2501
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Gfeller D, Bassani-Sternberg M, Schmidt J, Luescher IF. Current tools for predicting cancer-specific T cell immunity. Oncoimmunology 2016; 5:e1177691. [PMID: 27622028 DOI: 10.1080/2162402x.2016.1177691] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022] Open
Abstract
Tumor exome and RNA sequencing data provide a systematic and unbiased view on cancer-specific expression, over-expression, and mutations of genes, which can be mined for personalized cancer vaccines and other immunotherapies. Of key interest are tumor-specific mutations, because T cells recognizing neoepitopes have the potential to be highly tumoricidal. Here, we review recent developments and technical advances in identifying MHC class I and class II-restricted tumor antigens, especially neoantigen derived MHC ligands, including in silico predictions, immune-peptidome analysis by mass spectrometry, and MHC ligand validation by biochemical methods on T cells.
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Affiliation(s)
- David Gfeller
- Ludwig Center for Cancer Research, University of Lausanne, Epalinges, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Julien Schmidt
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
| | - Immanuel F Luescher
- Ludwig Center for Cancer Research, University of Lausanne , Epalinges, Switzerland
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2502
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Mandal R, Chan TA. Personalized Oncology Meets Immunology: The Path toward Precision Immunotherapy. Cancer Discov 2016; 6:703-13. [PMID: 27107038 DOI: 10.1158/2159-8290.cd-16-0146] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/31/2016] [Indexed: 12/17/2022]
Abstract
UNLABELLED Personalized oncology aims to tailor therapy by targeting the unique genetic characteristics of a patient's tumor, whereas cancer immunotherapy focuses on activating the patient's immune system to control the tumor. The fusion of these ostensibly separate strategies has created a new dimension for personalized cancer immunotherapy. This entails the development of next-generation cancer vaccines that target neoantigens as well as the use of mutational signatures as predictive biomarkers for clinical response. The optimal use of immunotherapeutic agents will hinge on a robust understanding of the mutational profile of a cancer's genome that significantly dictates antitumor immunity and immunotherapeutic response. SIGNIFICANCE Cancer immunotherapy has provided substantial clinical benefit in a significant number of patients with advanced disease. However, the need for more precise immunotherapies and predictive biomarkers remains pressing. Recent progress in these areas has been promising and has created a framework for precision immune-oncology. Cancer Discov; 6(7); 703-13. ©2016 AACR.
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Affiliation(s)
- Rajarsi Mandal
- Head and Neck Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York. Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York. Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York.
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2503
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Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, Stevens J, Lane WJ, Dellagatta JL, Steelman S, Sougnez C, Cibulskis K, Kiezun A, Hacohen N, Brusic V, Wu CJ, Getz G. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol 2016; 33:1152-8. [PMID: 26372948 PMCID: PMC4747795 DOI: 10.1038/nbt.3344] [Citation(s) in RCA: 489] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/12/2015] [Indexed: 12/17/2022]
Abstract
Detection of somatic mutations in HLA genes using whole-exome sequencing (WES) is hampered by the high polymorphism of the HLA loci, which prevents alignment of sequencing reads to the human reference genome. We describe a computational pipeline that enables accurate inference of germline alleles of class I HLA-A, -B and -C genes and subsequent detection of mutations in these genes using the inferred alleles as a reference. Analysis of WES data from 7,930 pairs of tumor and healthy tissue from the same patient revealed 298 non-silent HLA mutations in tumors from 266 patients. These 298 mutations are enriched for likely functional mutations, including putative loss-of-function events. Recurrence of mutations suggested that these ‘hotspot’ sites were positively selected. Cancers with recurrent somatic HLA mutations were associated with upregulation of signatures of cytolytic activity characteristic of tumor infiltration by effector lymphocytes, supporting immune evasion by altered HLA function as a contributory mechanism in cancer.
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2504
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Riaz N, Morris L, Havel JJ, Makarov V, Desrichard A, Chan TA. The role of neoantigens in response to immune checkpoint blockade. Int Immunol 2016; 28:411-9. [PMID: 27048318 DOI: 10.1093/intimm/dxw019] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 03/30/2016] [Indexed: 12/17/2022] Open
Abstract
Immune checkpoint blockade has demonstrated substantial promise for the treatment of several advanced malignancies. These agents activate the immune system to attack tumor cells. For example, agents targeting CTLA4 and programmed cell death 1 (PD-1) have resulted in impressive response rates and, in some cases, durable remissions. Neoantigens are mutations that encode immunologically active proteins that can cause the immune system to recognize the affected cell as foreign. Recent data have made it clear that these mutations are, in large part, the functional targets of immune checkpoint blockade. This review summarizes the key discoveries leading up to this important conclusion and discusses possible applications of neoantigens in cancer therapy.
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Affiliation(s)
| | - Luc Morris
- Human Oncology and Pathogenesis Program and Department of Surgery, Memorial Sloan Kettering Cancer Center, Box 20, 1275 York Avenue, New York, NY 10065, USA
| | | | | | | | - Timothy A Chan
- Department of Radiation Oncology, Human Oncology and Pathogenesis Program and
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2505
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Lund T. Treatment Opportunities for Colorectal Liver Metastases. EUROPEAN MEDICAL JOURNAL 2016. [DOI: 10.33590/emj/10311794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Colorectal liver metastases (CLM) are the most common hepatic malignancy and are caused by disseminated tumour cells (DTCs) seeded early in the tumourigenesis of colorectal cancer. Despite optimal treatment, CLM are associated with high mortality rates. This review provides an overview of three promising strategies to extend survival in CLM: treatment of DTCs, immunotherapy, and new surgical resection techniques.
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Affiliation(s)
- Tormod Lund
- Surgical Department, Vestre Viken Hospital Trust, Drammen, Norway
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2506
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Salgado R, Denkert C, Campbell C, Savas P, Nuciforo P, Nucifero P, Aura C, de Azambuja E, Eidtmann H, Ellis CE, Baselga J, Piccart-Gebhart MJ, Michiels S, Bradbury I, Sotiriou C, Loi S. Tumor-Infiltrating Lymphocytes and Associations With Pathological Complete Response and Event-Free Survival in HER2-Positive Early-Stage Breast Cancer Treated With Lapatinib and Trastuzumab: A Secondary Analysis of the NeoALTTO Trial. JAMA Oncol 2016; 1:448-54. [PMID: 26181252 DOI: 10.1001/jamaoncol.2015.0830] [Citation(s) in RCA: 440] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
IMPORTANCE The presence of tumor-infiltrating lymphocytes (TILs) is associated with improved outcomes in human epidermal growth factor receptor 2 (HER2)-positive early breast cancer treated with adjuvant trastuzumab and chemotherapy. The prognostic associations in the neoadjuvant setting of other anti-HER2 agents and combinations are unknown. OBJECTIVE To determine associations between presence of TILs, pathological complete response (pCR), and event-free survival (EFS) end points in patients with early breast cancer treated with trastuzumab, lapatinib, or the combination. DESIGN, SETTING, AND PARTICIPANTS The NeoALTTO trial (Neoadjuvant Lapatinib and/or Trastuzumab Treatment Optimization) randomly assigned 455 women with HER2-positive early-stage breast cancer between January 5, 2008, and May 27, 2010, to 1 of 3 neoadjuvant treatment arms: trastuzumab, lapatinib, or the combination for 6 weeks followed by the addition of weekly paclitaxel for 12 weeks, followed by 3 cycles of fluorouracil, epirubicin, and cyclophosphamide after surgery. The primary end point used in this study was pCR in the breast and lymph nodes, with a secondary end point of EFS. We evaluated levels of percentage of TILs using hematoxylin-eosin-stained core biopsy sections taken at diagnosis (prior to treatment) in a prospectively defined retrospective analysis. MAIN OUTCOMES AND MEASURES Levels of TILs were examined for their associations with efficacy end points adjusted for prognostic clinicopathological factors including PIK3CA genotype. RESULTS Of the 455 patients, 387 (85.1%) tumor samples were used for the present analysis. The median (interquartile range [IQR]) level of TILs was 12.5% (5.0%-30.0%), with levels lower in hormone receptor-positive (10.0% [5.0%-22.5%]) vs hormone receptor-negative (12.5% [3.0%-35.0%]) samples (P = .02). For the pCR end point, levels of TILs greater than 5% were associated with higher pCR rates independent of treatment group (adjusted odds ratio, 2.60 [95% CI, 1.26-5.39]; P = .01). With a median (IQR) follow-up time of 3.77 (3.50-4.22) years, every 1% increase in TILs was associated with a 3% decrease in the rate of an event (adjusted hazard ratio, 0.97 [95% CI, 0.95-0.99]; P = .002) across all treatment groups. CONCLUSIONS AND RELEVANCE The presence of TILs at diagnosis is an independent, positive, prognostic marker in HER2-positive early breast cancer treated with neoadjuvant anti-HER2 agents and chemotherapy for both pCR and EFS end points. TRIAL REGISTRATION clinicaltrials.gov Identifier: NCT00553358.
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Affiliation(s)
- Roberto Salgado
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium2Department of Pathology, Gasthuis Zusters Antwerpen Hospitals, Antwerp, Belgium
| | - Carsten Denkert
- Institute of Pathology, Charité-Universitätsmedizin, Berlin, Germany4German Cancer Consortium, Berlin, Germany
| | - Christine Campbell
- Frontier Science (Scotland) Ltd, Grampian View, Kincraig, Kingussie, United Kingdom
| | - Peter Savas
- Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Claudia Aura
- Val d'Hebron Institute of Oncology, Barcelona, Spain
| | - Evandro de Azambuja
- Breast European Adjuvant Study Team, Institut Jules Bordet, Brussels, Belgium
| | - Holger Eidtmann
- Department of Obstetrics and Gynecology, Campus Kiel, University Hospital Kiel, Kiel, Germany
| | | | - Jose Baselga
- Memorial Sloan-Kettering Cancer Center, New York, New York
| | | | - Stefan Michiels
- Centre de Recherche en Epidémiologie et Santé des Populations, INSERM U1018, Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Université Paris-Sud, Villejuif, France
| | - Ian Bradbury
- Frontier Science (Scotland) Ltd, Grampian View, Kincraig, Kingussie, United Kingdom
| | - Christos Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Sherene Loi
- Division of Clinical Medicine and Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
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2507
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Yao J, Caballero OL, Huang Y, Lin C, Rimoldi D, Behren A, Cebon JS, Hung MC, Weinstein JN, Strausberg RL, Zhao Q. Altered Expression and Splicing of ESRP1 in Malignant Melanoma Correlates with Epithelial-Mesenchymal Status and Tumor-Associated Immune Cytolytic Activity. Cancer Immunol Res 2016; 4:552-61. [PMID: 27045022 DOI: 10.1158/2326-6066.cir-15-0255] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/03/2016] [Indexed: 11/16/2022]
Abstract
Melanoma is one of the major cancer types for which new immune-based cancer treatments have achieved promising results. However, anti-PD-1 and anti-CTLA-4 therapies are effective only in some patients. Hence, predictive molecular markers for the development of clinical strategies targeting immune checkpoints are needed. Using The Cancer Genome Atlas (TCGA) RNAseq data, we found that expression of ESRP1, encoding a master splicing regulator in the epithelial-mesenchymal transition (EMT), was inversely correlated with tumor-associated immune cytolytic activity. That association holds up across multiple TCGA tumor types, suggesting a link between tumor EMT status and infiltrating lymphocyte activity. In melanoma, ESRP1 mainly exists in a melanocyte-specific truncated form transcribed from exon 13. This was validated by analyzing CCLE cell line data, public CAGE data, and RT-PCR in primary cultured melanoma cell lines. Based on ESRP1 expression, we divided TCGA melanoma cases into ESRP1-low, -truncated, and -full-length groups. ESRP1-truncated tumors comprise approximately two thirds of melanoma samples and reside in an apparent transitional state between epithelial and mesenchymal phenotypes. ESRP1 full-length tumors express epithelial markers and constitute about 5% of melanoma samples. In contrast, ESRP1-low tumors express mesenchymal markers and are high in immune cytolytic activity as well as PD-L2 and CTLA-4 expression. Those tumors are associated with better patient survival. Results from our study suggest a path toward the use of ESRP1 and other EMT markers as informative biomarkers for immunotherapy. Cancer Immunol Res; 4(6); 552-61. ©2016 AACR.
