1
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Sekeres MA, Montesinos P, Novak J, Wang J, Jeyakumar D, Tomlinson B, Mayer J, Jou E, Robak T, Taussig DC, Dombret H, Merchant A, Shaik N, O'Brien T, Roh W, Liu X, Ma W, DiRienzo CG, Chan G, Cortes JE. Glasdegib plus intensive or non-intensive chemotherapy for untreated acute myeloid leukemia: results from the randomized, phase 3 BRIGHT AML 1019 trial. Leukemia 2023; 37:2017-2026. [PMID: 37604981 PMCID: PMC10539167 DOI: 10.1038/s41375-023-02001-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023]
Abstract
This is the primary report of the randomized, placebo-controlled phase 3 BRIGHT AML 1019 clinical trial of glasdegib in combination with intensive chemotherapy (cytarabine and daunorubicin) or non-intensive chemotherapy (azacitidine) in patients with untreated acute myeloid leukemia. Overall survival (primary endpoint) was similar between the glasdegib and placebo arms in the intensive (n = 404; hazard ratio [HR] 1.05; 95% confidence interval [CI]: 0.782-1.408; two-sided p = 0.749) and non-intensive (n = 325; HR 0.99; 95% CI: 0.768-1.289; two-sided p = 0.969) studies. The proportion of patients who experienced treatment-emergent adverse events was similar for glasdegib versus placebo (intensive: 99.0% vs. 98.5%; non-intensive: 99.4% vs. 98.8%). The most common treatment-emergent adverse events were nausea, febrile neutropenia, and anemia in the intensive study and anemia, constipation, and nausea in the non-intensive study. The addition of glasdegib to either cytarabine and daunorubicin or azacitidine did not significantly improve overall survival and the primary efficacy endpoint for the BRIGHT AML 1019 phase 3 trial was not met. Clinical trial registration: ClinicalTrials.gov: NCT03416179.
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Affiliation(s)
- Mikkael A Sekeres
- Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA.
| | - Pau Montesinos
- Hospital Universitari i Politècnic La Fe, Valencia, Spain
- CIBERONC, Instituto Carlos III, Madrid, Spain
| | - Jan Novak
- Department of Internal Medicine and Hematology, University Hospital Kralovske Vinohrady, Prague, Czech Republic
- Department of Haematology, 3rd Faculty of Medicine, Charles University and Faculty Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Jianxiang Wang
- Department of Clinical Hematology, Institute of Hematology and Blood Diseases Hospital, Tianjin, China
| | - Deepa Jeyakumar
- University of California, Irvine, Chao Family Comprehensive Cancer Center, Orange, CA, USA
| | - Benjamin Tomlinson
- Division of Hematology, University Hospitals of Cleveland Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Jiri Mayer
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Erin Jou
- Department of Hematology/Oncology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Manhasset, NY, USA
| | - Tadeusz Robak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | - Hervé Dombret
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Akil Merchant
- Division of Hematology and Cellular Therapy, Cedars Sinai Cancer, Los Angeles, CA, USA
| | | | | | - Whijae Roh
- Pfizer Oncology, Pfizer Inc, San Diego, CA, USA
| | - Xueli Liu
- Pfizer Oncology, Pfizer Inc, San Diego, CA, USA
| | - Wendy Ma
- Pfizer Oncology, Pfizer Inc, San Diego, CA, USA
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2
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Bill R, Wirapati P, Messemaker M, Roh W, Zitti B, Duval F, Kiss M, Park JC, Saal TM, Hoelzl J, Tarussio D, Benedetti F, Tissot S, Kandalaft L, Varrone M, Ciriello G, McKee TA, Monnier Y, Mermod M, Blaum EM, Gushterova I, Gonye ALK, Hacohen N, Getz G, Mempel TR, Klein AM, Weissleder R, Faquin WC, Sadow PM, Lin D, Pai SI, Sade-Feldman M, Pittet MJ. CXCL9:SPP1 macrophage polarity identifies a network of cellular programs that control human cancers. Science 2023; 381:515-524. [PMID: 37535729 PMCID: PMC10755760 DOI: 10.1126/science.ade2292] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 06/22/2023] [Indexed: 08/05/2023]
Abstract
Tumor microenvironments (TMEs) influence cancer progression but are complex and often differ between patients. Considering that microenvironment variations may reveal rules governing intratumoral cellular programs and disease outcome, we focused on tumor-to-tumor variation to examine 52 head and neck squamous cell carcinomas. We found that macrophage polarity-defined by CXCL9 and SPP1 (CS) expression but not by conventional M1 and M2 markers-had a noticeably strong prognostic association. CS macrophage polarity also identified a highly coordinated network of either pro- or antitumor variables, which involved each tumor-associated cell type and was spatially organized. We extended these findings to other cancer indications. Overall, these results suggest that, despite their complexity, TMEs coordinate coherent responses that control human cancers and for which CS macrophage polarity is a relevant yet simple variable.
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Affiliation(s)
- Ruben Bill
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Pratyaksha Wirapati
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Marius Messemaker
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Division of Molecular Oncology and Immunology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Beatrice Zitti
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Florent Duval
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Máté Kiss
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
| | - Jong Chul Park
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Talia M Saal
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
| | - Jan Hoelzl
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Tarussio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Fabrizio Benedetti
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Stéphanie Tissot
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Lana Kandalaft
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Oncology, Center for Experimental Therapeutics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Marco Varrone
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Giovanni Ciriello
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne (UNIL), Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Thomas A McKee
- Division of Clinical Pathology, Diagnostic Department, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Yan Monnier
- Department of Otorhinolaryngology-Head and Neck Surgery, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Maxime Mermod
- Department of Otorhinolaryngology-Head and Neck Surgery, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Emily M Blaum
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Irena Gushterova
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Anna L K Gonye
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Nir Hacohen
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thorsten R Mempel
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - Allon M Klein
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - William C Faquin
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Peter M Sadow
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Derrick Lin
- Department of Otolaryngology Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Sara I Pai
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Moshe Sade-Feldman
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
| | - Mikael J Pittet
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA, USA
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Department of Oncology, Geneva University Hospitals (HUG), Geneva, Switzerland
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3
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Roh W, Geffen Y, Cha H, Miller M, Anand S, Kim J, Heiman DI, Gainor JF, Laird PW, Cherniack AD, Ock CY, Lee SH, Getz G. High-Resolution Profiling of Lung Adenocarcinoma Identifies Expression Subtypes with Specific Biomarkers and Clinically Relevant Vulnerabilities. Cancer Res 2022; 82:3917-3931. [PMID: 36040373 PMCID: PMC9718502 DOI: 10.1158/0008-5472.can-22-0432] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/30/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022]
Abstract
Lung adenocarcinoma (LUAD) is one of the most common cancer types and has various treatment options. Better biomarkers to predict therapeutic response are needed to guide choice of treatment modality and to improve precision medicine. Here, we used a consensus hierarchical clustering approach on 509 LUAD cases from The Cancer Genome Atlas to identify five robust LUAD expression subtypes. Genomic and proteomic data from patient samples and cell lines was then integrated to help define biomarkers of response to targeted therapies and immunotherapies. This approach defined subtypes with unique proteogenomic and dependency profiles. Subtype 4 (S4)-associated cell lines exhibited specific vulnerability to loss of CDK6 and CDK6-cyclin D3 complex gene (CCND3). Subtype 3 (S3) was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling. Experimental validation showed that S3-associated cell lines responded to MET inhibitors, leading to increased expression of programmed death-ligand 1 (PD-L1). In an independent real-world patient dataset, patients with S3 tumors were enriched with responders to immune checkpoint blockade. Genomic features in S3 and S4 were further identified as biomarkers for enabling clinical diagnosis of these subtypes. Overall, our consensus hierarchical clustering approach identified robust tumor expression subtypes, and our subsequent integrative analysis of genomics, proteomics, and CRISPR screening data revealed subtype-specific biology and vulnerabilities. These LUAD expression subtypes and their biomarkers could help identify patients likely to respond to CDK4/6, MET, or PD-L1 inhibitors, potentially improving patient outcome. SIGNIFICANCE Integrative analysis of multiomic and drug dependency data uncovers robust lung adenocarcinoma expression subtypes with unique therapeutic vulnerabilities and subtype-specific biomarkers of response.
