151
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152
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Ivanova M, Tsvetkova G, Lukanov T, Stoimenov A, Hadjiev E, Shivarov V. Probable HLA-mediated immunoediting of JAK2 V617F-driven oncogenesis. Exp Hematol 2020; 92:75-88.e10. [DOI: 10.1016/j.exphem.2020.09.200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 09/27/2020] [Indexed: 12/13/2022]
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153
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Anagnostou V, Bruhm DC, Niknafs N, White JR, Shao XM, Sidhom JW, Stein J, Tsai HL, Wang H, Belcaid Z, Murray J, Balan A, Ferreira L, Ross-Macdonald P, Wind-Rotolo M, Baras AS, Taube J, Karchin R, Scharpf RB, Grasso C, Ribas A, Pardoll DM, Topalian SL, Velculescu VE. Integrative Tumor and Immune Cell Multi-omic Analyses Predict Response to Immune Checkpoint Blockade in Melanoma. CELL REPORTS MEDICINE 2020; 1:100139. [PMID: 33294860 PMCID: PMC7691441 DOI: 10.1016/j.xcrm.2020.100139] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/10/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
In this study, we incorporate analyses of genome-wide sequence and structural alterations with pre- and on-therapy transcriptomic and T cell repertoire features in immunotherapy-naive melanoma patients treated with immune checkpoint blockade. Although tumor mutation burden is associated with improved treatment response, the mutation frequency in expressed genes is superior in predicting outcome. Increased T cell density in baseline tumors and dynamic changes in regression or expansion of the T cell repertoire during therapy distinguish responders from non-responders. Transcriptome analyses reveal an increased abundance of B cell subsets in tumors from responders and patterns of molecular response related to expressed mutation elimination or retention that reflect clinical outcome. High-dimensional genomic, transcriptomic, and immune repertoire data were integrated into a multi-modal predictor of response. These findings identify genomic and transcriptomic characteristics of tumors and immune cells that predict response to immune checkpoint blockade and highlight the importance of pre-existing T and B cell immunity in therapeutic outcomes. Unmet need for integrated molecular models that interpret immunotherapy response Genomic, transcriptomic, and T and B cell sequence data integration by machine learning T cell dynamism is a hallmark of response to immune checkpoint blockade The combined contributions of B, T, and tumor cell features predict clinical outcome
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Affiliation(s)
- Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xiaoshan M Shao
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - John William Sidhom
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Julie Stein
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hua-Ling Tsai
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hao Wang
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Zineb Belcaid
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Joseph Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Leonardo Ferreira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | | | - Alexander S Baras
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Janis Taube
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Rachel Karchin
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Catherine Grasso
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Drew M Pardoll
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Suzanne L Topalian
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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154
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Cummings AL, Gukasyan J, Lu HY, Grogan T, Sunga G, Fares CM, Hornstein N, Zaretsky J, Carroll J, Bachrach B, Akingbemi WO, Li D, Noor Z, Lisberg A, Goldman JW, Elashoff D, Bui AAT, Ribas A, Dubinett SM, Rossetti M, Garon EB. Mutational landscape influences immunotherapy outcomes among patients with non-small-cell lung cancer with human leukocyte antigen supertype B44. ACTA ACUST UNITED AC 2020; 1:1167-1175. [DOI: 10.1038/s43018-020-00140-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/06/2020] [Indexed: 12/30/2022]
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155
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Ivanova M, Shivarov V. HLA genotyping meets response to immune checkpoint inhibitors prediction: A story just started. Int J Immunogenet 2020; 48:193-200. [PMID: 33112034 DOI: 10.1111/iji.12517] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/06/2020] [Accepted: 10/13/2020] [Indexed: 12/27/2022]
Abstract
The implementation of the immune checkpoint blockade as a therapeutic option in contemporary oncology is one of the significant immunological achievements in the last century. Constantly accumulating evidence suggests that the response to immune checkpoint inhibitors (ICIs) is not universal. Therefore, it is critical to identify determinants for response, resistance and adverse effects of immune checkpoint therapy that could be developed as prognostic and predictive markers. Recent large scale analyses of cancer genome data revealed the key role of HLA class I and class II molecules in cancer immunoediting, and it appears that HLA diversity can predict response to ICIs. In the present review, we summarize the emerging data on the role of HLA germline variations as a marker for response to ICIs.