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Affiliation(s)
- Jun Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Otavia L Caballero
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Orygen Biotecnologia, SA., São Paulo, SP, Brazil
| | - Ying Huang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Calvin Lin
- Regeneron Pharmaceuticals Inc., Tarrytown, New York
| | - Donata Rimoldi
- Clinical Tumor Biology and Immunotherapy Unit, Ludwig Center, University of Lausanne, Switzerland, Lausanne, Switzerland
| | - Andreas Behren
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Jonathan S Cebon
- Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute, Victoria, Australia
| | - Mien-Chie Hung
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Qi Zhao
- Ludwig Collaborative Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland. Regeneron Pharmaceuticals Inc., Tarrytown, New York.
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2508
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Bedognetti D, Maccalli C, Bader SBA, Marincola FM, Seliger B. Checkpoint Inhibitors and Their Application in Breast Cancer. Breast Care (Basel) 2016; 11:108-15. [PMID: 27239172 PMCID: PMC4881248 DOI: 10.1159/000445335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Immune checkpoints are crucial for the maintenance of self-tolerance and for the modulation of immune responses in order to minimize tissue damage. Tumor cells take advantage of these mechanisms to evade immune recognition. A significant proportion of tumors, including breast cancers, can express co-inhibitory molecules that are important formediating the escape from T cell-mediated immune surveillance. The interaction of inhibitory receptors with their ligands can be blocked by specific molecules. Monoclonal antibodies (mAbs) directed against the cytotoxic T lymphocyte-associated antigen-4 (CTLA4) and, more recently, against the programmed cell death protein 1 (PD1), have been approved for the therapy of melanoma (anti-CTLA4 and anti-PD1 mAbs) and non-small cell lung cancer (anti-PD1 mAbs). Moreover, inhibition of PD1 signaling has shown extremely promising signs of activity in breast cancer. An increasing number of molecules directed against other immune checkpoints are currently under clinical development. In this review, we summarize the evidence supporting the implementation of checkpoint inhibition in breast cancer by reviewing in detail data on PD-L1 expression and its regulation. In addition, opportunities to boost anti-tumor immunity in breast cancer with checkpoint inhibitor-based immunotherapies alone and in combination with other treatment options will be discussed.
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Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Cristina Maccalli
- Tumor Biology, Immunology, and Therapy Section, Division of Translational Medicine, Sidra Medical and Research Center, Doha, Qatar
| | - Salha B.J. Al Bader
- National Center for Cancer Care and Research (NCCCR), and Hamad General Hospital, Doha, Qatar
| | - Francesco M. Marincola
- Office of the Chief Research Officer (CRO), Sidra Medical and Research Center, Doha, Qatar
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
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2509
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Novosiadly R, Kalos M. High-content molecular profiling of T-cell therapy in oncology. MOLECULAR THERAPY-ONCOLYTICS 2016; 3:16009. [PMID: 27626060 PMCID: PMC5008264 DOI: 10.1038/mto.2016.9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 12/19/2022]
Abstract
Recent clinical data have revealed the remarkable potential for T-cell-modulating agents to induce potent and durable responses in a subset of cancer patients. In this review, we discuss molecular approaches, platforms, and strategies that enable a broader interrogation of the activity of agents that modulate the activity of tumor-specific T cells, to more comprehensively understand how and why the agents succeed and fail, as well as examples of data sets generated in clinical trials that have provided important insights into the biological activity of T-cell therapies and that support further rational development of this exciting treatment modality.
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Affiliation(s)
- Ruslan Novosiadly
- Department of Cancer Immunobiology, Eli Lilly and Company , New York, New York, USA
| | - Michael Kalos
- Department of Cancer Immunobiology, Eli Lilly and Company , New York, New York, USA
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2510
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McGranahan N, Furness AJS, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, Watkins TBK, Shafi S, Murugaesu N, Mitter R, Akarca AU, Linares J, Marafioti T, Henry JY, Van Allen EM, Miao D, Schilling B, Schadendorf D, Garraway LA, Makarov V, Rizvi NA, Snyder A, Hellmann MD, Merghoub T, Wolchok JD, Shukla SA, Wu CJ, Peggs KS, Chan TA, Hadrup SR, Quezada SA, Swanton C. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science 2016; 351:1463-9. [PMID: 26940869 PMCID: PMC4984254 DOI: 10.1126/science.aaf1490] [Citation(s) in RCA: 2264] [Impact Index Per Article: 283.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 02/11/2016] [Indexed: 12/12/2022]
Abstract
As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy-induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens.
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Affiliation(s)
- Nicholas McGranahan
- The Francis Crick Institute, London WC2A 3LY, UK. Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London (UCL), London WC1E 6BT, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Andrew J S Furness
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Sofie Ramskov
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1970 Frederiksberg C, Denmark
| | - Rikke Lyngaa
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1970 Frederiksberg C, Denmark
| | - Sunil Kumar Saini
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1970 Frederiksberg C, Denmark
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Gareth A Wilson
- The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Nicolai J Birkbak
- The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Crispin T Hiley
- The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Thomas B K Watkins
- The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | - Nirupa Murugaesu
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK
| | | | - Ayse U Akarca
- Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. Department of Cellular Pathology, UCL, London WC1E 6BT, UK
| | - Joseph Linares
- Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. Department of Cellular Pathology, UCL, London WC1E 6BT, UK
| | - Teresa Marafioti
- Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK. Department of Cellular Pathology, UCL, London WC1E 6BT, UK
| | - Jake Y Henry
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Diana Miao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bastian Schilling
- Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany. German Cancer Consortium (DKTK), 69121 Heidelberg, Germany
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital, University Duisburg-Essen, 45147 Essen, Germany. German Cancer Consortium (DKTK), 69121 Heidelberg, Germany
| | - Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Naiyer A Rizvi
- Hematology/Oncology Division, 177 Fort Washington Avenue, Columbia University, New York, NY 10032, USA
| | - Alexandra Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Weill Cornell Medical College, New York, NY 10065, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Weill Cornell Medical College, New York, NY 10065, USA
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Ludwig Collaborative Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Weill Cornell Medical College, New York, NY 10065, USA. Ludwig Collaborative Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sachet A Shukla
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Department of Internal Medicine, Brigham and Woman's Hospital, Boston, MA 02115, USA
| | - Karl S Peggs
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sine R Hadrup
- Section for Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark, 1970 Frederiksberg C, Denmark
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK. Cancer Immunology Unit, UCL Cancer Institute, UCL, London WC1E 6BT, UK.
| | - Charles Swanton
- The Francis Crick Institute, London WC2A 3LY, UK. Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London WC1E 6BT, UK.
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2511
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Abstract
The recognition of functional roles for transcribed long non-coding RNA (lncRNA) has provided a new dimension to our understanding of cellular physiology and disease pathogenesis. LncRNAs are a large group of structurally complex RNA genes that can interact with DNA, RNA, or protein molecules to modulate gene expression and to exert cellular effects through diverse mechanisms. The emerging knowledge regarding their functional roles and their aberrant expression in disease states emphasizes the potential for lncRNA to serve as targets for therapeutic intervention. In this concise review, we outline the mechanisms of action of lncRNAs, their functional cellular roles, and their involvement in disease. Using liver cancer as an example, we provide an overview of the emerging opportunities and potential approaches to target lncRNA-dependent mechanisms for therapeutic purposes.
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2512
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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2513
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Strickland KC, Howitt BE, Shukla SA, Rodig S, Ritterhouse LL, Liu JF, Garber JE, Chowdhury D, Wu CJ, D'Andrea AD, Matulonis UA, Konstantinopoulos PA. Association and prognostic significance of BRCA1/2-mutation status with neoantigen load, number of tumor-infiltrating lymphocytes and expression of PD-1/PD-L1 in high grade serous ovarian cancer. Oncotarget 2016. [PMID: 26871470 DOI: 10.18632/oncotarget.7277]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Immune checkpoint inhibitors (e.g., anti-PD-1 and anti-PD-L1 antibodies) have demonstrated remarkable efficacy against hypermutated cancers such as melanomas and lung carcinomas. One explanation for this effect is that hypermutated lesions harbor more tumor-specific neoantigens that stimulate recruitment of an increased number of tumor-infiltrating lymphocytes (TILs), which is counterbalanced by overexpression of immune checkpoints such as PD-1 or PD-L1. Given that BRCA1/2-mutated high grade serous ovarian cancers (HGSOCs) exhibit a higher mutational load and a unique mutational signature with an elevated number of larger indels up to 50 bp, we hypothesized that they may also harbor more tumor-specific neoantigens, and, therefore, exhibit increased TILs and PD-1/PD-L1 expression. Here, we report significantly higher predicted neoantigens in BRCA1/2-mutated tumors compared to tumors without alterations in homologous recombination (HR) genes (HR-proficient tumors). Tumors with higher neoantigen load were associated with improved overall survival and higher expression of immune genes associated with tumor cytotoxicity such as genes of the TCR, the IFN-gamma and the TNFR pathways. Furthermore, immunohistochemistry studies demonstrated that BRCA1/2-mutated tumors exhibited significantly increased CD3+ and CD8+ TILs, as well as elevated expression of PD-1 and PD-L1 in tumor-associated immune cells compared to HR-proficient tumors. Survival analysis showed that both BRCA1/2-mutation status and number of TILs were independently associated with outcome. Of note, two distinct groups of HGSOCs, one with very poor prognosis (HR proficient with low number of TILs) and one with very good prognosis (BRCA1/2-mutated tumors with high number of TILs) were defined. These findings support a link between BRCA1/2-mutation status, immunogenicity and survival, and suggesting that BRCA1/2-mutated HGSOCs may be more sensitive to PD-1/PD-L1 inhibitors compared to HR-proficient HGSOCs.
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Affiliation(s)
- Kyle C Strickland
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brooke E Howitt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sachet A Shukla
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott Rodig
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren L Ritterhouse
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Joyce F Liu
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Judy E Garber
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Dipanjan Chowdhury
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Catherine J Wu
- The Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Alan D D'Andrea
- Division of Genomic Stability and DNA Repair, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ursula A Matulonis
- Medical Gynecologic Oncology Program, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
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2514
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Kakimi K, Karasaki T, Matsushita H, Sugie T. Advances in personalized cancer immunotherapy. Breast Cancer 2016; 24:16-24. [PMID: 27000871 DOI: 10.1007/s12282-016-0688-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 03/03/2016] [Indexed: 01/13/2023]
Abstract
There are currently three major approaches to T cell-based cancer immunotherapy, namely, active vaccination, adoptive cell transfer therapy and immune checkpoint blockade. Recently, this latter approach has demonstrated remarkable clinical benefits, putting cancer immunotherapy under the spotlight. Better understanding of the dynamics of anti-tumor immune responses (the "Cancer-Immunity Cycle") is crucial for the further development of this form of treatment. Tumors employ multiple strategies to escape from anti-tumor immunity, some of which result from the selection of cancer cells with immunosuppressive activity by the process of cancer immunoediting. Apart from this selective process, anti-tumor immune responses can also be inhibited in multiple different ways which vary from patient to patient. This implies that cancer immunotherapy must be personalized to (1) identify the rate-limiting steps in any given patient, (2) identify and combine strategies to overcome these hurdles, and (3) proceed with the next round of the "Cancer-Immunity Cycle". Cancer cells have genetic alterations which can provide the immune system with targets by which to recognize and eradicate the tumor. Mutated proteins expressed exclusively in cancer cells and recognizable by the immune system are known as neoantigens. The development of next-generation sequencing technology has made it possible to determine the genetic landscape of human cancer and facilitated the utilization of genomic information to identify such candidate neoantigens in individual cancers. Future immunotherapies will need to be personalized in terms of the identification of both patient-specific immunosuppressive mechanisms and target neoantigens.
