OS with PD-L1 blockade, independent of CD8+ T cell signals. We then derive gene signatures corresponding to the dominant B cell subsets present in NSCLC from single-cell RNA sequencing (RNA-seq) data. Importantly, we find increased plasma cell signatures to be predictive of OS in patients treated with atezolizumab, but not chemotherapy. B and plasma cells are also associated with the presence of tertiary lymphoid structures and organized lymphoid aggregates. Our results suggest an important contribution of B and plasma cells to the efficacy of PD-L1 blockade in NSCLC.
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Affiliation(s)
- Namrata S Patil
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.
| | - Barzin Y Nabet
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA.
| | - Sören Müller
- Oncology Bioinformatics, Genentech, Inc., South San Francisco, CA, USA
| | - Hartmut Koeppen
- Research Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Wei Zou
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | | | - Amelia Au-Yeung
- OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Shyam Srivats
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Jason H Cheng
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Chikara Takahashi
- OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | | | - Avantika S Chitre
- Cancer Immunology Research, Genentech, Inc., South San Francisco, CA, USA
| | - Jane L Grogan
- Cancer Immunology Research, Genentech, Inc., South San Francisco, CA, USA
| | - Linda Rangell
- Research Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Sangeeta Jayakar
- Research Pathology, Genentech, Inc., South San Francisco, CA, USA
| | - Maureen Peterson
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - Allison W Hsia
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - William E O'Gorman
- OMNI Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | | | - Romain Banchereau
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
| | - David S Shames
- Oncology Biomarker Development, Genentech, Inc., South San Francisco, CA, USA
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10
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Leader AM, Grout JA, Maier BB, Nabet BY, Park MD, Tabachnikova A, Chang C, Walker L, Lansky A, Le Berichel J, Troncoso L, Malissen N, Davila M, Martin JC, Magri G, Tuballes K, Zhao Z, Petralia F, Samstein R, D'Amore NR, Thurston G, Kamphorst AO, Wolf A, Flores R, Wang P, Müller S, Mellman I, Beasley MB, Salmon H, Rahman AH, Marron TU, Kenigsberg E, Merad M. Single-cell analysis of human non-small cell lung cancer lesions refines tumor classification and patient stratification. Cancer Cell 2021; 39:1594-1609.e12. [PMID: 34767762 PMCID: PMC8728963 DOI: 10.1016/j.ccell.2021.10.009] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 01/25/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022]
Abstract
Immunotherapy is a mainstay of non-small cell lung cancer (NSCLC) management. While tumor mutational burden (TMB) correlates with response to immunotherapy, little is known about the relationship between the baseline immune response and tumor genotype. Using single-cell RNA sequencing, we profiled 361,929 cells from 35 early-stage NSCLC lesions. We identified a cellular module consisting of PDCD1+CXCL13+ activated T cells, IgG+ plasma cells, and SPP1+ macrophages, referred to as the lung cancer activation module (LCAMhi). We confirmed LCAMhi enrichment in multiple NSCLC cohorts, and paired CITE-seq established an antibody panel to identify LCAMhi lesions. LCAM presence was found to be independent of overall immune cell content and correlated with TMB, cancer testis antigens, and TP53 mutations. High baseline LCAM scores correlated with enhanced NSCLC response to immunotherapy even in patients with above median TMB, suggesting that immune cell composition, while correlated with TMB, may be a nonredundant biomarker of response to immunotherapy.
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Affiliation(s)
- Andrew M Leader
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John A Grout
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barbara B Maier
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Barzin Y Nabet
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Matthew D Park
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra Tabachnikova
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christie Chang
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura Walker
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alona Lansky
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Le Berichel
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanna Troncoso
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nausicaa Malissen
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Dermatology and Skin Cancer, APHM, CHU Timone, Aix-Marseille University, Marseille, France
| | - Melanie Davila
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C Martin
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Nantes Université, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, 44000 Nantes, France; CHU Nantes, Nantes Université, Laboratoire d'Immunologie, 44000 Nantes, France
| | - Giuliana Magri
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kevin Tuballes
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Zhao
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Samstein
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Radiation Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalie Roy D'Amore
- Immuno-oncology Drug Discovery Unit, Millennium Pharmaceuticals, Inc. a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Tokyo, Japan
| | - Gavin Thurston
- Department of Oncology & Angiogenesis, Regeneron Pharmaceuticals Inc., Tarrytown, NY, USA
| | - Alice O Kamphorst
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrea Wolf
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raja Flores
- Department of Thoracic Surgery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sören Müller
- Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Ira Mellman
- Department of Cancer Immunology, Genentech, South San Francisco, CA, USA
| | - Mary Beth Beasley
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hélène Salmon
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb H Rahman
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas U Marron
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ephraim Kenigsberg
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Miriam Merad
- The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Institute for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Moding EJ, Nabet BY, Alizadeh AA, Diehn M. Detecting Liquid Remnants of Solid Tumors: Circulating Tumor DNA Minimal Residual Disease. Cancer Discov 2021; 11:2968-2986. [PMID: 34785539 PMCID: PMC8976700 DOI: 10.1158/2159-8290.cd-21-0634] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Growing evidence demonstrates that circulating tumor DNA (ctDNA) minimal residual disease (MRD) following treatment for solid tumors predicts relapse. These results suggest that ctDNA MRD could identify candidates for adjuvant therapy and measure response to such treatment. Importantly, factors such as assay type, amount of ctDNA release, and technical and biological background can affect ctDNA MRD results. Furthermore, the clinical utility of ctDNA MRD for treatment personalization remains to be fully established. Here, we review the evidence supporting the value of ctDNA MRD in solid cancers and highlight key considerations in the application of this potentially transformative biomarker. SIGNIFICANCE ctDNA analysis enables detection of MRD and predicts relapse after definitive treatment for solid cancers, thereby promising to revolutionize personalization of adjuvant and consolidation therapies.
