1
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Xin K, Wei X, Shao J, Chen F, Liu Q, Liu B. Establishment of a novel tumor neoantigen prediction tool for personalized vaccine design. Hum Vaccin Immunother 2024; 20:2300881. [PMID: 38214336 DOI: 10.1080/21645515.2023.2300881] [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: 09/06/2023] [Accepted: 12/28/2023] [Indexed: 01/13/2024] Open
Abstract
The personalized neoantigen nanovaccine (PNVAC) platform for patients with gastric cancer we established previously exhibited promising anti-tumor immunoreaction. However, limited by the ability of traditional neoantigen prediction tools, a portion of epitopes failed to induce specific immune response. In order to filter out more neoantigens to optimize our PNVAC platform, we develop a novel neoantigen prediction model, NUCC. This prediction tool trained through a deep learning approach exhibits better neoantigen prediction performance than other prediction tools, not only in two independent epitope datasets, but also in a totally new epitope dataset we construct from scratch, including 25 patients with advance gastric cancer and 150 candidate mutant peptides, 13 of which prove to be neoantigen by immunogenicity test in vitro. Our work lay the foundation for the improvement of our PNVAC platform for gastric cancer in the future.
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Affiliation(s)
- Kai Xin
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Xiao Wei
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Jie Shao
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Fangjun Chen
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Qin Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Baorui Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
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2
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Bulashevska A, Nacsa Z, Lang F, Braun M, Machyna M, Diken M, Childs L, König R. Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy. Front Immunol 2024; 15:1394003. [PMID: 38868767 PMCID: PMC11167095 DOI: 10.3389/fimmu.2024.1394003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular focus on neoantigens as promising targets for personalized treatments. The convergence of immunogenomics, bioinformatics, and artificial intelligence (AI) has propelled the development of innovative neoantigen discovery tools and pipelines. These tools have revolutionized our ability to identify tumor-specific antigens, providing the foundation for precision cancer immunotherapy. AI-driven algorithms can process extensive amounts of data, identify patterns, and make predictions that were once challenging to achieve. However, the integration of AI comes with its own set of challenges, leaving space for further research. With particular focus on the computational approaches, in this article we have explored the current landscape of neoantigen prediction, the fundamental concepts behind, the challenges and their potential solutions providing a comprehensive overview of this rapidly evolving field.
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Affiliation(s)
- Alla Bulashevska
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Zsófia Nacsa
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Franziska Lang
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Markus Braun
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Martin Machyna
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Liam Childs
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
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3
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Yang X, Huang K, Yang D, Zhao W, Zhou X. Biomedical Big Data Technologies, Applications, and Challenges for Precision Medicine: A Review. GLOBAL CHALLENGES (HOBOKEN, NJ) 2024; 8:2300163. [PMID: 38223896 PMCID: PMC10784210 DOI: 10.1002/gch2.202300163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 09/20/2023] [Indexed: 01/16/2024]
Abstract
The explosive growth of biomedical Big Data presents both significant opportunities and challenges in the realm of knowledge discovery and translational applications within precision medicine. Efficient management, analysis, and interpretation of big data can pave the way for groundbreaking advancements in precision medicine. However, the unprecedented strides in the automated collection of large-scale molecular and clinical data have also introduced formidable challenges in terms of data analysis and interpretation, necessitating the development of novel computational approaches. Some potential challenges include the curse of dimensionality, data heterogeneity, missing data, class imbalance, and scalability issues. This overview article focuses on the recent progress and breakthroughs in the application of big data within precision medicine. Key aspects are summarized, including content, data sources, technologies, tools, challenges, and existing gaps. Nine fields-Datawarehouse and data management, electronic medical record, biomedical imaging informatics, Artificial intelligence-aided surgical design and surgery optimization, omics data, health monitoring data, knowledge graph, public health informatics, and security and privacy-are discussed.
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Affiliation(s)
- Xue Yang
- Department of Pancreatic Surgery and West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
| | - Kexin Huang
- Department of Pancreatic Surgery and West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu610041China
| | - Dewei Yang
- College of Advanced Manufacturing EngineeringChongqing University of Posts and TelecommunicationsChongqingChongqing400000China
| | - Weiling Zhao
- Center for Systems MedicineSchool of Biomedical InformaticsUTHealth at HoustonHoustonTX77030USA
| | - Xiaobo Zhou
- Center for Systems MedicineSchool of Biomedical InformaticsUTHealth at HoustonHoustonTX77030USA
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4
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Pang Z, Lu MM, Zhang Y, Gao Y, Bai JJ, Gu JY, Xie L, Wu WZ. Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges. Biomark Res 2023; 11:104. [PMID: 38037114 PMCID: PMC10690996 DOI: 10.1186/s40364-023-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising approach for cancer therapy with an expectation of no significant side effects. In the human body, mature T cells are armed with an incredible diversity of T cell receptors (TCRs) that theoretically react to the variety of random mutations generated by tumor cells. The outcomes, however, of current clinical trials using TCR-T cell therapies are not very successful especially involving solid tumors. The therapy still faces numerous challenges in the efficient screening of tumor-specific antigens and their cognate TCRs. In this review, we first introduce TCR structure-based antigen recognition and signaling, then describe recent advances in neoantigens and their specific TCR screening technologies, and finally summarize ongoing clinical trials of TCR-T therapies against neoantigens. More importantly, we also present the current challenges of TCR-T cell-based immunotherapies, e.g., the safety of viral vectors, the mismatch of T cell receptor, the impediment of suppressive tumor microenvironment. Finally, we highlight new insights and directions for personalized TCR-T therapy.
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Affiliation(s)
- Zhi Pang
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Man-Man Lu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yu Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan Gao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jin-Jin Bai
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Ying Gu
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Wei-Zhong Wu
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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5
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [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: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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6
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Tian J, Ma J. The Value of Microbes in Cancer Neoantigen Immunotherapy. Pharmaceutics 2023; 15:2138. [PMID: 37631352 PMCID: PMC10459105 DOI: 10.3390/pharmaceutics15082138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Tumor neoantigens are widely used in cancer immunotherapy, and a growing body of research suggests that microbes play an important role in these neoantigen-based immunotherapeutic processes. The human body and its surrounding environment are filled with a large number of microbes that are in long-term interaction with the organism. The microbiota can modulate our immune system, help activate neoantigen-reactive T cells, and play a great role in the process of targeting tumor neoantigens for therapy. Recent studies have revealed the interconnection between microbes and neoantigens, which can cross-react with each other through molecular mimicry, providing theoretical guidance for more relevant studies. The current applications of microbes in immunotherapy against tumor neoantigens are mainly focused on cancer vaccine development and immunotherapy with immune checkpoint inhibitors. This article summarizes the related fields and suggests the importance of microbes in immunotherapy against neoantigens.
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Affiliation(s)
- Junrui Tian
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China;
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha 410078, China
| | - Jian Ma
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China;
- Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha 410078, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha 410078, China
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7
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Wu J, Chen W, Zhou Y, Chi Y, Hua X, Wu J, Gu X, Chen S, Zhou Z. TSNAdb v2.0: The Updated Version of Tumor-specific Neoantigen Database. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:259-266. [PMID: 36209954 PMCID: PMC10626054 DOI: 10.1016/j.gpb.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 09/24/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
In recent years, neoantigens have been recognized as ideal targets for tumor immunotherapy. With the development of neoantigen-based tumor immunotherapy, comprehensive neoantigen databases are urgently needed to meet the growing demand for clinical studies. We have built the tumor-specific neoantigen database (TSNAdb) previously, which has attracted much attention. In this study, we provide TSNAdb v2.0, an updated version of the TSNAdb. TSNAdb v2.0 offers several new features, including (1) adopting more stringent criteria for neoantigen identification, (2) providing predicted neoantigens derived from three types of somatic mutations, and (3) collecting experimentally validated neoantigens and dividing them according to the experimental level. TSNAdb v2.0 is freely available at https://pgx.zju.edu.cn/tsnadb/.
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Affiliation(s)
- Jingcheng Wu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenfan Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuxuan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Xiansheng Hua
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Jian Wu
- The Second Affiliated Hospital of School of Medicine, and School of Public Health, Zhejiang University, Hangzhou 310058, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China.
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8
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Biswas N, Chakrabarti S, Padul V, Jones LD, Ashili S. Designing neoantigen cancer vaccines, trials, and outcomes. Front Immunol 2023; 14:1105420. [PMID: 36845151 PMCID: PMC9947792 DOI: 10.3389/fimmu.2023.1105420] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Neoantigen vaccines are based on epitopes of antigenic parts of mutant proteins expressed in cancer cells. These highly immunogenic antigens may trigger the immune system to combat cancer cells. Improvements in sequencing technology and computational tools have resulted in several clinical trials of neoantigen vaccines on cancer patients. In this review, we have looked into the design of the vaccines which are undergoing several clinical trials. We have discussed the criteria, processes, and challenges associated with the design of neoantigens. We searched different databases to track the ongoing clinical trials and their reported outcomes. We observed, in several trials, the vaccines boost the immune system to combat the cancer cells while maintaining a reasonable margin of safety. Detection of neoantigens has led to the development of several databases. Adjuvants also play a catalytic role in improving the efficacy of the vaccine. Through this review, we can conclude that the efficacy of vaccines can make it a potential treatment across different types of cancers.