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Affiliation(s)
- Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
| | - Takahiro Karasaki
- Department of Immunotherapeutics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Tomoharu Sugie
- Department of Surgery, Kansai Medical University, Hirakata, Japan
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2515
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Kardos J, Chai S, Mose LE, Selitsky SR, Krishnan B, Saito R, Iglesia MD, Milowsky MI, Parker JS, Kim WY, Vincent BG. Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight 2016; 1:e85902. [PMID: 27699256 DOI: 10.1172/jci.insight.85902] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We report the discovery of a claudin-low molecular subtype of high-grade bladder cancer that shares characteristics with the homonymous subtype of breast cancer. Claudin-low bladder tumors were enriched for multiple genetic features including increased rates of RB1, EP300, and NCOR1 mutations; increased frequency of EGFR amplification; decreased rates of FGFR3, ELF3, and KDM6A mutations; and decreased frequency of PPARG amplification. While claudin-low tumors showed the highest expression of immune gene signatures, they also demonstrated gene expression patterns consistent with those observed in active immunosuppression. This did not appear to be due to differences in predicted neoantigen burden, but rather was associated with broad upregulation of cytokine and chemokine levels from low PPARG activity, allowing unopposed NFKB activity. Taken together, these results define a molecular subtype of bladder cancer with distinct molecular features and an immunologic profile that would, in theory, be primed for immunotherapeutic response.
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Affiliation(s)
- Jordan Kardos
- Lineberger Comprehensive Cancer Center.,Department of Genetics
| | - Shengjie Chai
- Lineberger Comprehensive Cancer Center.,Department of Microbiology/Immunology.,Curriculum in Bioinformatics and Computational Biology
| | | | | | | | | | | | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center.,Department of Medicine, Division of Hematology/Oncology, and.,Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center.,Department of Genetics
| | - William Y Kim
- Lineberger Comprehensive Cancer Center.,Department of Genetics.,Department of Medicine, Division of Hematology/Oncology, and.,Department of Urology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center.,Department of Medicine, Division of Hematology/Oncology, and
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2516
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Loi S, Dushyanthen S, Beavis PA, Salgado R, Denkert C, Savas P, Combs S, Rimm DL, Giltnane JM, Estrada MV, Sánchez V, Sanders ME, Cook RS, Pilkinton MA, Mallal SA, Wang K, Miller VA, Stephens PJ, Yelensky R, Doimi FD, Gómez H, Ryzhov SV, Darcy PK, Arteaga CL, Balko JM. RAS/MAPK Activation Is Associated with Reduced Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancer: Therapeutic Cooperation Between MEK and PD-1/PD-L1 Immune Checkpoint Inhibitors. Clin Cancer Res 2016; 22:1499-509. [PMID: 26515496 PMCID: PMC4794351 DOI: 10.1158/1078-0432.ccr-15-1125] [Citation(s) in RCA: 384] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/21/2015] [Indexed: 02/07/2023]
Abstract
PURPOSE Tumor-infiltrating lymphocytes (TIL) in the residual disease (RD) of triple-negative breast cancers (TNBC) after neoadjuvant chemotherapy (NAC) are associated with improved survival, but insight into tumor cell-autonomous molecular pathways affecting these features are lacking. EXPERIMENTAL DESIGN We analyzed TILs in the RD of clinically and molecularly characterized TNBCs after NAC and explored therapeutic strategies targeting combinations of MEK inhibitors with PD-1/PD-L1-targeted immunotherapy in mouse models of breast cancer. RESULTS Presence of TILs in the RD was significantly associated with improved prognosis. Genetic or transcriptomic alterations in Ras-MAPK signaling were significantly correlated with lower TILs. MEK inhibition upregulated cell surface MHC expression and PD-L1 in TNBC cells both in vivo and in vitro. Moreover, combined MEK and PD-L1/PD-1 inhibition enhanced antitumor immune responses in mouse models of breast cancer. CONCLUSIONS These data suggest the possibility that Ras-MAPK pathway activation promotes immune-evasion in TNBC, and support clinical trials combining MEK- and PD-L1-targeted therapies. Furthermore, Ras/MAPK activation and MHC expression may be predictive biomarkers of response to immune checkpoint inhibitors.
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Affiliation(s)
- Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.
| | | | - Paul A Beavis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Institute Jules Bordet, Brussels, Department of Pathology, GZA Antwerp, Belgium
| | - Carsten Denkert
- Charité University and German Cancer Consortium (DKTK), Berlin, Germany
| | - Peter Savas
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Susan Combs
- Departments of Pathology and Medicine, Yale University, New Haven, Connecticut
| | - David L Rimm
- Departments of Pathology and Medicine, Yale University, New Haven, Connecticut
| | - Jennifer M Giltnane
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Monica V Estrada
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Violeta Sánchez
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Melinda E Sanders
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Rebecca S Cook
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Mark A Pilkinton
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Simon A Mallal
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Kai Wang
- Foundation Medicine, Cambridge, Massachusetts
| | | | | | | | - Franco D Doimi
- Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Perú
| | - Henry Gómez
- Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Perú
| | | | - Phillip K Darcy
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Carlos L Arteaga
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Justin M Balko
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee.
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2517
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Loi S, Dushyanthen S, Beavis PA, Salgado R, Denkert C, Savas P, Combs S, Rimm DL, Giltnane JM, Estrada MV, Sánchez V, Sanders ME, Cook RS, Pilkinton MA, Mallal SA, Wang K, Miller VA, Stephens PJ, Yelensky R, Doimi FD, Gómez H, Ryzhov SV, Darcy PK, Arteaga CL, Balko JM. RAS/MAPK Activation Is Associated with Reduced Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancer: Therapeutic Cooperation Between MEK and PD-1/PD-L1 Immune Checkpoint Inhibitors. Clin Cancer Res 2016. [PMID: 26515496 DOI: 10.1158/1078-0432.ccr-15-1125.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Tumor-infiltrating lymphocytes (TIL) in the residual disease (RD) of triple-negative breast cancers (TNBC) after neoadjuvant chemotherapy (NAC) are associated with improved survival, but insight into tumor cell-autonomous molecular pathways affecting these features are lacking. EXPERIMENTAL DESIGN We analyzed TILs in the RD of clinically and molecularly characterized TNBCs after NAC and explored therapeutic strategies targeting combinations of MEK inhibitors with PD-1/PD-L1-targeted immunotherapy in mouse models of breast cancer. RESULTS Presence of TILs in the RD was significantly associated with improved prognosis. Genetic or transcriptomic alterations in Ras-MAPK signaling were significantly correlated with lower TILs. MEK inhibition upregulated cell surface MHC expression and PD-L1 in TNBC cells both in vivo and in vitro. Moreover, combined MEK and PD-L1/PD-1 inhibition enhanced antitumor immune responses in mouse models of breast cancer. CONCLUSIONS These data suggest the possibility that Ras-MAPK pathway activation promotes immune-evasion in TNBC, and support clinical trials combining MEK- and PD-L1-targeted therapies. Furthermore, Ras/MAPK activation and MHC expression may be predictive biomarkers of response to immune checkpoint inhibitors.
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Affiliation(s)
- Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia.
| | | | - Paul A Beavis
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Institute Jules Bordet, Brussels, Department of Pathology, GZA Antwerp, Belgium
| | - Carsten Denkert
- Charité University and German Cancer Consortium (DKTK), Berlin, Germany
| | - Peter Savas
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Susan Combs
- Departments of Pathology and Medicine, Yale University, New Haven, Connecticut
| | - David L Rimm
- Departments of Pathology and Medicine, Yale University, New Haven, Connecticut
| | - Jennifer M Giltnane
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Monica V Estrada
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Violeta Sánchez
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Melinda E Sanders
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee
| | - Rebecca S Cook
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Mark A Pilkinton
- Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Simon A Mallal
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Kai Wang
- Foundation Medicine, Cambridge, Massachusetts
| | | | | | | | - Franco D Doimi
- Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Perú
| | - Henry Gómez
- Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Perú
| | | | - Phillip K Darcy
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia. Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Carlos L Arteaga
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee
| | - Justin M Balko
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee. Department of Medicine, Vanderbilt University, Nashville, Tennessee.
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2518
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Matsushita H, Sato Y, Karasaki T, Nakagawa T, Kume H, Ogawa S, Homma Y, Kakimi K. Neoantigen Load, Antigen Presentation Machinery, and Immune Signatures Determine Prognosis in Clear Cell Renal Cell Carcinoma. Cancer Immunol Res 2016; 4:463-71. [PMID: 26980598 DOI: 10.1158/2326-6066.cir-15-0225] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/05/2016] [Indexed: 11/16/2022]
Abstract
Tumors commonly harbor multiple genetic alterations, some of which initiate tumorigenesis. Among these, some tumor-specific somatic mutations resulting in mutated protein have the potential to induce antitumor immune responses. To examine the relevance of the latter to immune responses in the tumor and to patient outcomes, we used datasets of whole-exome and RNA sequencing from 97 clear cell renal cell carcinoma (ccRCC) patients to identify neoepitopes predicted to be presented by each patient's autologous HLA molecules. We found that the number of nonsilent or missense mutations did not correlate with patient prognosis. However, combining the number of HLA-restricted neoepitopes with the cell surface expression of HLA or β2-microglobulin(β2M) revealed that an A-neo(hi)/HLA-A(hi) or ABC-neo(hi)/β2M(hi) phenotype correlated with better clinical outcomes. Higher expression of immune-related genes from CD8 T cells and their effector molecules [CD8A, perforin (PRF1) and granzyme A (GZMA)], however, did not correlate with prognosis. This may have been due to the observed correlation of these genes with the expression of other genes that were associated with immunosuppression in the tumor microenvironment (CTLA-4, PD-1, LAG-3, PD-L1, PD-L2, IDO1, and IL10). This suggested that abundant neoepitopes associated with greater antitumor effector immune responses were counterbalanced by a strongly immunosuppressive microenvironment. Therefore, immunosuppressive molecules should be considered high-priority targets for modulating immune responses in patients with ccRCC. Blockade of these molecular pathways could be combined with immunotherapies targeting neoantigens to achieve synergistic antitumor activity. Cancer Immunol Res; 4(5); 463-71. ©2016 AACR.
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Affiliation(s)
- Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Yusuke Sato
- Department of Urology, The University of Tokyo Hospital, Tokyo, Japan. Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahiro Karasaki
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | - Tohru Nakagawa
- Department of Urology, The University of Tokyo Hospital, Tokyo, Japan
| | - Haruki Kume
- Department of Urology, The University of Tokyo Hospital, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yukio Homma
- Department of Urology, The University of Tokyo Hospital, Tokyo, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan.