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Affiliation(s)
- 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
| | - Barzin Y. Nabet
- 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
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Current address: Department of Oncology Biomarker Development, Genentech, South San Francisco, CA 94080, USA
| | - Ash A. Alizadeh
- Stanford Cancer Institute, 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
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- 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
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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12
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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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13
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Gay CM, Stewart CA, Diao L, Nabet BY, Fujimoto J, Solis LM, Lu W, Xi Y, Cardnell RJ, Vokes NI, Ramkumar K, Swisher SG, Roth JA, Glisson BS, Shames DS, Wistuba II, Wang J, Minna J, Heymach JV, Byers LA. Abstract 22: A novel, inflamed small cell lung cancer transcriptional subtype, SCLC-I, defines a subset of patients with distinct immunotherapy vulnerability. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-22] [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
Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with dismal survival outcomes and no established predictive biomarkers. The landmark randomized, phase III IMpower133 trial established the new frontline standard of care for extensive-stage SCLC (ES-SCLC) as etoposide/platinum (EP) plus immune checkpoint blockade (ICB) [anti-PD-L1; atezolizumab (atezo)] based on an overall survival (OS) benefit compared to EP plus placebo. However, this survival benefit is limited in unselected populations, emphasizing the need for predictive biomarkers. Preclinically, there is emerging evidence of transcriptional heterogeneity among SCLC tumors, but the impact on therapeutic benefit remains undefined. Using non-negative matrix factorization (NMF) analysis of gene expression data from 81 SCLC tumors samples, we previously identified four subtypes, including three defined largely by differential expression of the transcription factors ASCL1 (SCLC-A), NEUROD1 (SCLC-N), and POU2F3 (SCLC-P), and a novel, fourth subtype with low expression of all three transcription factor signatures.
Method and Results
Using transcriptional and proteomic data from patient tumors and tumor-derived models, we molecularly characterized each of the four identified subtypes. The previously undescribed fourth subtype, dubbed SCLC-Inflamed (SCLC-I) showed high expression of non-neuroendocrine transcription factors (e.g. REST) and markers of EMT. Most distinctly, relative to the “cold” immune microenvironment typical of SCLC tumors, SCLC-I tumors possess markedly higher expression of interferon-γ signatures and immune checkpoints, including CD274 (PD-L1). Furthermore, cell type deconvolution using CIBERSORTx identified significantly higher infiltration into SCLC-I tumors by multiple immune cell types including T-cells, NK cells, macrophages, and dendritic cells. We predicted SCLC-I might derive disproportionate benefit from ICB due to its inflamed features. To test this, we applied our NMF-derived gene signature to 276 treatment-naïve, ES-SCLC patient tumors from the IMpower133 trial to assign patient subtype. The distribution of subtypes was as follows: SCLC-A 51%, SCLC-N 23%, SCLC-I 18% and SCLC-P 7%. While there was a trend toward OS benefit with the addition of atezo in each subtype, the benefit was numerically greater in SCLC-I. Specifically, median OS (atezo vs placebo arm) in months (mo) was 18.2 mo vs 10.4 mo for SCLC-I tumors, while median OS for the other three subtypes ranged from 9.6-10.9 mo (atezo arm) and 6.0-10.6 mo (placebo arm).
Conclusion
Unbiased transcriptional analyses identify four subtypes with distinct tumor and immune features. While all subtypes experienced improved OS with addition of anti-PD-L1 to frontline EP, SCLC-I patients appear to experience the most durable benefit.
Citation Format: Carl M. Gay, C. Allison Stewart, Lixia Diao, Barzin Y. Nabet, Junya Fujimoto, Luisa M. Solis, Wei Lu, Yuanxin Xi, Robert J. Cardnell, Natalie I. Vokes, Kavya Ramkumar, Stephen G. Swisher, Jack A. Roth, Bonnie S. Glisson, David S. Shames, Ignacio I. Wistuba, Jing Wang, John Minna, John V. Heymach, Lauren A. Byers. A novel, inflamed small cell lung cancer transcriptional subtype, SCLC-I, defines a subset of patients with distinct immunotherapy vulnerability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 22.
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Affiliation(s)
- Carl M. Gay
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lixia Diao
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Junya Fujimoto
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luisa M. Solis
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wei Lu
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yuanxin Xi
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Kavya Ramkumar
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jack A. Roth
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Jing Wang
- 1University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Minna
- 3University of Texas Southwestern Medical Center, Dallas, TX
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14
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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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15
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Gay CM, Stewart CA, Park EM, Diao L, Groves SM, Heeke S, Nabet BY, Fujimoto J, Solis LM, Lu W, Xi Y, Cardnell RJ, Wang Q, Fabbri G, Cargill KR, Vokes NI, Ramkumar K, Zhang B, Della Corte CM, Robson P, Swisher SG, Roth JA, Glisson BS, Shames DS, Wistuba II, Wang J, Quaranta V, Minna J, Heymach JV, Byers LA. Patterns of transcription factor programs and immune pathway activation define four major subtypes of SCLC with distinct therapeutic vulnerabilities. Cancer Cell 2021; 39:346-360.e7. [PMID: 33482121 PMCID: PMC8143037 DOI: 10.1016/j.ccell.2020.12.014] [Citation(s) in RCA: 393] [Impact Index Per Article: 131.0] [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: 06/15/2020] [Revised: 10/28/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]
Abstract
Despite molecular and clinical heterogeneity, small cell lung cancer (SCLC) is treated as a single entity with predictably poor results. Using tumor expression data and non-negative matrix factorization, we identify four SCLC subtypes defined largely by differential expression of transcription factors ASCL1, NEUROD1, and POU2F3 or low expression of all three transcription factor signatures accompanied by an Inflamed gene signature (SCLC-A, N, P, and I, respectively). SCLC-I experiences the greatest benefit from the addition of immunotherapy to chemotherapy, while the other subtypes each have distinct vulnerabilities, including to inhibitors of PARP, Aurora kinases, or BCL-2. Cisplatin treatment of SCLC-A patient-derived xenografts induces intratumoral shifts toward SCLC-I, supporting subtype switching as a mechanism of acquired platinum resistance. We propose that matching baseline tumor subtype to therapy, as well as manipulating subtype switching on therapy, may enhance depth and duration of response for SCLC patients.
