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Sotirov S, Dimitrov I. Tumor-Derived Antigenic Peptides as Potential Cancer Vaccines. Int J Mol Sci 2024; 25:4934. [PMID: 38732150 PMCID: PMC11084719 DOI: 10.3390/ijms25094934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Peptide antigens derived from tumors have been observed to elicit protective immune responses, categorized as either tumor-associated antigens (TAAs) or tumor-specific antigens (TSAs). Subunit cancer vaccines incorporating these antigens have shown promise in inducing protective immune responses, leading to cancer prevention or eradication. Over recent years, peptide-based cancer vaccines have gained popularity as a treatment modality and are often combined with other forms of cancer therapy. Several clinical trials have explored the safety and efficacy of peptide-based cancer vaccines, with promising outcomes. Advancements in techniques such as whole-exome sequencing, next-generation sequencing, and in silico methods have facilitated the identification of antigens, making it increasingly feasible. Furthermore, the development of novel delivery methods and a deeper understanding of tumor immune evasion mechanisms have heightened the interest in these vaccines among researchers. This article provides an overview of novel insights regarding advancements in the field of peptide-based vaccines as a promising therapeutic avenue for cancer treatment. It summarizes existing computational methods for tumor neoantigen prediction, ongoing clinical trials involving peptide-based cancer vaccines, and recent studies on human vaccination experiments.
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Affiliation(s)
| | - Ivan Dimitrov
- Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, 2, Dunav Str., 1000 Sofia, Bulgaria;
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2
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Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol 2024; 12:1343938. [PMID: 38745861 PMCID: PMC11091292 DOI: 10.3389/fcell.2024.1343938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024] Open
Abstract
This review examines the complex role of Pin1 in the development and treatment of cancer. Pin1 is the only peptidyl-prolyl isomerase (PPIase) that can recognize and isomerize phosphorylated Ser/Thr-Pro peptide bonds. Pin1 catalyzes a structural change in phosphorylated Ser/Thr-Pro motifs that can modulate protein function and thereby impact cell cycle regulation and tumorigenesis. The molecular mechanisms by which Pin1 contributes to oncogenesis are reviewed, including Pin1 overexpression and its correlation with poor cancer prognosis, and the contribution of Pin1 to aggressive tumor phenotypes involved in therapeutic resistance is discussed, with an emphasis on cancer stem cells, the epithelial-to-mesenchymal transition (EMT), and immunosuppression. The therapeutic potential of Pin1 inhibition in cancer is discussed, along with the promise and the difficulties in identifying potent, drug-like, small-molecule Pin1 inhibitors. The available evidence supports the efficacy of targeting Pin1 as a novel cancer therapeutic by analyzing the role of Pin1 in a complex network of cancer-driving pathways and illustrating the potential of synergistic drug combinations with Pin1 inhibitors for treating aggressive and drug-resistant tumors.
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Affiliation(s)
- Robert Stewart
- Department of Biochemistry, Western University, London, ON, Canada
| | - Shaunik Sharma
- Department of Biochemistry, Western University, London, ON, Canada
| | - Timothy Wu
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sho Okuda
- Department of Biochemistry, Western University, London, ON, Canada
| | - George Xie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brian Shilton
- Department of Biochemistry, Western University, London, ON, Canada
| | - Kun Ping Lu
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
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3
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Dhanushkumar T, M E S, Selvam PK, Rambabu M, Dasegowda KR, Vasudevan K, George Priya Doss C. Advancements and hurdles in the development of a vaccine for triple-negative breast cancer: A comprehensive review of multi-omics and immunomics strategies. Life Sci 2024; 337:122360. [PMID: 38135117 DOI: 10.1016/j.lfs.2023.122360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023]
Abstract
Triple-Negative Breast Cancer (TNBC) presents a significant challenge in oncology due to its aggressive behavior and limited therapeutic options. This review explores the potential of immunotherapy, particularly vaccine-based approaches, in addressing TNBC. It delves into the role of immunoinformatics in creating effective vaccines against TNBC. The review first underscores the distinct attributes of TNBC and the importance of tumor antigens in vaccine development. It then elaborates on antigen detection techniques such as exome sequencing, HLA typing, and RNA sequencing, which are instrumental in identifying TNBC-specific antigens and selecting vaccine candidates. The discussion then shifts to the in-silico vaccine development process, encompassing antigen selection, epitope prediction, and rational vaccine design. This process merges computational simulations with immunological insights. The role of Artificial Intelligence (AI) in expediting the prediction of antigens and epitopes is also emphasized. The review concludes by encapsulating how Immunoinformatics can augment the design of TNBC vaccines, integrating tumor antigens, advanced detection methods, in-silico strategies, and AI-driven insights to advance TNBC immunotherapy. This could potentially pave the way for more targeted and efficacious treatments.
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Affiliation(s)
- T Dhanushkumar
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Santhosh M E
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Prasanna Kumar Selvam
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Majji Rambabu
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - K R Dasegowda
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India
| | - Karthick Vasudevan
- Department of Biotechnology, School of Applied Sciences, REVA University, Bengaluru 560064, India.
| | - C George Priya Doss
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of BioSciences and Technology, Vellore Institute of Technology (VIT), Vellore, India.
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Li B, Jing P, Zheng G, Pi C, Zhang L, Yin Z, Xu L, Qiu J, Gu H, Qiu T, Fang J. Neo-intline: integrated pipeline enables neoantigen design through the in-silico presentation of T-cell epitope. Signal Transduct Target Ther 2023; 8:397. [PMID: 37848417 PMCID: PMC10582007 DOI: 10.1038/s41392-023-01644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/19/2023] Open
Abstract
Neoantigen vaccines are one of the most effective immunotherapies for personalized tumour treatment. The current immunogen design of neoantigen vaccines is usually based on whole-genome sequencing (WGS) and bioinformatics prediction that focuses on the prediction of binding affinity between peptide and MHC molecules, ignoring other peptide-presenting related steps. This may result in a gap between high prediction accuracy and relatively low clinical effectiveness. In this study, we designed an integrated in-silico pipeline, Neo-intline, which started from the SNPs and indels of the tumour samples to simulate the presentation process of peptides in-vivo through an integrated calculation model. Validation on the benchmark dataset of TESLA and clinically validated neoantigens illustrated that neo-intline could outperform current state-of-the-art tools on both sample level and melanoma level. Furthermore, by taking the mouse melanoma model as an example, we verified the effectiveness of 20 neoantigens, including 10 MHC-I and 10 MHC-II peptides. The in-vitro and in-vivo experiments showed that both peptides predicted by Neo-intline could recruit corresponding CD4+ T cells and CD8+ T cells to induce a T-cell-mediated cellular immune response. Moreover, although the therapeutic effect of neoantigen vaccines alone is not sufficient, combinations with other specific therapies, such as broad-spectrum immune-enhanced adjuvants of granulocyte-macrophage colony-stimulating factor (GM-CSF) and polyinosinic-polycytidylic acid (poly(I:C)), or immune checkpoint inhibitors, such as PD-1/PD-L1 antibodies, can illustrate significant anticancer effects on melanoma. Neo-intline can be used as a benchmark process for the design and screening of immunogenic targets for neoantigen vaccines.
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Affiliation(s)
- Bingyu Li
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, Henan, China
| | - Ping Jing
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Genhui Zheng
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
- Oden Institute for Computational Engineering and Sciences (ICES), University of Texas at Austin, Austin, TX, USA
| | - Chenyu Pi
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Lu Zhang
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Zuojing Yin
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lijun Xu
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
- School of Basic Medical Sciences, Henan University of Science and Technology, Luoyang, Henan, China
| | - Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Hua Gu
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China.
| | - Jianmin Fang
- Laboratory of Molecular Medicine, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji Hospital, Tongji University Suzhou Institute, Tongji University, Shanghai, China.
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Moeckel C, Bakhl K, Georgakopoulos-Soares I, Zaravinos A. The Efficacy of Tumor Mutation Burden as a Biomarker of Response to Immune Checkpoint Inhibitors. Int J Mol Sci 2023; 24:ijms24076710. [PMID: 37047684 PMCID: PMC10095310 DOI: 10.3390/ijms24076710] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/21/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023] Open
Abstract
Cancer is one of the leading causes of death in the world; therefore, extensive research has been dedicated to exploring potential therapeutics, including immune checkpoint inhibitors (ICIs). Initially, programmed-death ligand-1 was the biomarker utilized to predict the efficacy of ICIs. However, its heterogeneous expression in the tumor microenvironment, which is critical to cancer progression, promoted the exploration of the tumor mutation burden (TMB). Research in various cancers, such as melanoma and lung cancer, has shown an association between high TMB and response to ICIs, increasing its predictive value. However, the TMB has failed to predict ICI response in numerous other cancers. Therefore, future research is needed to analyze the variations between cancer types and establish TMB cutoffs in order to create a more standardized methodology for using the TMB clinically. In this review, we aim to explore current research on the efficacy of the TMB as a biomarker, discuss current approaches to overcoming immunoresistance to ICIs, and highlight new trends in the field such as liquid biopsies, next generation sequencing, chimeric antigen receptor T-cell therapy, and personalized tumor vaccines.
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Affiliation(s)
- Camille Moeckel
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Katrina Bakhl
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ilias Georgakopoulos-Soares
- Department of Biochemistry and Molecular Biology, Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Apostolos Zaravinos
- Department of Life Sciences, European University Cyprus, Diogenis Str., 6, Nicosia 2404, Cyprus
- Cancer Genetics, Genomics and Systems Biology Laboratory, Basic and Translational Cancer Research Center (BTCRC), Nicosia 1516, Cyprus
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Maqsood Q, Sumrin A, Iqbal M, Hussain N, Mahnoor M, Zafar Saleem M, Perveen R. A Winning New Combination? Toward Clinical Application in Oncology. Cancer Control 2023; 30:10732748231175240. [PMID: 37166227 PMCID: PMC10184224 DOI: 10.1177/10732748231175240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/04/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023] Open
Abstract
Immunotherapy has substantial attention in oncology due to the success of CTLA-4 and PD-1 inhibitors in the treatment of melanoma, lung cancer, head and neck cancer, renal cell carcinoma, and Hodgkin's lymphoma. A deeper understanding of interaction of tumor with its environment and the immune system provides best guide for oncology research. Recent studies in oncology have explained how a tumor alters antigen presentation, avoids detection, and activation of the host immune system to live and develop. Understanding the connections between the tumor and the immune system has resulted in several innovative therapy options. The extensive field of gene therapy has provided a number of cutting-edge medicines that are expected to play an important role in lowering cancer-related mortality. This article explains the history, important breakthroughs, and future prospects for three separate gene therapy treatment modalities: immunotherapy, oncolytic virotherapy, and gene transfer. Immunotherapies have completely changed how cancer is treated, especially for individuals whose condition was previously thought to be incurable. Examples include ACT (adoptive cell therapy) and ICB (immune checkpoint blockade). This review article will discuss the relationship between the immune response to cancer and the mechanisms of immunotherapy resistance. It will cover combination drugs authorized by the US Food and Drug Administration and provide a thorough overview of how these drugs are doing clinically right now. Cytokines, vaccines, and other soluble immunoregulatory agents, innate immune modifiers, ACT, virotherapy, and other treatment modalities will all be covered in detail.