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Affiliation(s)
- Milena Ivanova
- Department of Clinical Immunology, University Hospital Alexandrovska, Medical University Sofia, Sofia, Bulgaria
| | - Velizar Shivarov
- Department of Genetics, St. Kliment Ohridski University, Sofia, Bulgaria
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156
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Hallqvist A, Rohlin A, Raghavan S. Immune checkpoint blockade and biomarkers of clinical response in non-small cell lung cancer. Scand J Immunol 2020; 92:e12980. [PMID: 33015859 PMCID: PMC7757202 DOI: 10.1111/sji.12980] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/21/2020] [Accepted: 09/25/2020] [Indexed: 12/26/2022]
Abstract
Immunotherapy with PD‐1 and PD‐L1 inhibitors has revolutionized the treatment for patients with NSCLC the last years with increased overall survival and in particular increased number of long‐time survivors in patients with metastatic disease. It is now a treatment of choice for patients with distant metastases (stage IV) and in conjunction with chemoradiotherapy for patients with limited spread confined to the chest (stage III). PD‐1 inhibition has been proven to be superior to standard chemotherapy, both as a single treatment and when combined with either chemotherapy or CTLA‐4 inhibition. Despite the success of immunotherapy, the majority of patients do not respond or relapse within a short time frame. Biomarkers that would help to properly select patients with a high likelihood of clinical response to PD‐1 and PD‐L1 inhibitors are scarce and far from optimal, and only one (PD‐L1 expression) has reached clinical practice. Thus for immunotherapy to be effective, the discovery and validation of additional biomarkers is critical for patient selection and prediction of clinical response. In this mini‐review, we give an overview of current clinical management of NSCLC including treatment landscape with regard to immunotherapy, as well as discuss the current genetic and immune cell biomarker studies and their potential for introduction into clinical practice.
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Affiliation(s)
- Andreas Hallqvist
- Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Department of Oncology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Anna Rohlin
- Laboratory Medicine, Institute of Biomedicine at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Unit of Genetic Analysis and Bioinformatics, Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sukanya Raghavan
- Department of Microbiology and Immunology, Institute of Biomedicine at the Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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157
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Castrillon JA, Eng C, Cheng F. Pharmacogenomics for immunotherapy and immune-related cardiotoxicity. Hum Mol Genet 2020; 29:R186-R196. [PMID: 32620943 PMCID: PMC7574958 DOI: 10.1093/hmg/ddaa137] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 12/20/2022] Open
Abstract
Immune checkpoint blockade (ICB) has become a standard of care in a subset of solid tumors. Although cancer survivorship has extended, rates of durable response of ICB remain poor; furthermore, cardiac adverse effects are emerging, which impact several mechanical aspects of the heart. Cardio-oncology programs implement a clinical assessment to curtail cardiovascular disease progression but are limited to the current clinical parameters used in cardiology. Pharmacogenomics provides the potential to unveil heritable and somatic genetic variations for guiding precision immunotherapy treatment to reduce the risk of immune-related cardiotoxicity. A better understanding of pharmacogenomics will optimize the current treatment selection and dosing of immunotherapy. Here, we summarize the recent pharmacogenomics studies in immunotherapy responsiveness and its related cardiotoxicity and highlight how patient genetics and epigenetics can facilitate researchers and clinicians in designing new approaches for precision immunotherapy. We highlight and discuss how single-cell technologies, human-induced pluripotent stem cells and systems pharmacogenomics accelerate future studies of precision cardio-oncology.
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Affiliation(s)
- Jessica A Castrillon
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Feixiong Cheng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
- Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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158
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DiNatale RG, Hakimi AA, Chan TA. Genomics-based immuno-oncology: bridging the gap between immunology and tumor biology. Hum Mol Genet 2020; 29:R214-R225. [PMID: 33029628 PMCID: PMC7574960 DOI: 10.1093/hmg/ddaa203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 09/05/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022] Open
Abstract
The first hypotheses about how the immune system affects cancers were proposed in the early 20th century. These early concepts about cancer immunosurveillance were further developed in the decades that followed, but a detailed understanding of cancer immunity remained elusive. It was only recently, through the advent of high-throughput technologies, that scientists gained the ability to profile tumors with a resolution that allowed for granular assessment of both tumor cells and the tumor microenvironment. The advent of immune checkpoint inhibitors (ICIs), which have proven to be effective cancer therapies in many malignancies, has spawned great interest in developing biomarkers for efficacy, an endeavor that highlighted the value of dissecting tumor immunity using large-scale methods. Response to ICI therapy has been shown to be a highly complex process, where the dynamics of tumor and immune cells is key to success. The need to understand the biologic mechanisms at the tumor-immune interface has given rise to the field of cancer immunogenomics, a discipline that aims to bridge the gap between cancer genomics and classical immunology. We provide a broad overview of this emerging branch of translational science, summarizing common platforms used and recent discoveries in the field, which are having direct clinical implications. Our discussion will be centered around the genetic foundations governing tumor immunity and molecular determinants associated with clinical benefit from ICI therapy. We emphasize the importance of molecular diversity as a driver of anti-tumor immunity and discuss how these factors can be probed using genomic approaches.