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Affiliation(s)
- Carl M Gay
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - C Allison Stewart
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth M Park
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah M Groves
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Simon Heeke
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barzin Y Nabet
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco CA, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Lu
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuanxin Xi
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert J Cardnell
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Kasey R Cargill
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Natalie I Vokes
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kavya Ramkumar
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bingnan Zhang
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carminia M Della Corte
- Department of Precision Medicine, Oncology Division, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bonnie S Glisson
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco CA, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Vito Quaranta
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, USA
| | - John Minna
- Department of Internal Medicine and Simmons Cancer Center, the University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John V Heymach
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren Averett Byers
- Department of Thoracic/Head & Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Chiou SH, Tseng D, Reuben A, Mallajosyula V, Molina IS, Conley S, Wilhelmy J, McSween AM, Yang X, Nishimiya D, Sinha R, Nabet BY, Wang C, Shrager JB, Berry MF, Backhus L, Lui NS, Wakelee HA, Neal JW, Padda SK, Berry GJ, Delaidelli A, Sorensen PH, Sotillo E, Tran P, Benson JA, Richards R, Labanieh L, Klysz DD, Louis DM, Feldman SA, Diehn M, Weissman IL, Zhang J, Wistuba II, Futreal PA, Heymach JV, Garcia KC, Mackall CL, Davis MM. Global analysis of shared T cell specificities in human non-small cell lung cancer enables HLA inference and antigen discovery. Immunity 2021; 54:586-602.e8. [PMID: 33691136 PMCID: PMC7960510 DOI: 10.1016/j.immuni.2021.02.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/08/2020] [Accepted: 02/11/2021] [Indexed: 12/12/2022]
Abstract
To identify disease-relevant T cell receptors (TCRs) with shared antigen specificity, we analyzed 778,938 TCRβ chain sequences from 178 non-small cell lung cancer patients using the GLIPH2 (grouping of lymphocyte interactions with paratope hotspots 2) algorithm. We identified over 66,000 shared specificity groups, of which 435 were clonally expanded and enriched in tumors compared to adjacent lung. The antigenic epitopes of one such tumor-enriched specificity group were identified using a yeast peptide-HLA A∗02:01 display library. These included a peptide from the epithelial protein TMEM161A, which is overexpressed in tumors and cross-reactive epitopes from Epstein-Barr virus and E. coli. Our findings suggest that this cross-reactivity may underlie the presence of virus-specific T cells in tumor infiltrates and that pathogen cross-reactivity may be a feature of multiple cancers. The approach and analytical pipelines generated in this work, as well as the specificity groups defined here, present a resource for understanding the T cell response in cancer.
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Affiliation(s)
- Shin-Heng Chiou
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Diane Tseng
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vamsee Mallajosyula
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Irene S Molina
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Stephanie Conley
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Julie Wilhelmy
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Alana M McSween
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Xinbo Yang
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Daisuke Nishimiya
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Chunlin Wang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Mark F Berry
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Leah Backhus
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Natalie S Lui
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Heather A Wakelee
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Joel W Neal
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Sukhmani K Padda
- Department of Medicine, Division of Oncology, Stanford University, Stanford, CA 94305, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, BC V5Z 1L3, Canada
| | - Elena Sotillo
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Patrick Tran
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Jalen A Benson
- Department of Cardiothoracic Surgery - Thoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Rebecca Richards
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Louai Labanieh
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dorota D Klysz
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - David M Louis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA
| | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA; Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine Institute, Stanford University, Stanford, CA 94305, USA
| | - Jianjun Zhang
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology and Structural Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Crystal L Mackall
- Center for Cancer Cell Therapy, Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Mark M Davis
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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17
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Wisdom AJ, Mowery YM, Hong CS, Himes JE, Nabet BY, Qin X, Zhang D, Chen L, Fradin H, Patel R, Bassil AM, Muise ES, King DA, Xu ES, Carpenter DJ, Kent CL, Smythe KS, Williams NT, Luo L, Ma Y, Alizadeh AA, Owzar K, Diehn M, Bradley T, Kirsch DG. Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy. Nat Commun 2020; 11:6410. [PMID: 33335088 PMCID: PMC7746723 DOI: 10.1038/s41467-020-19917-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023] Open
Abstract
Immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Most preclinical immunotherapy studies utilize transplant tumor models, which overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate immunoediting, decreased neoantigen expression, and tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors, revealing striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in both models, only transplant tumors are enriched for activated CD8+ T cells. The immune microenvironment of primary murine sarcomas resembles most human sarcomas, while transplant sarcomas resemble the most inflamed human sarcomas. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients with a sarcoma immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.
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Affiliation(s)
- Amy J Wisdom
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Yvonne M Mowery
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA.
- Duke Cancer Institute, Durham, NC, 27708, USA.
| | - Cierra S Hong
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Jonathon E Himes
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Barzin Y Nabet
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, 94080, USA
| | - Xiaodi Qin
- Duke Cancer Institute, Durham, NC, 27708, USA
| | | | - Lan Chen
- Merck & Co., Inc, Kenilworth, NJ, 07033, USA
| | - Hélène Fradin
- Duke Center for Genomic and Computational Biology, Durham, NC, 27708, USA
| | - Rutulkumar Patel
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Alex M Bassil
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | | | - Daniel A King
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Eric S Xu
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - David J Carpenter
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Collin L Kent
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | | | - Nerissa T Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
- 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
| | - Kouros Owzar
- Duke Cancer Institute, Durham, NC, 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC, 27710, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- Department of Radiation Oncology, Stanford University, Stanford, CA, 94305, USA
| | - Todd Bradley
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA
- Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - David G Kirsch
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27708, USA.
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, 27708, USA.
- Duke Cancer Institute, Durham, NC, 27708, USA.