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Affiliation(s)
- Nupur Biswas
- Rhenix Lifesciences, Hyderabad, India,*Correspondence: Nupur Biswas, ;
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9
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Cai Y, Chen R, Gao S, Li W, Liu Y, Su G, Song M, Jiang M, Jiang C, Zhang X. Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy. Front Oncol 2023; 12:1054231. [PMID: 36698417 PMCID: PMC9868469 DOI: 10.3389/fonc.2022.1054231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
The field of cancer neoantigen investigation has developed swiftly in the past decade. Predicting novel and true neoantigens derived from large multi-omics data became difficult but critical challenges. The rise of Artificial Intelligence (AI) or Machine Learning (ML) in biomedicine application has brought benefits to strengthen the current computational pipeline for neoantigen prediction. ML algorithms offer powerful tools to recognize the multidimensional nature of the omics data and therefore extract the key neoantigen features enabling a successful discovery of new neoantigens. The present review aims to outline the significant technology progress of machine learning approaches, especially the newly deep learning tools and pipelines, that were recently applied in neoantigen prediction. In this review article, we summarize the current state-of-the-art tools developed to predict neoantigens. The standard workflow includes calling genetic variants in paired tumor and blood samples, and rating the binding affinity between mutated peptide, MHC (I and II) and T cell receptor (TCR), followed by characterizing the immunogenicity of tumor epitopes. More specifically, we highlight the outstanding feature extraction tools and multi-layer neural network architectures in typical ML models. It is noted that more integrated neoantigen-predicting pipelines are constructed with hybrid or combined ML algorithms instead of conventional machine learning models. In addition, the trends and challenges in further optimizing and integrating the existing pipelines are discussed.
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Affiliation(s)
- Yu Cai
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Rui Chen
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Shenghan Gao
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Wenqing Li
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Yuru Liu
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Guodong Su
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mingming Song
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mengju Jiang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Chao Jiang
- Department of Neurology, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
| | - Xi Zhang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
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10
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 152] [Impact Index Per Article: 152.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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11
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Wu J, Zhou Z. TSNAD and TSNAdb: The Useful Toolkit for Clinical Application of Tumor-Specific Neoantigens. Methods Mol Biol 2023; 2673:167-174. [PMID: 37258913 DOI: 10.1007/978-1-0716-3239-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Tumor-specific neoantigens play important roles in tumor immunotherapy. How to predict neoantigens accurately and efficiently has attracted much attention. TSNAD is the first one-stop neoantigen prediction tool from next-generation sequencing data, and TSNAdb provides both predicted and validated neoantigens based on pan-cancer immunogenomics analyses. In this chapter, we describe the usage of TSNAD and TSNAdb for the clinical application of neoantigens. The latest version of TSNAD is available at https://pgx.zju.edu.cn/tsnad , and the latest version of TSNAdb is available at https://pgx.zju.edu.cn/tsnadb .
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Affiliation(s)
- Jingcheng Wu
- Innovative Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhan Zhou
- Innovative Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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12
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Kang W, Tong Y, Zhang W, Jian M, Zhang A, Ren G, Fan H, Yang J. Computational Biology Predicts the Efficacy of Tumor Immune Checkpoint Blockade. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6087751. [PMID: 36212709 PMCID: PMC9534640 DOI: 10.1155/2022/6087751] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/09/2022] [Accepted: 09/16/2022] [Indexed: 12/02/2022]
Abstract
Tumor immunotherapy is considered as one of the most promising methods in cancer treatment in recent years. Immune checkpoint blockade (ICB) can activate immune cells to destroy tumors by relieving the inhibitory pathway of tumor cells to immune cells. In silico prediction of the ICB response is an important step toward achieving effective and personalized cancer immunotherapy. Although immune checkpoint inhibitors have shown exciting clinical effects in the treatment of many types of tumors, there are still some clinical problems in practical application, such as low response rate and large individualized differences. How to predict the efficacy of effective individualized immune checkpoint inhibitors for tumor patients based on specific biomarkers and computational models is one of the key issues in the immunotherapy of this kind of tumor. In our work, from the five levels of genome level, transcription level, epigenetic level, microbial taxonomy level, and the immune cell infiltration profile level, the biomarkers and in silico calculation methods that affect the efficacy of tumor immune checkpoint inhibitors are comprehensively summarized.
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Affiliation(s)
- Wenyi Kang
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000 Hubei, China
| | - Yao Tong
- School of Medicine, Wuhan University of Science and Technology, Wuhan, China 430061
| | - Weijia Zhang
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000 Hubei, China
| | - Mengru Jian
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000 Hubei, China
| | - Anqi Zhang
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000 Hubei, China
| | - Guoqing Ren
- Department of Laboratory Medicine, Chuzhou Maternal and Child Health Care and Family Planning Service Center, Chuzhou 239000, China
| | - Hao Fan
- Huanggang Central Hospital of Yangtze University, Huanggang 43800, China
| | - Jiyuan Yang
- Department of Oncology, The First Affiliated Hospital of Yangtze University, Jingzhou, 434000 Hubei, China
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13
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Alarcon NO, Jaramillo M, Mansour HM, Sun B. Therapeutic Cancer Vaccines—Antigen Discovery and Adjuvant Delivery Platforms. Pharmaceutics 2022; 14:pharmaceutics14071448. [PMID: 35890342 PMCID: PMC9325128 DOI: 10.3390/pharmaceutics14071448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 12/15/2022] Open
Abstract
For decades, vaccines have played a significant role in protecting public and personal health against infectious diseases and proved their great potential in battling cancers as well. This review focused on the current progress of therapeutic subunit vaccines for cancer immunotherapy. Antigens and adjuvants are key components of vaccine formulations. We summarized several classes of tumor antigens and bioinformatic approaches of identification of tumor neoantigens. Pattern recognition receptor (PRR)-targeting adjuvants and their targeted delivery platforms have been extensively discussed. In addition, we emphasized the interplay between multiple adjuvants and their combined delivery for cancer immunotherapy.
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Affiliation(s)
- Neftali Ortega Alarcon
- Skaggs Pharmaceutical Sciences Center, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (N.O.A.); (M.J.); (H.M.M.)
| | - Maddy Jaramillo
- Skaggs Pharmaceutical Sciences Center, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (N.O.A.); (M.J.); (H.M.M.)
| | - Heidi M. Mansour
- Skaggs Pharmaceutical Sciences Center, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (N.O.A.); (M.J.); (H.M.M.)
- The University of Arizona Cancer Center, Tucson, AZ 85721, USA
- Department of Medicine, College of Medicine, The University of Arizona, Tucson, AZ 85724, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
| | - Bo Sun
- Skaggs Pharmaceutical Sciences Center, College of Pharmacy, The University of Arizona, Tucson, AZ 85721, USA; (N.O.A.); (M.J.); (H.M.M.)
- The University of Arizona Cancer Center, Tucson, AZ 85721, USA
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
- Correspondence: ; Tel.: +1-520-621-6420
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14
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ProGeo-Neo v2.0: A One-Stop Software for Neoantigen Prediction and Filtering Based on the Proteogenomics Strategy. Genes (Basel) 2022; 13:genes13050783. [PMID: 35627168 PMCID: PMC9141370 DOI: 10.3390/genes13050783] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/15/2023] Open
Abstract
A proteogenomics-based neoantigen prediction pipeline, namely ProGeo-neo, was previously developed by our team to predict neoantigens, allowing the identification of class-I major histocompatibility complex (MHC) binding peptides based on single-nucleotide variation (SNV) mutations. To improve it, we here present an updated pipeline, i.e., ProGeo-neo v2.0, in which a one-stop software solution was proposed to identify neoantigens based on the paired tumor-normal whole genome sequencing (WGS)/whole exome sequencing (WES) data in FASTQ format. Preferably, in ProGeo-neo v2.0, several new features are provided. In addition to the identification of MHC-I neoantigens, the new version supports the prediction of MHC class II-restricted neoantigens, i.e., peptides up to 30-mer in length. Moreover, the source of neoantigens has been expanded, allowing more candidate neoantigens to be identified, such as in-frame insertion-deletion (indels) mutations, frameshift mutations, and gene fusion analysis. In addition, we propose two more efficient screening approaches, including an in-group authentic neoantigen peptides database and two more stringent thresholds. The range of candidate peptides was effectively narrowed down to those that are more likely to elicit an immune response, providing a more meaningful reference for subsequent experimental validation. Compared to ProGeo-neo, the ProGeo-neo v2.0 performed well based on the same dataset, including updated functionality and improved accuracy.