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Affiliation(s)
- Renzo G DiNatale
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - A Ari Hakimi
- Urology Department, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195, USA
- Lerner Research Institute and Taussig Cancer Center, Cleveland Clinic, Cleveland, OH 44195, USA
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159
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Krishna C, Chowell D, Gönen M, Elhanati Y, Chan TA. Genetic and environmental determinants of human TCR repertoire diversity. Immun Ageing 2020; 17:26. [PMID: 32944053 PMCID: PMC7487954 DOI: 10.1186/s12979-020-00195-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/06/2020] [Indexed: 12/22/2022]
Abstract
T cell discrimination of self and non-self is the foundation of the adaptive immune response, and is orchestrated by the interaction between T cell receptors (TCRs) and their cognate ligands presented by major histocompatibility (MHC) molecules. However, the impact of host immunogenetic variation on the diversity of the TCR repertoire remains unclear. Here, we analyzed a cohort of 666 individuals with TCR repertoire sequencing. We show that TCR repertoire diversity is positively associated with polymorphism at the human leukocyte antigen class I (HLA-I) loci, and diminishes with age and cytomegalovirus (CMV) infection. Moreover, our analysis revealed that HLA-I polymorphism and age independently shape the repertoire in healthy individuals. Our data elucidate key determinants of human TCR repertoire diversity, and suggest a mechanism underlying the evolutionary fitness advantage of HLA-I heterozygosity.
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Affiliation(s)
- Chirag Krishna
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Sloan Kettering Institute for Cancer Research, New York, NY 10065 USA
| | - Yuval Elhanati
- Department of Epidemiology and Biostatistics, Sloan Kettering Institute for Cancer Research, New York, NY 10065 USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
| | - Timothy A. Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065 USA
- Weill Cornell School of Medicine, New York, NY 10065 USA
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH 44195 USA
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160
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Genome-wide identification of differentially methylated promoters and enhancers associated with response to anti-PD-1 therapy in non-small cell lung cancer. Exp Mol Med 2020; 52:1550-1563. [PMID: 32879421 PMCID: PMC8080767 DOI: 10.1038/s12276-020-00493-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/22/2020] [Accepted: 07/14/2020] [Indexed: 12/22/2022] Open
Abstract
Although approved programmed cell death protein (PD)-1 inhibitors show durable responses, clinical benefits to these agents are only seen in one-third of patients in most cancer types. Therefore, strategies for improving the response to PD-1 inhibitor for treating various cancers including non-small cell lung cancer (NSCLC) are urgently needed. Compared with genome and transcriptome, tumor DNA methylome in anti-PD-1 response was relatively unexplored. We compared the pre-treatment methylation status of cis-regulatory elements between responders and non-responders to treatment with nivolumab or pembrolizumab using the Infinium Methylation EPIC Array, which can profile ~850,000 CpG sites, including ~350,000 CpG sites located in enhancer regions. Then, we analyzed differentially methylated regions overlapping promoters (pDMRs) or enhancers (eDMRs) between responders and non-responders to PD-1 inhibitors. We identified 1007 pDMRs and 607 eDMRs associated with the anti-PD-1 response. We also identified 1109 and 1173 target genes putatively regulated by these pDMRs and eDMRs, respectively. We found that eDMRs contribute to the epigenetic regulation of the anti-PD-1 response more than pDMRs. Hypomethylated pDMRs of Cytohesin 1 Interacting Protein (CYTIP) and TNF superfamily member 8 (TNFSF8) were more predictive than programmed cell death protein ligand 1 (PD-L1) expression for anti-PD-1 response and progression-free survival (PFS) and overall survival (OS) in a validation cohort, suggesting their potential as predictive biomarkers for anti-PD-1 immunotherapy. The catalog of promoters and enhancers differentially methylated between responders and non-responders to PD-1 inhibitors presented herein will guide the development of biomarkers and therapeutic strategies for improving anti-PD-1 immunotherapy in NSCLC.