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2519
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Madore J, Strbenac D, Vilain R, Menzies AM, Yang JYH, Thompson JF, Long GV, Mann GJ, Scolyer RA, Wilmott JS. PD-L1 Negative Status is Associated with Lower Mutation Burden, Differential Expression of Immune-Related Genes, and Worse Survival in Stage III Melanoma. Clin Cancer Res 2016; 22:3915-23. [PMID: 26960397 DOI: 10.1158/1078-0432.ccr-15-1714] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 02/22/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE Understanding why some melanomas test negative for PD-L1 by IHC may have implications for the application of anti-PD-1 therapies in melanoma management. This study sought to determine somatic mutation and gene expression patterns associated with tumor cell PD-L1 expression, or lack thereof, in stage III metastatic melanoma to better define therapeutically relevant patient subgroups. EXPERIMENTAL DESIGN IHC for PD-L1 was assessed in 52 American Joint Committee on Cancer stage III melanoma lymph node specimens and compared with specimen-matched comprehensive clinicopathologic, genomic, and transcriptomic data. RESULTS PD-L1-negative status was associated with lower nonsynonymous mutation (NSM) burden (P = 0.017) and worse melanoma-specific survival [HR = 0.28 (0.12-0.66), P = 0.002] in stage III melanoma. Gene set enrichment analysis identified an immune-related gene expression signature in PD-L1-positive tumors. There was a marked increase in cytotoxic T-cell and macrophage-specific genes in PD-L1-positive melanomas. CD8A(high) gene expression was associated with better melanoma-specific survival [HR = 0.2 (0.05-0.87), P = 0.017] and restricted to PD-L1-positive stage III specimens. NF1 mutations were restricted to PD-L1-positive tumors (P = 0.041). CONCLUSIONS Tumor negative PD-L1 status in stage III melanoma lymph node metastasis is a marker of worse patient survival and is associated with a poor immune response gene signature. Lower NSM levels were associated with PD-L1-negative status suggesting differences in somatic mutation profiles are a determinant of PD-L1-associated antitumor immunity in stage III melanoma. Clin Cancer Res; 22(15); 3915-23. ©2016 AACR.
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Affiliation(s)
- Jason Madore
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
| | - Dario Strbenac
- School of Mathematics and Statistics, The University of Sydney Camperdown, New South Wales, Australia
| | - Ricardo Vilain
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia. Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia. Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia
| | - Jeen Y H Yang
- School of Mathematics and Statistics, The University of Sydney Camperdown, New South Wales, Australia
| | - John F Thompson
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia. Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia. Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, New South Wales, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Centre for Cancer Research, The University of Sydney at Westmead Millennium Institute, Westmead, New South Wales, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia. Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia.
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia. Sydney Medical School, The University of Sydney, Camperdown, New South Wales, Australia
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2520
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Bedognetti D, Hendrickx W, Ceccarelli M, Miller LD, Seliger B. Disentangling the relationship between tumor genetic programs and immune responsiveness. Curr Opin Immunol 2016; 39:150-8. [PMID: 26967649 DOI: 10.1016/j.coi.2016.02.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/13/2022]
Abstract
Correlative studies in humans have demonstrated that an active immune microenvironment characterized by the presence of a T-helper 1 immune response typifies a tumor phenotype associated with better outcome and increased responsiveness to immune manipulation. This phenotype also signifies the counter activation of immune-regulatory mechanisms. Variables modulating the development of an effective anti-tumor immune response are increasingly scrutinized as potential therapeutic targets. Genetic alterations of cancer cells that functionally influence intratumoral immune response include mutational load, specific mutations of genes involved in oncogenic pathways and copy number aberrations involving chemokine and cytokine genes. Inhibiting oncogenic pathways that prevent the development of the immune-favorable cancer phenotype may complement modern immunotherapeutic approaches.
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Affiliation(s)
- Davide Bedognetti
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar.
| | - Wouter Hendrickx
- Tumor Biology, Immunology and Therapy Section, Division of Translational Medicine, Research Branch, Sidra Medical and Research Center, Doha, Qatar
| | - Michele Ceccarelli
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Halle, Germany
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2521
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Bernstein MB, Krishnan S, Hodge JW, Chang JY. Immunotherapy and stereotactic ablative radiotherapy (ISABR): a curative approach? Nat Rev Clin Oncol 2016; 13:516-24. [PMID: 26951040 DOI: 10.1038/nrclinonc.2016.30] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conventional radiotherapy, in addition to its well-established tumoricidal effects, can also activate the host immune system. Radiation therapy modulates tumour phenotypes, enhances antigen presentation and tumour immunogenicity, increases production of cytokines and alters the tumour microenvironment, enabling destruction of the tumour by the immune system. Investigating the combination of radiotherapy with immunotherapeutic agents, which also promote the host antitumour immune response is, therefore, a logical progression. As the spectrum of clinical use of stereotactic radiotherapy continues to broaden, the question arose as to whether the ablative radiation doses used can also stimulate immune responses and, if so, whether we can amplify these effects by combining immunotherapy and stereotactic ablative radiotherapy (SABR). In this Perspectives article, we explore the preclinical and clinical evidence supporting activation of the immune system following SABR. We then examine studies that provide data on the effectiveness of combining these two techniques - immunotherapy and SABR - in an approach that we have termed 'ISABR'. Lastly, we provide general guiding principles for the development of future clinical trials to investigate the efficacy of ISABR in the hope of generating further interest in these exciting developments.
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Affiliation(s)
- Michael B Bernstein
- Division of Radiation Oncology, MD Anderson Cancer Center, Unit 97, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - Sunil Krishnan
- Division of Radiation Oncology, MD Anderson Cancer Center, Unit 97, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
| | - James W Hodge
- Laboratory of Tumor Immunology and Biology, Center for Cancer Research, National Cancer Institute, Building 10, Room 8B13, Bethesda, Maryland 20892-1750, USA
| | - Joe Y Chang
- Division of Radiation Oncology, MD Anderson Cancer Center, Unit 97, 1515 Holcombe Boulevard, Houston, Texas 77030, USA
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2522
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Schalper KA, Kaftan E, Herbst RS. Predictive Biomarkers for PD-1 Axis Therapies: The Hidden Treasure or a Call for Research. Clin Cancer Res 2016; 22:2102-4. [PMID: 26957559 DOI: 10.1158/1078-0432.ccr-16-0169] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 02/14/2016] [Indexed: 12/26/2022]
Abstract
Blockade of the PD-1 axis has emerged as an effective anticancer immunotherapy against various tumor types. Diverse studies have identified biomarkers associated with response to these therapies. However, the clinical use of such tests is limited by their variable performance and restricted understanding of their biologic significance. Clin Cancer Res; 22(9); 2102-4. ©2016 AACRSee related article by Ock et al., p. 2261.
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Affiliation(s)
- Kurt A Schalper
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut. Medical Oncology, Yale School of Medicine and Yale Cancer Center, New Haven, Connecticut. Translational Immuno-oncology Laboratory, Yale Cancer Center, New Haven, Connecticut.
| | - Edward Kaftan
- Medical Oncology, Yale School of Medicine and Yale Cancer Center, New Haven, Connecticut. Translational Immuno-oncology Laboratory, Yale Cancer Center, New Haven, Connecticut
| | - Roy S Herbst
- Medical Oncology, Yale School of Medicine and Yale Cancer Center, New Haven, Connecticut
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2523
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Kloor M, von Knebel Doeberitz M. The Immune Biology of Microsatellite-Unstable Cancer. Trends Cancer 2016; 2:121-133. [PMID: 28741532 DOI: 10.1016/j.trecan.2016.02.004] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/03/2016] [Accepted: 02/09/2016] [Indexed: 12/16/2022]
Abstract
Deficient DNA mismatch repair (MMR) boosts the accumulation of frameshift mutations in genes encompassing coding microsatellites (cMS). This results in the translation of proteins with mutation-induced frameshift peptides (neoantigens) rendering microsatellite-unstable (MSI) cancers highly immunogenic. MSI cancers express a defined set of neoantigens resulting from functionally relevant driver mutations, which are shared by most MSI cancers. Patients with MSI cancers and healthy individuals affected by Lynch syndrome, an inherited predisposition for MSI cancers, develop specific immune responses against these neoantigens. In this review, we summarize our current understanding of the immune biology of MSI cancers and outline new concepts and research directions to develop not only therapeutic treatments, but also preventive vaccines based on the MSI cancer genome landscapes.
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Affiliation(s)
- Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
| | - Magnus von Knebel Doeberitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Clinical Cooperation Unit (CCU 105) of the German Cancer Research Center and Molecular Medicine Partner Unit (MMPU) of the European Molecular Biology Laboratory, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
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2524
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Kawaguchi K, Suzuki E, Yamaguchi A, Yamamoto M, Morita S, Toi M. Altered expression of major immune regulatory molecules in peripheral blood immune cells associated with breast cancer. Breast Cancer 2016; 24:111-120. [PMID: 26942414 PMCID: PMC5216091 DOI: 10.1007/s12282-016-0682-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 02/18/2016] [Indexed: 01/05/2023]
Abstract
BACKGROUND The purpose of this study was to clarify the alterations of major immune regulators in peripheral blood mononuclear cells (PBMCs) of cancer patients and to analyze the association with the disease progression in breast cancer patients. METHODS The study included 6 healthy volunteers (HVs), 12 primary breast cancer (PBC) patients, and 30 metastatic breast cancer (MBC) patients. The expression of immune regulators such as, CCR6, CD4, CD8, CD14, CD40, CD56, CD80, CTLA4, CXCR4, FOXP3, IDO-1, IDO-2, NKG2D, NRP-1, PD-1, and PD-L1 mRNA in PBMCs was measured by quantitative RT-PCR. Analysis of variance with contrasts was performed to find expression patterns of the three groups (HVs, PBC, MBC). RESULTS We clarified the alterations of mRNA of major immune regulators PD-L1, FOXP3, CD80, CD40, and CD14 in PBMCs of cancer patients and the association of these alternations with disease progression. Furthermore, PD-L1 expression was correlated with serum interferon-γ production. CONCLUSION Our data suggested that mRNA expressions of PD-L1, FOXP3, CD80, CD40 and CD14 in PBMCs are affected by disease progression. Understanding the roles of these various interactions will be of importance to future studies aiming to uncover biomarkers for predicting response to immune therapy.
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Affiliation(s)
- Kosuke Kawaguchi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Eiji Suzuki
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
| | - Ayane Yamaguchi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Michio Yamamoto
- Department of Biomedical Statistics and Bioinformatics, Kyoto University, Kyoto, Japan
| | - Satoshi Morita
- Department of Biomedical Statistics and Bioinformatics, Kyoto University, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Graduate School of Medicine, Kyoto University, 54 Shogoin-kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
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2525
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Bailey P, Chang DK, Nones K, Johns AL, Patch AM, Gingras MC, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, Murtaugh LC, Harliwong I, Idrisoglu S, Manning S, Nourbakhsh E, Wani S, Fink L, Holmes O, Chin V, Anderson MJ, Kazakoff S, Leonard C, Newell F, Waddell N, Wood S, Xu Q, Wilson PJ, Cloonan N, Kassahn KS, Taylor D, Quek K, Robertson A, Pantano L, Mincarelli L, Sanchez LN, Evers L, Wu J, Pinese M, Cowley MJ, Jones MD, Colvin EK, Nagrial AM, Humphrey ES, Chantrill LA, Mawson A, Humphris J, Chou A, Pajic M, Scarlett CJ, Pinho AV, Giry-Laterriere M, Rooman I, Samra JS, Kench JG, Lovell JA, Merrett ND, Toon CW, Epari K, Nguyen NQ, Barbour A, Zeps N, Moran-Jones K, Jamieson NB, Graham JS, Duthie F, Oien K, Hair J, Grützmann R, Maitra A, Iacobuzio-Donahue CA, Wolfgang CL, Morgan RA, Lawlor RT, Corbo V, Bassi C, Rusev B, Capelli P, Salvia R, Tortora G, Mukhopadhyay D, Petersen GM, Munzy DM, Fisher WE, Karim SA, Eshleman JR, Hruban RH, Pilarsky C, Morton JP, Sansom OJ, Scarpa A, Musgrove EA, Bailey UMH, Hofmann O, Sutherland RL, Wheeler DA, Gill AJ, Gibbs RA, Pearson JV, Waddell N, Biankin AV, Grimmond SM. Genomic analyses identify molecular subtypes of pancreatic cancer. Nature 2016; 531:47-52. [PMID: 26909576 DOI: 10.1038/nature16965] [Citation(s) in RCA: 2337] [Impact Index Per Article: 292.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 12/30/2015] [Indexed: 12/12/2022]
Abstract
Integrated genomic analysis of 456 pancreatic ductal adenocarcinomas identified 32 recurrently mutated genes that aggregate into 10 pathways: KRAS, TGF-β, WNT, NOTCH, ROBO/SLIT signalling, G1/S transition, SWI-SNF, chromatin modification, DNA repair and RNA processing. Expression analysis defined 4 subtypes: (1) squamous; (2) pancreatic progenitor; (3) immunogenic; and (4) aberrantly differentiated endocrine exocrine (ADEX) that correlate with histopathological characteristics. Squamous tumours are enriched for TP53 and KDM6A mutations, upregulation of the TP63∆N transcriptional network, hypermethylation of pancreatic endodermal cell-fate determining genes and have a poor prognosis. Pancreatic progenitor tumours preferentially express genes involved in early pancreatic development (FOXA2/3, PDX1 and MNX1). ADEX tumours displayed upregulation of genes that regulate networks involved in KRAS activation, exocrine (NR5A2 and RBPJL), and endocrine differentiation (NEUROD1 and NKX2-2). Immunogenic tumours contained upregulated immune networks including pathways involved in acquired immune suppression. These data infer differences in the molecular evolution of pancreatic cancer subtypes and identify opportunities for therapeutic development.