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Affiliation(s)
- Whijae Roh
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Yifat Geffen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Cancer Center and Dept. of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Hongui Cha
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Mendy Miller
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Shankara Anand
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Jaegil Kim
- GSK inc. 196 Broadway, Cambridge, Massachusetts
| | - David I Heiman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Justin F Gainor
- Center for Thoracic Cancers, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | | | - Andrew D Cherniack
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | | | - Se-Hoon Lee
- Division of Hematology/Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Gad Getz
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts.,Cancer Center and Dept. of Pathology, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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4
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Roh W, Geffen Y, Miller M, Anand S, Kim J, Heiman D, Meyerson M, Laird P, Cherniack A, Getz G. Abstract 2151: Identification and proteogenomic characterization of novel lung adenocarcinoma subtypes with therapeutic relevance. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2151] [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
Lung adenocarcinoma (LUAD) is one of the most common cancer types with various available treatment modalities. However, better biomarkers of response are still needed for further improving precision medicine. Therefore, a robust LUAD subtyping can substantially aid in determining the most effective therapies that target subtype-specific vulnerabilities. In this study, we integrated multiple datasets: (i) the full 509 LUAD patient cohort from The Cancer Genome Atlas (TCGA) project, (ii) cancer vulnerability data in LUAD cell lines from the Broad Institute’s DependencyMap, and (iii) proteomic data from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) LUAD patients. Using these datasets, we identified 5 expression subtypes (S1-S5) with unique proteogenomic and dependency profiles that increased the resolution of previously defined subtypes (Proximal Inflammatory [PI]; Proximal Proliferative [PP]; and Terminal Respiratory Unit [TRU]). S4-associated cell lines exhibited specific vulnerability to CDK6 and CDK6-cyclin D3 complex gene, CCND3. S3 was characterized by dependency on CDK4, immune-related expression patterns, and altered MET signaling. Experimental validation showed that S3-associated cell lines responded to MET inhibitors, which also led to increased PD-L1 expression. Finally, we identified a small set of biomarkers for S3 and S4 that could be used in the clinic to classify patients into our therapeutically relevant subtypes. Overall, our lung adenocarcinoma expression subtypes, especially S3 that represents 20% of LUAD patients and S4 that represents 25% of LUAD patients, and their biomarkers could help identify patients likely to respond to CDK4/6, MET, or PD-L1 inhibitors, potentially improving patient outcome.
Citation Format: Whijae Roh, Yifat Geffen, Mendy Miller, Shankara Anand, Jaegil Kim, David Heiman, Matthew Meyerson, Peter Laird, Andrew Cherniack, NCI CCG Tumor Molecular Pathology (TMP) Analysis Working Group, Gad Getz. Identification and proteogenomic characterization of novel lung adenocarcinoma subtypes with therapeutic relevance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2151.
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Affiliation(s)
| | | | | | | | | | | | - Matthew Meyerson
- 3Dana-Farber Cancer Institute, Harvard Medical School, Broad Institute, Cambridge, MA
| | | | | | - Gad Getz
- 6The Broad Institute, Massachusetts General Hospital, Harvard Medical School, Cambridge, MA
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5
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Andrews MC, Duong CPM, Gopalakrishnan V, Iebba V, Chen WS, Derosa L, Khan MAW, Cogdill AP, White MG, Wong MC, Ferrere G, Fluckiger A, Roberti MP, Opolon P, Alou MT, Yonekura S, Roh W, Spencer CN, Curbelo IF, Vence L, Reuben A, Johnson S, Arora R, Morad G, Lastrapes M, Baruch EN, Little L, Gumbs C, Cooper ZA, Prieto PA, Wani K, Lazar AJ, Tetzlaff MT, Hudgens CW, Callahan MK, Adamow M, Postow MA, Ariyan CE, Gaudreau PO, Nezi L, Raoult D, Mihalcioiu C, Elkrief A, Pezo RC, Haydu LE, Simon JM, Tawbi HA, McQuade J, Hwu P, Hwu WJ, Amaria RN, Burton EM, Woodman SE, Watowich S, Diab A, Patel SP, Glitza IC, Wong MK, Zhao L, Zhang J, Ajami NJ, Petrosino J, Jenq RR, Davies MA, Gershenwald JE, Futreal PA, Sharma P, Allison JP, Routy B, Zitvogel L, Wargo JA. Gut microbiota signatures are associated with toxicity to combined CTLA-4 and PD-1 blockade. Nat Med 2021; 27:1432-1441. [PMID: 34239137 PMCID: PMC11107795 DOI: 10.1038/s41591-021-01406-6] [Citation(s) in RCA: 199] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Treatment with combined immune checkpoint blockade (CICB) targeting CTLA-4 and PD-1 is associated with clinical benefit across tumor types, but also a high rate of immune-related adverse events. Insights into biomarkers and mechanisms of response and toxicity to CICB are needed. To address this, we profiled the blood, tumor and gut microbiome of 77 patients with advanced melanoma treated with CICB, with a high rate of any ≥grade 3 immune-related adverse events (49%) with parallel studies in pre-clinical models. Tumor-associated immune and genomic biomarkers of response to CICB were similar to those identified for ICB monotherapy, and toxicity from CICB was associated with a more diverse peripheral T-cell repertoire. Profiling of gut microbiota demonstrated a significantly higher abundance of Bacteroides intestinalis in patients with toxicity, with upregulation of mucosal IL-1β in patient samples of colitis and in pre-clinical models. Together, these data offer potential new therapeutic angles for targeting toxicity to CICB.
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Affiliation(s)
- Miles C Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia
- Deparment of Medicine, Monash University, Melbourne, Victoria, Australia
| | - Connie P M Duong
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | | | - Valerio Iebba
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Wei-Shen Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Dermatology, University of South Florida Morsani College of Medicine, Tampa, FL, USA
| | - Lisa Derosa
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Md Abdul Wadud Khan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandria P Cogdill
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael G White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew C Wong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gladys Ferrere
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Aurélie Fluckiger
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Maria P Roberti
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Paule Opolon
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
| | - Maryam Tidjani Alou
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Satoru Yonekura
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Whijae Roh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine N Spencer
- Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Irina Fernandez Curbelo
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luis Vence
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Golnaz Morad
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Lastrapes
- MD Anderson Cancer Center University of Texas Health Graduate School of Biomedical Sciences (GSBS), Houston, TX, USA
| | - Erez N Baruch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Peter A Prieto
- Department of Surgery, University of Rochester Medical Center, Rochester, NY, USA
| | - Khalida Wani
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Courtney W Hudgens
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Margaret K Callahan
- Department of Informatics, Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Adamow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Division of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael A Postow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Division of Immunology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte E Ariyan
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pierre-Olivier Gaudreau
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luigi Nezi
- Istituto Europeo di Oncologia, Milan, Italy
| | - Didier Raoult
- Aix-Marseille Université, MEPHI, IRD, IHU Méditerranée Infection, Marseille, France
| | - Catalin Mihalcioiu
- Department of Medicine, Faculty of Medicine and Health Sciences, McGill University Health Centre, Montreal, Quebec, Canada
| | - Arielle Elkrief
- Cedars Cancer Center, McGill University Health Centre, Montreal, Quebec, Canada
| | - Rossanna C Pezo
- Division of Medical Oncology, University of Toronto, Sunnybrook Odette Cancer Centre, Toronto, Ontario, Canada
| | - Lauren E Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Julie M Simon
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hussein A Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elizabeth M Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott E Woodman
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie Watowich
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael K Wong
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Li Zhao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Petrosino
- Department of Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Padmanee Sharma
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bertrand Routy
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus (GRCC), Villejuif, France.
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France.
- Université Paris-Saclay, Faculté de Médecine Kremlin-Bicêtre, Le Kremlin-Bicêtre, France.
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Hong X, Roh W, Sullivan RJ, Wong KHK, Wittner BS, Guo H, Dubash TD, Sade-Feldman M, Wesley B, Horwitz E, Boland GM, Marvin DL, Bonesteel T, Lu C, Aguet F, Burr R, Freeman SS, Parida L, Calhoun K, Jewett MK, Nieman LT, Hacohen N, Näär AM, Ting DT, Toner M, Stott SL, Getz G, Maheswaran S, Haber DA. The Lipogenic Regulator SREBP2 Induces Transferrin in Circulating Melanoma Cells and Suppresses Ferroptosis. Cancer Discov 2020; 11:678-695. [PMID: 33203734 DOI: 10.1158/2159-8290.cd-19-1500] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 09/22/2020] [Accepted: 11/12/2020] [Indexed: 12/20/2022]
Abstract
Circulating tumor cells (CTC) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastasis. We show that single CTCs from patients with melanoma coordinately upregulate lipogenesis and iron homeostasis pathways. These are correlated with both intrinsic and acquired resistance to BRAF inhibitors across clonal cultures of BRAF-mutant CTCs. The lipogenesis regulator SREBP2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species, and lipid peroxidation, thereby conferring resistance to inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic antioxidants ferrostatin-1 and vitamin E. In a prospective melanoma cohort, presence of CTCs with high lipogenic and iron metabolic RNA signatures is correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBP2-driven iron homeostatic pathways contribute to cancer progression, drug resistance, and metastasis. SIGNIFICANCE: Through single-cell analysis of primary and cultured melanoma CTCs, we have uncovered intrinsic cancer cell heterogeneity within lipogenic and iron homeostatic pathways that modulates resistance to BRAF inhibitors and to ferroptosis inducers. Activation of these pathways within CTCs is correlated with adverse clinical outcome, pointing to therapeutic opportunities.This article is highlighted in the In This Issue feature, p. 521.
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Affiliation(s)
- Xin Hong
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ryan J Sullivan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keith H K Wong
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
| | - Ben S Wittner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Hongshan Guo
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Taronish D Dubash
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Moshe Sade-Feldman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Benjamin Wesley
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Elad Horwitz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Genevieve M Boland
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dieuwke L Marvin
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Todd Bonesteel
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - François Aguet
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Risa Burr
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | | | - Laxmi Parida
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Katherine Calhoun
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Michelle K Jewett
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Linda T Nieman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - Nir Hacohen
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Anders M Näär
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
| | - David T Ting
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Mehmet Toner
- Center for Engineering in Medicine, Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Shriners Hospitals for Children, Boston, Massachusetts
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shannon L Stott
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Howard Hughes Medical Institute, Bethesda, Maryland
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Surgery, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, Massachusetts.
- Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- IBM Research, Yorktown Heights, New York
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7
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Lee WC, Reuben A, Hu X, McGranahan N, Chen R, Jalali A, Negrao MV, Hubert SM, Tang C, Wu CC, Lucas AS, Roh W, Suda K, Kim J, Tan AC, Peng DH, Lu W, Tang X, Chow CW, Fujimoto J, Behrens C, Kalhor N, Fukumura K, Coyle M, Thornton R, Gumbs C, Li J, Wu CJ, Little L, Roarty E, Song X, Lee JJ, Sulman EP, Rao G, Swisher S, Diao L, Wang J, Heymach JV, Huse JT, Scheet P, Wistuba II, Gibbons DL, Futreal PA, Zhang J, Gomez D, Zhang J. Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity. Genome Biol 2020; 21:271. [PMID: 33148332 PMCID: PMC7640699 DOI: 10.1186/s13059-020-02175-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary. RESULTS We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases. CONCLUSIONS Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.
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Affiliation(s)
- Won-Chul Lee
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Runzhe Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ali Jalali
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX, USA
| | - Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad Tang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anthony San Lucas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Whijae Roh
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kenichi Suda
- Department of Thoracic Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Japan
| | - Jihye Kim
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aik-Choon Tan
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kazutaka Fukumura
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcus Coyle
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rebecca Thornton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chang-Jiun Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik P Sulman
- New York University Langone School of Medicine, New York, NY, USA
| | - Ganesh Rao
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephen Swisher
- Department of Thoracic Surgery, 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
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel Gomez
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Current Address: Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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8
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Hong X, Roh W, Sullivan RJ, Wong KH, Wittner BS, Guo H, Dubash TD, Sade-Feldman M, Wesley BK, Boland GM, Marvin DL, Bonesteel T, Lu C, Horwitz E, Aguet F, Freeman SS, Calhoun K, Jewett MK, Nieman LT, Hacohen N, Näär AM, Ting DT, Toner M, Stott SL, Getz G, Maheswaran S, Haber DA. Abstract 6073: The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-6073] [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
Circulating tumor cells (CTCs) are shed by cancers into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastatic outgrowth. Clonally derived cultured CTCs from patients with BRAF-mutant melanoma reveal upregulation of lipogenesis and iron homeostasis pathways, correlated with their baseline and acquired drug resistance. In CTCs, the lipogenesis regulator SREBP directly induces transcription of the iron carrier Transferrin (TF), thereby reducing intracellular reactive oxygen species (ROS) and lipid peroxidation, and conferring resistance to BRAF inhibitors and inducers of ferroptosis. Knockdown of endogenous TF impairs tumorigenesis by melanoma CTCs; their associated soft agar clonogenic defect is rescued by the lipophilic anti-oxidants Ferrostatin-1 or Vitamin E, and by cholesterol. Single cell RNA-seq of patient-derived melanoma CTCs identifies a subset with high lipogenic, iron metabolic and proliferative signatures, correlated with adverse clinical outcome. Together, the coordinated regulation of these SREBP-driven pathways contributes to cancer progression, drug resistance and metastasis.
Citation Format: Xin Hong, Whijae Roh, Ryan J. Sullivan, Keith H. Wong, Ben S. Wittner, HongShan Guo, Taronish D. Dubash, Moshe Sade-Feldman, Ben K. Wesley, Genevieve M. Boland, Dieuwke L. Marvin, Todd Bonesteel, Chenyue Lu, Elad Horwitz, François Aguet, Samuel S. Freeman, Katherine Calhoun, Michelle K. Jewett, Linda T. Nieman, Nir Hacohen, Anders M. Näär, David T. Ting, Mehmet Toner, Shannon L. Stott, Gad Getz, Shyamala Maheswaran, Daniel A. Haber. The lipogenic regulator SREBP induces Transferrin in circulating melanoma cells, suppressing their susceptibility to ferroptosis [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 6073.
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Affiliation(s)
- Xin Hong
- 1MGH/Harvard Medical School, Charlestown, MA
| | - Whijae Roh
- 2Broad Institute of Harvard and MIT, Charlestown, MA
| | | | | | | | | | | | | | | | | | | | | | - Chenyue Lu
- 1MGH/Harvard Medical School, Charlestown, MA
| | | | | | | | - Katherine Calhoun
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | - Michelle K. Jewett
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | | | - Nir Hacohen
- 1MGH/Harvard Medical School, Charlestown, MA
| | | | | | - Mehmet Toner
- 3Center for Engineering in Medicine/Harvard Medical School, Charlestown, MA
| | | | - Gad Getz
- 2Broad Institute of Harvard and MIT, Charlestown, MA
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9
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Vidula N, Dubash T, Lawrence MS, Simoneau A, Niemierko A, Blouch E, Nagy B, Roh W, Chirn B, Reeves BA, Malvarosa G, Lennerz J, Isakoff SJ, Juric D, Micalizzi D, Wander S, Spring L, Moy B, Shannon K, Younger J, Lanman R, Toner M, Iafrate AJ, Getz G, Zou L, Ellisen LW, Maheswaran S, Haber DA, Bardia A. Identification of Somatically Acquired BRCA1/2 Mutations by cfDNA Analysis in Patients with Metastatic Breast Cancer. Clin Cancer Res 2020; 26:4852-4862. [PMID: 32571788 DOI: 10.1158/1078-0432.ccr-20-0638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/15/2020] [Accepted: 06/17/2020] [Indexed: 01/11/2023]
Abstract
PURPOSE Plasma genotyping may identify mutations in potentially "actionable" cancer genes, such as BRCA1/2, but their clinical significance is not well-defined. We evaluated the characteristics of somatically acquired BRCA1/2 mutations in patients with metastatic breast cancer (MBC). EXPERIMENTAL DESIGN Patients with MBC undergoing routine cell-free DNA (cfDNA) next-generation sequencing (73-gene panel) before starting a new therapy were included. Somatic BRCA1/2 mutations were classified as known germline pathogenic mutations or novel variants, and linked to clinicopathologic characteristics. The effect of the PARP inhibitor, olaparib, was assessed in vitro, using cultured circulating tumor cells (CTCs) from a patient with a somatically acquired BRCA1 mutation and a second patient with an acquired BRCA2 mutation. RESULTS Among 215 patients with MBC, 29 (13.5%) had somatic cfDNA BRCA1/2 mutations [nine (4%) known germline pathogenic and rest (9%) novel variants]. Known germline pathogenic BRCA1/2 mutations were common in younger patients (P = 0.008), those with triple-negative disease (P = 0.022), and they were more likely to be protein-truncating alterations and be associated with TP53 mutations. Functional analysis of a CTC culture harboring a somatic BRCA1 mutation demonstrated high sensitivity to PARP inhibition, while another CTC culture harboring a somatic BRCA2 mutation showed no differential sensitivity. Across the entire cohort, APOBEC mutational signatures (COSMIC Signatures 2 and 13) and the "BRCA" mutational signature (COSMIC Signature 3) were present in BRCA1/2-mutant and wild-type cases, demonstrating the high mutational burden associated with advanced MBC. CONCLUSIONS Somatic BRCA1/2 mutations are readily detectable in MBC by cfDNA analysis, and may be present as both known germline pathogenic and novel variants.
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Affiliation(s)
- Neelima Vidula
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts.
| | - Taronish Dubash
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | | | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Andrzej Niemierko
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Erica Blouch
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Becky Nagy
- Guardant Health, Inc., Redwood City, California
| | - Whijae Roh
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Brian Chirn
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Brittany A Reeves
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts
| | - Giuliana Malvarosa
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jochen Lennerz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Steven J Isakoff
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Douglas Micalizzi
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Seth Wander
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Laura Spring
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Beverly Moy
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Kristen Shannon
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Jerry Younger
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | | | - Mehmet Toner
- Center for Engineering in Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Gad Getz
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Leif W Ellisen
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Shyamala Maheswaran
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Daniel A Haber
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, Massachusetts
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10
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Mitra A, Andrews MC, Roh W, De Macedo MP, Hudgens CW, Carapeto F, Singh S, Reuben A, Wang F, Mao X, Song X, Wani K, Tippen S, Ng KS, Schalck A, Sakellariou-Thompson DA, Chen E, Reddy SM, Spencer CN, Wiesnoski D, Little LD, Gumbs C, Cooper ZA, Burton EM, Hwu P, Davies MA, Zhang J, Bernatchez C, Navin N, Sharma P, Allison JP, Wargo JA, Yee C, Tetzlaff MT, Hwu WJ, Lazar AJ, Futreal PA. Spatially resolved analyses link genomic and immune diversity and reveal unfavorable neutrophil activation in melanoma. Nat Commun 2020; 11:1839. [PMID: 32296058 PMCID: PMC7160105 DOI: 10.1038/s41467-020-15538-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Complex tumor microenvironmental (TME) features influence the outcome of cancer immunotherapy (IO). Here we perform immunogenomic analyses on 67 intratumor sub-regions of a PD-1 inhibitor-resistant melanoma tumor and 2 additional metastases arising over 8 years, to characterize TME interactions. We identify spatially distinct evolution of copy number alterations influencing local immune composition. Sub-regions with chromosome 7 gain display a relative lack of leukocyte infiltrate but evidence of neutrophil activation, recapitulated in The Cancer Genome Atlas (TCGA) samples, and associated with lack of response to IO across three clinical cohorts. Whether neutrophil activation represents cause or consequence of local tumor necrosis requires further study. Analyses of T-cell clonotypes reveal the presence of recurrent priming events manifesting in a dominant T-cell clonotype over many years. Our findings highlight the links between marked levels of genomic and immune heterogeneity within the physical space of a tumor, with implications for biomarker evaluation and immunotherapy response.