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161
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Subbiah V, Solit D, Chan T, Kurzrock R. The FDA approval of pembrolizumab for adult and pediatric patients with tumor mutational burden (TMB) ≥10: a decision centered on empowering patients and their physicians. Ann Oncol 2020; 31:1115-1118. [DOI: 10.1016/j.annonc.2020.07.002] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/05/2020] [Indexed: 12/16/2022] Open
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162
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A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion. Nat Rev Immunol 2020; 21:116-128. [PMID: 32820267 DOI: 10.1038/s41577-020-0390-6] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
The remarkable success of immune checkpoint inhibitors demonstrates the potential of tumour-specific CD8+ T cells to prevent and treat cancer. Although the number of lives saved by immunotherapy mounts, only a relatively small fraction of patients are cured. Here, we review two of the factors that limit the application of CD8+ T cell immunotherapies: difficulties in identifying tumour-specific peptides presented by MHC class I molecules and the ability of tumour cells to impair antigen presentation as they evolve under T cell selection. We describe recent advances in understanding how peptides are generated from non-canonical translation of defective ribosomal products, relate this to the dysregulated translation that is a feature of carcinogenesis and propose dysregulated translation as an important new source of tumour-specific peptides. We discuss how the synthesis and function of components of the antigen-processing and presentation pathway, including the recently described immunoribosome, are manipulated by tumours for immunoevasion and point to common druggable targets that may enhance immunotherapy.
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163
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Donoghue MTA, Schram AM, Hyman DM, Taylor BS. Discovery through clinical sequencing in oncology. ACTA ACUST UNITED AC 2020; 1:774-783. [PMID: 35122052 PMCID: PMC8985175 DOI: 10.1038/s43018-020-0100-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
The molecular characterization of tumors now informs clinical cancer care for many patients. This advent of molecular oncology is driven by the expanding number of therapeutic biomarkers that can predict sensitivity to both approved and investigational agents. Beyond its role in driving clinical trial enrollments and guiding therapy in individual patients, large-scale clinical genomics in oncology also represents a rapidly expanding research resource for translational scientific discovery. Here, we review the progress, opportunities, and challenges of scientific and translational discovery from prospective clinical genomic screening programs now routinely conducted in cancer patients.
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164
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Roerden M, Nelde A, Heitmann JS, Klein R, Rammensee HG, Bethge WA, Walz JS. HLA Evolutionary Divergence as a Prognostic Marker for AML Patients Undergoing Allogeneic Stem Cell Transplantation. Cancers (Basel) 2020; 12:cancers12071835. [PMID: 32650450 PMCID: PMC7408841 DOI: 10.3390/cancers12071835] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/03/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
The diversity of human leukocyte antigens (HLAs) enables the presentation of immense repertoires of peptides, including tumor-associated antigens (TAAs). As a surrogate for immunopeptidome diversity, the HLA evolutionary divergence (HED) between individual HLA alleles might directly define the ability to present TAAs, a prerequisite for graft-versus-leukemia effects. We therefore analyzed the impact of HED on survival within a cohort of 171 acute myeloid leukemia (AML) patients after matched donor allogeneic hematopoietic stem cell transplantation (HSCT). Low HED (<25th percentile) of HLA class I (HEDclass I) or HLA-DR antigens (HEDDR) was a strong determinant for adverse overall survival after allogeneic HSCT (OS), with a hazard ratio for death of 1.9 (95% CI 1.2–3.2) and 2.1 (95% CI 1.3–3.4), respectively. Defining a cutoff value for the combined HEDtotal (HEDclass I and HEDDR), the respective 5 year OS was 29.7% and 64.9% in patients with low and high HEDtotal (p < 0.001), respectively. Furthermore, the risk of relapse was significantly higher in patients with low HEDtotal (hazard ratio (HR) 2.2, 95% CI 1.3–3.6) and event-free survival (EFS) was significantly reduced (5 year EFS 25.7% versus 54.4%, p < 0.001). We here introduce HED, a fundamental metric of immunopeptidome diversity, as a novel prognostic factor for AML patients undergoing allogeneic HSCT.