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Affiliation(s)
- Quratulain Maqsood
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Aleena Sumrin
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Maryam Iqbal
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Nazim Hussain
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Muhammada Mahnoor
- Department of Rehabilitation Sciences, Akhtar Saeed Medical & Dental College, Lahore, Pakistan
| | - Muhammad Zafar Saleem
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
| | - Rukhsana Perveen
- Centre for Applied Molecular Biology, University of the Punjab Quaid-i-Azam Campus, Lahore, Pakistan
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7
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Ti W, Wei T, Wang J, Cheng Y. Comparative Analysis of Mutation Status and Immune Landscape for Squamous Cell Carcinomas at Different Anatomical sites. Front Immunol 2022; 13:947712. [PMID: 35935970 PMCID: PMC9354879 DOI: 10.3389/fimmu.2022.947712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 06/20/2022] [Indexed: 11/25/2022] Open
Abstract
Objective It has been controversial whether tumor mutation burden (TMB) affects the prognosis and the efficacy of immunotherapy in different tumor types. We provided a comprehensive analysis of mutation status and immune landscape of squamous cell carcinomas (SCCs) from four sites in order to investigate the relationship of TMB with prognosis and immune cell infiltration in different SCCs. Methods The transcriptome profiles and somatic mutation data of SCCs downloaded from the Cancer Genome Atlas (the Cancer Genome Atlas) database were analyzed and visualized. Then, TMB was calculated to analyze its correlations with prognosis and clinical features. Differentially expressed genes (DEGs) between the high and low TMB groups were screened for functional enrichment analysis. CIBERSORT algorithm was used to compare differences of immune cell infiltration between two groups in different SCCs. In addition, immune DEGs associated with prognosis were identified and risk prediction model was constructed via Cox regression analysis. Results Missense mutation was the most dominant mutation type in SCCs. The difference was that the top10 mutated genes varied widely among different SCCs. High TMB group had better prognosis in lung squamous cell carcinoma (LUSC) and cervical squamous cell carcinoma (CESC), while the result was reverse in head and neck squamous cell carcinoma (HNSCC) and esophageal squamous cell carcinoma (ESCC). In addition, patients with older age, smoking history, earlier pathological stage and no lymphatic invasion had higher TMB. The identified DEGs were mainly enriched in the regulation of immune system, muscular system and the activity of epidermal cells. The proportions of CD8+T cells, CD4+ memory T cells, follicular helper T cells, macrophages were distinct between two groups. The prognosis-related hub genes (CHGB, INHBA, LCN1 and VEGFC) screened were associated with poor prognosis. Conclusion This study reveals the mutation status and immune cell infiltration of SCCs at different anatomical sites. TMB is closely related to the prognosis of SCCs, and its effects on prognosis are diverse in different SCCs, which might result from the situation of immune cell infiltration. These findings contribute to the exploration of biomarkers for predicting the efficacy of immunotherapy in SCCs and providing innovative insights for accurate application of immunotherapy.
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Affiliation(s)
| | | | - Jianbo Wang
- *Correspondence: Yufeng Cheng, ; Jianbo Wang,
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Catanzaro E, Feron O, Skirtach AG, Krysko DV. Immunogenic Cell Death and Role of Nanomaterials Serving as Therapeutic Vaccine for Personalized Cancer Immunotherapy. Front Immunol 2022; 13:925290. [PMID: 35844506 PMCID: PMC9280641 DOI: 10.3389/fimmu.2022.925290] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/02/2022] [Indexed: 07/20/2023] Open
Abstract
Immunogenic cell death (ICD) is a rapidly growing research area representing one of the emerging therapeutic strategies of cancer immunotherapy. ICD is an umbrella term covering several cell death modalities including apoptosis, necroptosis, ferroptosis and pyroptosis, and is the product of a balanced combination of adjuvanticity (damage-associated molecular patterns and chemokines/cytokines) and antigenicity (tumor associated antigens). Only a limited number of anti-cancer therapies are available to induce ICD in experimental cancer therapies and even much less is available for clinical use. To overcome this limitation, nanomaterials can be used to increase the immunogenicity of cancer cells killed by anti-cancer therapy, which in themselves are not necessarily immunogenic. In this review, we outline the current state of knowledge of ICD modalities and discuss achievements in using nanomaterials to increase the immunogenicity of dying cancer cells. The emerging trends in modulating the immunogenicity of dying cancer cells in experimental and translational cancer therapies and the challenges facing them are described. In conclusion, nanomaterials are expected to drive further progress in their use to increase efficacy of anti-cancer therapy based on ICD induction and in the future, it is necessary to validate these strategies in clinical settings, which will be a challenging research area.
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Affiliation(s)
- Elena Catanzaro
- Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Olivier Feron
- Cancer Translational Research Laboratory, Pole of Pharmacology and Therapeutics, Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Brussels, Belgium
| | - André G. Skirtach
- Cancer Research Institute Ghent, Ghent, Belgium
- Nano-BioTechnology Laboratory, Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Dmitri V. Krysko
- Cell Death Investigation and Therapy (CDIT) Laboratory, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
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Fu M, Huang Y, Peng X, Li X, Luo N, Zhu W, Yang F, Chen Z, Ma S, Zhang Y, Li Q, Hu G. Development of Tumor Mutation Burden-Related Prognostic Model and Novel Biomarker Identification in Stomach Adenocarcinoma. Front Cell Dev Biol 2022; 10:790920. [PMID: 35399509 PMCID: PMC8983817 DOI: 10.3389/fcell.2022.790920] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Background: Stomach adenocarcinoma (STAD) is one of the most common tumors. Tumor mutation burden (TMB) has been linked to immunotherapy response. We wanted to see if there was any link between TMB and cancer prognosis. Methods: The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases were used to obtain mutation data, gene expression profiles, and clinical data. We looked at the differences in gene expression and immune markers between low and high TMB groups, built an immune prognostic model, and created a dynamic nomograph App that may be used in the clinic. Simultaneously, We ran the immunotherapy prediction and model comparison at the same time. Finally, model gene mutation and copy number variation (CNV) were displayed. The cellular functional experiments were used to investigate the potential role of GLP2R in gastric cancer. Results: Firstly, basic mutation information and differences in immune infiltration in STAD are revealed. Secondly, the prognostic model developed by us has good accuracy, and the corresponding dynamic nomograph Apps online and immunotherapy prediction facilitate clinical transformation. Furthermore, GLP2R knockdown significantly inhibited the proliferation, migration of gastric cancer cells in vitro. Conclusion: Our findings imply that TMB plays a significant role in the prognosis of STAD patients from a biological perspective. GLP2R may serve as a potential target for gastric cancer.
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Affiliation(s)
- Min Fu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongbiao Huang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohong Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Na Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenjun Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ziqi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengling Ma
- Department of Medical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yuanyuan Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
| | - Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Yuanyuan Zhang, ; Qianxia Li, ; Guangyuan Hu,
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10
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Ke CH, Wang YS, Chiang HC, Wu HY, Liu WJ, Huang CC, Huang YC, Lin CS. Xenograft cancer vaccines prepared from immunodeficient mice increase tumor antigen diversity and host T cell efficiency against colorectal cancers. Cancer Lett 2022; 526:66-75. [PMID: 34808284 DOI: 10.1016/j.canlet.2021.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 12/15/2022]
Abstract
Autologous cancer vaccines (ACVs) are a desirable approach for personalized medicine, but the efficiency of ACVs remains unsatisfactory due to their low immunogenicity. This study developed a platform that can enhance the immunogenicity of ACVs by transplanting the tumors into immunodeficient mice. The CT26 cell line was inoculated into severe combined immunodeficient mice (SCID) for vaccine preparation where escalates tumor development, subsequently diversifying the tumor antigenic topology. CT26/SCID cancer vaccines significantly inhibited tumor growth, increased the amount of tumor infiltrating lymphocytes, and triggered Th-1 predominant immune responses. Tumor antigenic profiles of CT26/SCID cells were further analyzed by liquid chromatography-tandem mass spectrometry. Compared to CT26 parental cells, a total of 428 differentially expressed proteins (DEPs) were detected. These DEPs revealed that CT26/SCID cells overexpressed several novel therapeutic targets, including KNG1, apoA-I and, β2-GPI, which can trigger cytotoxic T cells towards Th-1 predominant immune responses and directly suppress proliferation in tumors. CT26/SCID cancer vaccines can be easily manufactured, while traits of triggering stronger antigen-specific Th-1 immune activity against tumors, are retained. Results of this study provide an effective proof-of-concept of an ACV for personalized cancer immunotherapy.
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Affiliation(s)
- Chiao-Hsu Ke
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd., 106319, Taipei, Taiwan
| | - Yu-Shan Wang
- Lab. 2612, Rekiin Biotech Inc., 114737, Taipei, Taiwan
| | | | - Hsin-Yi Wu
- Instrumentation Center, National Taiwan University, 106319, Taipei, Taiwan
| | - Wang-Jing Liu
- Department of Earth and Life Science, University of Taipei, 1 Ai-Guo West Road, Taipei, 100234, Taipei, Taiwan
| | | | - Yi-Chun Huang
- Lab. 2612, Rekiin Biotech Inc., 114737, Taipei, Taiwan
| | - Chen-Si Lin
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No.1 Sec.4 Roosevelt Rd., 106319, Taipei, Taiwan.
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11
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Zou B, Guo D, Kong P, Wang Y, Cheng X, Cui Y. Integrative Genomic Analyses of 1,145 Patient Samples Reveal New Biomarkers in Esophageal Squamous Cell Carcinoma. Front Mol Biosci 2022; 8:792779. [PMID: 35127817 PMCID: PMC8814608 DOI: 10.3389/fmolb.2021.792779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022] Open
Abstract
Due to the lack of effective diagnostic markers and therapeutic targets, esophageal squamous cell carcinoma (ESCC) shows a poor 5 years survival rate of less than 30%. To explore the potential therapeutic targets of ESCC, we integrated and reanalyzed the mutation data of WGS (whole genome sequencing) or WES (whole exome sequencing) from a total of 1,145 samples in 7 large ESCC cohorts, including 270 ESCC gene expression data. Two new mutation signatures and 20 driver genes were identified in our study. Among them, AP3S1, MUC16, and RPS15 were reported for the first time. We also discovered that the KMT2D was associated with the multiple clinical characteristics of ESCC, and KMT2D knockdown cells showed enhanced cell migration and cell invasion. Furthermore, a few neoantigens were shared between ESCC patients. For ESCC, compared to TMB, neoantigen might be treated as a better immunotherapy biomarker. Our research expands the understanding of ESCC mutations and helps the identification of ESCC biomarkers, especially for immunotherapy biomarkers.
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Affiliation(s)
- Binbin Zou
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Dinghe Guo
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Pengzhou Kong
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Yanqiang Wang
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
| | - Xiaolong Cheng
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
| | - Yongping Cui
- Key Laboratory of Cellular Physiology of the Ministry of Education, Shanxi Medical University, Taiyuan, China
- Department of Pathology, Shanxi Medical University, Taiyuan, China
- Shenzhen Peking University-Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Peking University Shenzhen Hospital, Shenzhen, China
- *Correspondence: Xiaolong Cheng, ; Yongping Cui,
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12
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Whiteside TL. Tumor-Infiltrating Lymphocytes and Their Role in Solid Tumor Progression. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 113:89-106. [PMID: 35165861 PMCID: PMC9113058 DOI: 10.1007/978-3-030-91311-3_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tumor-infiltrating lymphocytes (TIL) are an important component of the tumor environment. Their role in tumor growth and progression has been debated for decades. Today, emphasis has shifted to beneficial effects of TIL for the host and to therapies optimizing the benefits by reducing immune suppression in the tumor microenvironment. Evidence indicates that when TILs are present in the tumor as dense aggregates of activated immune cells, tumor prognosis and responses to therapy are favorable. Gene signatures and protein profiling of TIL at the population and single-cell levels provide clues not only about their phenotype and numbers but also about TIL potential functions in the tumor. Correlations of the TIL data with clinicopathological tumor characteristics, clinical outcome, and patients' survival indicate that TILs exert influence on the disease progression, especially in colorectal carcinomas and breast cancer. At the same time, the recognition that TIL signatures vary with time and cancer progression has initiated investigations of TIL as potential prognostic biomarkers. Multiple mechanisms are utilized by tumors to subvert the host immune system. The balance between pro- and antitumor responses of TIL largely depends on the tumor microenvironment, which is unique in each cancer patient. This balance is orchestrated by the tumor and thus is shifted toward the promotion of tumor growth. Changes occurring in TIL during tumor progression appear to serve as a measure of tumor aggressiveness and potentially provide a key to selecting therapeutic strategies and inform about prognosis.