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15
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Liang H, Xu Y, Chen M, Zhao J, Zhong W, Liu X, Gao X, Li S, Li J, Guo C, Jia H, Wang M. Characterization of Somatic Mutations That Affect Neoantigens in Non-Small Cell Lung Cancer. Front Immunol 2022; 12:749461. [PMID: 35356154 PMCID: PMC8959482 DOI: 10.3389/fimmu.2021.749461] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/27/2021] [Indexed: 12/17/2022] Open
Abstract
Purpose Immune checkpoint inhibitors (ICIs) have recently emerged as an important option for treating patients with advanced non-small cell lung cancer (NSCLC). Neoantigens are important biomarkers and potential immunotherapy targets that play important roles in the prognosis and treatment of patients with NSCLC. This study aimed to evaluate and characterize the relationships between somatic mutations and potential neoantigens in specimens from patients who underwent surgical treatment for NSCLC. Patients and Methods This prospective study evaluated specimens from patients with NSCLC who underwent surgical treatment at the Peking Union Medical College, China, from June 2019 to September 2019. Whole-exome sequencing was performed for tumor tissues and corresponding normal tissues. Candidate neoantigens were predicted using generative software, and the relationships between various mutation characteristics and number of neoantigens were evaluated. Results Neoantigen-related gene mutations were less frequent than mutations affecting the whole genome. Genes with high neoantigen burden had more types and higher frequencies of mutations. The number of candidate neoantigens was positively correlated with missense mutations, code shift insertions/deletions, split-site variations, and nonsense mutations. However, in the multiple linear regression analysis, only missense mutations were positively correlated with the number of neoantigens. The number of neoantigens was also positively correlated with base transversions (A>C/C>A, T>G/G>T, and C>G/G>C) and negatively correlated with base transitions (A>G/G>A and C>T/T>C). Conclusion The number of candidate neoantigens in NSCLC specimens was associated with mutation frequency, type of mutation, and type of base substitution.
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Affiliation(s)
- Hongge Liang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjiang Chen
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhong
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyan Liu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoxing Gao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He Jia
- Department of Biological Information, Beijing Neoantigen Biotechnology Co., Ltd., Beijing, China
| | - Mengzhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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16
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Dhall A, Jain S, Sharma N, Naorem LD, Kaur D, Patiyal S, Raghava GPS. In silico tools and databases for designing cancer immunotherapy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 129:1-50. [PMID: 35305716 DOI: 10.1016/bs.apcsb.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Immunotherapy is a rapidly growing therapy for cancer which have numerous benefits over conventional treatments like surgery, chemotherapy, and radiation. Overall survival of cancer patients has improved significantly due to the use of immunotherapy. It acts as a novel pillar for treating different malignancies from their primary to the metastatic stage. Recent preferments in high-throughput sequencing and computational immunology leads to the development of targeted immunotherapy for precision oncology. In the last few decades, several computational methods and resources have been developed for designing immunotherapy against cancer. In this review, we have summarized cancer-associated genomic, transcriptomic, and mutation profile repositories. We have also enlisted in silico methods for the prediction of vaccine candidates, HLA binders, cytokines inducing peptides, and potential neoepitopes. Of note, we have incorporated the most important bioinformatics pipelines and resources for the designing of cancer immunotherapy. Moreover, to facilitate the scientific community, we have developed a web portal entitled ImmCancer (https://webs.iiitd.edu.in/raghava/immcancer/), comprises cancer immunotherapy tools and repositories.
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Affiliation(s)
- Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Shipra Jain
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Neelam Sharma
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Leimarembi Devi Naorem
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Dilraj Kaur
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi, India.
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17
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Fotakis G, Trajanoski Z, Rieder D. Computational cancer neoantigen prediction: current status and recent advances. IMMUNO-ONCOLOGY TECHNOLOGY 2021; 12:100052. [PMID: 35755950 PMCID: PMC9216660 DOI: 10.1016/j.iotech.2021.100052] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the last few decades, immunotherapy has shown significant therapeutic efficacy in a broad range of cancer types. Antitumor immune responses are contingent on the recognition of tumor-specific antigens, which are termed neoantigens. Tumor neoantigens are ideal targets for immunotherapy since they can be recognized as non-self antigens by the host immune system and thus are able to elicit an antitumor T-cell response. There are an increasing number of studies that highlight the importance of tumor neoantigens in immunoediting and in the sensitivity to immune checkpoint blockade. Therefore, one of the most fundamental tasks in the field of immuno-oncology research is the identification of patient-specific neoantigens. To this end, a plethora of computational approaches have been developed in order to predict tumor-specific aberrant peptides and quantify their likelihood of binding to patients' human leukocyte antigen molecules in order to be recognized by T cells. In this review, we systematically summarize and present the most recent advances in computational neoantigen prediction, and discuss the challenges and novel methods that are being developed to resolve them. Tumors have the ability to acquire immune escape mechanisms. Tumor-specific aberrant peptides (neoantigens) can elicit an immune response by the host immune system. The identification of neoantigens is one of the most fundamental tasks in the field of immuno-oncology research. A plethora of computational approaches have been developed in order to predict patient-specificneoantigens.
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Affiliation(s)
- G Fotakis
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Z Trajanoski
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - D Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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18
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Schaap-Johansen AL, Vujović M, Borch A, Hadrup SR, Marcatili P. T Cell Epitope Prediction and Its Application to Immunotherapy. Front Immunol 2021; 12:712488. [PMID: 34603286 PMCID: PMC8479193 DOI: 10.3389/fimmu.2021.712488] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022] Open
Abstract
T cells play a crucial role in controlling and driving the immune response with their ability to discriminate peptides derived from healthy as well as pathogenic proteins. In this review, we focus on the currently available computational tools for epitope prediction, with a particular focus on tools aimed at identifying neoepitopes, i.e. cancer-specific peptides and their potential for use in immunotherapy for cancer treatment. This review will cover how these tools work, what kind of data they use, as well as pros and cons in their respective applications.
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Affiliation(s)
| | - Milena Vujović
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Paolo Marcatili
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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19
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Zhou Z, Wu J, Ren J, Chen W, Zhao W, Gu X, Chi Y, He Q, Yang B, Wu J, Chen S. TSNAD v2.0: A one-stop software solution for tumor-specific neoantigen detection. Comput Struct Biotechnol J 2021; 19:4510-4516. [PMID: 34471496 PMCID: PMC8385119 DOI: 10.1016/j.csbj.2021.08.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/10/2021] [Accepted: 08/10/2021] [Indexed: 12/30/2022] Open
Abstract
TSNAD is a one-stop software solution for predicting neoantigens from the whole genome/exome sequencing data of tumor-normal pairs. Here we present TSNAD v2.0 which provides several new features such as the function of RNA-Seq analysis including gene expression and gene fusion analysis, the support of different versions of the reference genome. Most importantly, we replace the NetMHCpan with DeepHLApan we developed previously, which considers both the binding between peptide and major histocompatibility complex (MHC) and the immunogenicity of the presented peptide-MHC complex (pMHC). TSNAD v2.0 achieves good performamce on a standard dataset. For better usage, we provide the Docker version and the web service of TSNAD v2.0. The source code of TSNAD v2.0 is freely available at https://github.com/jiujiezz/tsnad. And the web service of TSNAD v2.0 is available at http://biopharm.zju.edu.cn/tsnad/.
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Affiliation(s)
- Zhan Zhou
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Jingcheng Wu
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Jianan Ren
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenfan Chen
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Polytechnic Institute, Zhejiang University, Hangzhou 310015, China
| | - Wenyi Zhao
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou 311121, China
| | - Qiaojun He
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Bo Yang
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China
| | - Jian Wu
- Collaborative Innovation Center of Artificial Intelligence by MOE and Zhejiang Provincial Government, College of Computer Science and Technology, Zhejiang University, Hangzhou 310027, China.,Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou 310018, China.,Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Shuqing Chen
- Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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20
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Tang L, Zhang R, Zhang X, Yang L. Personalized Neoantigen-Pulsed DC Vaccines: Advances in Clinical Applications. Front Oncol 2021; 11:701777. [PMID: 34381724 PMCID: PMC8350509 DOI: 10.3389/fonc.2021.701777] [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] [Received: 04/28/2021] [Accepted: 07/12/2021] [Indexed: 02/05/2023] Open
Abstract
In the past few decades, great progress has been made in the clinical application of dendritic cell (DC) vaccines loaded with personalized neoantigens. Personalized neoantigens are antigens arising from somatic mutations in cancers, with specificity to each patient. DC vaccines work based on the fundamental characteristics of DCs, which are professional antigen-presenting cells (APCs), responsible for the uptake, processing, and presentation of antigens to T cells to activate immune responses. Neoantigens can exert their antitumor effects only after they are taken up by APCs and presented to T cells. In recent years, neoantigen-based personalized tumor therapeutic vaccines have proven to be safe, immunogenic and feasible treatment strategies in patients with melanoma and glioblastoma that provide new hope in the treatment of cancer patients and a new approach to cure cancer. In addition, according to ClinicalTrials.gov, hundreds of registered DC vaccine trials are either completed or ongoing worldwide, of which 9 are in early phase I, 191 in phase I, 166 in phase II and 8 in phase III. Hundreds of clinical studies on therapeutic tumor vaccines globally have proven that DC vaccines are stable, reliable and very safe. However, in this process, many other factors still limit the effectiveness of the vaccine. This review will focus on the current research progress on personalized neoantigen-pulsed DC vaccines, their limitations and future research directions of DC vaccines loaded with neoantigens. This review aims to provide a better understanding of DCs biology and manipulation of activated DCs for DCs researchers to produce the next generation of highly efficient cancer vaccines for patients.