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Affiliation(s)
- Malte Roerden
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Correspondence: (M.R.); (J.S.W.)
| | - Annika Nelde
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany;
| | - Jonas S. Heitmann
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Reinhild Klein
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
| | - Hans-Georg Rammensee
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany;
- German Cancer Consortium (DKTK), DKFZ Partner Site Tübingen, 72076 Tübingen, Germany
| | - Wolfgang A. Bethge
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
| | - Juliane S. Walz
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, 72076 Tübingen, Germany; (R.K.); (W.A.B.)
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany; (A.N.); (J.S.H.)
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, 72076 Tübingen, Germany
- Correspondence: (M.R.); (J.S.W.)
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165
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Moreira M, Pobel C, Epaillard N, Simonaggio A, Oudard S, Vano YA. Resistance to cancer immunotherapy in metastatic renal cell carcinoma. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2020; 3:454-471. [PMID: 35582435 PMCID: PMC8992500 DOI: 10.20517/cdr.2020.16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/06/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022]
Abstract
The prognosis of metastatic clear cell renal cell carcinoma (mccRCC) has changed dramatically over the years with the emergence of immune checkpoint inhibitors (ICI) used alone, or in combination with another ICI, or with vascular endothelial growth factor receptor tyrosine kinase inhibitor. Although major response rates have been observed with ICI, many patients do not respond, reflecting primary resistance, and durable responses remain exceptional, reflecting secondary resistance. Factors contributing to primary and acquired resistance are manifold, including patient-intrinsic factors, tumor cell-intrinsic factors and factors associated with the tumoral microenvironment (TME). While some mechanisms of resistance are common to several tumor types, others are specific to mccRCC. Predictive biomarkers and alternative strategies are needed to overcome this resistance. This review provides an overview of the major ICI resistance mechanisms, highlights the potential of the TME to induce resistance to ICI, and discusses the predictive biomarkers available to guide therapeutic choice.
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Affiliation(s)
- Marco Moreira
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris F-75006, France.,Both authors contributed equally
| | - Cedric Pobel
- Department of Medical Oncology, European Hospital Georges Pompidou - APHP, Paris 75015, France.,University François Rabelais, Tours 37200, France.,Both authors contributed equally
| | - Nicolas Epaillard
- Department of Medical Oncology, European Hospital Georges Pompidou - APHP, Paris 75015, France
| | - Audrey Simonaggio
- Department of Medical Oncology, European Hospital Georges Pompidou - APHP, Paris 75015, France
| | - Stéphane Oudard
- Department of Medical Oncology, European Hospital Georges Pompidou - APHP, Paris 75015, France.,INSERM UMR-S1147, Paris 75006, France
| | - Yann-Alexandre Vano
- Centre de Recherche des Cordeliers, INSERM, Université de Paris, Sorbonne Université, Paris F-75006, France.,Department of Medical Oncology, European Hospital Georges Pompidou - APHP, Paris 75015, France
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166
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Immuno-Metabolism and Microenvironment in Cancer: Key Players for Immunotherapy. Int J Mol Sci 2020; 21:ijms21124414. [PMID: 32575899 PMCID: PMC7352562 DOI: 10.3390/ijms21124414] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs) have changed therapeutic algorithms in several malignancies, although intrinsic and secondary resistance is still an issue. In this context, the dysregulation of immuno-metabolism plays a leading role both in the tumor microenvironment (TME) and at the host level. In this review, we summarize the most important immune-metabolic factors and how they could be exploited therapeutically. At the cellular level, an increased concentration of extracellular adenosine as well as the depletion of tryptophan and uncontrolled activation of the PI3K/AKT pathway induces an immune-tolerant TME, reducing the response to ICIs. Moreover, aberrant angiogenesis induces a hypoxic environment by recruiting VEGF, Treg cells and immune-suppressive tumor associated macrophages (TAMs). On the other hand, factors such as gender and body mass index seem to affect the response to ICIs, while the microbiome composition (and its alterations) modulates both the response and the development of immune-related adverse events. Exploiting these complex mechanisms is the next goal in immunotherapy. The most successful strategy to date has been the combination of antiangiogenic drugs and ICIs, which prolonged the survival of patients with non-small-cell lung cancer (NSCLC) and hepatocellular carcinoma (HCC), while results from tryptophan pathway inhibition studies are inconclusive. New exciting strategies include targeting the adenosine pathway, TAMs and the microbiota with fecal microbiome transplantation.