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Affiliation(s)
- Theresa L Whiteside
- Departments of Pathology and Immunology, University of Pittsburgh School of Medicine, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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13
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Pignochino Y, Crisafulli G, Giordano G, Merlini A, Berrino E, Centomo ML, Chiabotto G, Brusco S, Basiricò M, Maldi E, Pisacane A, Leuci V, Sangiolo D, D’Ambrosio L, Aglietta M, Kasper B, Bardelli A, Grignani G. PARP1 Inhibitor and Trabectedin Combination Does Not Increase Tumor Mutational Burden in Advanced Sarcomas-A Preclinical and Translational Study. Cancers (Basel) 2021; 13:cancers13246295. [PMID: 34944915 PMCID: PMC8699802 DOI: 10.3390/cancers13246295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/09/2021] [Accepted: 12/13/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Immunotherapy has revolutionized cancer treatment, but not for all tumor types. Indeed, sarcomas are considered “immune-cold” tumors, which are relatively unresponsive to immunotherapy. One strategy to potentiate immunotherapy efficacy is to increase tumor immunogenicity, for instance by boosting the number of candidate targets (neoantigens) to be recognized by the immune system. Tumor mutational burden indicates the number of somatic mutations identified in the tumor and normalized per megabase. Tumor mutational burden is considered as an acceptable, measurable surrogate of tumor neoantigens. Here, we explored whether the combination of two DNA-damaging agents, trabectedin and olaparib, could increase tumor mutational burden in sarcomas, to prime subsequent immunotherapy. We found no variation in tumor mutational burden after trabectedin + olaparib in preclinical and clinical samples. Therefore, other aspects should be considered to increase sarcoma immunogenicity, by exploiting different pathways such as the potential modulation of the tumor microenvironment induced by trabectedin + olaparib. Abstract Drug-induced tumor mutational burden (TMB) may contribute to unleashing the immune response in relatively “immune-cold” tumors, such as sarcomas. We previously showed that PARP1 inhibition perpetuates the DNA damage induced by the chemotherapeutic agent trabectedin in both preclinical models and sarcoma patients. In the present work, we explored acquired genetic changes in DNA repair genes, mutational signatures, and TMB in a translational platform composed of cell lines, xenografts, and tumor samples from patients treated with trabectedin and olaparib combination, compared to cells treated with temozolomide, an alkylating agent that induces hypermutation. Whole-exome and targeted panel sequencing data analyses revealed that three cycles of trabectedin and olaparib combination neither affected the mutational profiles, DNA repair gene status, or copy number alterations, nor increased TMB both in homologous recombinant-defective and proficient cells or in xenografts. Moreover, TMB was not increased in tumor specimens derived from trabectedin- and olaparib-treated patients (5–6 cycles) when compared to pre-treatment biopsies. Conversely, repeated treatments with temozolomide induced a massive TMB increase in the SJSA-1 osteosarcoma model. In conclusion, a trabectedin and olaparib combination did not show mutagenic effects and is unlikely to prime subsequent immune-therapeutic interventions based on TMB increase. On the other hand, these findings are reassuring in the increasing warning of treatment-induced hematologic malignancies correlated to PARP1 inhibitor use.
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Affiliation(s)
- Ymera Pignochino
- Department of Clinical and Biological Sciences, University of Torino, 10100 Torino, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Giovanni Crisafulli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giorgia Giordano
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Alessandra Merlini
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
- Correspondence: ; Tel.: +39-0119933623
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Medical Sciences, University of Torino, 10100 Torino, Italy;
| | - Maria Laura Centomo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Torino, 10100 Torino, Italy;
| | - Silvia Brusco
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Marco Basiricò
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Elena Maldi
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Alberto Pisacane
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Valeria Leuci
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
| | - Dario Sangiolo
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Lorenzo D’Ambrosio
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Cardinal Massaia Hospital, 14100 Asti, Italy
| | - Massimo Aglietta
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Bernd Kasper
- Sarcoma Unit, Mannheim University Medical Center, University of Heidelberg, 68167 Mannheim, Germany;
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
- Department of Oncology, University of Torino, 10100 Torino, Italy
| | - Giovanni Grignani
- Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy; (G.C.); (G.G.); (E.B.); (M.L.C.); (S.B.); (M.B.); (E.M.); (A.P.); (V.L.); (D.S.); (L.D.); (M.A.); (A.B.); (G.G.)
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14
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Gao Z, Chen J, Tao Y, Wang Q, Peng S, Yu S, Zeng J, Li K, Xie Z, Huang H. Immune Signatures Combined With BRCA1-Associated Protein 1 Mutations Predict Prognosis and Immunotherapy Efficacy in Clear Cell Renal Cell Carcinoma. Front Cell Dev Biol 2021; 9:747985. [PMID: 34733850 PMCID: PMC8558467 DOI: 10.3389/fcell.2021.747985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/20/2021] [Indexed: 12/19/2022] Open
Abstract
Immunotherapy is gradually emerging in the field of tumor treatment. However, because of the complexity of the tumor microenvironment (TME), some patients cannot benefit from immunotherapy. Therefore, we comprehensively analyzed the TME and gene mutations of ccRCC to identify a comprehensive index that could more accurately guide the immunotherapy of patients with ccRCC. We divided ccRCC patients into two groups based on immune infiltration activity. Next, we investigated the differentially expressed genes (DEGs) and constructed a prognostic immune score using univariate Cox regression analysis, unsupervised cluster analysis, and principal component analysis (PCA) and validated its predictive power in both internal and total sets. Subsequently, the gene mutations in the groups were investigated, and patients suitable for immunotherapy were selected in combination with the immune score. The prognosis of the immune score-low group was significantly worse than that of the immune score-high group. The patients with BRCA1-associated protein 1 (BAP1) mutation had a poor prognosis. Thus, this study indicated that establishing an immune score model combined with BAP1 mutation can better predict the prognosis of patients, screen suitable ccRCC patients for immunotherapy, and select more appropriate drug combinations.
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Affiliation(s)
- Ze Gao
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Junxiu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yiran Tao
- Department of Urology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qiong Wang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Shirong Peng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shunli Yu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jianwen Zeng
- Department of Urology, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Kaiwen Li
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhongqiu Xie
- Department of Pathology, School of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Hai Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.,Department of Urology, Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
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15
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Liao JY, Zhang S. Safety and Efficacy of Personalized Cancer Vaccines in Combination With Immune Checkpoint Inhibitors in Cancer Treatment. Front Oncol 2021; 11:663264. [PMID: 34123821 PMCID: PMC8193725 DOI: 10.3389/fonc.2021.663264] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
Cancer immunotherapy can induce sustained responses in patients with cancers in a broad range of tissues, however, these treatments require the optimized combined therapeutic strategies. Despite immune checkpoint inhibitors (ICIs) have lasting clinical benefit, researchers are trying to combine them with other treatment modalities, and among them the combination with personalized cancer vaccines is attractive. Neoantigens, arising from mutations in cancer cells, can elicit strong immune response without central tolerance and out-target effects, which is a truly personalized method. Growing studies show that the combination can elevate the antitumor efficacy with acceptable safety and minimal additional toxicity compared with single agent vaccine or ICI. Herein, we have searched these preclinical and clinical trials and summarized safety and efficacy of personalized cancer vaccines combined with ICIs in several malignancies. Meanwhile, we discuss the rationale of the combination and future challenges.
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Affiliation(s)
- Juan-Yan Liao
- Department of Biotherapy, Cancer Center, West China Hospital of Sichuan University, Chengdu, China
- Sichuan Clinical Research Center of Biotherapy, Chengdu, China
| | - Shuang Zhang
- Department of Biotherapy, Cancer Center, West China Hospital of Sichuan University, Chengdu, China
- Sichuan Clinical Research Center of Biotherapy, Chengdu, China
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16
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Zeng Y, Zhang W, Li Z, Zheng Y, Wang Y, Chen G, Qiu L, Ke K, Su X, Cai Z, Liu J, Liu X. Personalized neoantigen-based immunotherapy for advanced collecting duct carcinoma: case report. J Immunother Cancer 2021; 8:jitc-2019-000217. [PMID: 32439798 PMCID: PMC7247377 DOI: 10.1136/jitc-2019-000217] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Collecting duct carcinoma (CDC) of the kidney is a rare and highly aggressive malignant tumor with the worst prognosis among all renal cancers. Nevertheless, the first-line treatments, including chemotherapy and target therapy, usually show poor response to CDC. Recent studies have suggested that immunotherapy targeting personal tumor-specific neoantigens could be a promising strategy for several solid cancers. However, whether it has therapeutic potential in CDC remains unclear. CASE PRESENTATION Here, we report a case of an Asian patient who underwent personalized neoantigen-based immunotherapy. The patient was diagnosed with metastatic CDC and suffered extensive tumor progression following sorafenib treatment. Based on the patient's own somatic mutational profile, a total of 13 neoantigens were identified and corresponding long-peptide vaccine and neoantigen-reactive T cells (NRTs) were prepared. After six cycles of neoantigen-based vaccination and T-cell immunotherapy, the patient was reported with stable disease status in tumor burden and significant alleviation of bone pain. Ex vivo interferon-γ enzyme-linked immunospot assay proved the reactivity to 12 of 13 neoantigens in peripheral blood mononuclear cells collected after immunotherapy, and the preferential reactivity to mutant peptides compared with corresponding wild-type peptides was also observed for 3 of the neoantigens. Surprisingly, biopsy sample collected from CDC sites after 3 months of immunotherapy showed decreased mutant allele frequency corresponding to 92% (12/13) of the neoantigens, indicating the elimination of tumor cells carrying these neoantigens. CONCLUSIONS Our case report demonstrated that the combined therapy of neoantigen peptide vaccination and NRT cell infusion showed certain efficacy in this CDC case, even when the patient carried only a relatively low tumor mutation burden. These results indicated that the personalized neoantigen-based immunotherapy was a promising new strategy for advanced CDC. TRIAL REGISTRATION NUMBER ChiCTR1800017836.
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Affiliation(s)
- Yongyi Zeng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Changhai Hospital of The Second Military Medical University, Shanghai 200433, China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Youshi Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Liman Qiu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Kun Ke
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xiaoping Su
- Institute of Cardiovascular Development and Translational Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China .,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China .,Mengchao Med-X Center, Fuzhou University, Fuzhou 350116, China
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17
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Zhang D, Lin Z, Wu M, Cai Z, Zheng Y, He L, Li Z, Zhou J, Sun L, Chen G, Zeng Y, Li J, Liu J, Yang H, Liu X. Cytosolic Delivery of Thiolated Neoantigen Nano-Vaccine Combined with Immune Checkpoint Blockade to Boost Anti-Cancer T Cell Immunity. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003504. [PMID: 33747739 PMCID: PMC7967047 DOI: 10.1002/advs.202003504] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/25/2020] [Indexed: 05/04/2023]
Abstract
Although tumor-specific neoantigen-based cancer vaccines hold tremendous potential, it still faces low cross-presentation associated with severe degradation via endocytosis pathway. Herein, a thiolated nano-vaccine allowing direct cytosolic delivery of neoantigen and Toll like receptor 9 agonist CpG-ODN is developed. This approach is capable of bypassing the endo-/lysosome degradation, increasing uptake and local concentration of neoantigen and CpG-ODN to activate antigen-presenting cells, significantly strengthening the anti-cancer T-cell immunity. In vivo immunization with thiolated nano-vaccine enhanced the lymph organ homing and promoted the antigen presentation on dendritic cells, effectively inhibited tumor growth, and significantly prolonged the survival of H22-bearing mice. Strikingly, further combination of the thiolated nano-vaccine with anti-programmed cell death protein-1 antibody (αPD-1) could efficiently reverse immunosuppression and enhance response rate of tumors, which led to enhanced tumor elimination, complete prevention of tumor re-challenge, and long-term survival above 150 d. Collectively, a versatile methodology to design cancer vaccines for strengthening anti-cancer T-cell immunity in solid tumors is presented, which could be further remarkably enhanced by combining with immune checkpoint inhibitors.