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Affiliation(s)
- Akash Mitra
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Quantitative Sciences Graduate Training Program, Graduate School of Biomedical Sciences, Houston, Texas, USA
| | - Miles C Andrews
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Olivia Newton-John Cancer Research Institute and School of Cancer Medicine, La Trobe University, Heidelberg, VIC, Australia
| | - Whijae Roh
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Courtney W Hudgens
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Fernando Carapeto
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shailbala Singh
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexandre Reuben
- Department of Thoracic Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xizeng Mao
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xingzhi Song
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Khalida Wani
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samantha Tippen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kwok-Shing Ng
- Institute for Personalized Cancer Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Aislyn Schalck
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Eveline Chen
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sangeetha M Reddy
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Diana Wiesnoski
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Latasha D Little
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Elizabeth M Burton
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Nicholas Navin
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - James P Allison
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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11
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Mitra A, Andrews MC, Roh W, Macedo MPD, Reuben A, Carapeto F, Wang F, Reddy SM, Wani K, Spencer C, Miller J, Schalck A, Little LD, Sakellariou-Thompson DA, Gumbs C, Hwu WJ, Bernatchez C, Zhang J, Hwu P, Navin N, Sharma P, Allison JP, Wargo J, Lazar AJ, Futreal PA. Abstract 3776: Spatially resolved immunogenomic analyses reveal diverse sub tumoral microenvironments in the context of melanoma immunotherapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3776] [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
Sustained periods of apparent clinical benefit despite lack of objective response are well known in a subpopulation of advanced melanoma patients. Inter-individual heterogeneity in response of separate tumors is common, characterizing complex overall response patterns. The molecular and cellular dynamics facilitating such long-term survival and heterogeneous response is poorly understood, particularly in the era of exposure to multiple potentially active therapies. We studied an exceptional case of long-term survival in a patient with non-responding metastatic melanoma in order to characterize the clonal and microenvironmental factors active across 3 time points.
We performed immunogenomic analyses of 3 metachronous tumors, including a systemic therapy-naïve mass, 67 intratumor sub-regions of a non-responding mass during PD-1 inhibitor therapy, and a post-PD-1 inhibitor mass. We profiled samples using whole exome sequencing, RNA-sequencing (RNA-seq), immunohistochemistry (IHC), and T cell receptor sequencing. Longitudinal, spatial, and cross-modal analyses were performed.
Longitudinal analyses identified mutations in several genes known to be associated with targeted or immune therapy resistance affecting distinct metastases. Genomic intratumoral heterogeneity (ITH) was primarily driven by subclonal copy number alterations that showed evidence of spatially-distinct evolution which may be in response to selective pressures at the tumor margin. RNA-seq revealed an unexpectedly high degree of ITH characterized by limited group-level gene or pathway associations with physical or immune characteristics of each site. Spatially-distinct pockets of immune activation and suppression were observed throughout the PD-1 inhibitor resistant metastasis despite a largely immune-excluded phenotype seen on IHC. A specific T cell Vβ CDR3 rearrangement was identified as dominant and recurrent not only across multiple spatial points within a single tumor mass, but also across metachronous tumors spanning the patient’s disease course. Immunophenotyping of the T cell population with single-cell RNA-seq suggested repeated T-cell priming events leading to the persistence of both activated and exhausted T cells bearing the same TCR-β at any given time.
Our findings highlight an unexpected level of genomic and immune heterogeneity in metastatic melanoma tumors of a long-term surviving patient. The observed degree of ITH across local tumor microenvironments reiterates the inherent limitations to identifying robust and reproducible predictive biomarkers of therapy response based on limited physical sampling of tumors. Further spatiotemporal analysis of metastatic lesions in the context of immune checkpoint blockade will be required to determine how the mechanisms driving convergent microenvironmental phenotypes may be harnessed for therapeutic gain.
Citation Format: Akash Mitra, Miles C. Andrews, Whijae Roh, Mariana P. de Macedo, Alexandre Reuben, Fernando Carapeto, Feng Wang, Sangeetha M. Reddy, Khalida Wani, Christine Spencer, John Miller, Aislyn Schalck, Latasha D. Little, Donald A. Sakellariou-Thompson, Curtis Gumbs, Wen-Jen Hwu, Chantale Bernatchez, Jianhua Zhang, Patrick Hwu, Nicholas Navin, Padmanee Sharma, James P. Allison, Jennifer Wargo, Alexander J. Lazar, Philip A. Futreal. Spatially resolved immunogenomic analyses reveal diverse sub tumoral microenvironments in the context of melanoma immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3776.
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Affiliation(s)
- Akash Mitra
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | - Feng Wang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Khalida Wani
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - John Miller
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aislyn Schalck
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Curtis Gumbs
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wen-Jen Hwu
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianhua Zhang
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick Hwu
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nicholas Navin
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Padmanee Sharma
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jennifer Wargo
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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12
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Lee WC, Gomez D, Zhang J, Reuben A, Jalali A, Roh W, Wu CC, Lu W, Chow CW, Fujimoto J, Antonoff M, Moran C, Sulman E, Rao G, Swisher S, Heymach J, Wistuba II, Futreal A, Zhang J. Abstract 2741: Comprehensive molecular profiling of primary tumors and paired distant metastases in non-small cell lung cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-2741] [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
Despite complete resection, many non-small cell lung cancer (NSCLC) patients still develop and succumb to distant metastases, which is a major cause of cancer-related death worldwide. However, our understanding of the molecular mechanisms driving metastasis is rudimentary. We performed whole exome sequencing, RNA sequencing (RNA-seq), methylation microarray, and immunohistochemistry using multiple immune markers on 8 pairs of NSCLC primary tumors and matched distant metastases including 7 metachronous brain and 1 synchronous liver metastases. On average, 60% of all somatic mutations (22% to 90%) and 86% of canonical cancer gene mutations were shared between primary tumors and paired distant metastases. Metastases also resembled paired primary tumors closely in regard to their mutational spectrum, copy number aberrations, allelic imbalance, and methylation profiles. Genomic aberrations unique to metastases were rather patient-specific than commonly observed across multiple patients. Of particular interest, subclonal architecture analysis suggested that monoclonal metastatic seeding is a prevalent mode of metastasis in NSCLC. We validated these findings in a large published dataset consisting of 38 pairs of primary lung tumors and matched distant metastases. RNA-seq showed gene expression profiles in metastases were similar to those of paired primary tumors. Metastases commonly up-regulated metabolism-associated pathways and down-regulated immune-related pathways, consistent with the immunohistochemical staining data for CD3, CD4, CD8, CD20, CD68, PD1, and PD-L1. Our data suggest that distant metastasis is a late event during carcinogenesis and that a majority of genomic and epigenetic aberrations occur before metastatic outgrowth. While molecular mechanisms underlying postsurgical distant metastasis seem to be variable among NSCLC patients, immune suppression may be a common characteristic of cancer cells with metastatic plasticity.
Citation Format: Won-Chul Lee, Daniel Gomez, Jianhua Zhang, Alexandre Reuben, Ali Jalali, Whijae Roh, Chia Chin Wu, Wei Lu, Chi-Wan Chow, Junya Fujimoto, Mara Antonoff, Cesar Moran, Erik Sulman, Ganesh Rao, Stephen Swisher, John Heymach, Ignacio I. Wistuba, Andrew Futreal, Jianjun Zhang. Comprehensive molecular profiling of primary tumors and paired distant metastases in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2741.