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MESH Headings
- Animals
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Carcinoma, Pancreatic Ductal/classification
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/immunology
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- DNA Methylation
- DNA-Binding Proteins/genetics
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- Genes, Neoplasm/genetics
- Genome, Human/genetics
- Genomics
- Hepatocyte Nuclear Factor 3-beta/genetics
- Hepatocyte Nuclear Factor 3-gamma/genetics
- Histone Demethylases/genetics
- Homeobox Protein Nkx-2.2
- Homeodomain Proteins/genetics
- Humans
- Mice
- Mutation/genetics
- Nuclear Proteins/genetics
- Pancreatic Neoplasms/classification
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/immunology
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Prognosis
- Receptors, Cytoplasmic and Nuclear/genetics
- Survival Analysis
- Trans-Activators/genetics
- Transcription Factors/genetics
- Transcription, Genetic
- Transcriptome
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Proteins/genetics
- Zebrafish Proteins
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Affiliation(s)
- Peter Bailey
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
| | - Katia Nones
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Amber L Johns
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Ann-Marie Patch
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - David K Miller
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Angelika N Christ
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Tim J C Bruxner
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Michael C Quinn
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Craig Nourse
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - L Charles Murtaugh
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Ivon Harliwong
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Senel Idrisoglu
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Suzanne Manning
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Ehsan Nourbakhsh
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Shivangi Wani
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Lynn Fink
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Oliver Holmes
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Venessa Chin
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Matthew J Anderson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Stephen Kazakoff
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Conrad Leonard
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Felicity Newell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nick Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Scott Wood
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Qinying Xu
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Peter J Wilson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Nicole Cloonan
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Karin S Kassahn
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Genetic and Molecular Pathology, SA Pathology, Adelaide, South Australia 5000, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Darrin Taylor
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Kelly Quek
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Alan Robertson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
| | - Lorena Pantano
- Harvard Chan Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Laura Mincarelli
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Luis N Sanchez
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Lisa Evers
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Jianmin Wu
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Mark Pinese
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Mark J Cowley
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Marc D Jones
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Emily K Colvin
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Adnan M Nagrial
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Emily S Humphrey
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Lorraine A Chantrill
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Macarthur Cancer Therapy Centre, Campbelltown Hospital, New South Wales 2560, Australia
| | - Amanda Mawson
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Jeremy Humphris
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Angela Chou
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Pathology. SydPath, St Vincent's Hospital, Sydney, NSW 2010, Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, New South Wales 2052, Australia
| | - Christopher J Scarlett
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- School of Environmental &Life Sciences, University of Newcastle, Ourimbah, New South Wales 2258, Australia
| | - Andreia V Pinho
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Marc Giry-Laterriere
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Ilse Rooman
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Jaswinder S Samra
- Department of Surgery, Royal North Shore Hospital, St Leonards, Sydney, New South Wales 2065, Australia
- University of Sydney, Sydney, New South Wales 2006, Australia
| | - James G Kench
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- University of Sydney, Sydney, New South Wales 2006, Australia
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Camperdown New South Wales 2050, Australia
| | - Jessica A Lovell
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Neil D Merrett
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
- School of Medicine, University of Western Sydney, Penrith, New South Wales 2175, Australia
| | - Christopher W Toon
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - Krishna Epari
- Fiona Stanley Hospital, Robin Warren Drive, Murdoch, Western Australia 6150, Australia
| | - Nam Q Nguyen
- Department of Gastroenterology, Royal Adelaide Hospital, North Terrace, Adelaide, South Australia 5000, Australia
| | - Andrew Barbour
- Department of Surgery, Princess Alexandra Hospital, Ipswich Rd, Woollongabba, Queensland 4102, Australia
| | - Nikolajs Zeps
- School of Surgery M507, University of Western Australia, 35 Stirling Hwy, Nedlands 6009, Australia and St John of God Pathology, 12 Salvado Rd, Subiaco, Western Australia 6008, Australia
| | - Kim Moran-Jones
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Academic Unit of Surgery, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G4 OSF, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Janet S Graham
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Department of Medical Oncology, Beatson West of Scotland Cancer Centre, 1053 Great Western Road, Glasgow G12 0YN, UK
| | - Fraser Duthie
- Department of Pathology, Southern General Hospital, Greater Glasgow &Clyde NHS, Glasgow G51 4TF, UK
| | - Karin Oien
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Pathology, Southern General Hospital, Greater Glasgow &Clyde NHS, Glasgow G51 4TF, UK
| | - Jane Hair
- GGC Bio-repository, Pathology Department, Southern General Hospital, 1345 Govan Road, Glasgow G51 4TY, UK
| | - Robert Grützmann
- Department of Surgery, TU Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | - Anirban Maitra
- Departments of Pathology and Translational Molecular Pathology, UT MD Anderson Cancer Center, Houston Texas 77030, USA
| | - Christine A Iacobuzio-Donahue
- The David M. Rubenstein Pancreatic Cancer Research Center and Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christopher L Wolfgang
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
- Department of Surgery, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Richard A Morgan
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Rita T Lawlor
- ARC-Net Applied Research on Cancer Centre, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University of Verona, Verona 37134, Italy
| | - Vincenzo Corbo
- ARC-Net Applied Research on Cancer Centre, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Claudio Bassi
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Borislav Rusev
- ARC-Net Applied Research on Cancer Centre, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Paola Capelli
- Department of Pathology and Diagnostics, University of Verona, Verona 37134, Italy
| | - Roberto Salvia
- Department of Surgery, Pancreas Institute, University and Hospital Trust of Verona, Verona 37134, Italy
| | - Giampaolo Tortora
- Department of Medical Oncology, Comprehensive Cancer Centre, University and Hospital Trust of Verona, Verona 37134, Italy
| | | | | | - Donna M Munzy
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
| | - William E Fisher
- Elkins Pancreas Center, Baylor College of Medicine, One Baylor Plaza, MS226, Houston, Texas 77030-3411, USA
| | - Saadia A Karim
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
| | - James R Eshleman
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Ralph H Hruban
- Department of Pathology, The Sol Goldman Pancreatic Cancer Research Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Christian Pilarsky
- Department of Surgery, TU Dresden, Fetscherstr. 74, 01307 Dresden, Germany
| | | | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow G61 1BD, UK
- Institute for Cancer Science, University of Glasgow, Glasgow G12 8QQ, UK
| | - Aldo Scarpa
- ARC-Net Applied Research on Cancer Centre, University and Hospital Trust of Verona, Verona 37134, Italy
- Department of Pathology and Diagnostics, University of Verona, Verona 37134, Italy
| | - Elizabeth A Musgrove
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Ulla-Maja Hagbo Bailey
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Oliver Hofmann
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- Harvard Chan Bioinformatics Core, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Robert L Sutherland
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
| | - David A Wheeler
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Anthony J Gill
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- University of Sydney, Sydney, New South Wales 2006, Australia
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Michael DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, USA
| | - John V Pearson
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Nicola Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- The Kinghorn Cancer Centre, 370 Victoria St, Darlinghurst, and the Cancer Research Program, Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, Sydney, New South Wales 2010, Australia
- Department of Surgery, Bankstown Hospital, Eldridge Road, Bankstown, Sydney, New South Wales 2200, Australia
- South Western Sydney Clinical School, Faculty of Medicine, University of New South Wales, Liverpool, New South Wales 2170, Australia
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, UK
| | - Sean M Grimmond
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
- University of Melbourne, Parkville, Victoria 3010, Australia
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2526
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Zou W, Wolchok JD, Chen L. PD-L1 (B7-H1) and PD-1 pathway blockade for cancer therapy: Mechanisms, response biomarkers, and combinations. Sci Transl Med 2016; 8:328rv4. [PMID: 26936508 PMCID: PMC4859220 DOI: 10.1126/scitranslmed.aad7118] [Citation(s) in RCA: 1746] [Impact Index Per Article: 218.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PD-L1 and PD-1 (PD) pathway blockade is a highly promising therapy and has elicited durable antitumor responses and long-term remissions in a subset of patients with a broad spectrum of cancers. How to improve, widen, and predict the clinical response to anti-PD therapy is a central theme in the field of cancer immunology and immunotherapy. Oncologic, immunologic, genetic, and biological studies focused on the human cancer microenvironment have yielded substantial insight into this issue. Here, we focus on tumor microenvironment and evaluate several potential therapeutic response markers including the PD-L1 and PD-1 expression pattern, genetic mutations within cancer cells and neoantigens, cancer epigenetics and effector T cell landscape, and microbiota. We further clarify the mechanisms of action of these markers and their roles in shaping, being shaped, and/or predicting therapeutic responses. We also discuss a variety of combinations with PD pathway blockade and their scientific rationales for cancer treatment.
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Affiliation(s)
- Weiping Zou
- Department of Surgery, University of Michigan School of Medicine, Ann Arbor, MI 48109, USA.
| | - Jedd D Wolchok
- Department of Medicine and the Ludwig Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Lieping Chen
- Department of Immunobiology, Yale University School of Medicine, New Haven CT 06519, USA.
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2527
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Marabelle A, Routy B, Michels J, Kroemer G, Zitvogel L. Prime time for immune-checkpoint targeted therapy at ASCO 2015. Oncoimmunology 2016; 5:e1068494. [PMID: 27141332 PMCID: PMC4839368 DOI: 10.1080/2162402x.2015.1068494] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 06/27/2015] [Indexed: 10/23/2022] Open
Abstract
Cancer immunotherapy has been one of the dominant topics in oral presentations and abstracts during the 2015 annual meeting of the American Society of Clinical Oncology (ASCO). The renewed interest in immunotherapy is explained by the wide spectrum of activity, the durability of tumor responses and the rapid clinical development of immune-checkpoint targeted monoclonal antibodies. These new drugs are currently revolutionizing the field of oncology. Here we highlight what were to us the most important results announced during the annual meeting of ASCO held in Chicago, IL from May, 29th to June, 2nd 2015. In addition, we searched all the posters/published abstracts pertinent to the field of immunooncology from this year conference. Among more than 400 published abstracts on this topic, we have grouped and briefly summarized the most relevant ones.