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18
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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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19
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Nabet BY, Esfahani MS, Moding EJ, Hamilton EG, Chabon JJ, Rizvi H, Steen CB, Chaudhuri AA, Liu CL, Hui AB, Almanza D, Stehr H, Gojenola L, Bonilla RF, Jin MC, Jeon YJ, Tseng D, Liu C, Merghoub T, Neal JW, Wakelee HA, Padda SK, Ramchandran KJ, Das M, Plodkowski AJ, Yoo C, Chen EL, Ko RB, Newman AM, Hellmann MD, Alizadeh AA, Diehn M. Noninvasive Early Identification of Therapeutic Benefit from Immune Checkpoint Inhibition. Cell 2020; 183:363-376.e13. [PMID: 33007267 PMCID: PMC7572899 DOI: 10.1016/j.cell.2020.09.001] [Citation(s) in RCA: 189] [Impact Index Per Article: 47.3] [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: 02/14/2020] [Revised: 06/18/2020] [Accepted: 08/28/2020] [Indexed: 12/30/2022]
Abstract
Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICIs) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we demonstrate that pre-treatment circulating tumor DNA (ctDNA) and peripheral CD8 T cell levels are independently associated with DCB. We further show that ctDNA dynamics after a single infusion can aid in identification of patients who will achieve DCB. Integrating these determinants, we developed and validated an entirely noninvasive multiparameter assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA-On-treatment) that robustly predicts which patients will achieve DCB with higher accuracy than any individual feature. Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICIs.
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Affiliation(s)
- Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Mohammad S Esfahani
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chloe B Steen
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Chih Long Liu
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Diego Almanza
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Program in Cancer Biology, Stanford University, Stanford, CA, USA
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Michael C Jin
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Young-Jun Jeon
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Diane Tseng
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Cailian Liu
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell School of Medicine, New York, NY, USA; Parker Institute for Cancer Immunotherapy at MSK, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joel W Neal
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Sukhmani K Padda
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Kavitha J Ramchandran
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Millie Das
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher Yoo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Emily L Chen
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Aaron M Newman
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Matthew D Hellmann
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell School of Medicine, New York, NY, USA; Parker Institute for Cancer Immunotherapy at MSK, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Department of Radiation Oncology, 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.
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20
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Steen CB, Luca B, Esfahani MS, Nabet BY, Sworder B, Farshidfar F, Kurtz D, Liu CL, Advani RH, Natkunam Y, Myklebust JH, Diehn M, Gentles A, Alizadeh A, Newman AM. Abstract 1557: Landscape of tumor cell states and cellular ecosystems in diffuse large B cell lymphoma. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The tumor microenvironment (TME) plays critical roles in cancer development, tumor progression, and susceptibility to therapy. However, the phenotypic states and interaction patterns of its underlying cell types remain poorly understood. To address this challenge, we developed a new computational framework, EcoTyper, for large-scale dissection of cell states and cellular communities (i.e., ecosystems) from tumor genomic profiles. EcoTyper integrates single-cell RNA sequencing (scRNA-seq) with CIBERSORTx, an algorithm for bulk RNA-seq deconvolution (Newman et al., Nat Biotechnol, 2019), to identify and validate cellular states and ecosystems that reflect fundamental distinctions in TME biology. Here we applied EcoTyper to diffuse large B cell lymphoma (DLBCL), an aggressive B cell malignancy with clinically distinct molecular subtypes and several immunologically-active therapies. We sought to determine whether EcoTyper could reveal novel biological variation in the DLBCL TME linked to tumor subtypes and genotypes, therapeutic responses, and clinical outcomes. We applied our approach to define transcriptional states from 13 cell types, including malignant, immune, and stromal cells, in over 1,500 DLBCL tumors. Remarkably, nearly all cell states identified by EcoTyper were validated in independent scRNA-seq and bulk RNA-seq datasets. Moreover, many cells states reflected novel phenotypic groupings, and the majority showed strong associations with overall survival, specific mutational profiles, and tumor molecular subtypes. Additionally, by identifying DLBCL tumors with similar communities of cellular states, we defined novel cellular ecosystems, or “ecotypes”, with distinct biological characteristics and clinical outcomes. Several ecotypes showed significant enrichments in canonical or novel tumor genotypes, suggesting an evolutionary interplay between the tumor and host TME. In summary, we developed a novel computational framework to dissect the TME at scale and present the most comprehensive atlas to date of cell states and cellular communities in DLBCL. Our approach is extensible to nearly any cancer type and may lead to the development of novel diagnostics and individualized immunotherapies.
Citation Format: Chloe B. Steen, Bogdan Luca, Mohammad S. Esfahani, Barzin Y. Nabet, Brian Sworder, Farshad Farshidfar, David Kurtz, Chih Long Liu, Ranjana H. Advani, Yasodha Natkunam, June H. Myklebust, Maximilian Diehn, Andrew Gentles, Ash Alizadeh, Aaron M. Newman. Landscape of tumor cell states and cellular ecosystems in diffuse large B cell lymphoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1557.
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21
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Nabet BY, Esfahani MS, Hamilton EG, Chabon JJ, Moding EJ, Rizvi H, Steen CB, Chaudhuri AA, Liu CL, Hui AB, Stehr H, Goljenola L, Jin MC, Jeon YJ, Tseng D, Merghoub T, Neal JW, Wakelee HA, Padda SK, Ramchandran KJ, Das M, Bonilla RF, Yoo C, Chen EL, Ko RB, Newman AM, Hellmann MD, Alizadeh AA, Diehn M. Abstract 5666: A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5666] [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
Although treatment of non-small cell lung cancer (NSCLC) with immune checkpoint inhibitors (ICI) can produce remarkably durable responses, most patients develop early disease progression. Furthermore, initial response assessment by conventional imaging is often unable to identify which patients will achieve durable clinical benefit (DCB). Here, we analyze 211 samples from 99 patients and demonstrate that pre-treatment circulating tumor DNA (ctDNA) and circulating immune profiles are independently associated with DCB. We further show that ctDNA dynamics after a single ICI infusion can identify the majority of patients who will achieve DCB. Integrating these determinants, we describe an entirely noninvasive multi-analyte assay (DIREct-On, Durable Immunotherapy Response Estimation by immune profiling and ctDNA- On-treatment) that robustly predicted DCB, and that was validated in two independent cohorts (AUC = 0.89-0.93, PPV = 92-100%, HR = 0.04-0.11). Taken together, these results demonstrate that integrated ctDNA and circulating immune cell profiling can provide accurate, noninvasive, and early forecasting of ultimate outcomes for NSCLC patients receiving ICI.