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Affiliation(s)
| | | | | | | | - Ali Jalali
- 2Baylor College of Medicine, Houston, TX
| | | | | | - Wei Lu
- 1MD Anderson Cancer Center, Houston, TX
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13
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Romano G, Chen PL, Song P, McQuade J, Liang R, Liu M, Roh W, Duose D, Carapeto F, Li J, Teh J, Aplin A, Chen M, Zhang J, Lazar A, Futreal PA, Amaria R, Zhang D, Wargo J, Kwong LN. Abstract 1838: A pre-existing rare PIK3CAE545K subpopulation confers clinical resistance to MEK plus CDK4/6 inhibition in NRAS melanoma and is dependent on S6K1 signaling. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1838] [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
Combined MEK and CDK4/6 inhibition (MEKi+CDK4i) has shown promising clinical outcomes in NRAS mutant melanoma patients. Here, we interrogated longitudinal biopsies from a patient who initially responded to MEKi+CDK4i therapy but subsequently developed resistance. Whole exome sequencing and functional validation identified an acquired PIK3CAE545K mutation as conferring drug resistance. We demonstrate that PIK3CAE545K pre-existed in a rare subpopulation that was missed by both clinical and research testing, but was revealed upon multi-region sampling due to PIK3CAE545K being non-uniformly distributed. This resistant population rapidly expanded after the initiation of MEKi+CDK4i therapy and persisted in all successive samples even after immune checkpoint therapy. Functional studies identified activated S6K1 as both a key marker and specific therapeutic vulnerability downstream of PIK3CAE545K-induced resistance. These results demonstrate that comprehensive analysis of pre-treatment samples can reveal rare pre-existing resistant subpopulations and posit S6K1 as a common downstream therapeutic nexus for the MAPK, CDK4/6, and PI3K pathways.
Citation Format: Gabriele Romano, Pei-Ling Chen, Ping Song, Jennifer McQuade, Roger Liang, Mingguang Liu, Whijae Roh, Dzifa Duose, Fernando Carapeto, Jun Li, Jessica Teh, Andrew Aplin, Merry Chen, Jianhua Zhang, Alexander Lazar, P Andrew Futreal, Rodabe Amaria, David Zhang, Jennifer Wargo, Lawrence N. Kwong. A pre-existing rare PIK3CAE545K subpopulation confers clinical resistance to MEK plus CDK4/6 inhibition in NRAS melanoma and is dependent on S6K1 signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1838.
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Affiliation(s)
| | | | | | | | | | | | - Whijae Roh
- 1UT MD Anderson Cancer Ctr., Houston, TX
| | | | | | - Jun Li
- 1UT MD Anderson Cancer Ctr., Houston, TX
| | - Jessica Teh
- 3Thomas Jefferson University, Philadelphia, PA
| | | | - Merry Chen
- 1UT MD Anderson Cancer Ctr., Houston, TX
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14
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Mitra A, Roh W, Reuben A, Wargo J, Lazar A, Futreal PA. Abstract 2099: Multi-spatial whole-lesion molecular heterogeneity analyses of an immunotherapy-resistant metastatic melanoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-2099] [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
Genomic and immune intratumor heterogeneity (ITH) can be a significant obstacle to treating patients with checkpoint blockade immunotherapy. The extent of ITH within a single lesion has begun to be addressed but there have been no comprehensive molecular analyses of an entire lesion, multiply sampled in three dimensions with reconstruction of the tumor in its host microenvironment reported thus far. This approach can allow a portrait of the entire tumor ecosystem to emerge and provide a richer, more comprehensive view of the interplay of microenvironment and tumor not bound by a single planar view of a complex entity. Here, we report on our analyses of an anti-CTLA4/anti-PD1 resistant metastatic lesion in toto with an attendant comparative longitudinal view of pre-immunotherapy lesion.
We performed 3-D reconstruction of metastasis obtained at palliative surgery from a patient progressing on anti-PD1 in the context of prior anti-CTLA4 therapy utilizing combined genomic (gene expression profiling, methylation, whole exome sequencing and neoantigen prediction) and immune (immunohistochemistry, RNA- and DNA- based T cell receptor sequencing) profiling of 67 distinct sampled regions from the entire lesion.
Limited point-mutation heterogeneity was found in melanoma driver genes across regions of metastasis. However, copy number alteration analysis revealed changes over time and space with gain of chromosome 7, loss of chromosome 10, and gain of chromosome 14 in certain regions. Differences in immune signatures were observed across regions of a tumor with pockets of immune activation and suppression throughout the metastasis. TCR profiling revealed the dominance of two distinct T cell clonotypes across different regions of the same met, suggesting spatial differences in tumor immunogenicity and T cell activation status. Neoantigen prediction and expression analyses were performed, revealing persistence of a predicted neoantigen detectable prior to CTLA-4 therapy, enriched in different regions of the tumor post-PD-1 blockade. Gene expression of this potential neo-antigen correlated with the distribution and dominance of a specific T cell subclone, suggesting a potential path of infiltration and migration of T cells through the lesion.
Our findings shed light on the three-dimensional genomic and immune landscape in metastatic melanoma in the context of treatment and resistance to immune checkpoint blockade. In particular, even when essentially “gated” on a relatively monotonous mutation landscape, immune intra-tumor heterogeneity can be substantial. This suggests that as immune markers move into the mainstream for use as biomarkers, the use of single biopsies to inform treatment choice may be confounded. These data further impress the need for comprehensive, integrated molecular phenotyping approaches to unravel immunotherapy response and resistance in metastatic melanoma.
Citation Format: Akash Mitra, Whijae Roh, Alexandre Reuben, Jennifer Wargo, Alexandar Lazar, Philip A. Futreal. Multi-spatial whole-lesion molecular heterogeneity analyses of an immunotherapy-resistant metastatic melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2099.
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Affiliation(s)
- Akash Mitra
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jennifer Wargo
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexandar Lazar
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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15
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Mitra A, Roh W, Reuben A, Macedo M, Carapeto FCL, Gumbs C, Zhang J, Woodman SE, Hwu P, Hwu WJ, Lazar AJ, Wargo JA, Futreal PA. Multi-spatial whole-lesion molecular heterogeneity of an immunotherapy-resistant metastatic melanoma. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.9568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Akash Mitra
- University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Curtis Gumbs
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianhua Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Patrick Hwu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wen-Jen Hwu
- University of Texas MD Anderson Cancer Center, Houston, TX
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16
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Romano G, Chen PL, Song P, McQuade JL, Liang RJ, Liu M, Roh W, Duose DY, Carapeto FCL, Li J, Teh JLF, Aplin AE, Chen M, Zhang J, Lazar AJ, Davies MA, Futreal PA, Amaria RN, Zhang DY, Wargo JA, Kwong LN. A Preexisting Rare PIK3CAE545K Subpopulation Confers Clinical Resistance to MEK plus CDK4/6 Inhibition in NRAS Melanoma and Is Dependent on S6K1 Signaling. Cancer Discov 2018; 8:556-567. [PMID: 29496665 PMCID: PMC5932238 DOI: 10.1158/2159-8290.cd-17-0745] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [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: 06/30/2017] [Revised: 01/22/2018] [Accepted: 02/23/2018] [Indexed: 12/14/2022]
Abstract
Combined MEK and CDK4/6 inhibition (MEKi + CDK4i) has shown promising clinical outcomes in patients with NRAS-mutant melanoma. Here, we interrogated longitudinal biopsies from a patient who initially responded to MEKi + CDK4i therapy but subsequently developed resistance. Whole-exome sequencing and functional validation identified an acquired PIK3CAE545K mutation as conferring drug resistance. We demonstrate that PIK3CAE545K preexisted in a rare subpopulation that was missed by both clinical and research testing, but was revealed upon multiregion sampling due to PIK3CAE545K being nonuniformly distributed. This resistant population rapidly expanded after the initiation of MEKi + CDK4i therapy and persisted in all successive samples even after immune checkpoint therapy and distant metastasis. Functional studies identified activated S6K1 as both a key marker and specific therapeutic vulnerability downstream of PIK3CAE545K-induced resistance. These results demonstrate that difficult-to-detect preexisting resistance mutations may exist more often than previously appreciated and also posit S6K1 as a common downstream therapeutic nexus for the MAPK, CDK4/6, and PI3K pathways.Significance: We report the first characterization of clinical acquired resistance to MEKi + CDK4i, identifying a rare preexisting PIK3CAE545K subpopulation that expands upon therapy and exhibits drug resistance. We suggest that single-region pretreatment biopsy is insufficient to detect rare, spatially segregated drug-resistant subclones. Inhibition of S6K1 is able to resensitize PIK3CAE545K-expressing NRAS-mutant melanoma cells to MEKi + CDK4i. Cancer Discov; 8(5); 556-67. ©2018 AACR.See related commentary by Sullivan, p. 532See related article by Teh et al., p. 568This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Gabriele Romano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ping Song
- Department of Bioengineering, Rice University, Houston, Texas
| | - Jennifer L McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roger J Liang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mingguang Liu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Whijae Roh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fernando C L Carapeto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jun Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jessica L F Teh
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Cutaneous Biology and Dermatology, Thomas Jefferson University, Philadelphia, Pennsylvania
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Merry Chen
- Department of Neurooncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Y Zhang
- Department of Bioengineering, Rice University, Houston, Texas
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Neurooncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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17
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Roh W, Chen PL, Reuben A, Spencer CN, Prieto PA, Miller JP, Gopalakrishnan V, Wang F, Cooper ZA, Reddy SM, Gumbs C, Little L, Chang Q, Chen WS, Wani K, De Macedo MP, Chen E, Austin-Breneman JL, Jiang H, Roszik J, Tetzlaff MT, Davies MA, Gershenwald JE, Tawbi H, Lazar AJ, Hwu P, Hwu WJ, Diab A, Glitza IC, Patel SP, Woodman SE, Amaria RN, Prieto VG, Hu J, Sharma P, Allison JP, Chin L, Zhang J, Wargo JA, Futreal PA. Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance. Sci Transl Med 2017; 9:9/379/eaah3560. [PMID: 28251903 DOI: 10.1126/scitranslmed.aah3560] [Citation(s) in RCA: 587] [Impact Index Per Article: 83.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/17/2016] [Accepted: 02/04/2017] [Indexed: 12/20/2022]
Abstract
Immune checkpoint blockade produces clinical benefit in many patients. However, better biomarkers of response are still needed, and mechanisms of resistance remain incompletely understood. To address this, we recently studied a cohort of melanoma patients treated with sequential checkpoint blockade against cytotoxic T lymphocyte antigen-4 (CTLA-4) followed by programmed death receptor-1 (PD-1) and identified immune markers of response and resistance. Building on these studies, we performed deep molecular profiling including T cell receptor sequencing and whole-exome sequencing within the same cohort and demonstrated that a more clonal T cell repertoire was predictive of response to PD-1 but not CTLA-4 blockade. Analysis of CNAs identified a higher burden of copy number loss in nonresponders to CTLA-4 and PD-1 blockade and found that it was associated with decreased expression of genes in immune-related pathways. The effect of mutational load and burden of copy number loss on response was nonredundant, suggesting the potential utility of a combinatorial biomarker to optimize patient care with checkpoint blockade therapy.