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Affiliation(s)
- Lin Tang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Rui Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Xiaoyu Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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21
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Zhang W, Zeng B, Lin H, Guan W, Mo J, Wu S, Wei Y, Zhang Q, Yu D, Li W, Chan GCF. CanImmunother: a manually curated database for identification of cancer immunotherapies associating with biomarkers, targets, and clinical effects. Oncoimmunology 2021; 10:1944553. [PMID: 34345532 PMCID: PMC8288037 DOI: 10.1080/2162402x.2021.1944553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/01/2022] Open
Abstract
As immunotherapy is evolving into an essential armamentarium against cancers, numerous translational studies associated with relevant biomarkers, targets, and clinical effects have been reported in recent years. However, a large amount of associated experimental data remains unexplored due to the difficulty in accessibility and utilization. Here, we established a comprehensive high-quality database for cancer immunotherapy called CanImmunother (http://www.biomedical-web.com/cancerit/) through manual curation on 4515 publications. CanImmunother contains 3267 experimentally validated associations between 218 cancer sub-types across 34 body parts and 484 immunotherapies with 642 biomarkers, 108 targets, and 121 control therapies. Each association was manually curated by professional curators, incorporated with valuable annotation and cross references, and assigned with an association score for prioritization. To help clinicians and researchers in identifying and discovering better cancer immunotherapy and their respective biomarkers and targets, CanImmunother offers user-friendly web applications including search, browse, excel table, association prioritization, and network visualization. CanImmunother presents a landscape of experimental cancer immunotherapy association data, serving as a useful resource to improve our insight and to facilitate further discovery of advanced immunotherapy options for cancer patients.
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Affiliation(s)
- Wenliang Zhang
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, China
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China
| | - Binghui Zeng
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Huancai Lin
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Wen Guan
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jing Mo
- Department of Bioinformatics, Outstanding Biotechnology Co., Ltd.-Shenzhen, Shenzhen, China
| | - Song Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yanjie Wei
- Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, China
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
| | - Qianshen Zhang
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dongsheng Yu
- Guangdong Provincial Key Laboratory of Stomatology, Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-sen University,Guangzhou, China
| | - Godfrey Chi-Fung Chan
- Department of Pediatrics, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine, The University of Hong Kong, Hong Kong
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22
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Chen I, Chen MY, Goedegebuure SP, Gillanders WE. Challenges targeting cancer neoantigens in 2021: a systematic literature review. Expert Rev Vaccines 2021; 20:827-837. [PMID: 34047245 DOI: 10.1080/14760584.2021.1935248] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Cancer neoantigens represent important targets of cancer immunotherapy. The goal of cancer neoantigen vaccines is to induce neoantigen-specific immune responses and antitumor immunity while minimizing the potential for autoimmune toxicity. Advances in sequencing technologies, neoantigen prediction algorithms, and other technologies have dramatically improved the ability to identify and prioritize cancer neoantigens. Unfortunately, results from preclinical studies and early phase clinical trials highlight important challenges to the successful clinical translation of neoantigen cancer vaccines.Areas covered: In this review, we provide an overview of current strategies for the identification and prioritization of cancer neoantigens with a particular emphasis on the two most common strategies used for neoantigen identification: (1) direct identification of peptide ligands eluted from peptide-MHC complexes, and (2) next-generation sequencing combined with neoantigen prediction algorithms. We highlight the limitations of current neoantigen prediction pipelines, and discuss broader challenges associated with cancer neoantigen vaccines including tumor purity/heterogeneity and the immunosuppressive tumor microenvironment.Expert opinion: Despite current limitations, neoantigen prediction is likely to improve rapidly based on advances in sequencing, machine learning, and information sharing. The successful development of robust cancer neoantigen prediction strategies is likely to have a significant impact, with the potential to facilitate cancer neoantigen vaccine design.
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Affiliation(s)
- Ina Chen
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA
| | - Michael Y Chen
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA.,The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University and Siteman Cancer Center in St. Louis, St Louis, Missouri, USA.,The Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St Louis, MO, USA
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23
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Nasrollahzadeh D, Roshandel G, Delhomme TM, Avogbe PH, Foll M, Saidi F, Poustchi H, Sotoudeh M, Malekzadeh R, Brennan P, Mckay J, Hainaut P, Abedi-Ardekani B. TP53 Targeted Deep Sequencing of Cell-Free DNA in Esophageal Squamous Cell Carcinoma Using Low-Quality Serum: Concordance with Tumor Mutation. Int J Mol Sci 2021; 22:5627. [PMID: 34073316 PMCID: PMC8197963 DOI: 10.3390/ijms22115627] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/17/2021] [Indexed: 12/30/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is emerging as a potential tumor biomarker. CfDNA-based biomarkers may be applicable in tumors without an available non-invasive screening method among at-risk populations. Esophageal squamous cell carcinoma (ESCC) and residents of the Asian cancer belt are examples of those malignancies and populations. Previous epidemiological studies using cfDNA have pointed to the need for high volumes of good quality plasma (i.e., >1 mL plasma with 0 or 1 cycles of freeze-thaw) rather than archival serum, which is often the main available source of cfDNA in retrospective studies. Here, we have investigated the concordance of TP53 mutations in tumor tissue and cfDNA extracted from archival serum left-over from 42 cases and 39 matched controls (age, gender, residence) in a high-risk area of Northern Iran (Golestan). Deep sequencing of TP53 coding regions was complemented with a specialized variant caller (Needlestack). Overall, 23% to 31% of mutations were concordantly detected in tumor and serum cfDNA (based on two false discovery rate thresholds). Concordance was positively correlated with high cfDNA concentration, smoking history (p-value = 0.02) and mutations with a high potential of neoantigen formation (OR; 95%CI = 1.9 (1.11-3.29)), suggesting that tumor DNA release in the bloodstream might reflect the effects of immune and inflammatory context on tumor cell turnover. We identified TP53 mutations in five controls, one of whom was subsequently diagnosed with ESCC. Overall, the results showed that cfDNA mutations can be reliably identified by deep sequencing of archival serum, with a rate of success comparable to plasma. Nonetheless, 70% non-identifiable mutations among cancer patients and 12% mutation detection in controls are the main challenges in applying cfDNA to detect tumor-related variants when blindly targeting whole coding regions of the TP53 gene in ESCC.
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Affiliation(s)
- Dariush Nasrollahzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Gholamreza Roshandel
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan 49177-44563, Iran;
| | - Tiffany Myriam Delhomme
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, 08036 Barcelona, Spain
| | - Patrice Hodonou Avogbe
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Matthieu Foll
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Farrokh Saidi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran 14117-13135, Iran; (D.N.); (F.S.); (H.P.); (M.S.); (R.M.)
| | - Paul Brennan
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - James Mckay
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm 1209 CNRS 5309 UGA, 38700 Grenoble, France;
| | - Behnoush Abedi-Ardekani
- Genomic Epidemiology Branch, International Agency for Research on Cancer/World Health Organization (IARC/WHO), 69000 Lyon, France; (T.M.D.); (P.H.A.); (M.F.); (P.B.); (J.M.)
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24
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Wang H, Ding Y, Chen Y, Jiang J, Chen Y, Lu J, Kong M, Mo F, Huang Y, Zhao W, Fang P, Chen X, Teng X, Xu N, Lu Y, Yu X, Li Z, Zhang J, Wang H, Bao X, Zhou D, Chi Y, Zhou T, Zhou Z, Chen S, Teng L. A novel genomic classification system of gastric cancer via integrating multidimensional genomic characteristics. Gastric Cancer 2021; 24:1227-1241. [PMID: 34095982 PMCID: PMC8502137 DOI: 10.1007/s10120-021-01201-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/21/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric cancer (GC) is one of the leading causes of cancer deaths with high heterogeneity. There is currently a paucity of clinically applicable molecular classification system to guide precise medicine. METHODS A total of 70 Chinese patients with GC were included in this study and whole-exome sequencing was performed. Unsupervised clustering was undertaken to identify genomic subgroups, based on mutational signature, copy number variation, neoantigen, clonality, and essential genomic alterations. Subgroups were characterized by clinicopathological factors, molecular features, and prognosis. RESULTS We identified 32 significantly mutated genes (SMGs), including TP53, ARID1A, PIK3CA, CDH1, and RHOA. Of these, PREX2, PIEZO1, and FSIP2 have not been previously reported in GC. Using a novel genome-based classification method that integrated multidimensional genomic features, we categorized GC into four subtypes with distinct clinical phenotypes and prognosis. Subtype 1, which was predominantly Lauren intestinal type, harbored recurrent TP53 mutation and ERBB2 amplification, high tumor mutation burden (TMB)/tumor neoantigen burden (TNB), and intratumoral heterogeneity, with a liver metastasis tendency. Subtype 2 tended to occur at an elder age, accompanying with frequent TP53 and SYNE1 mutations, high TMB/TNB, and was associated with poor prognosis. Subtype 3 and subtype 4 included patients with mainly diffuse/mixed type tumors, high frequency of peritoneal metastasis, and genomical stability, whereas subtype 4 was associated with a favorable prognosis. CONCLUSIONS By integrating multidimensional genomic characteristics, we proposed a novel genomic classification system of GC associated with clinical phenotypes and provided a new insight to facilitate genome-guided risk stratification and disease management.