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Affiliation(s)
- Da Zhang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of ChemistryFuzhou UniversityFuzhou350002P. R. China
| | - Ziguo Lin
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
| | - Ming Wu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Zhixiong Cai
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Youshi Zheng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Lei He
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Jie Zhou
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of ChemistryFuzhou UniversityFuzhou350002P. R. China
| | - Liqin Sun
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of ChemistryFuzhou UniversityFuzhou350002P. R. China
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Yongyi Zeng
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
| | - Juan Li
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of ChemistryFuzhou UniversityFuzhou350002P. R. China
| | - Jingfeng Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou350002P. R. China
| | - Huanghao Yang
- The Key Lab of Analysis and Detection Technology for Food Safety of the MOE, Fujian Provincial Key Laboratory of Analysis and Detection Technology for Food Safety, College of ChemistryFuzhou UniversityFuzhou350002P. R. China
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian ProvinceMengchao Hepatobiliary Hospital of Fujian Medical UniversityFuzhou350025P. R. China
- Mengchao Med‐X CenterFuzhou UniversityFuzhou350116P. R. China
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, Fujian Institute of Research on the Structure of MatterChinese Academy of SciencesFuzhou350002P. R. China
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18
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Shukla A, Cloutier M, Appiya Santharam M, Ramanathan S, Ilangumaran S. The MHC Class-I Transactivator NLRC5: Implications to Cancer Immunology and Potential Applications to Cancer Immunotherapy. Int J Mol Sci 2021; 22:ijms22041964. [PMID: 33671123 PMCID: PMC7922096 DOI: 10.3390/ijms22041964] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
The immune system constantly monitors the emergence of cancerous cells and eliminates them. CD8+ cytotoxic T lymphocytes (CTLs), which kill tumor cells and provide antitumor immunity, select their targets by recognizing tumor antigenic peptides presented by MHC class-I (MHC-I) molecules. Cancer cells circumvent immune surveillance using diverse strategies. A key mechanism of cancer immune evasion is downregulation of MHC-I and key proteins of the antigen processing and presentation machinery (APM). Even though impaired MHC-I expression in cancers is well-known, reversing the MHC-I defects remains the least advanced area of tumor immunology. The discoveries that NLRC5 is the key transcriptional activator of MHC-I and APM genes, and genetic lesions and epigenetic modifications of NLRC5 are the most common cause of MHC-I defects in cancers, have raised the hopes for restoring MHC-I expression. Here, we provide an overview of cancer immunity mediated by CD8+ T cells and the functions of NLRC5 in MHC-I antigen presentation pathways. We describe the impressive advances made in understanding the regulation of NLRC5 expression, the data supporting the antitumor functions of NLRC5 and a few reports that argue for a pro-tumorigenic role. Finally, we explore the possible avenues of exploiting NLRC5 for cancer immunotherapy.
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Affiliation(s)
- Akhil Shukla
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Maryse Cloutier
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Madanraj Appiya Santharam
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
| | - Sheela Ramanathan
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
| | - Subburaj Ilangumaran
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada; (A.S.); (M.C.); (M.A.S.); (S.R.)
- CRCHUS, Centre Hospitalier de l’Université de Sherbrooke, Sherbrooke, QC J1H5N4, Canada
- Correspondence: ; Tel.: +1-819-346-1110 (ext. 14834)
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19
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Roviello G, Catalano M, Nobili S, Santi R, Mini E, Nesi G. Focus on Biochemical and Clinical Predictors of Response to Immune Checkpoint Inhibitors in Metastatic Urothelial Carcinoma: Where Do We Stand? Int J Mol Sci 2020; 21:E7935. [PMID: 33114616 PMCID: PMC7662285 DOI: 10.3390/ijms21217935] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/13/2020] [Accepted: 10/22/2020] [Indexed: 12/24/2022] Open
Abstract
Urothelial bladder cancer is one of the most lethal cancers worldwide with barely 5% five-year survival in patients with metastatic disease. Intravesical immunotherapy with Bacillus Calmette-Guérin and platinum-based chemotherapy are currently the standard of care for non-muscle invasive and advanced or metastatic urothelial cancer (mUC), respectively. Recently, a subset of patients with locally advanced or mUC has shown to be responsive to immune checkpoint inhibitors (ICIs), e.g., the anti-cytotoxic T-lymphocyte-associated protein 4 and programmed cell death -1/programmed death-ligand1 (PD-1/PD-L1) antibodies. Due to the relevant clinical benefit of immunotherapy for mUC, in 2016, the United States Food and Drug Administration (FDA) approved five immunotherapeutic agents as second-line or first-line treatments for patients with advanced bladder cancer who did not profit from or were ineligible for standard therapy. In this review, we discuss the role of immunotherapy in bladder cancer and recent clinical applications of PD-1/PD-L1 blockade in mUC. Furthermore, we evaluate a variable response rate to ICIs treatment and outline potential biomarkers predictive of immunotherapy response.
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Affiliation(s)
- Giandomenico Roviello
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy; (S.N.); (E.M.)
| | - Martina Catalano
- School of Human Health Sciences, University of Florence, Largo Brambilla 3, 50134 Florence, Italy;
| | - Stefania Nobili
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy; (S.N.); (E.M.)
| | - Raffaella Santi
- Department of Pathology, Careggi University Hospital, University of Firenze, 50139 Firenze, Italy;
| | - Enrico Mini
- Department of Health Sciences, Section of Clinical Pharmacology and Oncology, University of Florence, Viale Pieraccini, 6, 50139 Florence, Italy; (S.N.); (E.M.)
| | - Gabriella Nesi
- Department of Health Sciences, University of Florence, Section of Pathological Anatomy, University Hospital of Florence, 50139 Florence, Italy;
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20
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Bracci L, Fragale A, Gabriele L, Moschella F. Towards a Systems Immunology Approach to Unravel Responses to Cancer Immunotherapy. Front Immunol 2020; 11:582744. [PMID: 33193392 PMCID: PMC7649803 DOI: 10.3389/fimmu.2020.582744] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
Immunotherapy, particularly immune checkpoint blockade and chimeric antigen receptor (CAR)-T cells, holds a great promise against cancer. These treatments have markedly improved survival in solid as well as in hematologic tumors previously considered incurable. However, durable responses occur in a fraction of patients, and existing biomarkers (e.g. PD-L1) have shown limited prediction power. This scenario highlights the need to dissect the complex interplay between immune and tumor cells to identify reliable biomarkers of response to be used for patients’ selection. In this context, systems immunology represents indeed the new frontier to address important clinical challenges in biomarker discovery. Through the integration of multiple layers of data obtained with several high-throughput approaches, systems immunology may give insights on the vast range of inter-individual differences and on the influences of genes and factors that cooperatively shape the individual immune response to a given treatment. In this Mini Review, we give an overview of the current high-throughput methodologies, including genomics, epigenomics, transcriptomics, metabolomics, proteomics, and multi-parametric phenotyping suitable for systems immunology as well as on the key steps of data integration and biological interpretation. Additionally, we review recent studies in which multi-omics technologies have been used to characterize mechanisms of response and to identify powerful biomarkers of response to checkpoint inhibitors, CAR-T cell therapy, dendritic cell-based and peptide-based cancer vaccines. We also highlight the need of favoring the collaboration of researchers with complementary expertise and of integrating multi-omics data into biological networks with the final goal of developing accurate markers of therapeutic response.
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Affiliation(s)
- Laura Bracci
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Fragale
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Lucia Gabriele
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Federica Moschella
- Tumor Immunology Unit, Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
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21
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Zhang H, Zhou X, Liu D, Zhu Y, Ma Q, Zhang Y. Progress and challenges of personalized neoantigens in the clinical treatment of tumors. MEDICINE IN DRUG DISCOVERY 2020. [DOI: 10.1016/j.medidd.2020.100030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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22
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Bellesoeur A, Torossian N, Amigorena S, Romano E. Advances in theranostic biomarkers for tumor immunotherapy. Curr Opin Chem Biol 2020; 56:79-90. [PMID: 32217357 DOI: 10.1016/j.cbpa.2020.02.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 01/05/2023]
Abstract
Cancer treatment has known a revolution with the emergence of immune checkpoint inhibitors. However, accurate theranostic biomarkers are lacking. In this review, we discuss different types of biomarkers currently under investigation. First, we focus on tissue biomarkers including PD-L1 expression by immunohistochemistry-the first Food and Drug Administration-approved biomarker-despite conflicting results. In addition, we report on novel biomarkers, including protein-based, molecular (tumor mutational load, immune signature…), circulating (neutrophil-to-lymphocyte ratio, serum cytokines…), and imaging-based biomarkers (radiomic signatures and positron-emission tomography using radiolabeled antibodies). We highlight the limitations of each candidate biomarker and finally discuss combinatorial approaches for their use and the opportunity to switch from a predictive strategy of biomarker research to an adaptive one in the field of cancer immunotherapy.
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Affiliation(s)
- Audrey Bellesoeur
- Dpt of Medical Oncology, Institut Curie, Paris, France; Dpt of Radio-pharmacology, Institut Curie-Hôpital René Huguenin, Saint-Cloud, France
| | | | - Sebastian Amigorena
- Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France
| | - Emanuela Romano
- Dpt of Medical Oncology, Institut Curie, Paris, France; Dpt of Drug Development and Innovation, Institut Curie, Paris, France; Center for Cancer Immunotherapy, INSERM U932, Institut Curie, PSL Research University, Paris, France.
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23
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The prognostic value of tumor mutational burden and immune cell infiltration in esophageal cancer patients with or without radiotherapy. Aging (Albany NY) 2020; 12:4603-4616. [PMID: 32165590 PMCID: PMC7093160 DOI: 10.18632/aging.102917] [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: 10/29/2019] [Accepted: 03/02/2020] [Indexed: 02/07/2023]
Abstract
Growing evidence highlighted the tumor mutational burden (TMB) as an important feature of carcinogenesis and therapeutic efficacy in esophageal cancer (EC). Our study aimed to explore the genomic landscape and the correlation between TMB and immune cell infiltration in EC patients with or without radiotherapy. The EC patients were categorized into high TMB (TMB-H) and low TMB (TMB-L) groups by the ESTIMATE algorithm, and subgroup analysis was performed based on receiving radiotherapy or not. Univariate regression analysis indicated TMB and TNM stages as high-risk prognostic factors (Hazard ratio > 1 and P < 0.05). Multivariate regression analysis suggested TMB as an independent prognostic factor (Hazard ratio = 1.051, P = 0.003). Kaplan-Meier analysis showed no significant difference of the overall survival (OS) between TMB-H and TMB-L groups (P = 0.082). However, EC patients without radiotherapy in the TMB-H group had significantly decreased OS (P = 0.038) and increased Tregs cell infiltration (P = 0.033). These results suggested TMB as a prognostic marker for EC patients. Especially for patients who did not receive radiotherapy, the prognosis of TMB-H patients was significantly poorer than that of TMB-L patients, which might result from the different regulatory T cell infiltration.