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167
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Power R, Lowery MA, Reynolds JV, Dunne MR. The Cancer-Immune Set Point in Oesophageal Cancer. Front Oncol 2020; 10:891. [PMID: 32582553 PMCID: PMC7287212 DOI: 10.3389/fonc.2020.00891] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022] Open
Abstract
Immunotherapy has achieved long-term disease control in a proportion of cancer patients, but determinants of clinical benefit remain unclear. A greater understanding of antitumor immunity on an individual basis is needed to facilitate a precision oncology approach. A conceptual framework called the "cancer-immune set point" has been proposed to describe the equilibrium between factors that promote or suppress anticancer immunity and can serve as a basis to understand the variability in clinical response to immune checkpoint blockade. Oesophageal cancer has a high mutational burden, develops from pre-existing chronic inflammatory lesions and is therefore anticipated to be sensitive to immune checkpoint inhibition. However, both tumour- and patient-specific factors including the immune microenvironment, the microbiome, obesity, and host genetics contribute to an immune set point that confers a lower-than-expected response to checkpoint blockade. Immunotherapy is therefore currently confined to latter lines of treatment of advanced disease, with no reliable predictive biomarker of response. In this review, we examine oesophageal cancer in the context of the cancer-immune set point, discuss factors that contribute to response to immunotherapeutic intervention, and propose areas requiring further investigation to improve treatment response.
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Affiliation(s)
- Robert Power
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
- Trinity St. James Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Maeve A. Lowery
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
- Trinity St. James Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - John V. Reynolds
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
- Trinity St. James Cancer Institute, Trinity College Dublin, Dublin, Ireland
| | - Margaret R. Dunne
- Department of Surgery, Trinity College Dublin, Dublin, Ireland
- Trinity St. James Cancer Institute, Trinity College Dublin, Dublin, Ireland
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168
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Fumet JD, Truntzer C, Yarchoan M, Ghiringhelli F. Tumour mutational burden as a biomarker for immunotherapy: Current data and emerging concepts. Eur J Cancer 2020; 131:40-50. [PMID: 32278982 DOI: 10.1016/j.ejca.2020.02.038] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/13/2020] [Indexed: 01/10/2023]
Abstract
Treatment with immune checkpoint inhibitors targeting programmed cell death protein 1 (PD-1) or its ligand (PD-L1) can generate durable responses in various cancer types, but only in a subset of patients. The use of predictive biomarkers for response to PD-1/PD-L1 inhibitors is critical for patient selection. Expression of PD-L1 has demonstrated utility in patient selection. Tumour mutational burden (TMB) is an emerging biomarker for response to PD-1/PD-L1 inhibitors. The evaluation of this biomarker is based on the hypothesis that a high number of mutations in somatic exonic regions will lead to an increase in neoantigen production, which could then be recognised by CD8+ T cells, resulting in improved immune responses. In this review, we will discuss rationale and implementation of TMB usage in patients, development of different methods to assess it, current limitations and technical issues to use this biomarker as a diagnostic test and propose future perspectives beyond TMB.
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Affiliation(s)
- Jean-David Fumet
- Department of Medical Oncology, Center GF Leclerc, Dijon, France; Research Platform in Biological Oncology, Dijon, France; GIMI Genetic and Immunology Medical Institute, Dijon, France; University of Burgundy-Franche Comté, Dijon, France; UMR INSERM 1231, Dijon, France
| | - Caroline Truntzer
- Research Platform in Biological Oncology, Dijon, France; GIMI Genetic and Immunology Medical Institute, Dijon, France; UMR INSERM 1231, Dijon, France
| | - Mark Yarchoan
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Francois Ghiringhelli
- Department of Medical Oncology, Center GF Leclerc, Dijon, France; Research Platform in Biological Oncology, Dijon, France; GIMI Genetic and Immunology Medical Institute, Dijon, France; University of Burgundy-Franche Comté, Dijon, France; UMR INSERM 1231, Dijon, France.
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169
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Henick BS. Elite Intratumoral T-cell Clonotypes (The 1%) Effect "Trickle-Down Cytotoxicity". Clin Cancer Res 2020; 26:1205-1207. [PMID: 31919138 DOI: 10.1158/1078-0432.ccr-19-3788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 11/16/2022]
Abstract
Careful study of T-cell clonal dynamics in patients with non-small cell lung cancer treated with neoadjuvant nivolumab suggests that successful trafficking of clones from a proliferative burst in the periphery to the tumor associates with major pathologic response. Integration of these findings with functional analysis may augment current therapeutic strategies.See related article by Zhang et al., p. 1327.
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