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Affiliation(s)
- Haiyong Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Yanyan Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Junjie Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Jun Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Mei Kong
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Fan Mo
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences & Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058 China ,Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou, 310051 China
| | - Yingying Huang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Wenyi Zhao
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences & Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058 China
| | - Ping Fang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Xiangliu Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Xiaodong Teng
- Department of Pathology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Yimin Lu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Xiongfei Yu
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Zhongqi Li
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Jing Zhang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Haohao Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Donghui Zhou
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Alibaba DAMO Academy, Hangzhou, 311121 China
| | - Tianhua Zhou
- Institute of Gastroenterology, Zhejiang University, Hangzhou, 310058 China
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences & Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058 China
| | - Shuqing Chen
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences & Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Zhejiang University, Hangzhou, 310058 China ,Hangzhou Neoantigen Therapeutics Co., Ltd., Hangzhou, 310051 China ,Institute of Drug Metabolism & Pharmaceutical Analysis & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Lisong Teng
- Department of Surgical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003 China
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25
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Sherafat E, Force J, Măndoiu II. Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy. BMC Bioinformatics 2020; 21:498. [PMID: 33375939 PMCID: PMC7772914 DOI: 10.1186/s12859-020-03813-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in cancer cells lead to tumor rejection. Since it is impractical to experimentally assess all candidate neoepitopes prior to vaccination, developing accurate methods for predicting tumor-rejection mediating neoepitopes (TRMNs) is critical for enabling routine clinical use of cancer vaccines. RESULTS In this paper we introduce Positive-unlabeled Learning using AuTOml (PLATO), a general semi-supervised approach to improving accuracy of model-based classifiers. PLATO generates a set of high confidence positive calls by applying a stringent filter to model-based predictions, then rescores remaining candidates by using positive-unlabeled learning. To achieve robust performance on clinical samples with large patient-to-patient variation, PLATO further integrates AutoML hyper-parameter tuning, classification threshold selection based on spies, and support for bootstrapping. CONCLUSIONS Experimental results on real datasets demonstrate that PLATO has improved performance compared to model-based approaches for two key steps in TRMN prediction, namely somatic variant calling from exome sequencing data and peptide identification from MS/MS data.
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Affiliation(s)
- Elham Sherafat
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Jordan Force
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Ion I Măndoiu
- Computer Science and Engineering Department, University of Connecticut, Storrs, CT, 06269, USA.
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26
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Gopanenko AV, Kosobokova EN, Kosorukov VS. Main Strategies for the Identification of Neoantigens. Cancers (Basel) 2020; 12:E2879. [PMID: 33036391 PMCID: PMC7600129 DOI: 10.3390/cancers12102879] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022] Open
Abstract
Genetic instability of tumors leads to the appearance of numerous tumor-specific somatic mutations that could potentially result in the production of mutated peptides that are presented on the cell surface by the MHC molecules. Peptides of this kind are commonly called neoantigens. Their presence on the cell surface specifically distinguishes tumors from healthy tissues. This feature makes neoantigens a promising target for immunotherapy. The rapid evolution of high-throughput genomics and proteomics makes it possible to implement these techniques in clinical practice. In particular, they provide useful tools for the investigation of neoantigens. The most valuable genomic approach to this problem is whole-exome sequencing coupled with RNA-seq. High-throughput mass-spectrometry is another option for direct identification of MHC-bound peptides, which is capable of revealing the entire MHC-bound peptidome. Finally, structure-based predictions could significantly improve the understanding of physicochemical and structural features that affect the immunogenicity of peptides. The development of pipelines combining such tools could improve the accuracy of the peptide selection process and decrease the required time. Here we present a review of the main existing approaches to investigating the neoantigens and suggest a possible ideal pipeline that takes into account all modern trends in the context of neoantigen discovery.
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Affiliation(s)
| | | | - Vyacheslav S. Kosorukov
- N.N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (A.V.G.); (E.N.K.)
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27
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Wood MA, Nguyen A, Struck AJ, Ellrott K, Nellore A, Thompson RF. neoepiscope improves neoepitope prediction with multivariant phasing. Bioinformatics 2020; 36:713-720. [PMID: 31424527 DOI: 10.1093/bioinformatics/btz653] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/22/2019] [Accepted: 08/16/2019] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION The vast majority of tools for neoepitope prediction from DNA sequencing of complementary tumor and normal patient samples do not consider germline context or the potential for the co-occurrence of two or more somatic variants on the same mRNA transcript. Without consideration of these phenomena, existing approaches are likely to produce both false-positive and false-negative results, resulting in an inaccurate and incomplete picture of the cancer neoepitope landscape. We developed neoepiscope chiefly to address this issue for single nucleotide variants (SNVs) and insertions/deletions (indels). RESULTS Herein, we illustrate how germline and somatic variant phasing affects neoepitope prediction across multiple datasets. We estimate that up to ∼5% of neoepitopes arising from SNVs and indels may require variant phasing for their accurate assessment. neoepiscope is performant, flexible and supports several major histocompatibility complex binding affinity prediction tools. AVAILABILITY AND IMPLEMENTATION neoepiscope is available on GitHub at https://github.com/pdxgx/neoepiscope under the MIT license. Scripts for reproducing results described in the text are available at https://github.com/pdxgx/neoepiscope-paper under the MIT license. Additional data from this study, including summaries of variant phasing incidence and benchmarking wallclock times, are available in Supplementary Files 1, 2 and 3. Supplementary File 1 contains Supplementary Table 1, Supplementary Figures 1 and 2, and descriptions of Supplementary Tables 2-8. Supplementary File 2 contains Supplementary Tables 2-6 and 8. Supplementary File 3 contains Supplementary Table 7. Raw sequencing data used for the analyses in this manuscript are available from the Sequence Read Archive under accessions PRJNA278450, PRJNA312948, PRJNA307199, PRJNA343789, PRJNA357321, PRJNA293912, PRJNA369259, PRJNA305077, PRJNA306070, PRJNA82745 and PRJNA324705; from the European Genome-phenome Archive under accessions EGAD00001004352 and EGAD00001002731; and by direct request to the authors. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mary A Wood
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
- Portland VA Research Foundation, Portland, OR 97239, USA
| | - Austin Nguyen
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
| | - Adam J Struck
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
| | - Kyle Ellrott
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
- Department of Biomedical Engineering, OR 97239, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
- Department of Biomedical Engineering, OR 97239, USA
- Department of Surgery, OR 97239, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97201, USA
- Portland VA Research Foundation, Portland, OR 97239, USA
- Department of Radiation Medicine, OR 97239, USA
- Department of Medical Informatics & Clinical Epidemiology, Oregon Health & Science University Portland, OR 97239, USA
- Division of Hospital and Specialty Medicine, VA Portland Healthcare System, Portland, OR 97239, USA
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28
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Mangalaparthi KK, Patel K, Khan AA, Manoharan M, Karunakaran C, Murugan S, Gupta R, Gupta R, Khanna-Gupta A, Chaudhuri A, Kumar P, Nair B, Kumar RV, Prasad TSK, Chatterjee A, Pandey A, Gowda H. Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort. Front Oncol 2020; 10:1457. [PMID: 32974170 PMCID: PMC7469928 DOI: 10.3389/fonc.2020.01457] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/09/2020] [Indexed: 12/18/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the most common histological subtype of esophageal cancer in India. Cigarette smoking and chewing tobacco are known risk factors associated with ESCC. However, genomic alterations associated with ESCC in India are not well-characterized. In this study, we carried out exome sequencing to characterize the mutational landscape of ESCC tumors from subjects with a varied history of tobacco usage. Whole exome sequence analysis of ESCC from an Indian cohort revealed several genes that were mutated or had copy number changes. ESCC from tobacco chewers had a higher frequency of C:G > A:T transversions and 2-fold enrichment for mutation signature 4 compared to smokers and non-users of tobacco. Genes, such as TP53, CSMD3, SYNE1, PIK3CA, and NOTCH1 were found to be frequently mutated in Indian cohort. Mutually exclusive mutation patterns were observed in PIK3CA-NOTCH1, DNAH5-ZFHX4, MUC16-FAT1, and ZFHX4-NOTCH1 gene pairs. Recurrent amplifications were observed in 3q22-3q29, 11q13.3-q13.4, 7q22.1-q31.1, and 8q24 regions. Approximately 53% of tumors had genomic alterations in PIK3CA making this pathway a promising candidate for targeted therapy. In conclusion, we observe enrichment of mutation signature 4 in ESCC tumors from patients with a history of tobacco chewing. This is likely due to direct exposure of esophagus to tobacco carcinogens when it is chewed and swallowed. Genomic alterations were frequently observed in PIK3CA-AKT pathway members independent of the history of tobacco usage. PIK3CA pathway can be potentially targeted in ESCC which currently has no effective targeted therapeutic options.
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Affiliation(s)
- Kiran K. Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Aafaque A. Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | | | | | | | - Ravi Gupta
- Medgenome Labs Pvt. Ltd., Bangalore, India
| | | | | | | | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha V. Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Manipal Academy of Higher Education, Manipal, India
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, United States
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, United States
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
- Manipal Academy of Higher Education, Manipal, India
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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29
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Zhang Z, Zhou C, Tang L, Gong Y, Wei Z, Zhang G, Wang F, Liu Q, Yu J. ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq. Aging (Albany NY) 2020; 12:14633-14648. [PMID: 32697765 PMCID: PMC7425491 DOI: 10.18632/aging.103516] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022]
Abstract
Cancer neoantigens have shown great potential in immunotherapy, while current software focuses on identifying neoantigens which are derived from SNVs, indels or gene fusions. Alternative splicing widely occurs in tumor samples and it has been proven to contribute to the generation of candidate neoantigens. Here we present ASNEO, which is an integrated computational pipeline for the identification of personalized Alternative Splicing based NEOantigens with RNA-seq. Our analyses showed that ASNEO could identify neopeptides which are presented by MHC I complex through mass spectrometry data validation. When ASNEO was applied to two immunotherapy-treated cohorts, we found that alternative splicing based neopeptides generally have a higher immune score than that of somatic neopeptides and alternative splicing based neopeptides could be a marker to predict patient survival pattern. Our identification of alternative splicing derived neopeptides would contribute to a more complete understanding of the tumor immune landscape. Prediction of patient-specific alternative splicing neopeptides has the potential to contribute to the development of personalized cancer vaccines.