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24
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Roudko V, Greenbaum B, Bhardwaj N. Computational Prediction and Validation of Tumor-Associated Neoantigens. Front Immunol 2020; 11:27. [PMID: 32117226 PMCID: PMC7025577 DOI: 10.3389/fimmu.2020.00027] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/08/2020] [Indexed: 12/30/2022] Open
Abstract
Tumor progression is typically accompanied by an accumulation of driver and passenger somatic mutations. A handful of those mutations occur in protein coding genes which introduce non-synonymous polymorphisms. Certain substitutions may give rise to novel, tumor-associated antigens or neoantigens, presentable by cancer cells to the host adaptive immune system. As antigen recognition is the core of an effective immune response, the identification of patient tumor specific antigens derived from transformed cells is of importance for immunotherapeutic approaches. Recent technological advances in DNA sequencing of tumor genomes, advances in gene expression analysis, algorithm development for antigen predictions and methods for T-cell receptor (TCR) repertoire sequencing have facilitated the selection of candidate immunogenic neoantigens. In this regard, multiple research groups have reported encouraging results of neoantigen-based cancer vaccines that generate tumor antigen specific immune responses, both in mouse models and clinical trials. Additionally, both the quantity and quality of neoantigens has been shown to have predictive value for clinical outcomes in checkpoint-blockade immunotherapy in certain tumor types. Neoantigen recognition by vaccination or through adoptive T cell therapy may have unprecedented potential to advance cancer immunotherapy in combination with other approaches. In our review we discuss three parameters regarding neoantigens: computational methods for epitope prediction, experimental methods for epitope immunogenicity validation and future directions for improvement of those methods. Within each section, we will describe the advantages and limitations of existing methods as well as highlight pressing fundamental problems to be addressed.
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Affiliation(s)
- Vladimir Roudko
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Center for Computational Immunology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Benjamin Greenbaum
- Center for Computational Immunology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Department of Pathology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
| | - Nina Bhardwaj
- Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, United States
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25
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Wu Z, Wang M, Liu Q, Liu Y, Zhu K, Chen L, Guo H, Li Y, Shi B. Identification of gene expression profiles and immune cell infiltration signatures between low and high tumor mutation burden groups in bladder cancer. Int J Med Sci 2020; 17:89-96. [PMID: 31929742 PMCID: PMC6945555 DOI: 10.7150/ijms.39056] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/14/2019] [Indexed: 12/23/2022] Open
Abstract
Bladder cancer is one of the most commonly diagnosed tumors and is results from the accumulation of somatic mutations in the DNA. Tumor mutation burden (TMB) has been associated with cancer immunotherapeutic response. In this study, we attempted to explore the correlation between TMB and cancer prognosis. Identify the different expressed genes and immune cell infiltration signatures between low and high TMB group. Mutation data, gene expression profiles and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database. Patients were divided into high and low TMB groups, allowing differentially expressed genes (DEGs) to be identified. Functional enrichment and protein-protein interaction (PPI) network analysis were used to identify the functions of the DEGs. And immune cell infiltration signatures were evaluated by CIBERSORT algorithm. These results shown that high TMB was significantly associated with prognosis. We obtained a list of TMB related genes which may influence the infiltrations of immune cells. We also found a higher proportion of CD8 T cells, CD4 T cells and NK cells in the high TMB group. Our data suggest that higher TMB tends to promote the infiltrations of T cells and NK cells and patients with higher TMB may achieve a more favorable prognosis in bladder cancer.
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Affiliation(s)
- Zonglong Wu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Muru Wang
- Division of Gastroenterology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Qinggang Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Yaxiao Liu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Kejia Zhu
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Lipeng Chen
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Hongda Guo
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Yan Li
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
| | - Benkang Shi
- Department of Urology, Qilu Hospital of Shandong University, Jinan, China
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26
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Blanc E, Holtgrewe M, Dhamodaran A, Messerschmidt C, Willimsky G, Blankenstein T, Beule D. Identification and ranking of recurrent neo-epitopes in cancer. BMC Med Genomics 2019; 12:171. [PMID: 31775766 PMCID: PMC6882202 DOI: 10.1186/s12920-019-0611-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/25/2019] [Indexed: 12/25/2022] Open
Abstract
Background Immune escape is one of the hallmarks of cancer and several new treatment approaches attempt to modulate and restore the immune system’s capability to target cancer cells. At the heart of the immune recognition process lies antigen presentation from somatic mutations. These neo-epitopes are emerging as attractive targets for cancer immunotherapy and new strategies for rapid identification of relevant candidates have become a priority. Methods We carefully screen TCGA data sets for recurrent somatic amino acid exchanges and apply MHC class I binding predictions. Results We propose a method for in silico selection and prioritization of candidates which have a high potential for neo-antigen generation and are likely to appear in multiple patients. While the percentage of patients carrying a specific neo-epitope and HLA-type combination is relatively small, the sheer number of new patients leads to surprisingly high reoccurence numbers. We identify 769 epitopes which are expected to occur in 77629 patients per year. Conclusion While our candidate list will definitely contain false positives, the results provide an objective order for wet-lab testing of reusable neo-epitopes. Thus recurrent neo-epitopes may be suitable to supplement existing personalized T cell treatment approaches with precision treatment options.
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Affiliation(s)
- Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Manuel Holtgrewe
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Arunraj Dhamodaran
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany
| | - Clemens Messerschmidt
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Gerald Willimsky
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
| | - Thomas Blankenstein
- Institute of Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Lindenberger Weg 80, Berlin, 13125, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.,Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, Charitéplatz 1, Berlin, 10117, Germany. .,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Robert-Rössle-Str. 10, Berlin, 13092, Germany.
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27
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Zhou C, Wei Z, Zhang Z, Zhang B, Zhu C, Chen K, Chuai G, Qu S, Xie L, Gao Y, Liu Q. pTuneos: prioritizing tumor neoantigens from next-generation sequencing data. Genome Med 2019; 11:67. [PMID: 31666118 PMCID: PMC6822339 DOI: 10.1186/s13073-019-0679-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Cancer neoantigens are expressed only in cancer cells and presented on the tumor cell surface in complex with major histocompatibility complex (MHC) class I proteins for recognition by cytotoxic T cells. Accurate and rapid identification of neoantigens play a pivotal role in cancer immunotherapy. Although several in silico tools for neoantigen prediction have been presented, limitations of these tools exist. RESULTS We developed pTuneos, a computational pipeline for prioritizing tumor neoantigens from next-generation sequencing data. We tested the performance of pTuneos on the melanoma cancer vaccine cohort data and tumor-infiltrating lymphocyte (TIL)-recognized neopeptide data. pTuneos is able to predict the MHC presentation and T cell recognition ability of the candidate neoantigens, and the actual immunogenicity of single-nucleotide variant (SNV)-based neopeptides considering their natural processing and presentation, surpassing the existing tools with a comprehensive and quantitative benchmark of their neoantigen prioritization performance and running time. pTuneos was further tested on The Cancer Genome Atlas (TCGA) cohort data as well as the melanoma and non-small cell lung cancer (NSCLC) cohort data undergoing checkpoint blockade immunotherapy. The overall neoantigen immunogenicity score proposed by pTuneos is demonstrated to be a powerful and pan-cancer marker for survival prediction compared to traditional well-established biomarkers. CONCLUSIONS In summary, pTuneos provides the state-of-the-art one-stop and user-friendly solution for prioritizing SNV-based candidate neoepitopes, which could help to advance research on next-generation cancer immunotherapies and personalized cancer vaccines. pTuneos is available at https://github.com/bm2-lab/pTuneos , with a Docker version for quick deployment at https://cloud.docker.com/u/bm2lab/repository/docker/bm2lab/ptuneos .
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Affiliation(s)
- Chi Zhou
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Zhiting Wei
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Zhanbing Zhang
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Biyu Zhang
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Chenyu Zhu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Ke Chen
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Guohui Chuai
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Sheng Qu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
- Department of Ophthalmology, Ninghai First Hospital, Ninghai, 310000, Zhejiang, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai, 201203, China
| | - Yong Gao
- Department of Digestive Oncology, Shanghai East Hospital, Tongji University, Shanghai, 200120, China
| | - Qi Liu
- Department of Endocrinology & Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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Protecting Tumors by Preventing Human Papilloma Virus Antigen Presentation: Insights from Emerging Bioinformatics Algorithms. Cancers (Basel) 2019; 11:cancers11101543. [PMID: 31614809 PMCID: PMC6826432 DOI: 10.3390/cancers11101543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Recent developments in bioinformatics technologies have led to advances in our understanding of how oncogenic viruses such as the human papilloma virus drive cancer progression and evade the host immune system. Here, we focus our review on understanding how these emerging bioinformatics technologies influence our understanding of how human papilloma virus (HPV) drives immune escape in cancers of the head and neck, and how these new informatics approaches may be generally applicable to other virally driven cancers. Indeed, these tools enable researchers to put existing data from genome wide association studies, in which high risk alleles have been identified, in the context of our current understanding of cellular processes regulating neoantigen presentation. In the future, these new bioinformatics approaches are highly likely to influence precision medicine-based decision making for the use of immunotherapies in virally driven cancers.
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Scheetz L, Park KS, Li Q, Lowenstein PR, Castro MG, Schwendeman A, Moon JJ. Engineering patient-specific cancer immunotherapies. Nat Biomed Eng 2019; 3:768-782. [PMID: 31406259 PMCID: PMC6783331 DOI: 10.1038/s41551-019-0436-x] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
Abstract
Research into the immunological processes implicated in cancer has yielded a basis for the range of immunotherapies that are now considered the fourth pillar of cancer treatment (alongside surgery, radiotherapy and chemotherapy). For some aggressive cancers, such as advanced non-small-cell lung carcinoma, combination immunotherapies have resulted in unprecedented treatment efficacy for responding patients, and have become frontline therapies. Individualized immunotherapy, enabled by the identification of patient-specific mutations, neoantigens and biomarkers, and facilitated by advances in genomics and proteomics, promises to broaden the responder patient population. In this Perspective, we give an overview of immunotherapies leveraging engineering approaches, including the design of biomaterials, delivery strategies and nanotechnology solutions, for the realization of individualized cancer treatments such as nanoparticle vaccines customized with neoantigens, cell therapies based on patient-derived dendritic cells and T cells, and combinations of theranostic strategies. Developments in precision cancer immunotherapy will increasingly rely on the adoption of engineering principles.
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Affiliation(s)
- Lindsay Scheetz
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - Kyung Soo Park
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Qiao Li
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Pedro R Lowenstein
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Maria G Castro
- Department of Neurosurgery, University of Michigan, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Anna Schwendeman
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI, USA.
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.