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Affiliation(s)
- Aurélien Marabelle
- Gustave Roussy Cancer Campus, Villejuif, France
- INSERM, U1015, Villejuif, France
| | - Bertrand Routy
- Gustave Roussy Cancer Campus, Villejuif, France
- INSERM, U1015, Villejuif, France
| | - Judith Michels
- Gustave Roussy Cancer Campus, Villejuif, France
- INSERM, U1015, Villejuif, France
| | - Guido Kroemer
- INSERM U848, Villejuif, France
- Metabolomics Platform, Institut Gustave Roussy Villejuif, France
- Equipe 11 labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, INSERM U1138, Paris, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France
- INSERM, U1015, Villejuif, France
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2528
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Meniawy TM, Lake RA, McDonnell AM, Millward MJ, Nowak AK. PD-L1 on peripheral blood T lymphocytes is prognostic in patients with non-small cell lung cancer (NSCLC) treated with EGFR inhibitors. Lung Cancer 2016; 93:9-16. [DOI: 10.1016/j.lungcan.2015.12.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/20/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
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2529
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Abstract
The immune system is capable of recognizing tumors and eliminates many early malignant cells. However, tumors evolve to evade immune attack, and the tumor microenvironment is immunosuppressive. Immune responses are regulated by a number of immunological checkpoints that promote protective immunity and maintain tolerance. T cell coinhibitory pathways restrict the strength and duration of immune responses, thereby limiting immune-mediated tissue damage, controlling resolution of inflammation, and maintaining tolerance to prevent autoimmunity. Tumors exploit these coinhibitory pathways to evade immune eradication. Blockade of the PD-1 and CTLA-4 checkpoints is proving to be an effective and durable cancer immunotherapy in a subset of patients with a variety of tumor types, and additional combinations are further improving response rates. In this review we discuss the immunoregulatory functions of coinhibitory pathways and their translation to effective immunotherapies for cancer.
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Affiliation(s)
- Susanne H Baumeister
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Division of Pediatric Hematology-Oncology, Boston Children's Hospital, Boston, Massachusetts 02115.,Harvard Medical School, Boston, Massachusetts 02115
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Harvard Medical School, Boston, Massachusetts 02115
| | - Glenn Dranoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215.,Novartis Institutes for BioMedical Research, Exploratory Immuno-oncology, Cambridge, Massachusetts 02139
| | - Arlene H Sharpe
- Department of Microbiology and Immunobiology, and Evergrande Center for Immunologic Diseases, Harvard Medical School, Boston, Massachusetts 02115;
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2530
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Ali HR, Dariush A, Provenzano E, Bardwell H, Abraham JE, Iddawela M, Vallier AL, Hiller L, Dunn JA, Bowden SJ, Hickish T, McAdam K, Houston S, Irwin MJ, Pharoah PDP, Brenton JD, Walton NA, Earl HM, Caldas C. Computational pathology of pre-treatment biopsies identifies lymphocyte density as a predictor of response to neoadjuvant chemotherapy in breast cancer. Breast Cancer Res 2016; 18:21. [PMID: 26882907 PMCID: PMC4755003 DOI: 10.1186/s13058-016-0682-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/01/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There is a need to improve prediction of response to chemotherapy in breast cancer in order to improve clinical management and this may be achieved by harnessing computational metrics of tissue pathology. We investigated the association between quantitative image metrics derived from computational analysis of digital pathology slides and response to chemotherapy in women with breast cancer who received neoadjuvant chemotherapy. METHODS We digitised tissue sections of both diagnostic and surgical samples of breast tumours from 768 patients enrolled in the Neo-tAnGo randomized controlled trial. We subjected digital images to systematic analysis optimised for detection of single cells. Machine-learning methods were used to classify cells as cancer, stromal or lymphocyte and we computed estimates of absolute numbers, relative fractions and cell densities using these data. Pathological complete response (pCR), a histological indicator of chemotherapy response, was the primary endpoint. Fifteen image metrics were tested for their association with pCR using univariate and multivariate logistic regression. RESULTS Median lymphocyte density proved most strongly associated with pCR on univariate analysis (OR 4.46, 95 % CI 2.34-8.50, p < 0.0001; observations = 614) and on multivariate analysis (OR 2.42, 95 % CI 1.08-5.40, p = 0.03; observations = 406) after adjustment for clinical factors. Further exploratory analyses revealed that in approximately one quarter of cases there was an increase in lymphocyte density in the tumour removed at surgery compared to diagnostic biopsies. A reduction in lymphocyte density at surgery was strongly associated with pCR (OR 0.28, 95 % CI 0.17-0.47, p < 0.0001; observations = 553). CONCLUSIONS A data-driven analysis of computational pathology reveals lymphocyte density as an independent predictor of pCR. Paradoxically an increase in lymphocyte density, following exposure to chemotherapy, is associated with a lack of pCR. Computational pathology can provide objective, quantitative and reproducible tissue metrics and represents a viable means of outcome prediction in breast cancer. TRIAL REGISTRATION ClinicalTrials.gov NCT00070278 ; 03/10/2003.
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Affiliation(s)
- H Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
- Department of Pathology, University of Cambridge, Cambridge, UK.
| | | | - Elena Provenzano
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Department of Histopathology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Helen Bardwell
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
| | - Jean E Abraham
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Mahesh Iddawela
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Present address: Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
| | - Anne-Laure Vallier
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Louise Hiller
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK.
| | - Janet A Dunn
- Warwick Clinical Trials Unit, University of Warwick, Coventry, UK.
| | - Sarah J Bowden
- Cancer Research UK Clinical Trials Unit, Institute for Cancer Studies, The University of Birmingham, Edgbaston, Birmingham, UK.
| | - Tamas Hickish
- Royal Bournemouth Hospital and Bournemouth University, Castle Lane East, Bournemouth, UK.
| | - Karen McAdam
- Peterborough and Stamford Hospitals NHS Foundation Trust and Cambridge University Hospital NHS Foundation Trust, Peterborough, UK.
| | - Stephen Houston
- Royal Surrey County Hospital NHS Foundation Trust, Egerton Road, Guildford, UK.
| | - Mike J Irwin
- Institute of Astronomy, University of Cambridge, Cambridge, UK.
| | - Paul D P Pharoah
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | | | - Helena M Earl
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK.
- Department of Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
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2531
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Pfirschke C, Engblom C, Rickelt S, Cortez-Retamozo V, Garris C, Pucci F, Yamazaki T, Poirier-Colame V, Newton A, Redouane Y, Lin YJ, Wojtkiewicz G, Iwamoto Y, Mino-Kenudson M, Huynh TG, Hynes RO, Freeman GJ, Kroemer G, Zitvogel L, Weissleder R, Pittet MJ. Immunogenic Chemotherapy Sensitizes Tumors to Checkpoint Blockade Therapy. Immunity 2016; 44:343-54. [PMID: 26872698 PMCID: PMC4758865 DOI: 10.1016/j.immuni.2015.11.024] [Citation(s) in RCA: 703] [Impact Index Per Article: 87.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/11/2015] [Accepted: 11/11/2015] [Indexed: 11/17/2022]
Abstract
Checkpoint blockade immunotherapies can be extraordinarily effective, but might benefit only the minority of patients whose tumors are pre-infiltrated by T cells. Here, using lung adenocarcinoma mouse models, including genetic models, we show that autochthonous tumors that lacked T cell infiltration and resisted current treatment options could be successfully sensitized to host antitumor T cell immunity when appropriately selected immunogenic drugs (e.g., oxaliplatin combined with cyclophosphamide for treatment against tumors expressing oncogenic Kras and lacking Trp53) were used. The antitumor response was triggered by direct drug actions on tumor cells, relied on innate immune sensing through toll-like receptor 4 signaling, and ultimately depended on CD8(+) T cell antitumor immunity. Furthermore, instigating tumor infiltration by T cells sensitized tumors to checkpoint inhibition and controlled cancer durably. These findings indicate that the proportion of cancers responding to checkpoint therapy can be feasibly and substantially expanded by combining checkpoint blockade with immunogenic drugs.
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Affiliation(s)
- Christina Pfirschke
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Camilla Engblom
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Virna Cortez-Retamozo
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Christopher Garris
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA; Graduate Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Ferdinando Pucci
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | | | | | - Andita Newton
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Younes Redouane
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Yi-Jang Lin
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Gregory Wojtkiewicz
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Yoshiko Iwamoto
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tiffany G Huynh
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Guido Kroemer
- Gustave Roussy Cancer Campus, 94805 Villejuif, France
| | | | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA
| | - Mikael J Pittet
- Center for Systems Biology, Massachusetts General Hospital Research Institute and Harvard Medical School, Boston, MA 02114, USA.
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2532
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Ward JP, Gubin MM, Schreiber RD. The Role of Neoantigens in Naturally Occurring and Therapeutically Induced Immune Responses to Cancer. Adv Immunol 2016; 130:25-74. [PMID: 26922999 DOI: 10.1016/bs.ai.2016.01.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Definitive experimental evidence from mouse cancer models and strong correlative clinical data gave rise to the Cancer Immunoediting concept that explains the dual host-protective and tumor-promoting actions of immunity on developing cancers. Tumor-specific neoantigens can serve as targets of spontaneously arising adaptive immunity to cancer and thereby determine the ultimate fate of developing tumors. Tumor-specific neoantigens can also function as optimal targets of cancer immunotherapy against established tumors. These antigens are derived from nonsynonymous mutations that occur during cellular transformation and, because they are foreign to the host genome, are not subject to central tolerance. In this review, we summarize the experimental evidence indicating that cancer neoantigens are the source of both spontaneously occurring and therapeutically induced immune responses against cancer. We also review the advances in genomics, bioinformatics, and cancer immunotherapy that have facilitated identification of neoantigens and have moved personalized cancer immunotherapies into clinical trials, with the promise of providing more specific, safer, more effective, and perhaps even more generalizable treatments to cancer patients than current immunotherapies.
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Affiliation(s)
- Jeffrey P Ward
- Washington University School of Medicine, St. Louis, MO, United States
| | - Matthew M Gubin
- Washington University School of Medicine, St. Louis, MO, United States
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2533
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Cherkasova E, Scrivani C, Doh S, Weisman Q, Takahashi Y, Harashima N, Yokoyama H, Srinivasan R, Linehan WM, Lerman MI, Childs RW. Detection of an Immunogenic HERV-E Envelope with Selective Expression in Clear Cell Kidney Cancer. Cancer Res 2016; 76:2177-85. [PMID: 26862115 DOI: 10.1158/0008-5472.can-15-3139] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/26/2016] [Indexed: 01/06/2023]
Abstract
VHL-deficient clear cell renal cell carcinomas (ccRCC), the most common form of kidney cancer, express transcripts derived from the novel human endogenous retrovirus HERV-E (named CT-RCC HERV-E). In this study, we define a transcript encoding the entire envelope gene of HERV-E as expressed selectively in ccRCC tumors, as distinct from normal kidney tissues or other tumor types. Sequence analysis of this envelope transcript revealed long open reading frames encoding putative surface and transmembrane envelope proteins. Retroviral envelopes are known to be capable of eliciting immunity in humans. Accordingly, we found that HLA-A*0201-restricted peptides predicted to be products of the CT-RCC HERV-E envelope transcript-stimulated CD8(+) T cells, which could recognize HLA-A*0201-positive HERV-E-expressing kidney tumor cells. Overall, our results offer evidence of unique HERV-E envelope peptides presented on the surface of ccRCC cells, offering potentially useful tumor-restricted targets for T-cell-based immunotherapy of kidney cancer. Cancer Res; 76(8); 2177-85. ©2016 AACR.
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Affiliation(s)
- Elena Cherkasova
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Claire Scrivani
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Susan Doh
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Quinn Weisman
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Yoshiyuki Takahashi
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Nanae Harashima
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Hisayuki Yokoyama
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | | | | | - Michael I Lerman
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland
| | - Richard W Childs
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, Maryland.
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2534
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Abstract
In recent years, the introduction and Federal Drug Administration approval of immune checkpoint inhibitor antibodies has dramatically improved the clinical outcomes for patients with advanced melanoma. These antagonist monoclonal antibodies are capable of unleashing dormant or exhausted antitumor immunity, which has led to durable complete and partial responses in a large number of patients. Ipilimumab targets the cytotoxic T lymphocyte-associated protein 4 (CTLA-4) receptor. Nivolumab and pembrolizumab target programmed cell death protein 1 (PD-1) receptors and have proven to be superior to ipilimumab alone. The combination of ipilimumab and nivolumab has yielded higher response rates, greater tumor shrinkage, and longer progression-free survival than either monotherapy alone. As other promising immunotherapies for melanoma proceed through clinical trials, future goals include defining the role of immune checkpoint inhibitors as adjuvant therapy, identifying optimal combination strategies, and developing reliable predictive biomarkers to guide treatment selection for individual patients.