Citation Format: Barzin Y. Nabet, Mohammad S. Esfahani, Emily G. Hamilton, Jacob J. Chabon, Everett J. Moding, Hira Rizvi, Chloe B. Steen, Aadel A. Chaudhuri, Chih Long Liu, Angela B. Hui, Henning Stehr, Linda Goljenola, Michael C. Jin, Young-Jun Jeon, Diane Tseng, Taha Merghoub, Joel W. Neal, Heather A. Wakelee, Sukhmani K. Padda, Kavitha J. Ramchandran, Millie Das, Rene F. Bonilla, Christopher Yoo, Emily L. Chen, Ryan B. Ko, Aaron M. Newman, Matthew D. Hellmann, Ash A. Alizadeh, Maximilian Diehn. A noninvasive approach for early prediction of therapeutic benefit from immune checkpoint inhibition for lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5666.
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Affiliation(s)
| | | | | | | | | | - Hira Rizvi
- 2Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | | | | | | | - Taha Merghoub
- 2Memorial Sloan Kettering Cancer Center, New York, NY
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22
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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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23
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Hellmann MD, Nabet BY, Rizvi H, Chaudhuri AA, Wells DK, Dunphy MPS, Chabon JJ, Liu CL, Hui AB, Arbour KC, Luo J, Preeshagul IR, Moding EJ, Almanza D, Bonilla RF, Sauter JL, Choi H, Tenet M, Abu-Akeel M, Plodkowski AJ, Perez Johnston R, Yoo CH, Ko RB, Stehr H, Gojenola L, Wakelee HA, Padda SK, Neal JW, Chaft JE, Kris MG, Rudin CM, Merghoub T, Li BT, Alizadeh AA, Diehn M. Circulating Tumor DNA Analysis to Assess Risk of Progression after Long-term Response to PD-(L)1 Blockade in NSCLC. Clin Cancer Res 2020; 26:2849-2858. [PMID: 32046999 DOI: 10.1158/1078-0432.ccr-19-3418] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/30/2022]
Abstract
PURPOSE Treatment with PD-(L)1 blockade can produce remarkably durable responses in patients with non-small cell lung cancer (NSCLC). However, a significant fraction of long-term responders ultimately progress and predictors of late progression are unknown. We hypothesized that circulating tumor DNA (ctDNA) analysis of long-term responders to PD-(L)1 blockade may differentiate those who will achieve ongoing benefit from those at risk of eventual progression. EXPERIMENTAL DESIGN In patients with advanced NSCLC achieving long-term benefit from PD-(L)1 blockade (progression-free survival ≥ 12 months), plasma was collected at a surveillance timepoint late during/after treatment to interrogate ctDNA by Cancer Personalized Profiling by Deep Sequencing. Tumor tissue was available for 24 patients and was profiled by whole-exome sequencing (n = 18) or by targeted sequencing (n = 6). RESULTS Thirty-one patients with NSCLC with long-term benefit to PD-(L)1 blockade were identified, and ctDNA was analyzed in surveillance blood samples collected at a median of 26.7 months after initiation of therapy. Nine patients also had baseline plasma samples available, and all had detectable ctDNA prior to therapy initiation. At the surveillance timepoint, 27 patients had undetectable ctDNA and 25 (93%) have remained progression-free; in contrast, all 4 patients with detectable ctDNA eventually progressed [Fisher P < 0.0001; positive predictive value = 1, 95% confidence interval (CI), 0.51-1; negative predictive value = 0.93 (95% CI, 0.80-0.99)]. CONCLUSIONS ctDNA analysis can noninvasively identify minimal residual disease in patients with long-term responses to PD-(L)1 blockade and predict the risk of eventual progression. If validated, ctDNA surveillance may facilitate personalization of the duration of immune checkpoint blockade and enable early intervention in patients at high risk for progression.
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Affiliation(s)
- Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York. .,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York.,Parker Center for Cancer Immunotherapy, San Francisco, California
| | - Barzin Y Nabet
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Daniel K Wells
- Parker Center for Cancer Immunotherapy, San Francisco, California
| | - Mark P S Dunphy
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jacob J Chabon
- Department of Radiation Oncology, Stanford University, Stanford, California.,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
| | - Angela B Hui
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Kathryn C Arbour
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jia Luo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabel R Preeshagul
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Diego Almanza
- Department of Radiation Oncology, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Jennifer L Sauter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hyejin Choi
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan Tenet
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mohsen Abu-Akeel
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rocio Perez Johnston
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, California
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, California
| | - Heather A Wakelee
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Sukhmani K Padda
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Joel W Neal
- Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University, Stanford, California
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark G Kris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Parker Center for Cancer Immunotherapy, San Francisco, California.,Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bob T Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell School of Medicine, New York, New York.,Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ash A Alizadeh
- Stanford Cancer Institute, 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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24
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Moding EJ, Liu Y, Nabet BY, Chabon JJ, Chaudhuri AA, Hui AB, Bonilla RF, Ko RB, Yoo CH, Gojenola L, Jones CD, He J, Qiao Y, Xu T, Heymach JV, Tsao A, Liao Z, Gomez DR, Das M, Padda SK, Ramchandran KJ, Neal JW, Wakelee HA, Loo BW, Lin SH, Alizadeh AA, Diehn M. Circulating Tumor DNA Dynamics Predict Benefit from Consolidation Immunotherapy in Locally Advanced Non-Small Cell Lung Cancer. Nat Cancer 2020; 1:176-183. [PMID: 34505064 PMCID: PMC8425388 DOI: 10.1038/s43018-019-0011-0] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022]
Abstract
Circulating tumor DNA (ctDNA) molecular residual disease (MRD) following curative-intent treatment strongly predicts recurrence in multiple tumor types, but whether further treatment can improve outcomes in patients with MRD remains unclear. We applied CAPP-Seq ctDNA analysis to 218 samples from 65 patients receiving chemoradiation therapy (CRT) for locally advanced NSCLC, including 28 patients receiving consolidation immune checkpoint inhibition (CICI). Patients with undetectable ctDNA after CRT had excellent outcomes whether or not they received CICI. Among such patients, one died from CICI-related pneumonitis, highlighting the potential utility of only treating patients with MRD. In contrast, patients with MRD after CRT who received CICI had significantly better outcomes than patients who did not receive CICI. Furthermore, the ctDNA response pattern early during CICI identified patients responding to consolidation therapy. Our results suggest that CICI improves outcomes for NSCLC patients with MRD and that ctDNA analysis may facilitate personalization of consolidation therapy.