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Narang P, Chen M, Sharma AA, Anderson KS, Wilson MA. The neoepitope landscape of breast cancer: implications for immunotherapy. BMC Cancer 2019; 19:200. [PMID: 30832597 PMCID: PMC6399957 DOI: 10.1186/s12885-019-5402-1] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Background Cancer immunotherapy with immune checkpoint blockade (CKB) is now standard of care for multiple cancers. The clinical response to CKB is associated with T cell immunity targeting cancer-induced mutations that generate novel HLA-binding epitopes (neoepitopes). Methods Here, we developed a rapid bioinformatics pipeline and filtering strategy, EpitopeHunter, to identify and prioritize clinically relevant neoepitopes from the landscape of somatic mutations. We used the pipeline to determine the frequency of neoepitopes from the TCGA dataset of invasive breast cancers. We predicted HLA class I-binding neoepitopes for 870 breast cancer samples and filtered the neoepitopes based on tumor transcript abundance. Results We found that the total mutational burden (TMB) was highest for triple-negative breast cancer, TNBC, (median = 63 mutations, range: 2–765); followed by HER-2(+) (median = 39 mutations, range: 1–1206); and lowest for ER/PR(+)HER-2(−) (median = 32 mutations, range: 1–2860). 40% of the nonsynonymous mutations led to the generation of predicted neoepitopes. The neoepitope load (NEL) is highly correlated with the mutational burden (R2 = 0.86). Conclusions Only half (51%) of the predicted neoepitopes are expressed at the RNA level (FPKM≥2), indicating the importance of assessing whether neoepitopes are transcribed. However, of all patients, 93% have at least one expressed predicted neoepitope, indicating that most breast cancer patients have the potential for neo-epitope targeted immunotherapy. Electronic supplementary material The online version of this article (10.1186/s12885-019-5402-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pooja Narang
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA
| | - Meixuan Chen
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA.,Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Amit A Sharma
- Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Karen S Anderson
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA. .,Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA. .,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
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31
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Abstract
Checkpoint inhibitor-based immunotherapies that target cytotoxic T lymphocyte antigen 4 (CTLA4) or the programmed cell death 1 (PD1) pathway have achieved impressive success in the treatment of different cancer types. Yet, only a subset of patients derive clinical benefit. It is thus critical to understand the determinants driving response, resistance and adverse effects. In this Review, we discuss recent work demonstrating that immune checkpoint inhibitor efficacy is affected by a combination of factors involving tumour genomics, host germline genetics, PD1 ligand 1 (PDL1) levels and other features of the tumour microenvironment, as well as the gut microbiome. We focus on recently identified molecular and cellular determinants of response. A better understanding of how these variables cooperate to affect tumour-host interactions is needed to optimize the implementation of precision immunotherapy.
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Affiliation(s)
- Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Diego Chowell
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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32
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Verma V, Sharma G, Singh A. Immunotherapy in extensive small cell lung cancer. Exp Hematol Oncol 2019; 8:5. [PMID: 30740266 PMCID: PMC6360752 DOI: 10.1186/s40164-019-0129-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Small cell lung cancer which constitutes about 15% of lung cancers is pathobiologically and clinically distinct from non small cell cancer. Histologically it is characterized by small cells with scant cytoplasm, absent or inconspicuous nucleoli, extensive necrosis, and expresses neuroendocrine markers. It is on a spectrum of neuroendocrine cancer that extend from typical carcinoids to large cell to small cell cancer. Clinically it behaves in a more malignant fashion with a rapid doubling time, early metastasis. They respond rapidly to cytotoxic treatment however tend to develop resistance soon. Immunotherapy with checkpoint inhibitors take advantage of PD 1 ligand-receptor axis between the tumor and T cells or CTLA4 on T cells which when engaged lead to inhibition of T cells. This inhibition helps tumors to evade immune surveillance. Checkpoint inhibitors break this axis by either binding to PD 1 ligands or PD 1 to CTLA4, thereby preventing tumors to evade the immune systems. This has led to remarkable responses in tumors. The immune related adverse effects can be severe however are experienced at much lower rates as compared to cytotoxic chemotherapy. Recently, CheckMate 032 has shown impressive response rates with Nivolumab and Nivolumab/Ipilimumab in relapsed small cell cancer. IMpower 133, a phase 3 trial showed that addition of Atezolizumab to Carbo/Etoposide led to a significant survival benefit in treatment naive extensive small cell cancer. This review will summarize recent developments and ongoing studies of immune therapy in extensive small cell cancer in addition to a brief summary of immune therapy landscape of Non small cell lung cancer. Investigational approaches to immune therapy have also been delineated.
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Affiliation(s)
- Vaibhav Verma
- 1Mon Health Medical Center, Morgantown, WV USA.,Morgantown, WV USA
| | - Geeti Sharma
- 3Steward Medical Group, Trumbull Medical Center, Youngstown, OH USA
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Chan TA, Yarchoan M, Jaffee E, Swanton C, Quezada SA, Stenzinger A, Peters S. Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic. Ann Oncol 2019; 30:44-56. [PMID: 30395155 PMCID: PMC6336005 DOI: 10.1093/annonc/mdy495] [Citation(s) in RCA: 1656] [Impact Index Per Article: 331.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Treatment with immune checkpoint blockade (ICB) with agents such as anti-programmed cell death protein 1 (PD-1), anti-programmed death-ligand 1 (PD-L1), and/or anti-cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) can result in impressive response rates and durable disease remission but only in a subset of patients with cancer. Expression of PD-L1 has demonstrated utility in selecting patients for response to ICB and has proven to be an important biomarker for patient selection. Tumor mutation burden (TMB) is emerging as a potential biomarker. However, refinement of interpretation and contextualization is required. Materials and methods In this review, we outline the evolution of TMB as a biomarker in oncology, delineate how TMB can be applied in the clinic, discuss current limitations as a diagnostic test, and highlight mechanistic insights unveiled by the study of TMB. We review available data to date studying TMB as a biomarker for response to ICB by tumor type, focusing on studies proposing a threshold for TMB as a predictive biomarker for ICB activity. Results High TMB consistently selects for benefit with ICB therapy. In lung, bladder and head and neck cancers, the current predictive TMB thresholds proposed approximate 200 non-synonymous somatic mutations by whole exome sequencing (WES). PD-L1 expression influences response to ICB in high TMB tumors with single agent PD-(L)1 antibodies; however, response may not be dependent on PD-L1 expression in the setting of anti-CTLA4 or anti-PD-1/CTLA-4 combination therapy. Disease-specific TMB thresholds for effective prediction of response in various other malignancies are not well established. Conclusions TMB, in concert with PD-L1 expression, has been demonstrated to be a useful biomarker for ICB selection across some cancer types; however, further prospective validation studies are required. TMB determination by selected targeted panels has been correlated with WES. Calibration and harmonization will be required for optimal utility and alignment across all platforms currently used internationally. Key challenges will need to be addressed before broader use in different tumor types.
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Affiliation(s)
- T A Chan
- Human Oncology and Pathogenesis Program; The Immunogenomics and Precision Oncology Program, Memorial Sloan Kettering Cancer Center, New York.
| | - M Yarchoan
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - E Jaffee
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, USA
| | - C Swanton
- Translational Cancer Therapeutics Laboratory, Francis Crick Institute, London
| | - S A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg; Germany and German Cancer Consortium (DKTK), Heidelberg Partner Site, Heidelberg, Germany
| | - S Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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34
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Novel Approaches to Immunotherapy in Triple Negative Breast Cancer. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2018. [DOI: 10.5812/ijcm.87024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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35
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Yi M, Qin S, Zhao W, Yu S, Chu Q, Wu K. The role of neoantigen in immune checkpoint blockade therapy. Exp Hematol Oncol 2018; 7:28. [PMID: 30473928 PMCID: PMC6240277 DOI: 10.1186/s40164-018-0120-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023] Open
Abstract
Immune checkpoint inhibitor induces tumor rejection by activated host immune system. The anti-tumor immune response consists of capture, presentation, recognition of neoantigen, as well as subsequent killing of tumor cell. Due to the interdependence among this series of stepwise events, neoantigen profoundly influences the efficacy of anti-immune checkpoint therapy. Moreover, the neoantigen-specific T cell reactivity is the cornerstone of multiple immunotherapies. In fact, several strategies targeting neoantigen have been attempted for synergetic effect with immune checkpoint inhibitor. Increasing neoantigen presentation to immune system by oncolytic virus, radiotherapy, or cancer vaccine is feasible to enhance neoantigen-specific T cell reactivity in theory. However, some obstacles have not been overcome in practice such as dynamic variation of neoantigen landscape, identification of potential neoantigen, maintenance of high T cell titer post vaccination. In addition, adoptive T cell transfer is another approach to enhance neoantigen-specific T cell reactivity, especially for patients with severe immunosuppression. In this review, we highlighted the advancements of neoantigen and innovative explorations of utilization of neoantigen repertoire in immune checkpoint blockade therapy.
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Affiliation(s)
- Ming Yi
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Shuang Qin
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Weiheng Zhao
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Shengnan Yu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Qian Chu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
| | - Kongming Wu
- Department of Oncology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030 China
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36
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Abstract
Somatic variations are frequent and important drivers in cancers. Amino acid substitutions can yield neoantigens that are detected by the immune system. Neoantigens can lead to immune response and tumor rejection. Although neoantigen load and occurrence have been widely studied, a detailed pan-cancer analysis of the occurrence and characterization of neoepitopes is missing. We investigated the proteome-wide amino acid substitutions in 8-, 9-, 10-, and 11-mer peptides in 30 cancer types with the NetMHC 4.0 software. 11,316,078 (0.24%) of the predicted 8-, 9-, 10-, and 11-mer peptides were highly likely neoepitope candidates and were derived from 95.44% of human proteins. Binding affinity to MHC molecules is just one of the many epitope features. The most likely epitopes are those which are detected by several MHCs and of several peptide lengths. 9-mer peptides are the most common among the high binding neoantigens. 0.17% of all variants yield more than 100 neoepitopes and are considered as the best candidates for any application. Amino acid distributions indicate that variants at all positions in neoepitopes of any length are, on average, more hydrophobic than the wild-type residues. We characterized properties of neoepitopes in 30 cancer types and estimated the likely numbers of tumor-derived epitopes that could induce an immune response. We found that amino acid distributions, at all positions in neoepitopes of all lengths, contain more hydrophobic residues than the wild-type sequences implying that the hydropathy nature of neoepitopes is an important property. The neoepitope characteristics can be employed for various applications including targeted cancer vaccine development for precision medicine.
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37
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Update on Tumor Neoantigens and Their Utility: Why It Is Good to Be Different. Trends Immunol 2018; 39:536-548. [PMID: 29751996 DOI: 10.1016/j.it.2018.04.005] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/18/2022]
Abstract
Antitumor rejection by the immune system is a complex process that is regulated by several factors. Among these factors are the quality and quantity of mutational events that occur in cancer cells. Perhaps one of the most important types of mutations that influence antitumor immunity is the neoantigen, that is, a non-self-antigen that arises as a result of somatic mutation. Recent work has demonstrated that neoantigens hold significant promise for developing new diagnostic and therapeutic modalities. Therapeutic targeting of neoantigens is important for achieving benefit following therapy with immune checkpoint blockade agents or for cancer vaccines targeting mutations. Here, we review our understanding of neoantigens and discuss new developments in the quest to use them in cancer immunotherapy.
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38
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Valentini D, Rao M, Meng Q, von Landenberg A, Bartek J, Sinclair G, Paraschoudi G, Jäger E, Harvey-Peredo I, Dodoo E, Maeurer M. Identification of neoepitopes recognized by tumor-infiltrating lymphocytes (TILs) from patients with glioma. Oncotarget 2018; 9:19469-19480. [PMID: 29731959 PMCID: PMC5929402 DOI: 10.18632/oncotarget.24955] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/24/2018] [Indexed: 12/16/2022] Open
Abstract
Neoepitope-specific T-cell responses have been shown to induce durable clinical responses in patients with advanced cancers. We explored the recognition patterns of tumor-infiltrating T lymphocytes (TILs) from patients with glioblastoma multiforme (GBM), the most fatal form of tumors of the central nervous system. Whole-genome sequencing was used for generating DNA sequences representing the entire spectrum of ‘private’ somatic mutations in GBM tumors from five patients, followed by 15-mer peptide prediction and subsequent peptide synthesis. For each mutated peptide sequence, the wildtype sequence was also synthesized and individually co-cultured with autologous GBM TILs, which had been expanded in vitro with a combination of interleukin (IL)-2, IL-15 and IL-21. After seven days of culture, interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α) and/or IL-17A production was measured by ELISA in culture supernatants, and used as an epitope-specific immune response readout. Mutated peptides that induced a strong cytokine response were considered to contain legitimate neoepitopes. TILs from 5/5 patients with GBM exhibited specific immune reactivity profiles to the nominal target peptides, defined by IFN-γ and/or TNF-α production, as well as IL-17A. Neoepitopes, defined by mutated peptides inducing IFN-γ and/or TNF-α production without or only minimal reactivity to the wildtype sequences, were found for each individual patient. CD8+ TILs dominated the patients’ responses to private neoepitopes. The present study shows that neoepitope-specific TIL reactivity constitutes an important arm of anti-tumor immune responses in patients with GBM, and thus a powerful tool for developing next-generation personalized immunotherapies.