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Affiliation(s)
- Zhanbing Zhang
- Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Chi Zhou
- Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Lihua Tang
- School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Yukang Gong
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Tongji University, Shanghai 200009, China
| | - Zhiting Wei
- Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Gongchen Zhang
- Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Feng Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Qi Liu
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Tongji University, Shanghai 200009, China.,Department of Endocrinology and Metabolism, Shanghai Tenth People's Hospital; Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai 200009, China
| | - Jing Yu
- Department of Ophthalmology, Shanghai Tenth People's Hospital, Tongji University, School of Medicine, Tongji University, Shanghai 200009, China
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30
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Zhao W, Wu J, Chen S, Zhou Z. Shared neoantigens: ideal targets for off-the-shelf cancer immunotherapy. Pharmacogenomics 2020; 21:637-645. [DOI: 10.2217/pgs-2019-0184] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neoantigen, as an important member of tumor-specific antigens, has attracted a great deal of attention as a target for immunotherapy. Neoantigens are potential targets for personalized vaccines and adoptive cell transfer therapies. However, most of the neoantigen-targeted immunotherapies in the process are customized and costly. So, we are inclined to find shared neoantigens suitable for more patients. With the help of existing neoantigen prediction algorithms, we found that the most frequent shared neoantigens occurred in more than 1% of patients for 17 tumor types and the ten most frequent shared neoantigens covered approximately 50% of pancreatic cancer patients, providing a potential list of targets for off-the-shelf immunotherapy.
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Affiliation(s)
- Wenyi Zhao
- Institute of Drug Metabolism & Pharmaceutical Analysis & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Collaborative Innovation Center for Artificial Intelligence, College of Computer Science & Technology, Zhejiang University, Hangzhou, 310027, China
| | - Jingcheng Wu
- Institute of Drug Metabolism & Pharmaceutical Analysis & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shuqing Chen
- Institute of Drug Metabolism & Pharmaceutical Analysis & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhan Zhou
- Institute of Drug Metabolism & Pharmaceutical Analysis & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Collaborative Innovation Center for Artificial Intelligence, College of Computer Science & Technology, Zhejiang University, Hangzhou, 310027, China
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31
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Prota G, Gileadi U, Rei M, Lechuga-Vieco AV, Chen JL, Galiani S, Bedard M, Lau VWC, Fanchi LF, Artibani M, Hu Z, Gordon S, Rehwinkel J, Enríquez JA, Ahmed AA, Schumacher TN, Cerundolo V. Enhanced Immunogenicity of Mitochondrial-Localized Proteins in Cancer Cells. Cancer Immunol Res 2020; 8:685-697. [PMID: 32205315 DOI: 10.1158/2326-6066.cir-19-0467] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 11/05/2019] [Accepted: 03/12/2020] [Indexed: 11/16/2022]
Abstract
Epitopes derived from mutated cancer proteins elicit strong antitumor T-cell responses that correlate with clinical efficacy in a proportion of patients. However, it remains unclear whether the subcellular localization of mutated proteins influences the efficiency of T-cell priming. To address this question, we compared the immunogenicity of NY-ESO-1 and OVA localized either in the cytosol or in mitochondria. We showed that tumors expressing mitochondrial-localized NY-ESO-1 and OVA proteins elicit significantdly higher frequencies of antigen-specific CD8+ T cells in vivo. We also demonstrated that this stronger immune response is dependent on the mitochondrial location of the antigenic proteins, which contributes to their higher steady-state amount, compared with cytosolic localized proteins. Consistent with these findings, we showed that injection of mitochondria purified from B16 melanoma cells can protect mice from a challenge with B16 cells, but not with irrelevant tumors. Finally, we extended these findings to cancer patients by demonstrating the presence of T-cell responses specific for mutated mitochondrial-localized proteins. These findings highlight the utility of prioritizing epitopes derived from mitochondrial-localized mutated proteins as targets for cancer vaccination strategies.
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Affiliation(s)
- Gennaro Prota
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.
| | - Uzi Gileadi
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Margarida Rei
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Ana Victoria Lechuga-Vieco
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ji-Li Chen
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Silvia Galiani
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Melissa Bedard
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Vivian Wing Chong Lau
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Lorenzo F Fanchi
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Mara Artibani
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, United Kingdom
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, United Kingdom
| | - Siamon Gordon
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- Chang Gung University, Graduate Institute of Biomedical Sciences, College of Medicine, Taoyuan City, Taiwan
| | - Jan Rehwinkel
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Jose A Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES), Madrid, Spain
| | - Ahmed A Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Women's Centre, John Radcliffe Hospital, United Kingdom
| | - Ton N Schumacher
- Division of Molecular Oncology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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32
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Li Y, Wang G, Tan X, Ouyang J, Zhang M, Song X, Liu Q, Leng Q, Chen L, Xie L. ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection. BMC Med Genomics 2020; 13:52. [PMID: 32241270 PMCID: PMC7118832 DOI: 10.1186/s12920-020-0683-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Neoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data. RESULTS Here we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only. CONCLUSIONS The pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
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Affiliation(s)
- Yuyu Li
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Guangzhi Wang
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Xiaoxiu Tan
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China
| | - Xiaofeng Song
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China
| | - Qi Liu
- Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 20009, China
| | - Qibin Leng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, 78 Heng Zhi Gang, Lu Hu Road, Guangzhou, 510095, China
| | - Lanming Chen
- Key Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), China Ministry of Agriculture; College of Food Science and Technology, Shanghai Ocean University, 999 Hu Cheng Huan Road, Shanghai, 201306, China.
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Keyuan Road, Shanghai, 201203, China.
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Coelho ACMF, Fonseca AL, Martins DL, Lins PBR, da Cunha LM, de Souza SJ. neoANT-HILL: an integrated tool for identification of potential neoantigens. BMC Med Genomics 2020; 13:30. [PMID: 32087727 PMCID: PMC7036241 DOI: 10.1186/s12920-020-0694-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/11/2020] [Indexed: 02/08/2023] Open
Abstract
Background Cancer neoantigens have attracted great interest in immunotherapy due to their capacity to elicit antitumoral responses. These molecules arise from somatic mutations in cancer cells, resulting in alterations on the original protein. Neoantigens identification remains a challenging task due largely to a high rate of false-positives. Results We have developed an efficient and automated pipeline for the identification of potential neoantigens. neoANT-HILL integrates several immunogenomic analyses to improve neoantigen detection from Next Generation Sequence (NGS) data. The pipeline has been compiled in a pre-built Docker image such that minimal computational background is required for download and setup. NeoANT-HILL was applied in The Cancer Genome Atlas (TCGA) melanoma dataset and found several putative neoantigens including ones derived from the recurrent RAC1:P29S and SERPINB3:E250K mutations. neoANT-HILL was also used to identify potential neoantigens in RNA-Seq data with a high sensitivity and specificity. Conclusion neoANT-HILL is a user-friendly tool with a graphical interface that performs neoantigens prediction efficiently. neoANT-HILL is able to process multiple samples, provides several binding predictors, enables quantification of tumor-infiltrating immune cells and considers RNA-Seq data for identifying potential neoantigens. The software is available through github at https://github.com/neoanthill/neoANT-HILL.
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Affiliation(s)
- Ana Carolina M F Coelho
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - André L Fonseca
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - Danilo L Martins
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - Paulo B R Lins
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil
| | - Lucas M da Cunha
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil.,PhD Program in Bioinformatics, UFRN, Natal, Brazil
| | - Sandro J de Souza
- Bioinformatics Multidisciplinary Enviroment (BioME), Institute Metropolis Digital, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil. .,Brain Institute, Federal University of Rio Grande do Norte, UFRN, Natal, Brazil. .,Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China.
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34
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Lancaster EM, Jablons D, Kratz JR. Applications of Next-Generation Sequencing in Neoantigen Prediction and Cancer Vaccine Development. Genet Test Mol Biomarkers 2020; 24:59-66. [DOI: 10.1089/gtmb.2018.0211] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Elizabeth M. Lancaster
- Thoracic Oncology Program, Department of Surgery, University of California, San Francisco, San Francisco, California
| | - David Jablons
- Thoracic Oncology Program, Department of Surgery, University of California, San Francisco, San Francisco, California
| | - Johannes R. Kratz
- Thoracic Oncology Program, Department of Surgery, University of California, San Francisco, San Francisco, California
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Wu J, Wang W, Zhang J, Zhou B, Zhao W, Su Z, Gu X, Wu J, Zhou Z, Chen S. DeepHLApan: A Deep Learning Approach for Neoantigen Prediction Considering Both HLA-Peptide Binding and Immunogenicity. Front Immunol 2019; 10:2559. [PMID: 31736974 PMCID: PMC6838785 DOI: 10.3389/fimmu.2019.02559] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Neoantigens play important roles in cancer immunotherapy. Current methods used for neoantigen prediction focus on the binding between human leukocyte antigens (HLAs) and peptides, which is insufficient for high-confidence neoantigen prediction. In this study, we apply deep learning techniques to predict neoantigens considering both the possibility of HLA-peptide binding (binding model) and the potential immunogenicity (immunogenicity model) of the peptide-HLA complex (pHLA). The binding model achieves comparable performance with other well-acknowledged tools on the latest Immune Epitope Database (IEDB) benchmark datasets and an independent mass spectrometry (MS) dataset. The immunogenicity model could significantly improve the prediction precision of neoantigens. The further application of our method to the mutations with pre-existing T-cell responses indicating its feasibility in clinical application. DeepHLApan is freely available at https://github.com/jiujiezz/deephlapan and http://biopharm.zju.edu.cn/deephlapan.