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Affiliation(s)
- Everett J Moding
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Yufei Liu
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barzin Y Nabet
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Washington University, St. Louis, MO, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Rene F Bonilla
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Ryan B Ko
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Christopher H Yoo
- Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Linda Gojenola
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Carol D Jones
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jianzhong He
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yawei Qiao
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ting Xu
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne Tsao
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhongxing Liao
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel R Gomez
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Millie Das
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
- Department of Medicine, VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sukhmani K Padda
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Kavitha J Ramchandran
- Division of Oncology, Department of Medicine, 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
| | - Steven H Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| | - Maximilian Diehn
- Department of Radiation Oncology, 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.
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25
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Osorio JC, Arbour KC, Le DT, Durham JN, Plodkowski AJ, Halpenny DF, Ginsberg MS, Sawan P, Crompton JG, Yu HA, Namakydoust A, Nabet BY, Chaft JE, Riely GJ, Rizvi H, Diaz LA, Hellmann MD. Lesion-Level Response Dynamics to Programmed Cell Death Protein (PD-1) Blockade. J Clin Oncol 2019; 37:3546-3555. [PMID: 31675272 DOI: 10.1200/jco.19.00709] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Response to programmed cell death protein 1 (PD-1) blockade is often conceptualized as resulting from reinvigoration of tumor-infiltrating lymphocytes. However, recruited antitumor immunity from the periphery may also be an important contributor to response. A detailed assessment of the response dynamics of individual metastasis could provide insight to the systemic and local features that mediate response and resistance to immunotherapy. MATERIALS AND METHODS Patients with metastatic non-small-cell lung cancer (NSCLC) or mismatch repair deficiency (MMRD) carcinoma treated with PD-1 monotherapy were evaluated independently. Absolute and percent change of each target lesion were quantified at each computed tomography scan using RECIST. Patterns of progression were predefined as systemic or mixed and were correlated with clinical outcomes. RESULTS A total of 761 individual lesions from 214 patients with NSCLC and 290 lesions from 78 patients with MMRD carcinoma were examined. Individual target lesion responses aligned with best overall response of each patient (85% NSCLC and 93% MMRD lesions responded in patients with partial response/complete response). In responding patients, timing of response was uniform (73% NSCLC and 76% MMRD lesions responded synchronously), and deeper responses were associated with prolonged progression-free survival and overall survival. By contrast, at progression, mixed progression was common (45% of NSCLC and 53% of MMRD) and associated with improved survival compared with those who experienced systemic progression (NSCLC hazard ratio [HR], 0.58; P = .001; MMRD HR, 0.40; P = .07). Organ sites had differential responses, with lymph node and liver metastasis among the most and least responsive, respectively. CONCLUSION Temporal-spatial patterns of response across individual metastases tend to be uniform, favoring the role of peripheral, clonally directed antitumor immunity as a key mediator of response to PD-1 blockade. In contrast, progression is more heterogeneous, potentially revealing the clinical importance of local features and intertumoral heterogeneity.
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Affiliation(s)
- Juan C Osorio
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kathryn C Arbour
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Dung T Le
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | | | - Peter Sawan
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Helena A Yu
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Azadeh Namakydoust
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Barzin Y Nabet
- Memorial Sloan Kettering Cancer Center, New York, NY.,Stanford University, Stanford, CA
| | - Jamie E Chaft
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Gregory J Riely
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Hira Rizvi
- Memorial Sloan Kettering Cancer Center, New York, NY
| | - Luis A Diaz
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY
| | - Matthew D Hellmann
- Memorial Sloan Kettering Cancer Center, New York, NY.,Weill Cornell Medical College, New York, NY.,Parker Institute for Cancer Immunotherapy, New York, NY
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26
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Abstract
Exosomes are small extracellular vesicles that contain genetic material, proteins, and lipids. They function as potent signaling molecules between cancer cells and the surrounding cells that comprise the tumor microenvironment (TME). Exosomes derived from both tumor and stromal cells have been implicated in all stages of cancer progression and play an important role in therapy resistance. Moreover, due to their nature as mediators of cell-cell communication, they are integral to TME-dependent therapy resistance. In this review, we discuss current exosome isolation and profiling techniques and their role in TME interactions and therapy resistance. We also explore emerging clinical applications of both exosomes as biomarkers, direct therapeutic targets, and engineered nanocarriers. In order to fully understand the TME, careful interrogation of exosomes and their cargo is critical. This understanding is a promising avenue for the development of effective clinical applications.
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Affiliation(s)
- Irene Li
- Stanford Cancer Biology Program, Stanford University, 318 Campus Drive, Stanford, CA 94305 USA
- Department of Radiology, Stanford University, 318 Campus Drive, Stanford, CA 94305 USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford University, 265 Campus Drive, Stanford, CA 94305 USA
- Stanford Cancer Institute, Stanford University, 265 Campus Drive, Stanford, CA 94305 USA
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27
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Dudley JC, Schroers-Martin J, Lazzareschi DV, Shi WY, Chen SB, Esfahani MS, Trivedi D, Chabon JJ, Chaudhuri AA, Stehr H, Liu CL, Lim H, Costa HA, Nabet BY, Sin MLY, Liao JC, Alizadeh AA, Diehn M. Detection and Surveillance of Bladder Cancer Using Urine Tumor DNA. Cancer Discov 2018; 9:500-509. [PMID: 30578357 DOI: 10.1158/2159-8290.cd-18-0825] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/02/2018] [Accepted: 12/18/2018] [Indexed: 01/14/2023]
Abstract
Current regimens for the detection and surveillance of bladder cancer are invasive and have suboptimal sensitivity. Here, we present a novel high-throughput sequencing (HTS) method for detection of urine tumor DNA (utDNA) called utDNA CAPP-Seq (uCAPP-Seq) and apply it to 67 healthy adults and 118 patients with early-stage bladder cancer who had urine collected either prior to treatment or during surveillance. Using this targeted sequencing approach, we detected a median of 6 mutations per patient with bladder cancer and observed surprisingly frequent mutations of the PLEKHS1 promoter (46%), suggesting these mutations represent a useful biomarker for detection of bladder cancer. We detected utDNA pretreatment in 93% of cases using a tumor mutation-informed approach and in 84% when blinded to tumor mutation status, with 96% to 100% specificity. In the surveillance setting, we detected utDNA in 91% of patients who ultimately recurred, with utDNA detection preceding clinical progression in 92% of cases. uCAPP-Seq outperformed a commonly used ancillary test (UroVysion, P = 0.02) and cytology and cystoscopy combined (P ≤ 0.006), detecting 100% of bladder cancer cases detected by cytology and 82% that cytology missed. Our results indicate that uCAPP-Seq is a promising approach for early detection and surveillance of bladder cancer. SIGNIFICANCE: This study shows that utDNA can be detected using HTS with high sensitivity and specificity in patients with early-stage bladder cancer and during post-treatment surveillance, significantly outperforming standard diagnostic modalities and facilitating noninvasive detection, genotyping, and monitoring.This article is highlighted in the In This Issue feature, p. 453.