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Affiliation(s)
- Davide Valentini
- Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Martin Rao
- Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden
| | - Qingda Meng
- Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden
| | - Anna von Landenberg
- Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden
| | - Jiri Bartek
- Department of Neurosurgery, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.,Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Georges Sinclair
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Georgia Paraschoudi
- Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden
| | - Elke Jäger
- Krankenhaus Nordwest, Division of Oncology and Hematology, Frankfurt, Germany
| | - Inti Harvey-Peredo
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Ernest Dodoo
- Department of Neurosurgery, Karolinska University Hospital, Stockholm, Sweden
| | - Markus Maeurer
- Centre for Allogeneic Stem Cell Transplantation (CAST), Karolinska University Hospital Huddinge, Stockholm, Sweden.,Therapeutic Immunology Unit (TIM), Department of Laboratory Medicine (LABMED), Karolinska Institutet, Stockholm, Sweden.,Krankenhaus Nordwest, Division of Oncology and Hematology, Frankfurt, Germany
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39
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Gul A, Erman B. Binding stability of peptides on major histocompatibility complex class I proteins: role of entropy and dynamics. Phys Biol 2018; 15:026005. [PMID: 29035272 DOI: 10.1088/1478-3975/aa93b8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Prediction of peptide binding on specific human leukocyte antigens (HLA) has long been studied with successful results. We herein describe the effects of entropy and dynamics by investigating the binding stabilities of 10 nanopeptides on various HLA Class I alleles using a theoretical model based on molecular dynamics simulations. The fluctuational entropies of the peptides are estimated over a temperature range of 310-460 K. The estimated entropies correlate well with experimental binding affinities of the peptides: peptides that have higher binding affinities have lower entropies compared to non-binders, which have significantly larger entropies. The computation of the entropies is based on a simple model that requires short molecular dynamics trajectories and allows for approximate but rapid determination. The paper draws attention to the long neglected dynamic aspects of peptide binding, and provides a fast computation scheme that allows for rapid scanning of large numbers of peptides on selected HLA antigens, which may be useful in defining the right peptides for personal immunotherapy.
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Affiliation(s)
- Ahmet Gul
- Istanbul Faculty of Medicine, Division of Rheumatology, Department of Internal Medicine, Istanbul University, Istanbul, Turkey
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40
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Baumgaertner P, Ioannidou K, Speiser DE. Immune Monitoring of Blood and Tumor Microenvironment. Oncoimmunology 2018. [DOI: 10.1007/978-3-319-62431-0_41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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41
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Roh W, Chen PL, Reuben A, Spencer CN, Prieto PA, Miller JP, Gopalakrishnan V, Wang F, Cooper ZA, Reddy SM, Gumbs C, Little L, Chang Q, Chen WS, Wani K, De Macedo MP, Chen E, Austin-Breneman JL, Jiang H, Roszik J, Tetzlaff MT, Davies MA, Gershenwald JE, Tawbi H, Lazar AJ, Hwu P, Hwu WJ, Diab A, Glitza IC, Patel SP, Woodman SE, Amaria RN, Prieto VG, Hu J, Sharma P, Allison JP, Chin L, Zhang J, Wargo JA, Futreal PA. Integrated molecular analysis of tumor biopsies on sequential CTLA-4 and PD-1 blockade reveals markers of response and resistance. Sci Transl Med 2017; 9:9/379/eaah3560. [PMID: 28251903 DOI: 10.1126/scitranslmed.aah3560] [Citation(s) in RCA: 603] [Impact Index Per Article: 86.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/17/2016] [Accepted: 02/04/2017] [Indexed: 12/20/2022]
Abstract
Immune checkpoint blockade produces clinical benefit in many patients. However, better biomarkers of response are still needed, and mechanisms of resistance remain incompletely understood. To address this, we recently studied a cohort of melanoma patients treated with sequential checkpoint blockade against cytotoxic T lymphocyte antigen-4 (CTLA-4) followed by programmed death receptor-1 (PD-1) and identified immune markers of response and resistance. Building on these studies, we performed deep molecular profiling including T cell receptor sequencing and whole-exome sequencing within the same cohort and demonstrated that a more clonal T cell repertoire was predictive of response to PD-1 but not CTLA-4 blockade. Analysis of CNAs identified a higher burden of copy number loss in nonresponders to CTLA-4 and PD-1 blockade and found that it was associated with decreased expression of genes in immune-related pathways. The effect of mutational load and burden of copy number loss on response was nonredundant, suggesting the potential utility of a combinatorial biomarker to optimize patient care with checkpoint blockade therapy.
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Affiliation(s)
- Whijae Roh
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Cancer Biology Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Pei-Ling Chen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine N Spencer
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peter A Prieto
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John P Miller
- Oncology Research for Biologics and Immunotherapy Translation, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Feng Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zachary A Cooper
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qing Chang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei-Shen Chen
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mariana Petaccia De Macedo
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Pathology Department, A.C.Camargo Cancer Center, São Paulo, SP-01509-010, Brazil
| | - Eveline Chen
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jacob L Austin-Breneman
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hong Jiang
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason Roszik
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T Tetzlaff
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hussein Tawbi
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander J Lazar
- Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wen-Jen Hwu
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Isabella C Glitza
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sapna P Patel
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E Woodman
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N Amaria
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Victor G Prieto
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James P Allison
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lynda Chin
- University of Texas System, Austin, TX 78701, USA
| | - Jianhua Zhang
- Applied Cancer Science Institute, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. .,Department of Surgical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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42
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Basanta D, Anderson ARA. Homeostasis Back and Forth: An Ecoevolutionary Perspective of Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a028332. [PMID: 28289244 DOI: 10.1101/cshperspect.a028332] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The role of genetic mutations in cancer is indisputable: They are a key source of tumor heterogeneity and drive its evolution to malignancy. But, the success of these new mutant cells relies on their ability to disrupt the homeostasis that characterizes healthy tissues. Mutated clones unable to break free from intrinsic and extrinsic homeostatic controls will fail to establish a tumor. Here, we will discuss, through the lens of mathematical and computational modeling, why an evolutionary view of cancer needs to be complemented by an ecological perspective to understand why cancer cells invade and subsequently transform their environment during progression. Importantly, this ecological perspective needs to account for tissue homeostasis in the organs that tumors invade, because they perturb the normal regulatory dynamics of these tissues, often coopting them for its own gain. Furthermore, given our current lack of success in treating advanced metastatic cancers through tumor-centric therapeutic strategies, we propose that treatments that aim to restore homeostasis could become a promising venue of clinical research. This ecoevolutionary view of cancer requires mechanistic mathematical models to both integrate clinical with biological data from different scales but also to detangle the dynamic feedback between the tumor and its environment. Importantly, for these models to be useful, they need to embrace a higher degree of complexity than many mathematical modelers are traditionally comfortable with.
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Affiliation(s)
- David Basanta
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, Florida 33612
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, Moffitt Cancer Center, Tampa, Florida 33612
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43
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Qin Y, Ekmekcioglu S, Forget MA, Szekvolgyi L, Hwu P, Grimm EA, Jazaeri AA, Roszik J. Cervical Cancer Neoantigen Landscape and Immune Activity is Associated with Human Papillomavirus Master Regulators. Front Immunol 2017; 8:689. [PMID: 28670312 PMCID: PMC5473350 DOI: 10.3389/fimmu.2017.00689] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/29/2017] [Indexed: 01/22/2023] Open
Abstract
Human papillomaviruses (HPVs) play a major role in development of cervical cancer, and HPV oncoproteins are being targeted by immunotherapies. Although these treatments show promising results in the clinic, many patients do not benefit or the durability is limited. In addition to HPV antigens, neoantigens derived from somatic mutations may also generate an effective immune response and represent an additional and distinct immunotherapy strategy against this and other HPV-associated cancers. To explore the landscape of neoantigens in cervix cancer, we predicted all possible mutated neopeptides in two large sequencing data sets and analyzed whether mutation and neoantigen load correlate with antigen presentation, infiltrating immune cell types, and a HPV-induced master regulator gene expression signature. We found that targetable neoantigens are detected in most tumors, and there are recurrent mutated peptides from known oncogenic driver genes (KRAS, MAPK1, PIK3CA, ERBB2, and ERBB3) that are predicted to be potentially immunogenic. Our studies show that HPV-induced master regulators are not only associated with HPV load but may also play crucial roles in relation to mutation and neoantigen load, and also the immune microenvironment of the tumor. A subset of these HPV-induced master regulators positively correlated with expression of immune-suppressor molecules such as PD-L1, TGFB1, and IL-10 suggesting that they may be involved in abrogating antitumor response induced by the presence of mutations and neoantigens. Based on these results, we predict that HPV master regulators identified in our study might be potentially effective targets in cervical cancer.
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Affiliation(s)
- Yong Qin
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Suhendan Ekmekcioglu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Lorant Szekvolgyi
- MTA-DE Momentum, Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Elizabeth A Grimm
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States.,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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44
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Schmidt J, Guillaume P, Dojcinovic D, Karbach J, Coukos G, Luescher I. In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. J Biol Chem 2017; 292:11840-11849. [PMID: 28536262 DOI: 10.1074/jbc.m117.789511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/11/2017] [Indexed: 11/06/2022] Open
Abstract
Tumor exomes provide comprehensive information on mutated, overexpressed genes and aberrant splicing, which can be exploited for personalized cancer immunotherapy. Of particular interest are mutated tumor antigen T-cell epitopes, because neoepitope-specific T cells often are tumoricidal. However, identifying tumor-specific T-cell epitopes is a major challenge. A widely used strategy relies on initial prediction of human leukocyte antigen-binding peptides by in silico algorithms, but the predictive power of this approach is unclear. Here, we used the human tumor antigen NY-ESO-1 (ESO) and the human leukocyte antigen variant HLA-A*0201 (A2) as a model and predicted in silico the 41 highest-affinity, A2-binding 8-11-mer peptides and assessed their binding, kinetic complex stability, and immunogenicity in A2-transgenic mice and on peripheral blood mononuclear cells from ESO-vaccinated melanoma patients. We found that 19 of the peptides strongly bound to A2, 10 of which formed stable A2-peptide complexes and induced CD8+ T cells in A2-transgenic mice. However, only 5 of the peptides induced cognate T cells in humans; these peptides exhibited strong binding and complex stability and contained multiple large hydrophobic and aromatic amino acids. These results were not predicted by in silico algorithms and provide new clues to improving T-cell epitope identification. In conclusion, our findings indicate that only a small fraction of in silico-predicted A2-binding ESO peptides are immunogenic in humans, namely those that have high peptide-binding strength and complex stability. This observation highlights the need for improving in silico predictions of peptide immunogenicity.