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Affiliation(s)
- Whijae Roh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Cancer Biology Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Pei-Ling Chen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine N Spencer
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter A Prieto
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John P Miller
- Oncology Research for Biologics and Immunotherapy Translation, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zachary A Cooper
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qing Chang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei-Shen Chen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mariana Petaccia De Macedo
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Pathology Department, A.C.Camargo Cancer Center, São Paulo, SP-01509-010, Brazil
| | - Eveline Chen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jacob L Austin-Breneman
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Jiang
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander J Lazar
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor G Prieto
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James P Allison
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lynda Chin
- University of Texas System, Austin, TX 78701, USA
| | - Jianhua Zhang
- Applied Cancer Science Institute, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. .,Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Lee WC, Gomez DR, Zhang J, Jalali A, Roh W, Reuben A, Lu W, Chow CW, Wu CC, Fujimoto J, Antonoff M, Moran C, Sulman EP, Rao G, Swisher S, Heymach J, Wistuba II, Futreal A, Zhang J. Comprehensive molecular and immune profiling of non-small cell lung cancer and matched distant metastases to suggest distinct molecular mechanisms underlying metastasis. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.8541] [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: 11/20/2022] Open
Abstract
8541 Background: Despite complete resection, many non-small cell lung cancer (NSCLC) patients still develop and succumb to distant metastases. Previous studies suggested distant metastasis may be due to genomic evolution and/or suppressed immune surveillance. However, the relationship between specific genomic alterations and immune surveillance has not been systemically studied. Methods: We performed whole exome sequencing, RNA-Seq, methylation microarray, immunohistochemistry using multiple immune markers, and T cell receptor sequencing on 7 pairs of NSCLC primary tumors and matched metastases including 6 metachronous brain and 1 synchronous liver metastases. Results: On average, 84% of all somatic mutations (54% to 97%) and all 28 canonical cancer gene mutations were shared between primary tumors and paired distant metastases. Metastases also resembled paired primary tumors closely in regard to somatic copy number aberration profiles, methylation profiles. Subclonal analysis showed almost identical clonal architectures in 4 of 7 pairs of primary tumor and metastasis comparable to the similarity observed between different regions within the same tumors. The other 3 pairs, however, displayed clear evidence of clonal evolution. We validated these findings in a published dataset consisting of 38 pairs of primary NSCLC tumors and matched distant metastases. The RNA-Seq data showed that 25 of the top 35 significantly down-regulated signaling pathways in metastases relative to primary tumors were related to immune activation, which was validated in an independent cohort of 41 primary NSCLC tumors and distant metastases using NanoString’s PanCancer Immune Profiling Panel. Conclusions: Our data suggest that molecular mechanisms underlying postsurgical distant metastasis may be variable among NSCLC patients. While genomic evolution may play a role in development of metastasis in some patients, distant metastasis may be early event during carcinogenesis without further genomic evolution in a substantial proportion of NSCLC patients. Furthermore, immune suppression may be a characteristic of cancer cells of metastatic capacity.
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Affiliation(s)
- Won-Chul Lee
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Jianhua Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ali Jalali
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Whijae Roh
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Wei Lu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chi-Wan Chow
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chia Chin Wu
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Junya Fujimoto
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mara Antonoff
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cesar Moran
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Erik P. Sulman
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ganesh Rao
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stephen Swisher
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Heymach
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jianjun Zhang
- The University of Texas MD Anderson Cancer Center, Houston, TX
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19
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Reuben A, Spencer CN, Prieto PA, Gopalakrishnan V, Reddy SM, Miller JP, Mao X, De Macedo MP, Chen J, Song X, Jiang H, Chen PL, Beird HC, Garber HR, Roh W, Wani K, Chen E, Haymaker C, Forget MA, Little LD, Gumbs C, Thornton RL, Hudgens CW, Chen WS, Austin-Breneman J, Sloane RS, Nezi L, Cogdill AP, Bernatchez C, Roszik J, Hwu P, Woodman SE, Chin L, Tawbi H, Davies MA, Gershenwald JE, Amaria RN, Glitza IC, Diab A, Patel SP, Hu J, Lee JE, Grimm EA, Tetzlaff MT, Lazar AJ, Wistuba II, Clise-Dwyer K, Carter BW, Zhang J, Futreal PA, Sharma P, Allison JP, Cooper ZA, Wargo JA. Genomic and immune heterogeneity are associated with differential responses to therapy in melanoma. NPJ Genom Med 2017; 2. [PMID: 28819565 PMCID: PMC5557036 DOI: 10.1038/s41525-017-0013-8] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Appreciation for genomic and immune heterogeneity in cancer has grown though the relationship of these factors to treatment response has not been thoroughly elucidated. To better understand this, we studied a large cohort of melanoma patients treated with targeted therapy or immune checkpoint blockade (n = 60). Heterogeneity in therapeutic responses via radiologic assessment was observed in the majority of patients. Synchronous melanoma metastases were analyzed via deep genomic and immune profiling, and revealed substantial genomic and immune heterogeneity in all patients studied, with considerable diversity in T cell frequency, and few shared T cell clones (<8% on average) across the cohort. Variables related to treatment response were identified via these approaches and through novel radiomic assessment. These data yield insight into differential therapeutic responses to targeted therapy and immune checkpoint blockade in melanoma, and have key translational implications in the age of precision medicine. Patients with metastatic melanoma display molecular and immune differences across tumor sites associated with differential drug responses. A team led by Jennifer Wargo from the University of Texas MD Anderson Cancer Center, Houston, USA, studied the radiological responses of 60 patients with metastatic melanoma, half of whom received targeted drug therapy and half of whom received an immune checkpoint inhibitor. The majority (83%) showed differences in responses across metastases. The group then profiled tumors in a subset, and found molecular and immune heterogeneity in different tumors within the same patient. Heterogeneity in mutational and immune profiles within tumors from individual patients could explain differences in treatment response. Knowing this, the authors emphasize the importance of acquiring biopsies from more than one tumor site in order to best tailor therapies to the features of metastatic cancer.
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Affiliation(s)
- Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Christine N Spencer
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Peter A Prieto
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Vancheswaran Gopalakrishnan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - John P Miller
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Xizeng Mao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Mariana Petaccia De Macedo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jiong Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Hong Jiang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Pei-Ling Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Hannah C Beird
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Haven R Garber
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Whijae Roh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Eveline Chen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Latasha D Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Rebecca L Thornton
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Courtney W Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Wei-Shen Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jacob Austin-Breneman
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Robert Szczepaniak Sloane
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Luigi Nezi
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Alexandria P Cogdill
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Elizabeth A Grimm
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Alexander J Lazar
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Karen Clise-Dwyer
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Brett W Carter
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Zachary A Cooper
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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20
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Chen PL, Roh W, Reuben A, Cooper ZA, Spencer CN, Prieto PA, Miller JP, Bassett RL, Gopalakrishnan V, Wani K, De Macedo MP, Austin-Breneman JL, Jiang H, Chang Q, Reddy SM, Chen WS, Tetzlaff MT, Broaddus RJ, Davies MA, Gershenwald JE, Haydu L, Lazar AJ, Patel SP, Hwu P, Hwu WJ, Diab A, Glitza IC, Woodman SE, Vence LM, Wistuba II, Amaria RN, Kwong LN, Prieto V, Davis RE, Ma W, Overwijk WW, Sharpe AH, Hu J, Futreal PA, Blando J, Sharma P, Allison JP, Chin L, Wargo JA. Analysis of Immune Signatures in Longitudinal Tumor Samples Yields Insight into Biomarkers of Response and Mechanisms of Resistance to Immune Checkpoint Blockade. Cancer Discov 2016; 6:827-37. [PMID: 27301722 DOI: 10.1158/2159-8290.cd-15-1545] [Citation(s) in RCA: 681] [Impact Index Per Article: 85.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/10/2016] [Indexed: 11/16/2022]
Abstract
UNLABELLED Immune checkpoint blockade represents a major breakthrough in cancer therapy; however, responses are not universal. Genomic and immune features in pretreatment tumor biopsies have been reported to correlate with response in patients with melanoma and other cancers, but robust biomarkers have not been identified. We studied a cohort of patients with metastatic melanoma initially treated with cytotoxic T-lymphocyte-associated antigen-4 (CTLA4) blockade (n = 53) followed by programmed death-1 (PD-1) blockade at progression (n = 46), and analyzed immune signatures in longitudinal tissue samples collected at multiple time points during therapy. In this study, we demonstrate that adaptive immune signatures in tumor biopsy samples obtained early during the course of treatment are highly predictive of response to immune checkpoint blockade and also demonstrate differential effects on the tumor microenvironment induced by CTLA4 and PD-1 blockade. Importantly, potential mechanisms of therapeutic resistance to immune checkpoint blockade were also identified. SIGNIFICANCE These studies demonstrate that adaptive immune signatures in early on-treatment tumor biopsies are predictive of response to checkpoint blockade and yield insight into mechanisms of therapeutic resistance. These concepts have far-reaching implications in this age of precision medicine and should be explored in immune checkpoint blockade treatment across cancer types. Cancer Discov; 6(8); 827-37. ©2016 AACR.See related commentary by Teng et al., p. 818This article is highlighted in the In This Issue feature, p. 803.