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Affiliation(s)
| | - Joseph Schroers-Martin
- Department of Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - William Y Shi
- Department of Pathology, Stanford University, Stanford, California
| | - Simon B Chen
- Department of Pathology, Stanford University, Stanford, California
| | | | - Dharati Trivedi
- Department of Urology, Stanford University, Stanford, California.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Jacob J Chabon
- Stanford Cancer Institute, Stanford University, Stanford, California
| | - Aadel A Chaudhuri
- Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Radiation Oncology, Stanford University, Stanford, California
| | - Henning Stehr
- Department of Pathology, Stanford University, Stanford, California
| | - Chih Long Liu
- Department of Medicine, Stanford University, Stanford, California.,Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Stanford University, Stanford, California
| | - Harumi Lim
- Department of Pathology, Stanford University, Stanford, California
| | - Helio A Costa
- Department of Pathology, Stanford University, Stanford, California
| | - Barzin Y Nabet
- Stanford Cancer Institute, Stanford University, Stanford, California
| | | | - Joseph C Liao
- Stanford Cancer Institute, Stanford University, Stanford, California.,Department of Urology, Stanford University, Stanford, California.,Veterans Affairs Palo Alto Health Care System, Palo Alto, California
| | - Ash A Alizadeh
- Department of Medicine, Stanford University, Stanford, California. .,Stanford Cancer Institute, Stanford University, Stanford, California.,Division of Oncology, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, California. .,Department of Radiation Oncology, Stanford University, Stanford, California.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California
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28
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Nabet BY, Qiu Y, Shabason JE, Wu TJ, Yoon T, Kim BC, Benci JL, DeMichele AM, Tchou J, Marcotrigiano J, Minn AJ. Exosome RNA Unshielding Couples Stromal Activation to Pattern Recognition Receptor Signaling in Cancer. Cell 2017; 170:352-366.e13. [PMID: 28709002 PMCID: PMC6611169 DOI: 10.1016/j.cell.2017.06.031] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 04/26/2017] [Accepted: 06/20/2017] [Indexed: 12/24/2022]
Abstract
Interactions between stromal fibroblasts and cancer cells generate signals for cancer progression, therapy resistance, and inflammatory responses. Although endogenous RNAs acting as damage-associated molecular patterns (DAMPs) for pattern recognition receptors (PRRs) may represent one such signal, these RNAs must remain unrecognized under non-pathological conditions. We show that triggering of stromal NOTCH-MYC by breast cancer cells results in a POL3-driven increase in RN7SL1, an endogenous RNA normally shielded by RNA binding proteins SRP9/14. This increase in RN7SL1 alters its stoichiometry with SRP9/14 and generates unshielded RN7SL1 in stromal exosomes. After exosome transfer to immune cells, unshielded RN7SL1 drives an inflammatory response. Upon transfer to breast cancer cells, unshielded RN7SL1 activates the PRR RIG-I to enhance tumor growth, metastasis, and therapy resistance. Corroborated by evidence from patient tumors and blood, these results demonstrate that regulation of RNA unshielding couples stromal activation with deployment of RNA DAMPs that promote aggressive features of cancer. VIDEO ABSTRACT.
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Affiliation(s)
- Barzin Y Nabet
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yu Qiu
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacob E Shabason
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tony J Wu
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Taewon Yoon
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian C Kim
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph L Benci
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angela M DeMichele
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Julia Tchou
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph Marcotrigiano
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Andy J Minn
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Basser Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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29
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Wu TJ, Nabet BY, Xu B, Boelens MC, Jonkers J, Minn AJ. Abstract A45: Exosome transfer from stromal to breast cancer cells regulates therapy resistance pathways in triple-negative breast cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.tme16-a45] [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
Breast cancer cells can achieve protection from DNA damage both through cell-autonomous mechanisms and intercellular communication with the tumor microenvironment. Previously, we described an Interferon-Related DNA Damage Resistance Signature comprising of a network of interferon-stimulated genes (ISGs) that promotes and clinically predicts chemotherapy and radiation resistance in breast cancer. Here, we examine the heterotypic tumor-stroma interactions that regulate ISGs. We show that STAT1 and other ISGs are induced in breast cancer cells following interaction with stroma. STAT1 induces NOTCH3 expression, explaining a requirement for juxtacrine signaling. Moreover, we report that stroma upregulates ISG expression in breast cancer cells through exosomes. Exosomes transferred from the stroma and ISG induction are both dependent on RAB27B. In mice, targeting these pathways abrogate stroma-mediated resistance and results in long-term tumor-free survival. Analysis of primary human tumors supports the role of anti-viral/NOTCH3 pathways in NOTCH signaling and stroma-mediated resistance. To determine whether these observations can further predict clinical efficacy, cell lines derived from a genetically engineered mouse model for p53-induced breast cancer, K14cre;Brca1F/F;p53F/F, were tested. We show that stroma induces breast cancer ISGs through exosomes, which in turn can induce signaling to activate NOTCH3 and regulate DNA damage resistance.