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Affiliation(s)
- Jason M Redman
- Georgetown Lombardi Comprehensive Cancer Center 3970 Reservoir Road, NW Research Building, Room E501, 20007, Washington DC, USA. .,Department of Medicine, Georgetown University Medical Center, Washington DC, USA.
| | - Geoffrey T Gibney
- Georgetown Lombardi Comprehensive Cancer Center 3970 Reservoir Road, NW Research Building, Room E501, 20007, Washington DC, USA. .,Department of Medicine, Georgetown University Medical Center, Washington DC, USA.
| | - Michael B Atkins
- Georgetown Lombardi Comprehensive Cancer Center 3970 Reservoir Road, NW Research Building, Room E501, 20007, Washington DC, USA. .,Department of Medicine, Georgetown University Medical Center, Washington DC, USA.
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2535
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Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution. PLoS Comput Biol 2016; 12:e1004731. [PMID: 26828429 PMCID: PMC4734774 DOI: 10.1371/journal.pcbi.1004731] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 01/04/2016] [Indexed: 01/06/2023] Open
Abstract
The vast majority of mutations in the exome of cancer cells are passengers, which do not affect the reproductive rate of the cell. Passengers can provide important information about the evolutionary history of an individual cancer, and serve as a molecular clock. Passengers can also become targets for immunotherapy or confer resistance to treatment. We study the stochastic expansion of a population of cancer cells describing the growth of primary tumors or metastatic lesions. We first analyze the process by looking forward in time and calculate the fixation probabilities and frequencies of successive passenger mutations ordered by their time of appearance. We compute the likelihood of specific evolutionary trees, thereby informing the phylogenetic reconstruction of cancer evolution in individual patients. Next, we derive results looking backward in time: for a given subclonal mutation we estimate the number of cancer cells that were present at the time when that mutation arose. We derive exact formulas for the expected numbers of subclonal mutations of any frequency. Fitting this formula to cancer sequencing data leads to an estimate for the ratio of birth and death rates of cancer cells during the early stages of clonal expansion. Cancer is the consequence of an evolutionary process, which lasts several decades, is impossible to observe during most of its time, and only becomes apparent in late stages. We use mathematical modeling to shed light on the evolutionary dynamics of cancer by studying the accumulation of passenger mutations. We show that the frequencies obtained by passenger mutations depend strongly on the ratio of death and birth rates of cancer cells. We use genetic data of colorectal cancer to estimate this important quantity in vivo. We estimate the size of the cancer cell population that was present when a specific mutation first emerged. Our theory informs the analysis of cancer sequencing data and the phylogenetic reconstruction of cancer evolution.
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2536
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Abstract
Advances in immunotherapy have resulted in remarkable clinical responses in some patients. However, one of the biggest challenges in cancer therapeutics is the development of resistant disease and disease progression on or after therapy. Given that many patients have now received various types of immunotherapy, we asked three scientists to give their views on the current evidence for whether acquired resistance to immunotherapy exists in patients and the future challenges posed by immunotherapy.
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Affiliation(s)
- Nicholas P. Restifo
- Center for Cancer Research, National Cancer Institute and Center for Regenerative Medicine, National Institutes of Health, Bldg 10/CRC, Room 3-5762, 9000 Rockville Pike, Bethesda, Maryland 20892, USA.
| | - Mark J. Smyth
- Immunology in Cancer and Infection Laboratory, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4006, Australia; and the School of Medicine, University of Queensland, Herston, Brisbane, Queensland 4006, Australia.
| | - Alexander Snyder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 300 East 66th Street, New York, New York 10065, USA.
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2537
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Ock CY, Keam B, Kim S, Lee JS, Kim M, Kim TM, Jeon YK, Kim DW, Chung DH, Heo DS. Pan-Cancer Immunogenomic Perspective on the Tumor Microenvironment Based on PD-L1 and CD8 T-Cell Infiltration. Clin Cancer Res 2016; 22:2261-70. [PMID: 26819449 DOI: 10.1158/1078-0432.ccr-15-2834] [Citation(s) in RCA: 189] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 01/11/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE There is currently no reliable biomarker to predict who would benefit from anti-PD-1/PD-L1 inhibitors. We comprehensively analyzed the immunogenomic properties in The Cancer Genome Atlas (TCGA) according to the classification of tumor into four groups based on PD-L1 status and tumor-infiltrating lymphocyte recruitment (TIL), a combination that has been suggested to be a theoretically reliable biomarker of anti-PD-1/PD-L1 inhibitors. EXPERIMENTAL DESIGN The RNA expression levels of PD-L1 and CD8A in the samples in the pan-cancer database of TCGA (N = 9,677) were analyzed. Based on their median values, the samples were classified into four tumor microenvironment immune types (TMIT). The mutational profiles, PD-L1 amplification, and viral association of the samples were compared according to the four TMITs. RESULTS The proportions of TMIT I, defined by high PD-L1 and CD8A expression, were high in lung adenocarcinoma (67.1%) and kidney clear cell carcinoma (64.8%) among solid cancers. The number of somatic mutations and the proportion of microsatellite instable-high tumor in TMIT I were significantly higher than those in other TMITs, respectively (P < 0.001). PD-L1 amplification and oncogenic virus infection were significantly associated with TMIT I, respectively (P < 0.001). A multivariate analysis confirmed that the number of somatic mutations, PD-L1 amplification, and Epstein-Barr virus/human papillomavirus infection were independently associated with TMIT I. CONCLUSIONS TMIT I is associated with a high mutational burden, PD-L1 amplification, and oncogenic viral infection. This integrative analysis highlights the importance of the assessment of both PD-L1 expression and TIL recruitment to predict responders to immune checkpoint inhibitors. Clin Cancer Res; 22(9); 2261-70. ©2016 AACRSee related commentary by Schalper et al., p. 2102.
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Affiliation(s)
- Chan-Young Ock
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Bhumsuk Keam
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.
| | - Sehui Kim
- Department of Pathology, Seoul National University Hospital Seoul, Korea
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea
| | - Tae Min Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Yoon Kyung Jeon
- Department of Pathology, Seoul National University Hospital Seoul, Korea
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Doo Hyun Chung
- Department of Pathology, Seoul National University Hospital Seoul, Korea
| | - Dae Seog Heo
- Department of Internal Medicine, Seoul National University Hospital, Seoul, Korea. Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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2538
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Nosho K, Sukawa Y, Adachi Y, Ito M, Mitsuhashi K, Kurihara H, Kanno S, Yamamoto I, Ishigami K, Igarashi H, Maruyama R, Imai K, Yamamoto H, Shinomura Y. Association of Fusobacterium nucleatum with immunity and molecular alterations in colorectal cancer. World J Gastroenterol 2016; 22:557-566. [PMID: 26811607 PMCID: PMC4716059 DOI: 10.3748/wjg.v22.i2.557] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/25/2015] [Accepted: 11/13/2015] [Indexed: 02/06/2023] Open
Abstract
The human intestinal microbiome plays a major role in human health and diseases, including colorectal cancer. Colorectal carcinogenesis represents a heterogeneous process with a differing set of somatic molecular alterations, influenced by diet, environmental and microbial exposures, and host immunity. Fusobacterium species are part of the human oral and intestinal microbiota. Metagenomic analyses have shown an enrichment of Fusobacterium nucleatum (F. nucleatum) in colorectal carcinoma tissue. Using 511 colorectal carcinomas from Japanese patients, we assessed the presence of F. nucleatum. Our results showed that the frequency of F. nucleatum positivity in the Japanese colorectal cancer was 8.6% (44/511), which was lower than that in United States cohort studies (13%). Similar to the United States studies, F. nucleatum positivity in Japanese colorectal cancers was significantly associated with microsatellite instability (MSI)-high status. Regarding the immune response in colorectal cancer, high levels of infiltrating T-cell subsets (i.e., CD3+, CD8+, CD45RO+, and FOXP3+ cells) have been associated with better patient prognosis. There is also evidence to indicate that molecular features of colorectal cancer, especially MSI, influence T-cell-mediated adaptive immunity. Concerning the association between the gut microbiome and immunity, F. nucleatum has been shown to expand myeloid-derived immune cells, which inhibit T-cell proliferation and induce T-cell apoptosis in colorectal cancer. This finding indicates that F. nucleatum possesses immunosuppressive activities by inhibiting human T-cell responses. Certain microRNAs are induced during the macrophage inflammatory response and have the ability to regulate host-cell responses to pathogens. MicroRNA-21 increases the levels of IL-10 and prostaglandin E2, which suppress antitumor T-cell-mediated adaptive immunity through the inhibition of the antigen-presenting capacities of dendritic cells and T-cell proliferation in colorectal cancer cells. Thus, emerging evidence may provide insights for strategies to target microbiota, immune cells and tumor molecular alterations for colorectal cancer prevention and treatment. Further investigation is needed to clarify the association of Fusobacterium with T-cells and microRNA expressions in colorectal cancer.
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2539
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Abstract
Background: Increasing evidence supporting the role of immune checkpoint blockade in cancer management has been bolstered by recent reports demonstrating significant and durable clinical responses across multiple tumour types, including metastatic urothelial carcinoma (mUC). The majority of these results are achieved via blockade of the programmed death (PD) axis, which like CTLA-4 blockade permits T-cell activation and immune-mediated anti-tumour activity- essentially harnessing the patient’s own immune system to mount an anti-neoplastic response. However, while clinical responses can be striking, our understanding of the biology of immune checkpoint blockade is only beginning to shed light on how to maximize and even improve patient outcomes with immune checkpoint blockade, especially in UC. Methods: We performed a literature review for immune checkpoint blockade with a focus on rationale for checkpoint therapy and outcomes in UC. We also highlight the advances made in other tumour types, with a focus on the recent 2015 meeting of the American Society for Clinical Oncology. Results: In heavily pre-treated UC, trials are suggesting objective response rates above 30% . These impressive results are seen across multiple different tumour types, especially those with high burden of DNA level mutations. Identification of prognostic biomarkers is currently under investigation, in order to improve patient selection. Interestingly, response to PD-1 directed therapy is seen even in patients with no evidence of PD-1 positivity on immunohistochemistry. This has led to the development of enhanced biomarkers including assessing DNA mutation rates and immune gene signatures, to improve patient selection. Conclusions: Immune checkpoint blockade is an exciting cancer treatment modality which is demonstrating impressive clinical results across multiple tumour types. For UC, anti-PD directed therapy represents a much needed treatment in the metastatic, post chemotherapy context. Potential for these agents to have clinical utility in non-metastatic UC is still to be assessed.
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Affiliation(s)
- S Bidnur
- Vancouver Prostate Centre, University of British Columbia , Vancouver, B.C, Canada
| | - R Savdie
- Vancouver Prostate Centre, University of British Columbia , Vancouver, B.C, Canada
| | - P C Black
- Vancouver Prostate Centre, University of British Columbia , Vancouver, B.C, Canada
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2540
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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2541
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Varn FS, Andrews EH, Mullins DW, Cheng C. Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles. Nat Commun 2016; 7:10248. [PMID: 26725977 PMCID: PMC4725766 DOI: 10.1038/ncomms10248] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 11/17/2015] [Indexed: 12/17/2022] Open
Abstract
Transcriptional programmes active in haematopoietic cells enable a variety of functions including dedifferentiation, innate immunity and adaptive immunity. Understanding how these programmes function in the context of cancer can provide valuable insights into host immune response, cancer severity and potential therapy response. Here we present a method that uses the transcriptomes of over 200 murine haematopoietic cells, to infer the lineage-specific haematopoietic activity present in human breast tumours. Correlating this activity with patient survival and tumour purity reveals that the transcriptional programmes of many cell types influence patient prognosis and are found in environments of high lymphocytic infiltration. Collectively, these results allow for a detailed and personalized assessment of the patient immune response to a tumour. When combined with routinely collected patient biopsy genomic data, this method can enable a richer understanding of the complex interplay between the host immune system and cancer.