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Affiliation(s)
- Julien Schmidt
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Philippe Guillaume
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | - Danijel Dojcinovic
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland
| | | | - George Coukos
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland; Department of Oncology, University Hospital of Lausanne, 1011 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig Institute for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.
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45
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Harao M, Forget MA, Roszik J, Gao H, Babiera GV, Krishnamurthy S, Chacon JA, Li S, Mittendorf EA, DeSnyder SM, Rockwood KF, Bernatchez C, Ueno NT, Radvanyi LG, Vence L, Haymaker C, Reuben JM. 4-1BB-Enhanced Expansion of CD8 + TIL from Triple-Negative Breast Cancer Unveils Mutation-Specific CD8 + T Cells. Cancer Immunol Res 2017; 5:439-445. [PMID: 28473315 DOI: 10.1158/2326-6066.cir-16-0364] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 11/16/2022]
Abstract
Triple-negative breast cancer (TNBC) highly infiltrated with CD8+ tumor-infiltrating lymphocytes (TIL) has been associated with improved prognosis. This observation led us to hypothesize that CD8+ TIL could be utilized in autologous adoptive cell therapy for TNBC, although this concept has proven to be challenging, given the difficulty in expanding CD8+ TILs in solid cancers other than in melanoma. To overcome this obstacle, we used an agonistic antibody (urelumab) to a TNFR family member, 4-1BB/CD137, which is expressed by recently activated CD8+ T cells. This approach was first utilized in melanoma and, in this study, led to advantageous growth of TILs for the majority of TNBC tumors tested. The agonistic antibody was only added in the initial setting of the culture and yet favored the propagation of CD8+ TILs from TNBC tumors. These expanded CD8+ TILs were capable of cytotoxic functions and were successfully utilized to demonstrate the presence of immunogenic mutations in autologous TNBC tumor tissue without recognition of the wild-type counterpart. Our findings open the way for a successful adoptive immunotherapy for TNBC. Cancer Immunol Res; 5(6); 439-45. ©2017 AACR.
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Affiliation(s)
- Michiko Harao
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas.,Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas.,Department of Genomic Medicine, The University of Texas MDACC, Houston, Texas
| | - Hui Gao
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Hematopathology, The University of Texas MDACC, Houston, Texas
| | - Gildy V Babiera
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Breast Surgical Oncology, The University of Texas MDACC, Houston, Texas
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Pathology, The University of Texas MDACC, Houston, Texas
| | - Jessica A Chacon
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Shumin Li
- Department of Immunology, The University of Texas MDACC, Houston, Texas
| | - Elizabeth A Mittendorf
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Breast Surgical Oncology, The University of Texas MDACC, Houston, Texas
| | - Sarah M DeSnyder
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Breast Surgical Oncology, The University of Texas MDACC, Houston, Texas
| | | | - Chantale Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Naoto T Ueno
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas.,Department of Breast Medical Oncology, The University of Texas MDACC, Houston, Texas
| | - Laszlo G Radvanyi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas
| | - Luis Vence
- Department of Immunology, The University of Texas MDACC, Houston, Texas
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center (MDACC), Houston, Texas.
| | - James M Reuben
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MDACC, Houston, Texas. .,Department of Hematopathology, The University of Texas MDACC, Houston, Texas
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46
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Riaz N, Havel JJ, Kendall SM, Makarov V, Walsh LA, Desrichard A, Weinhold N, Chan TA. Recurrent SERPINB3 and SERPINB4 mutations in patients who respond to anti-CTLA4 immunotherapy. Nat Genet 2016; 48:1327-1329. [PMID: 27668655 PMCID: PMC5553281 DOI: 10.1038/ng.3677] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 08/26/2016] [Indexed: 12/22/2022]
Abstract
Immune checkpoint blockade has shown significant promise as an anticancer treatment, yet the determinants of response are not completely understood. Here we show that somatic mutations in SERPINB3 and SERPINB4 are associated with survival after anti-CTLA4 immunotherapy in two independent cohorts of patients with melanoma (n = 174). Interestingly, serpins are homologs of the well-known ovalbumin antigen and are associated with autoimmunity. Our findings have implications for the personalization of immunotherapy.
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Affiliation(s)
- Nadeem Riaz
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Sviatoslav M Kendall
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Vladimir Makarov
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Logan A Walsh
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Alexis Desrichard
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Nils Weinhold
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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47
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Bailey P, Chang DK, Forget MA, Lucas FAS, Alvarez HA, Haymaker C, Chattopadhyay C, Kim SH, Ekmekcioglu S, Grimm EA, Biankin AV, Hwu P, Maitra A, Roszik J. Exploiting the neoantigen landscape for immunotherapy of pancreatic ductal adenocarcinoma. Sci Rep 2016; 6:35848. [PMID: 27762323 PMCID: PMC5071896 DOI: 10.1038/srep35848] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/06/2016] [Indexed: 02/06/2023] Open
Abstract
Immunotherapy approaches for pancreatic ductal adenocarcinoma (PDAC) have met with limited success. It has been postulated that a low mutation load may lead to a paucity of T cells within the tumor microenvironment (TME). However, it is also possible that while neoantigens are present, an effective immune response cannot be generated due to an immune suppressive TME. To discern whether targetable neoantigens exist in PDAC, we performed a comprehensive study using genomic profiles of 221 PDAC cases extracted from public databases. Our findings reveal that: (a) nearly all PDAC samples harbor potentially targetable neoantigens; (b) T cells are present but generally show a reduced activation signature; and (c) markers of efficient antigen presentation are associated with a reduced signature of markers characterizing cytotoxic T cells. These findings suggest that despite the presence of tumor specific neoepitopes, T cell activation is actively suppressed in PDAC. Further, we identify iNOS as a potential mediator of immune suppression that might be actionable using pharmacological avenues.
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Affiliation(s)
- Peter Bailey
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
| | - David K. Chang
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
- 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
| | - Marie-Andrée Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Francis A. San Lucas
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Hector A. Alvarez
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Chandrani Chattopadhyay
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Sun-Hee Kim
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Suhendan Ekmekcioglu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Elizabeth A. Grimm
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Andrew V. Biankin
- Wolfson Wohl Cancer Research Centre, Institute for Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow G61 1BD, UK
- West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
- 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
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Anirban Maitra
- Departments of Pathology and Translational Molecular Pathology, Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
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48
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Li Y, Kobayashi K, Mona MM, Satomi C, Okano S, Inoue H, Tani K, Takahashi A. Immunogenic FEAT protein circulates in the bloodstream of cancer patients. J Transl Med 2016; 14:275. [PMID: 27659353 PMCID: PMC5034574 DOI: 10.1186/s12967-016-1034-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 09/12/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND FEAT is an intracellular protein that potently drives tumorigenesis in vivo. It is only weakly expressed in normal human tissues, including the testis. In contrast, FEAT is aberrantly upregulated in most human cancers. The present study was designed to investigate whether FEAT is applicable to tumor immunotherapy and whether FEAT is discernible in the bloodstream as a molecular biomarker of human cancers. METHODS Two mouse FEAT peptides with predicted affinities for major histocompatibility complex H-2Kb and H-2Db were injected subcutaneously into C57BL/6 mice before subcutaneous transplantation of isogenic B16-F10 melanoma cells. Intracellular localization of FEAT was determined by immunogold electron microscopy. Immunoprecipitation was performed to determine whether FEAT was present in blood from cancer patients. A sandwich enzyme-linked immunosorbent assay was used to measure FEAT concentrations in plasma from 30 cancer patients and eight healthy volunteers. RESULTS The vaccination experiments demonstrated that FEAT was immunogenic, and that immune responses against FEAT were induced without deleterious side effects in mice. Electron microscopy revealed localization of FEAT in the cytoplasm, mitochondria, and nucleus. Immunoprecipitation identified FEAT in the blood plasma from cancer patients, while FEAT was not detected in plasma exosomes. Plasma FEAT levels were significantly higher in the presence of cancers. CONCLUSIONS These findings suggest that FEAT is a candidate for applications in early diagnosis and prevention of some cancers.
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Affiliation(s)
- Yan Li
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan.,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Kyosuke Kobayashi
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan
| | - Marwa M Mona
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan.,Department of Medical Biochemistry, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Chikako Satomi
- Division of Translational Cancer Research, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shinji Okano
- Department of Innovative Applied Oncology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Inoue
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan
| | - Kenzaburo Tani
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan.,Division of ALA Advanced Medical Research, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Atsushi Takahashi
- Division of Molecular and Clinical Genetics, Kyushu University, Fukuoka, Japan. .,Division of Translational Cancer Research, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. .,Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.
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49
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Wargo JA, Reddy SM, Reuben A, Sharma P. Monitoring immune responses in the tumor microenvironment. Curr Opin Immunol 2016; 41:23-31. [PMID: 27240055 DOI: 10.1016/j.coi.2016.05.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 05/12/2016] [Indexed: 12/15/2022]
Abstract
Immune monitoring in the tumor microenvironment allows for important insights into immune mechanisms of response and resistance to various cancer treatments; however clinical challenges exist using current strategies. Significant questions remain regarding monitoring of archival versus fresh tissue, assessment of static versus dynamic markers, evaluation of limited tissue samples, and the translation of insights gained from immunologically 'hot' tumors such as melanoma to other 'cold' tumor microenvironments prevalent in other cancer types. Current and emerging immune monitoring strategies will be examined herein, and genomic-based assays complementing these techniques will also be discussed. Finally, host genomic and external environmental factors influencing anti-tumor immune responses will be considered, including the role of the gut microbiome. Though optimal immune monitoring techniques are in evolution, great promise exists in recent advances that will help guide patient selection as far as type, sequence, and combination of therapeutic regimens to enhance anti-tumor immunity and clinical responses.
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Affiliation(s)
- Jennifer A Wargo
- Department of Surgical Oncology, Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Sangeetha M Reddy
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Unit 463, Houston, TX 77030, USA
| | - Alexandre Reuben
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Padmanee Sharma
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 1155 Pressler Street, Unit 1374, Houston, TX 77030, USA.
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50
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Opportunities for immunotherapy in microsatellite instable colorectal cancer. Cancer Immunol Immunother 2016; 65:1249-59. [PMID: 27060000 PMCID: PMC5035655 DOI: 10.1007/s00262-016-1832-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/23/2016] [Indexed: 12/22/2022]
Abstract
Microsatellite instability (MSI), the somatic accumulation of length variations in repetitive DNA sequences called microsatellites, is frequently observed in both hereditary and sporadic colorectal cancer (CRC). It has been established that defects in the DNA mismatch repair (MMR) pathway underlie the development of MSI in CRC. After the inactivation of the DNA MMR pathway, misincorporations, insertions and deletions introduced by DNA polymerase slippage are not properly recognized and corrected. Specific genomic regions, including microsatellites, are more prone for DNA polymerase slippage and, therefore, more susceptible for the introduction of these mutations if the DNA MMR capacity is lost. Some of these susceptible genomic regions are located within the coding regions of genes. Insertions and deletions in these regions may alter their reading frame, potentially resulting in the transcription and translation of frameshift peptides with c-terminally altered amino acid sequences. These frameshift peptides are called neoantigens and are highly immunogenic, which explains the enhanced immunogenicity of MSI CRC. Neoantigens contribute to increased infiltration of tumor tissue with activated neoantigen-specific cytotoxic T lymphocytes, a hallmark of MSI tumors. Currently, neoantigen-based vaccination is being studied in a clinical trial for Lynch syndrome and in a trial for sporadic MSI CRC of advanced stage. In this Focussed Research Review, we summarize current knowledge on molecular mechanisms and address immunological features of tumors with MSI. Finally, we describe their implications for immunotherapeutic approaches and provide an outlook on next-generation immunotherapy involving neoantigens and combinatorial therapies in the setting of MSI CRC.
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