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Affiliation(s)
- Pei-Ling Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Whijae Roh
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zachary A Cooper
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Christine N Spencer
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter A Prieto
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John P Miller
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mariana Petaccia De Macedo
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jacob L Austin-Breneman
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hong Jiang
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qing Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sangeetha M Reddy
- Department of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wei-Shen Chen
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael T Tetzlaff
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Russell J Broaddus
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lauren Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexander J Lazar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luis M Vence
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Victor Prieto
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - R Eric Davis
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wencai Ma
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Willem W Overwijk
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Jianhua Hu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jorge Blando
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Padmanee Sharma
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James P Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lynda Chin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Song S, Roh W, Kim B, Lee S, Sung H. Effects of intravenous anaesthetics on cyclopiazonic acid-induced contractions in isolated rat aorta. J Cardiothorac Vasc Anesth 2016. [DOI: 10.1053/j.jvca.2016.03.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Reuben A, Spencer C, Roszik J, Miller J, Kwong L, Jiang H, Haymaker C, Chen PL, Austin-Breneman J, Roh W, Little L, Cao Y, Garber H, Forget MA, Gopalakrishnan V, Amaria R, Davies M, Bernatchez C, Roger E, Cuentas P, Rodriguez J, Tetzlaff M, Woodman S, Dwyer K, Sharma P, Allison J, Chin L, Futreal A, Cooper Z, Wargo J. Molecular and immune heterogeneity in synchronous melanoma metastases. J Immunother Cancer 2015. [PMCID: PMC4649346 DOI: 10.1186/2051-1426-3-s2-p262] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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23
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Reuben A, Cooper ZA, Roh W, Cao Y, Austin-Breneman J, Jiang H, Amaria RN, Chen PL, Tetzlaff MT, Chin L, Futreal A, Davies MA, Wargo JA. Abstract 1301: Inter- and intra-tumoral immune and genomic heterogeneity in patients with metastatic melanoma. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1301] [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
There have been significant advances in the treatment of metastatic melanoma via the use of targeted and immunotherapy, however a significant proportion of patients still progress on treatment. Intense research efforts to better understand resistance are underway, and multiple molecular resistance mechanisms to targeted therapy have been identified. Appreciation of intratumoral genetic heterogeneity as a contributor to resistance to therapy is growing, although immune heterogeneity in multiple solid tumors within a same patient has been less well characterized. The goal of the present study is to better understand the leukocyte infiltrate in multiple melanoma tumors within the same patient at the time of disease progression, with the potential to identify actionable strategies to overcome resistance to therapy. In this study, we prospectively evaluated 8 tumors from 4 patients on either targeted or immunotherapy. Tissues were evaluated by polychromatic flow cytometry, complemented with immunohistochemical (IHC) analysis of tissue sections. Specifically, we utilized 5 distinct flow cytometry panels comprising 35 antibodies and an 11-marker IHC antibody panel to better understand the intratumoral leukocyte composition as well as presence of immune checkpoint molecules PD-1 and PD-L1. Results demonstrate significant immune heterogeneity between different melanoma tumors within the same patient in the majority of patients studied. Of note, there were significant differences in CD4+, CD8+, and regulatory T cells (p<0.05) with similar activation markers but differences in T cell memory markers. Furthermore, deep TCR sequencing data revealed that T cell populations infiltrating distinct tumors within the same patient presented different specificities, as, in aggregate, ∼92% of T cell clones detected were restricted to one tumor. This inter-tumoral leukocyte and T cell heterogeneity within the same patient may correspond to differential mutations as determined by whole exome sequencing and this analysis is currently underway. Together, these data suggest that there may be significant immune heterogeneity between tumors within a single patient with metastatic melanoma. This has important clinical implications, as a single tumor biopsy sample may not be representative of the immune profile of multiple tumors within the same individual. One could contemplate that this may account for variable responses to therapy, however this is a hypothesis that needs to be tested carefully in a much larger data set. Nonetheless, these findings may have significant implications for the treatment of melanoma and other cancers.
Citation Format: Alexandre Reuben, Zachary A. Cooper, Whijae Roh, Yu Cao, Jacob Austin-Breneman, Hong Jiang, Rodabe N. Amaria, Pei-Ling Chen, Michael T. Tetzlaff, Lynda Chin, Andrew Futreal, Michael A. Davies, Jennifer A. Wargo. Inter- and intra-tumoral immune and genomic heterogeneity in patients with metastatic melanoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1301. doi:10.1158/1538-7445.AM2015-1301
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Affiliation(s)
| | | | | | - Yu Cao
- MD Anderson Cancer Center, Houston, TX
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Takahashi K, Roh W, Zhang J, Propotopov A, Patel K, Strickland S, Kim A, Vnencak-Jones C, Pelletier S, Parmar S, Garcia-Manero G, Kornblau S, Chin L, Kantarjian H, Futreal PA, Ravandi F. Clonal evolution of acute myeloid leukemia relapsed after 19 years of remission. Am J Hematol 2015; 90:E134-5. [PMID: 25801490 DOI: 10.1002/ajh.24009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 03/12/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Koichi Takahashi
- Department of Leukemia; , University of Texas MD Anderson Cancer Center; Houston Texas
- Department of Hematology and Oncology, Graduate School of Medicine; Kyoto University; Kyoto Japan
| | - Whijae Roh
- Department of Genomic Medicine; , University of Texas MD Anderson Cancer Center; Houston Texas
- Program in Cancer Biology; , University of Texas Graduate School of Biomedical Sciences; Houston Texas
| | - Jianhua Zhang
- Institute of Applied Cancer Science; University of Texas MD Anderson Cancer Center; Houston Texas
| | - Alexei Propotopov
- Institute of Applied Cancer Science; University of Texas MD Anderson Cancer Center; Houston Texas
| | - Keyur Patel
- Department of Hematopathology; , University of Texas MD Anderson Cancer Center; Houston Texas
| | | | - Annette Kim
- Vanderbilt-Ingram Cancer Center; Nashville Tennessee
| | | | - Sarah Pelletier
- Department of Leukemia; , University of Texas MD Anderson Cancer Center; Houston Texas
| | - Simrit Parmar
- Department of Stem Cell Transplant; , University of Texas MD Anderson Cancer Center; Houston Texas
| | | | - Steven Kornblau
- Department of Leukemia; , University of Texas MD Anderson Cancer Center; Houston Texas
| | - Lynda Chin
- Department of Genomic Medicine; , University of Texas MD Anderson Cancer Center; Houston Texas
- Institute of Applied Cancer Science; University of Texas MD Anderson Cancer Center; Houston Texas
| | - Hagop Kantarjian
- Department of Leukemia; , University of Texas MD Anderson Cancer Center; Houston Texas
| | - P. Andrew Futreal
- Department of Genomic Medicine; , University of Texas MD Anderson Cancer Center; Houston Texas
| | - Farhad Ravandi
- Department of Leukemia; , University of Texas MD Anderson Cancer Center; Houston Texas
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Wang Y, Navin N, Waters J, Leung M, Unruh A, Shi X, Roh W, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Meric-Bernstam F, Michor F, Zhao R. Abstract LB-310: Single cell genome sequencing reveals clonal stability and diversity in breast cancer. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-lb-310] [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
Human breast cancers often display intratumor genomic heterogeneity. This clonal diversity confounds the clinical diagnosis and basic research of cancer, because single samples may not represent that tumor as a whole. Sequencing breast tumor cohorts en masse has identified many prevalent mutations, but has limited ability for resolving subclonal diversity. Here, we developed a whole-genome and exome single-cell sequencing approach (Nuc-Seq) using G2/M cells. To validate our method, we applied Nuc-Seq to sequence the whole genomes of two single cells from a genetically monoclonal breast cancer cell line (SK-BR-3) at high coverage depth (61X ± 5 sem, n=2) and breadth (83.70% ± 3.40 sem, n=2) to detect somatic mutations. Our analysis suggests that Nuc-Seq generates low allelic dropout rates (9.73% ± 2.19%) and low false positive error rates for point mutations (FPR = 1.24e-6). We then applied this method to sequence single normal and tumor cells from an estrogen-receptor positive breast cancer and a triple-negative ductal carcinoma at base-pair resolution. In parallel, we performed single cell copy number profiling. In both tumors, we observed a large number of rare variants that were not detected by sequencing the bulk tumor en masse. In contrast, we find that single cell copy number profiles are highly similar. Our data suggest that aneuploid rearrangements occurred early in tumor evolution and remained highly stable as the tumor mass expanded. In contrast we find that point mutations evolved gradually, generating extensive clonal diversity. Many of the diverse mutations were shown to occur at low frequencies (0.03 -10%) in the tumor mass by targeted duplex sequencing. Mathematical modeling suggests that the triple-negative tumor cells have an increased mutation rate (13.3X), while the ER+ tumor cells do not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