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Affiliation(s)
- Jingcheng Wu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Wenzhe Wang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Jiucheng Zhang
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Binbin Zhou
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Wenyi Zhao
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Zhixi Su
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Jian Wu
- College of Computer Science and Technology, Zhejiang University, Hangzhou, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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36
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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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Richters MM, Xia H, Campbell KM, Gillanders WE, Griffith OL, Griffith M. Best practices for bioinformatic characterization of neoantigens for clinical utility. Genome Med 2019; 11:56. [PMID: 31462330 PMCID: PMC6714459 DOI: 10.1186/s13073-019-0666-2] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/16/2019] [Indexed: 12/13/2022] Open
Abstract
Neoantigens are newly formed peptides created from somatic mutations that are capable of inducing tumor-specific T cell recognition. Recently, researchers and clinicians have leveraged next generation sequencing technologies to identify neoantigens and to create personalized immunotherapies for cancer treatment. To create a personalized cancer vaccine, neoantigens must be computationally predicted from matched tumor-normal sequencing data, and then ranked according to their predicted capability in stimulating a T cell response. This candidate neoantigen prediction process involves multiple steps, including somatic mutation identification, HLA typing, peptide processing, and peptide-MHC binding prediction. The general workflow has been utilized for many preclinical and clinical trials, but there is no current consensus approach and few established best practices. In this article, we review recent discoveries, summarize the available computational tools, and provide analysis considerations for each step, including neoantigen prediction, prioritization, delivery, and validation methods. In addition to reviewing the current state of neoantigen analysis, we provide practical guidance, specific recommendations, and extensive discussion of critical concepts and points of confusion in the practice of neoantigen characterization for clinical use. Finally, we outline necessary areas of development, including the need to improve HLA class II typing accuracy, to expand software support for diverse neoantigen sources, and to incorporate clinical response data to improve neoantigen prediction algorithms. The ultimate goal of neoantigen characterization workflows is to create personalized vaccines that improve patient outcomes in diverse cancer types.
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Affiliation(s)
- Megan M Richters
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Huiming Xia
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Katie M Campbell
- Division of Hematology and Oncology, Medical Plaza Driveway, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, 90024, USA
| | - William E Gillanders
- Department of Surgery, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Obi L Griffith
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Malachi Griffith
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Forest Park Avenue, Washington University School of Medicine, St. Louis, MO, 63108, USA.
- Siteman Cancer Center, Parkview Place, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Department of Genetics, South Euclid Avenue, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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Smith CC, Selitsky SR, Chai S, Armistead PM, Vincent BG, Serody JS. Alternative tumour-specific antigens. Nat Rev Cancer 2019; 19:465-478. [PMID: 31278396 PMCID: PMC6874891 DOI: 10.1038/s41568-019-0162-4] [Citation(s) in RCA: 200] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
The study of tumour-specific antigens (TSAs) as targets for antitumour therapies has accelerated within the past decade. The most commonly studied class of TSAs are those derived from non-synonymous single-nucleotide variants (SNVs), or SNV neoantigens. However, to increase the repertoire of available therapeutic TSA targets, 'alternative TSAs', defined here as high-specificity tumour antigens arising from non-SNV genomic sources, have recently been evaluated. Among these alternative TSAs are antigens derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other processes. Unlike the patient-specific nature of SNV neoantigens, some alternative TSAs may have the advantage of being widely shared by multiple tumours, allowing for universal, off-the-shelf therapies. In this Opinion article, we will outline the biology, available computational tools, preclinical and/or clinical studies and relevant cancers for each alternative TSA class, as well as discuss both current challenges preventing the therapeutic application of alternative TSAs and potential solutions to aid in their clinical translation.
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Affiliation(s)
- Christof C Smith
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sara R Selitsky
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Bioinformatics Core, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Marsico Hall, Chapel Hill, NC, USA
| | - Shengjie Chai
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paul M Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Benjamin G Vincent
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Jonathan S Serody
- Department of Microbiology and Immunology, UNC School of Medicine, Marsico Hall, Chapel Hill, NC, USA.
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Hematology/Oncology, Department of Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Program in Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Neoantigens Derived from Recurrently Mutated Genes as Potential Immunotherapy Targets for Gastric Cancer. BIOMED RESEARCH INTERNATIONAL 2019; 2019:8103142. [PMID: 31312661 PMCID: PMC6595338 DOI: 10.1155/2019/8103142] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/12/2019] [Indexed: 12/30/2022]
Abstract
Neoantigens are optimal tumor-specific targets for T-cell based immunotherapy, especially for patients with “undruggable” mutated driver genes. T-cell immunotherapy can be a “universal” treatment for HLA genotype patients sharing same oncogenic mutations. To identify potential neoantigens for therapy in gastric cancer, 32 gastric cancer patients were enrolled in our study. Whole exome sequencing data from these patients was processed by TSNAD software to detect cancer somatic mutations and predict neoantigens. The somatic mutations between different patients suggested a high interpatient heterogeneity. C>A and C>T substitutions are common, suggesting an active nucleotide excision repair. The number of predicted neoantigens was significantly higher in patients at stage T1a compared to in patients at T2 or T4b. Six genes (PIK3CA, FAT4, BRCA2, GNAQ, LRP1B, and PREX2) were found as recurrently mutated driver genes in our study. Combining with highly frequent HLA alleles, several neoantigens derived from six recurrently mutated genes were considered as potential targets for further immunotherapy.
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Schenck RO, Lakatos E, Gatenbee C, Graham TA, Anderson ARA. NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. BMC Bioinformatics 2019; 20:264. [PMID: 31117948 PMCID: PMC6532147 DOI: 10.1186/s12859-019-2876-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 05/06/2019] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Next generation sequencing has yielded an unparalleled means of quickly determining the molecular make-up of patient tumors. In conjunction with emerging, effective immunotherapeutics for a number of cancers, this rapid data generation necessitates a paired high-throughput means of predicting and assessing neoantigens from tumor variants that may stimulate immune response. RESULTS Here we offer NeoPredPipe (Neoantigen Prediction Pipeline) as a contiguous means of predicting putative neoantigens and their corresponding recognition potentials for both single and multi-region tumor samples. NeoPredPipe is able to quickly provide summary information for researchers, and clinicians alike, on predicted neoantigen burdens while providing high-level insights into tumor heterogeneity given somatic mutation calls and, optionally, patient HLA haplotypes. Given an example dataset we show how NeoPredPipe is able to rapidly provide insights into neoantigen heterogeneity, burden, and immune stimulation potential. CONCLUSIONS Through the integration of widely adopted tools for neoantigen discovery NeoPredPipe offers a contiguous means of processing single and multi-region sequence data. NeoPredPipe is user-friendly and adaptable for high-throughput performance. NeoPredPipe is freely available at https://github.com/MathOnco/NeoPredPipe .
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Affiliation(s)
- Ryan O Schenck
- Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, EC1M, UK
| | - Chandler Gatenbee
- Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, EC1M, UK
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Wu J, Zhao W, Zhou B, Su Z, Gu X, Zhou Z, Chen S. TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:276-282. [PMID: 30223042 PMCID: PMC6203688 DOI: 10.1016/j.gpb.2018.06.003] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/18/2018] [Accepted: 06/25/2018] [Indexed: 12/13/2022]
Abstract
Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database (TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen (HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas (TCGA) and The Cancer Immunome Atlas (TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients, which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy. TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb.
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Affiliation(s)
- Jingcheng Wu
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenyi Zhao
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Binbin Zhou
- College of Computer Science and Technology, Zhejiang University, Hangzhou 310013, China
| | - Zhixi Su
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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The perfect personalized cancer therapy: cancer vaccines against neoantigens. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:86. [PMID: 29678194 PMCID: PMC5910567 DOI: 10.1186/s13046-018-0751-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023]
Abstract
In the advent of Immune Checkpoint inhibitors (ICI) and of CAR-T adoptive T-cells, the new frontier in Oncology is Cancer Immunotherapy because of its ability to provide long term clinical benefit in metastatic disease in several solid and liquid tumor types. It is now clear that ICI acts by unmasking preexisting immune responses as well as by inducing de novo responses against tumor neoantigens. Thanks to theprogress made in genomics technologies and the evolution of bioinformatics, neoantigens represent ideal targets, due to their specific expression in cancer tissue and the potential lack of side effects. In this review, we discuss the promise of preclinical and clinical results with mutation-derived neoantigen cancer vaccines (NCVs) along with the current limitations from bioinformatics prediction to manufacturing an effective new therapeutic approach.