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Affiliation(s)
- Frederick S Varn
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Erik H Andrews
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - David W Mullins
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA
| | - Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA.,Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA.,Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire 03766, USA
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2542
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Lipinski KA, Barber LJ, Davies MN, Ashenden M, Sottoriva A, Gerlinger M. Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine. Trends Cancer 2016; 2:49-63. [PMID: 26949746 PMCID: PMC4756277 DOI: 10.1016/j.trecan.2015.11.003] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/01/2023]
Abstract
The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.
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Affiliation(s)
- Kamil A Lipinski
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Louise J Barber
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Matthew N Davies
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Matthew Ashenden
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Marco Gerlinger
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Gastrointestinal Cancer Unit, The Royal Marsden Hospital, London, UK.
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2543
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Kelderman S, Kvistborg P. Tumor antigens in human cancer control. Biochim Biophys Acta Rev Cancer 2016; 1865:83-89. [DOI: 10.1016/j.bbcan.2015.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/27/2015] [Accepted: 10/30/2015] [Indexed: 01/10/2023]
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2544
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2545
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Meng C, Helm D, Frejno M, Kuster B. moCluster: Identifying Joint Patterns Across Multiple Omics Data Sets. J Proteome Res 2015; 15:755-65. [PMID: 26653205 DOI: 10.1021/acs.jproteome.5b00824] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Increasingly, multiple omics approaches are being applied to understand the complexity of biological systems. Yet, computational approaches that enable the efficient integration of such data are not well developed. Here, we describe a novel algorithm, termed moCluster, which discovers joint patterns among multiple omics data. The method first employs a multiblock multivariate analysis to define a set of latent variables representing joint patterns across input data sets, which is further passed to an ordinary clustering algorithm in order to discover joint clusters. Using simulated data, we show that moCluster's performance is not compromised by issues present in iCluster/iCluster+ (notably, the nondeterministic solution) and that it operates 100× to 1000× faster than iCluster/iCluster+. We used moCluster to cluster proteomic and transcriptomic data from the NCI-60 cell line panel. The resulting cluster model revealed different phenotypes across cellular subtypes, such as doubling time and drug response. Applying moCluster to methylation, mRNA, and protein data from a large study on colorectal cancer patients identified four molecular subtypes, including one characterized by microsatellite instability and high expression of genes/proteins involved in immunity, such as PDL1, a target of multiple drugs currently in development. The other three subtypes have not been discovered before using single data sets, which clearly illustrates the molecular complexity of oncogenesis and the need for holistic, multidata analysis strategies.
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Affiliation(s)
| | | | - Martin Frejno
- Department of Oncology, University of Oxford , Oxford OX3 7DQ, United Kingdom
| | - Bernhard Kuster
- Center for Integrated Protein Science Munich (CIPSM) , Emil-Erlenmeyer-Forum 5, Freising 85354, Germany
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2546
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Mouw KW, D'Andrea AD, Konstantinopoulos PA. Nucleotide excision repair (NER) alterations as evolving biomarkers and therapeutic targets in epithelial cancers. Oncoscience 2015; 2:942-3. [PMID: 26909362 PMCID: PMC4741401 DOI: 10.18632/oncoscience.283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 12/28/2015] [Indexed: 12/30/2022] Open
Affiliation(s)
- Kent W Mouw
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
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2547
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Hugo W, Shi H, Sun L, Piva M, Song C, Kong X, Moriceau G, Hong A, Dahlman KB, Johnson DB, Sosman JA, Ribas A, Lo RS. Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance. Cell 2015; 162:1271-85. [PMID: 26359985 DOI: 10.1016/j.cell.2015.07.061] [Citation(s) in RCA: 457] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 06/20/2015] [Accepted: 07/31/2015] [Indexed: 12/15/2022]
Abstract
Clinically acquired resistance to MAPK inhibitor (MAPKi) therapies for melanoma cannot be fully explained by genomic mechanisms and may be accompanied by co-evolution of intra-tumoral immunity. We sought to discover non-genomic mechanisms of acquired resistance and dynamic immune compositions by a comparative, transcriptomic-methylomic analysis of patient-matched melanoma tumors biopsied before therapy and during disease progression. Transcriptomic alterations across resistant tumors were highly recurrent, in contrast to mutations, and were frequently correlated with differential methylation of tumor cell-intrinsic CpG sites. We identified in the tumor cell compartment supra-physiologic c-MET up-expression, infra-physiologic LEF1 down-expression and YAP1 signature enrichment as drivers of acquired resistance. Importantly, high intra-tumoral cytolytic T cell inflammation prior to MAPKi therapy preceded CD8 T cell deficiency/exhaustion and loss of antigen presentation in half of disease-progressive melanomas, suggesting cross-resistance to salvage anti-PD-1/PD-L1 immunotherapy. Thus, melanoma acquires MAPKi resistance with highly dynamic and recurrent non-genomic alterations and co-evolving intra-tumoral immunity.
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Affiliation(s)
- Willy Hugo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Hubing Shi
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Lu Sun
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Marco Piva
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Chunying Song
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Xiangju Kong
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Aayoung Hong
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Kimberly B Dahlman
- Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Douglas B Johnson
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Jeffrey A Sosman
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA; Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Antoni Ribas
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; Division of Hematology and Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; Division of Surgical Oncology, Department of Surgery, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA; David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095-1662, USA.
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2548
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Abstract
The clinical relevance of the host immune system in breast cancer has long been unexplored. Studies developed over the past decade have highlighted the biological heterogeneity of breast cancer, prompting researchers to investigate whether the role of the immune system in this malignancy is similar across different molecular subtypes of the disease. The presence of high levels of lymphocytic infiltration has been consistently associated with a more-favourable prognosis in patients with early stage triple-negative and HER2-positive breast cancer. These infiltrates seem to reflect favourable host antitumour immune responses, suggesting that immune activation is important for improving survival outcomes. In this Review, we discuss the composition of the immune infiltrates observed in breast cancers, as well as data supporting the clinical relevance of host antitumour immunity, as represented by lymphocytic infiltration, and how this biomarker could be used in the clinical setting. We also discuss the rationale for enhancing immunity in breast cancer, including early data on the efficacy of T-cell checkpoint inhibition in this setting.
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2549
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Galluzzi L, Buqué A, Kepp O, Zitvogel L, Kroemer G. Immunological Effects of Conventional Chemotherapy and Targeted Anticancer Agents. Cancer Cell 2015; 28:690-714. [PMID: 26678337 DOI: 10.1016/j.ccell.2015.10.012] [Citation(s) in RCA: 1112] [Impact Index Per Article: 123.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 10/05/2015] [Accepted: 10/23/2015] [Indexed: 11/23/2022]
Abstract
The tremendous clinical success of checkpoint blockers illustrates the potential of reestablishing latent immunosurveillance for cancer therapy. Although largely neglected in the clinical practice, accumulating evidence indicates that the efficacy of conventional and targeted anticancer agents does not only involve direct cytostatic/cytotoxic effects, but also relies on the (re)activation of tumor-targeting immune responses. Chemotherapy can promote such responses by increasing the immunogenicity of malignant cells, or by inhibiting immunosuppressive circuitries that are established by developing neoplasms. These immunological "side" effects of chemotherapy are desirable, and their in-depth comprehension will facilitate the design of novel combinatorial regimens with improved clinical efficacy.
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Affiliation(s)
- Lorenzo Galluzzi
- Equipe 11 Labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - Aitziber Buqué
- Equipe 11 Labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - Oliver Kepp
- Equipe 11 Labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France
| | - Laurence Zitvogel
- Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France; INSERM, U1015, 94805 Villejuif, France; Center of Clinical Investigations in Biotherapies of Cancer (CICBT) 507, 94805 Villejuif, France; Université Paris Sud/Paris XI, 94270 Le Kremlin-Bicêtre, France.
| | - Guido Kroemer
- Equipe 11 Labellisée Ligue contre le Cancer, Centre de Recherche des Cordeliers, 75006 Paris, France; INSERM, U1138, 75006 Paris, France; Université Paris Descartes/Paris V, Sorbonne Paris Cité, 75006 Paris, France; Université Pierre et Marie Curie/Paris VI, 75006 Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Comprehensive Cancer Institute, 94805 Villejuif, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France; Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, 17176 Stockholm, Sweden.
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2550
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Peng W, Chen JQ, Liu C, Malu S, Creasy C, Tetzlaff MT, Xu C, McKenzie JA, Zhang C, Liang X, Williams LJ, Deng W, Chen G, Mbofung R, Lazar AJ, Torres-Cabala CA, Cooper ZA, Chen PL, Tieu TN, Spranger S, Yu X, Bernatchez C, Forget MA, Haymaker C, Amaria R, McQuade JL, Glitza IC, Cascone T, Li HS, Kwong LN, Heffernan TP, Hu J, Bassett RL, Bosenberg MW, Woodman SE, Overwijk WW, Lizée G, Roszik J, Gajewski TF, Wargo JA, Gershenwald JE, Radvanyi L, Davies MA, Hwu P. Loss of PTEN Promotes Resistance to T Cell-Mediated Immunotherapy. Cancer Discov 2015. [PMID: 26645196 DOI: 10.1158/2159-8290.cd-15-0283.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED T cell-mediated immunotherapies are promising cancer treatments. However, most patients still fail to respond to these therapies. The molecular determinants of immune resistance are poorly understood. We show that loss of PTEN in tumor cells in preclinical models of melanoma inhibits T cell-mediated tumor killing and decreases T-cell trafficking into tumors. In patients, PTEN loss correlates with decreased T-cell infiltration at tumor sites, reduced likelihood of successful T-cell expansion from resected tumors, and inferior outcomes with PD-1 inhibitor therapy. PTEN loss in tumor cells increased the expression of immunosuppressive cytokines, resulting in decreased T-cell infiltration in tumors, and inhibited autophagy, which decreased T cell-mediated cell death. Treatment with a selective PI3Kβ inhibitor improved the efficacy of both anti-PD-1 and anti-CTLA-4 antibodies in murine models. Together, these findings demonstrate that PTEN loss promotes immune resistance and support the rationale to explore combinations of immunotherapies and PI3K-AKT pathway inhibitors. SIGNIFICANCE This study adds to the growing evidence that oncogenic pathways in tumors can promote resistance to the antitumor immune response. As PTEN loss and PI3K-AKT pathway activation occur in multiple tumor types, the results support the rationale to further evaluate combinatorial strategies targeting the PI3K-AKT pathway to increase the efficacy of immunotherapy.
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Affiliation(s)
- Weiyi Peng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jie Qing Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chengwen Liu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shruti Malu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caitlin Creasy
- Department of Melanoma Medical Oncology, 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. Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunyu Xu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jodi A McKenzie
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chunlei Zhang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiaoxuan Liang
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leila J Williams
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wanleng Deng
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guo Chen
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rina Mbofung
- Department of Melanoma Medical 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
| | - Carlos A Torres-Cabala
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zachary A Cooper
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Pei-Ling Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trang N Tieu
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stefani Spranger
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Xiaoxing Yu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Marie-Andree Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rodabe Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L McQuade
- Division of Cancer Medicine, 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
| | - Tina Cascone
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Haiyan S Li
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lawrence N Kwong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Timothy P Heffernan
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Hu
- Department of Biostatistics, 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
| | - Marcus W Bosenberg
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, 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
| | - Gregory Lizée
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Genomic Medicine, 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
| | - Laszlo Radvanyi
- Department of Melanoma Medical Oncology, 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.
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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