Citation Format: Yong Wang, Nicholas Navin, Jill Waters, Marco Leung, Anna Unruh, Xiuqing Shi, Whijae Roh, Ken Chen, Paul Scheet, Selina Vattathil, Han Liang, Asha Multani, Hong Zhang, Funda Meric-Bernstam, Franziska Michor, Rui Zhao. Single cell genome sequencing reveals clonal stability and diversity in breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-310. doi:10.1158/1538-7445.AM2014-LB-310
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Affiliation(s)
- Yong Wang
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | | | - Anna Unruh
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | - Whijae Roh
- 1UT MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | | | - Han Liang
- 1UT MD Anderson Cancer Center, Houston, TX
| | | | - Hong Zhang
- 1UT MD Anderson Cancer Center, Houston, TX
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Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE. Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 2014; 512:155-60. [PMID: 25079324 PMCID: PMC4158312 DOI: 10.1038/nature13600] [Citation(s) in RCA: 711] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 06/23/2014] [Indexed: 12/16/2022]
Abstract
Sequencing studies of breast tumor cohorts have identified many prevalent mutations, but provide limited insight into the genomic diversity within tumors. Here, we developed a whole-genome and exome single cell sequencing approach called Nuc-Seq that utilizes G2/M nuclei to achieve 91% mean coverage breadth. We applied this method to sequence single normal and tumor nuclei from an estrogen-receptor positive breast cancer and a triple-negative ductal carcinoma. In parallel, we performed single nuclei copy number profiling. Our data show that aneuploid rearrangements occurred early in tumor evolution and remained highly stable as the tumor masses clonally expanded. In contrast, point mutations evolved gradually, generating extensive clonal diversity. Many of the diverse mutations were shown to occur at low frequencies (<10%) in the tumor mass by targeted single-molecule sequencing. Using mathematical modeling we found that the triple-negative tumor cells had an increased mutation rate (13.3X) while the ER+ tumor cells did not. These findings have important implications for the diagnosis, therapeutic treatment and evolution of chemoresistance in breast cancer.
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Affiliation(s)
- Yong Wang
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Jill Waters
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Marco L Leung
- 1] The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA [2] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
| | - Anna Unruh
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Whijae Roh
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Xiuqing Shi
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Ken Chen
- The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA
| | - Paul Scheet
- 1] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [2] The University of Texas MD Anderson Cancer Center, Department of Epidemiology, Houston, Texas 77030, USA
| | - Selina Vattathil
- 1] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [2] The University of Texas MD Anderson Cancer Center, Department of Epidemiology, Houston, Texas 77030, USA
| | - Han Liang
- The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA
| | - Asha Multani
- The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA
| | - Hong Zhang
- The University of Texas MD Anderson Cancer Center, Department of Pathology, Houston, Texas 77030, USA
| | - Rui Zhao
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02215, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02215, USA
| | - Funda Meric-Bernstam
- The University of Texas MD Anderson Cancer Center Department of Investigational Cancer Therapeutics, Houston, Texas 77030, USA
| | - Nicholas E Navin
- 1] The University of Texas MD Anderson Cancer Center, Department of Genetics, Houston, Texas 77030, USA [2] The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA [3] The University of Texas MD Anderson Cancer Center, Department of Bioinformatics and Computational Biology, Houston, Texas 77030, USA
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Lee JH, Yeon JH, Kim H, Roh W, Chae J, Park HO, Kim DM. The natural anticancer agent plumbagin induces potent cytotoxicity in MCF-7 human breast cancer cells by inhibiting a PI-5 kinase for ROS generation. PLoS One 2012; 7:e45023. [PMID: 23028742 PMCID: PMC3441601 DOI: 10.1371/journal.pone.0045023] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/11/2012] [Indexed: 02/06/2023] Open
Abstract
Drug-induced haploinsufficiency (DIH) in yeast has been considered a valuable tool for drug target identification. A plant metabolite, plumbagin, has potent anticancer activity via reactive oxygen species (ROS) generation. However, the detailed molecular targets of plumbagin for ROS generation are not understood. Here, using DIH and heterozygous deletion mutants of the fission yeast Schizosaccharomyces pombe, we identified 1, 4-phopshatidylinositol 5-kinase (PI5K) its3 as a new molecular target of plumbagin for ROS generation. Plumbagin showed potent anti-proliferative activity (GI(50); 10 µM) and induced cell elongation and septum formation in wild-type S. pombe. Furthermore, plumbagin dramatically increased the intracellular ROS level, and pretreatment with the ROS scavenger, N-acetyl cysteine (NAC), protected against growth inhibition by plumbagin, suggesting that ROS play a crucial role in the anti-proliferative activity in S. pombe. Interestingly, significant DIH was observed in an its3-deleted heterozygous mutant, in which ROS generation by plumbagin was higher than that in wild-type cells, implying that its3 contributes to ROS generation by plumbagin in this yeast. In MCF7 human breast cancer cells, plumbagin significantly decreased the level of a human ortholog, 1, 4-phopshatidylinositol 5-kinase (PI5K)-1B, of yeast its3, and knockdown of PI5K-1B using siPI5K-1B increased the ROS level and decreased cell viability. Taken together, these results clearly show that PI5K-1B plays a crucial role in ROS generation as a new molecular target of plumbagin. Moreover, drug target screening using DIH in S. pombe deletion mutants is a valuable tool for identifying molecular targets of anticancer agents.
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Affiliation(s)
- Ju-Hee Lee
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Ji-Hyun Yeon
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Hanna Kim
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Whijae Roh
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Jeiwook Chae
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Han-Oh Park
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
| | - Dong-Myung Kim
- S. pombe Research Team, Gene-to-Drug Division, Bioneer Corporation, Daejeon, Republic of Korea
- * E-mail:
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Uchida T, Mills K, Kuo CH, Roh W, Tung YC, Garner AL, Koide K, Thouless M, Takayama S. External compression-induced fracture patterning on the surface of poly(dimethylsiloxane) cubes and microspheres. Langmuir 2009; 25:3102-3107. [PMID: 19437776 PMCID: PMC2772125 DOI: 10.1021/la801986k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This article describes a method for creating submicrometer surface patterns on cubes and microspheres. In this method, PDMS cubes and microspheres are exposed to oxygen plasma, which creates a very thin, hard, surface-modified layer on a compliant substrate. These are then compressed, causing the layer to crack in patterns dictated by the distribution of tensile stresses in the surface layer. Cracks with submicrometer widths were generated on 1 cm3 cubes and 800-microm-diameter microspheres, and the resulting crack patterns were observed. Finite-element simulations of the tensile stress distributions reveal that the fracture patterns arise from different mechanisms in the cubes and spheres. In particular, pattern formation is associated with frictional contact in the cubes but not in the microspheres, where geometrical effects associated with changes in the cross-sectional area along the axis lead to the generation of tensile stress. These observations and analyses provide a foundation on which to predict and guide crack pattern formation on a wide variety of small 3D objects. In anticipation of future applications in materials science and biology, we demonstrate the selective deposition of compounds into the cracks to make them functionally differentiable from the rest of the surface.
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Affiliation(s)
- Tomoyuki Uchida
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - K.L. Mills
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chuan-Hsien Kuo
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Whijae Roh
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yi-Chung Tung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda L. Garner
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - M.D. Thouless
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shuichi Takayama
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Macromolecular Science and Engineering Program, University of Michigan, Ann Arbor, MI 48109, USA
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Russell T, Roh W, Marciante J. Incoherent beam combining using stimulated Brillouin scattering in multimode fibers. Opt Express 2001; 8:246-254. [PMID: 19417811 DOI: 10.1364/oe.8.000246] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A beam combining technique for producing a single, spatially coherent beam from two mutually incoherent (temporally and spatially) lasers is demonstrated and the spatial coherence properties of the resulting beam are characterized. The technique is based on simultaneous excitation of stimulated Brillouin scattering by two independent lasers operating at two different wavelengths in a long multimode optical fiber. Though spectrally independent, the resulting Stokes beams produce essentially identical intensity distributions corresponding to the fundamental fiber mode.
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