Citation Format: Tony J. Wu, Barzin Y. Nabet, Bihui Xu, Mirjam C. Boelens, Jos Jonkers, Andy J. Minn. Exosome transfer from stromal to breast cancer cells regulates therapy resistance pathways in triple-negative breast cancer. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr A45.
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Affiliation(s)
- Tony J. Wu
- 1University of Pennsylvania, Philadelphia, PA,
| | | | - Bihui Xu
- 1University of Pennsylvania, Philadelphia, PA,
| | | | - Jos Jonkers
- 2Netherlands Cancer Institute, Amsterdam, The Netherlands
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Reina CP, Nabet BY, Young PD, Pittman RN. Basal and stress-induced Hsp70 are modulated by ataxin-3. Cell Stress Chaperones 2012; 17:729-42. [PMID: 22777893 PMCID: PMC3468683 DOI: 10.1007/s12192-012-0346-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 05/11/2012] [Accepted: 06/07/2012] [Indexed: 12/24/2022] Open
Abstract
Regulation of basal and induced levels of hsp70 is critical for cellular homeostasis. Ataxin-3 is a deubiquitinase with several cellular functions including transcriptional regulation and maintenance of protein homeostasis. While investigating potential roles of ataxin-3 in response to cellular stress, it appeared that ataxin-3 regulated hsp70. Basal levels of hsp70 were lower in ataxin-3 knockout (KO) mouse brain from 2 to 63 weeks of age and hsp70 was also lower in fibroblasts from ataxin-3 KO mice. Transfecting KO cells with ataxin-3 rescued basal levels of hsp70 protein. Western blots of representative chaperones including hsp110, hsp90, hsp70, hsc70, hsp60, hsp40/hdj2, and hsp25 indicated that only hsp70 was appreciably altered in KO fibroblasts and KO mouse brain. Turnover of hsp70 protein was similar in wild-type (WT) and KO cells; however, basal hsp70 promoter reporter activity was decreased in ataxin-3 KO cells. Transfecting ataxin-3 restored hsp70 basal promoter activity in KO fibroblasts to levels of promoter activity in WT cells; however, mutations that inactivated deubiquitinase activity or the ubiquitin interacting motifs did not restore full activity to hsp70 basal promoter activity. Hsp70 protein and promoter activity were higher in WT compared to KO cells exposed to heat shock and azetidine-2-carboxylic acid, but WT and KO cells had similar levels in response to cadmium. Heat shock factor-1 had decreased levels and increased turnover in ataxin-3 KO fibroblasts. Data in this study are consistent with ataxin-3 regulating basal level of hsp70 as well as modulating hsp70 in response to a subset of cellular stresses.
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Affiliation(s)
- Christopher P. Reina
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
- Present Address: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854 USA
| | - Barzin Y. Nabet
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
- Present Address: Department of Cancer Biology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Peter D. Young
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
| | - Randall N. Pittman
- Department of Pharmacology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104 USA
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Gilad O, Nabet BY, Ragland RL, Schoppy DW, Smith KD, Durham AC, Brown EJ. Combining ATR suppression with oncogenic Ras synergistically increases genomic instability, causing synthetic lethality or tumorigenesis in a dosage-dependent manner. Cancer Res 2010; 70:9693-702. [PMID: 21098704 DOI: 10.1158/0008-5472.can-10-2286] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [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] [Indexed: 12/17/2022]
Abstract
Previous studies indicate that oncogenic stress activates the ATR-Chk1 pathway. Here, we show that ATR-Chk1 pathway engagement is essential for limiting genomic instability following oncogenic Ras transformation. ATR pathway inhibition in combination with oncogenic Ras expression synergistically increased genomic instability, as quantified by chromatid breaks, sister chromatid exchanges, and H2AX phosphorylation. This level of instability was significantly greater than that observed following ATR suppression in untransformed control cells. In addition, consistent with a deficiency in long-term genome maintenance, hypomorphic ATR pathway reduction to 16% of normal levels was synthetic lethal with oncogenic Ras expression in cultured cells. Notably, elevated genomic instability and synthetic lethality following suppression of ATR were not due to accelerated cycling rates in Ras-transformed cells, indicating that these synergistic effects were generated on a per-cell-cycle basis. In contrast to the synthetic lethal effects of hypomorphic ATR suppression, subtle reduction of ATR expression (haploinsufficiency) in combination with endogenous levels of K-ras(G12D) expression elevated the incidence of lung adenocarcinoma, spindle cell sarcoma, and thymic lymphoma in p53 heterozygous mice. K-ras(G12D)-induced tumorigenesis in ATR(+/-)p53(+/-) mice was associated with intrachromosomal deletions and loss of wild-type p53. These findings indicate that synergistic increases in genomic instability following ATR reduction in oncogenic Ras-transformed cells can produce 2 distinct biological outcomes: synthetic lethality upon significant suppression of ATR expression and tumor promotion in the context of ATR haploinsufficiency. These results highlight the importance of the ATR pathway both as a barrier to malignant progression and as a potential target for cancer treatment.
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MESH Headings
- Animals
- Antineoplastic Agents, Hormonal/pharmacology
- Ataxia Telangiectasia Mutated Proteins
- Blotting, Western
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Transformation, Neoplastic/genetics
- Cells, Cultured
- Checkpoint Kinase 1
- Dose-Response Relationship, Drug
- Female
- Gene Expression Regulation, Neoplastic
- Genes, ras/genetics
- Genomic Instability
- Male
- Mice
- Mice, 129 Strain
- Mice, Inbred C57BL
- Mice, Knockout
- NIH 3T3 Cells
- Neoplasms, Experimental/genetics
- Neoplasms, Experimental/metabolism
- Neoplasms, Experimental/pathology
- Protein Kinases/genetics
- Protein Kinases/metabolism
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- RNA Interference
- Recombination, Genetic/drug effects
- Reverse Transcriptase Polymerase Chain Reaction
- Signal Transduction
- Tamoxifen/pharmacology
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
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Affiliation(s)
- Oren Gilad
- Abramson Family Cancer Research Institute and Department of Cancer Biology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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