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Wood MA, Paralkar M, Paralkar MP, Nguyen A, Struck AJ, Ellrott K, Margolin A, Nellore A, Thompson RF. Population-level distribution and putative immunogenicity of cancer neoepitopes. BMC Cancer 2018; 18:414. [PMID: 29653567 PMCID: PMC5899330 DOI: 10.1186/s12885-018-4325-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/03/2018] [Indexed: 02/08/2023] Open
Abstract
Background Tumor neoantigens are drivers of cancer immunotherapy response; however, current prediction tools produce many candidates requiring further prioritization. Additional filtration criteria and population-level understanding may assist with prioritization. Herein, we show neoepitope immunogenicity is related to measures of peptide novelty and report population-level behavior of these and other metrics. Methods We propose four peptide novelty metrics to refine predicted neoantigenicity: tumor vs. paired normal peptide binding affinity difference, tumor vs. paired normal peptide sequence similarity, tumor vs. closest human peptide sequence similarity, and tumor vs. closest microbial peptide sequence similarity. We apply these metrics to neoepitopes predicted from somatic missense mutations in The Cancer Genome Atlas (TCGA) and a cohort of melanoma patients, and to a group of peptides with neoepitope-specific immune response data using an extension of pVAC-Seq (Hundal et al., pVAC-Seq: a genome-guided in silico approach to identifying tumor neoantigens. Genome Med 8:11, 2016). Results We show neoepitope burden varies across TCGA diseases and HLA alleles, with surprisingly low repetition of neoepitope sequences across patients or neoepitope preferences among sets of HLA alleles. Only 20.3% of predicted neoepitopes across TCGA patients displayed novel binding change based on our binding affinity difference criteria. Similarity of amino acid sequence was typically high between paired tumor-normal epitopes, but in 24.6% of cases, neoepitopes were more similar to other human peptides, or bacterial (56.8% of cases) or viral peptides (15.5% of cases), than their paired normal counterparts. Applied to peptides with neoepitope-specific immune response, a linear model incorporating neoepitope binding affinity, protein sequence similarity between neoepitopes and their closest viral peptides, and paired binding affinity difference was able to predict immunogenicity (AUROC = 0.66). Conclusions Our proposed prioritization criteria emphasize neoepitope novelty and refine patient neoepitope predictions for focus on biologically meaningful candidate neoantigens. We have demonstrated that neoepitopes should be considered not only with respect to their paired normal epitope, but to the entire human proteome, and bacterial and viral peptides, with potential implications for neoepitope immunogenicity and personalized vaccines for cancer treatment. We conclude that putative neoantigens are highly variable across individuals as a function of cancer genetics and personalized HLA repertoire, while the overall behavior of filtration criteria reflects predictable patterns. Electronic supplementary material The online version of this article (10.1186/s12885-018-4325-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mary A Wood
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Portland VA Research Foundation, Portland, OR, USA
| | - Mayur Paralkar
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Carnegie Mellon University, Pittsburgh, PA, USA
| | - Mihir P Paralkar
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Carnegie Mellon University, Pittsburgh, PA, USA
| | - Austin Nguyen
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Oregon State University, Corvallis, OR, USA
| | - Adam J Struck
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA
| | - Kyle Ellrott
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Adam Margolin
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA.,Department of Surgery, Oregon Health and Science University, Portland, OR, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health and Science University, Portland, OR, USA. .,Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA. .,Department of Radiation Medicine, Oregon Health and Science University, Portland, OR, USA. .,VA Portland Health Care System, Portland, OR, USA.
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Kiyotani K, Chan HT, Nakamura Y. Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens. Cancer Sci 2018; 109:542-549. [PMID: 29288513 PMCID: PMC5834780 DOI: 10.1111/cas.13498] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/23/2017] [Accepted: 12/25/2017] [Indexed: 12/15/2022] Open
Abstract
Utilizing the host immune system to eradicate cancer cells has been the most investigated subject in the cancer research field in recent years. However, most of the studies have focused on highly variable responses from immunotherapies such as immune checkpoint inhibitors, from which the majority of patients experienced no or minimum clinical benefit. Advances in genomic sequencing technologies have improved our understanding of immunopharmacogenomics and allowed us to identify novel cancer-specific immune targets. Highly tumor-specific antigens, neoantigens, are generated by somatic mutations that are not present in normal cells. It is plausible that by targeting antigens with high tumor-specificity, such as neoantigens, the likelihood of toxic effects is very limited. However, understanding the interaction between neoantigens and the host immune system remains a significant challenge. This review focuses on the potential use of neoantigen-targeted immunotherapies in cancer treatment and the recent progress of different strategies in predicting, identifying, and validating neoantigens. Successful identification of highly tumor-specific antigens accelerates the development of personalized immunotherapy with no or minimum adverse effects and with a broader coverage of patients.
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Affiliation(s)
- Kazuma Kiyotani
- Project for ImmunogenomicsCancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Hiu Ting Chan
- Project for ImmunogenomicsCancer Precision Medicine CenterJapanese Foundation for Cancer ResearchTokyoJapan
| | - Yusuke Nakamura
- Department of MedicineThe University of ChicagoChicagoILUSA
- Department of SurgeryThe University of ChicagoChicagoILUSA
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González S, Volkova N, Beer P, Gerstung M. Immuno-oncology from the perspective of somatic evolution. Semin Cancer Biol 2017; 52:75-85. [PMID: 29223477 DOI: 10.1016/j.semcancer.2017.12.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/29/2017] [Accepted: 12/05/2017] [Indexed: 12/30/2022]
Abstract
The past years have witnessed significant success for cancer immunotherapies that activate a patient's immune system against their cancer cells. At the same time our understanding of the genetic changes driving tumor evolution have progressed dramatically. The study of cancer genomes has shown that tumors are best understood as cell populations governed by the rules of evolution, leading to the emergence and spread of cell lineages with pathogenic mutations. Moreover, somatic evolution can explain the acquisition of mutations conferring drug resistance in the ever-lasting battle for reaching even fitter cell states. Here, we review the current state of the art of somatic cancer evolution and mechanisms of immune control and escape. We also revisit the principles of immunotherapy from the perspective of somatic evolution and discuss the basic rules of resistance to immunotherapies as dictated by evolution.
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Affiliation(s)
- Santiago González
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nadezda Volkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Philip Beer
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
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46
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Towards In Silico Prediction of the Immune-Checkpoint Blockade Response. Trends Pharmacol Sci 2017; 38:1041-1051. [PMID: 29089139 DOI: 10.1016/j.tips.2017.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 12/19/2022]
Abstract
Cancer immunotherapy with immune-checkpoint blockade (ICB) is considered a promising strategy for cancer treatment. Identifying predictive biomarkers and developing efficient computational models to predict the ICB response are important issues for successful immunotherapy. Here, we present a concise and intuitive survey of the computational issues for ICB response prediction, providing a summary of the available predictive biomarkers and building of one-stop machine-learning models that integrate biomarkers calculable from high-throughput sequencing (HTS) data. Several points for discussion are highlighted to inspire further research for improving ICB treatment. Continuing efforts are required to improve ICB response prediction and to identify novel predictive biomarkers by taking advantage of the rapid development of computational models and HTS techniques for effective and personalized cancer immunotherapy.
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47
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Zhou Z, Wu S, Lai J, Shi Y, Qiu C, Chen Z, Wang Y, Gu X, Zhou J, Chen S. Identification of trunk mutations in gastric carcinoma: a case study. BMC Med Genomics 2017; 10:49. [PMID: 28716121 PMCID: PMC5520061 DOI: 10.1186/s12920-017-0285-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/13/2017] [Indexed: 02/06/2023] Open
Abstract
Background Intratumor heterogeneity (ITH) poses an urgent challenge for cancer precision medicine because it can cause drug resistance against cancer target therapy and immunotherapy. The search for trunk mutations that are present in all cancer cells is therefore critical for each patient. Case presentation In this study, we aimed to evaluate the efficiency of multiregional sequencing for the identification of trunk mutations present in all regions of a tumor as a case study. We applied multiregional whole-exome sequencing (WES) to investigate the genetic heterogeneity and homogeneity of a case of gastric carcinoma. Approximately 83% of common missense mutations present in two samples and approximately 89% of common missense mutations present in three samples were trunk mutations. Notably, trunk mutations appeared to have higher variant allele frequencies (VAFs) than non-trunk mutations. Conclusions Our results indicate that small-scale multiregional sampling and subsequent screening of low VAF somatic mutations might be a cost-effective strategy for identifying the majority of trunk mutations in gastric carcinoma. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0285-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhan Zhou
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Shanshan Wu
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Jun Lai
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Yuan Shi
- Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang, Hangzhou, 310058, China
| | - Chixiao Qiu
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China
| | - Zhe Chen
- Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang, Hangzhou, 310058, China
| | - Yufeng Wang
- Department of Biology and South Texas Center for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Xun Gu
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Jie Zhou
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China.
| | - Shuqing Chen
- College of Pharmaceutical Sciences, Zhejiang University, Zhejiang, Hangzhou, 310058, China. .,International Center for Precision Medicine, Zhejiang California International NanoSystems Institute, Zhejiang, Hangzhou, 310058, China.
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