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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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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3
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Ramirez CA, Becker-Hapak M, Singhal K, Russler-Germain DA, Frenkel F, Barnell EK, McClain ED, Desai S, Schappe T, Onyeador OC, Kudryashova O, Belousov V, Bagaev A, Ocheredko E, Kiwala S, Hundal J, Skidmore ZL, Watkins MP, Mooney TB, Walker JR, Krysiak K, Gomez F, Fronick CC, Fulton RS, Schreiber RD, Mehta-Shah N, Cashen AF, Kahl BS, Ataullakhanov R, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma. Blood Adv 2024; 8:4035-4049. [PMID: 38713894 DOI: 10.1182/bloodadvances.2022007792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024] Open
Abstract
ABSTRACT Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR repertoire from healthy individuals using RNA-seq data. An average of 52 somatic mutations per patient (range, 2-172) were identified, and ≥2 (median, 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all 4 patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field. This trial was registered at www.ClinicalTrials.gov as #NCT03121677.
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Affiliation(s)
- Cody A Ramirez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | | | - Kartik Singhal
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - David A Russler-Germain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Erica K Barnell
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Ethan D McClain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sweta Desai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy Schappe
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Zachary L Skidmore
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Marcus P Watkins
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Thomas B Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Kilannin Krysiak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Felicia Gomez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Catrina C Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert D Schreiber
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Neha Mehta-Shah
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Amanda F Cashen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Brad S Kahl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Nancy L Bartlett
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Obi L Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Todd A Fehniger
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
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4
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Meng W, Takeuchi Y, Ward JP, Sultan H, Arthur CD, Mardis ER, Artyomov MN, Lichti CF, Schreiber RD. Improvement of Tumor Neoantigen Detection by High-Field Asymmetric Waveform Ion Mobility Mass Spectrometry. Cancer Immunol Res 2024; 12:988-1006. [PMID: 38768391 DOI: 10.1158/2326-6066.cir-23-0900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 03/05/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Cancer neoantigens have been shown to elicit cancer-specific T-cell responses and have garnered much attention for their roles in both spontaneous and therapeutically induced antitumor responses. Mass spectrometry (MS) profiling of tumor immunopeptidomes has been used, in part, to identify MHC-bound mutant neoantigen ligands. However, under standard conditions, MS-based detection of such rare but clinically relevant neoantigens is relatively insensitive, requiring 300 million cells or more. Here, to quantitatively define the minimum detectable amounts of therapeutically relevant MHC-I and MHC-II neoantigen peptides, we analyzed different dilutions of immunopeptidomes isolated from the well-characterized T3 mouse methylcholanthrene (MCA)-induced cell line by MS. Using either data-dependent acquisition or parallel reaction monitoring (PRM), we established the minimum amount of material required to detect the major T3 neoantigens in the presence or absence of high field asymmetric waveform ion mobility spectrometry (FAIMS). This analysis yielded a 14-fold enhancement of sensitivity in detecting the major T3 MHC-I neoantigen (mLama4) with FAIMS-PRM compared with PRM without FAIMS, allowing ex vivo detection of this neoantigen from an individual 100 mg T3 tumor. These findings were then extended to two other independent MCA-sarcoma lines (1956 and F244). This study demonstrates that FAIMS substantially increases the sensitivity of MS-based characterization of validated neoantigens from tumors.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
| | - Yoshiko Takeuchi
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
| | - Jeffrey P Ward
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
- Department of Medicine, Washington University School of Medicine, Saint Louis, Missouri
| | - Hussein Sultan
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
| | - Cora D Arthur
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine at Nationwide Children's Hospital, Columbus, Ohio
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, Missouri
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5
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Cai Y, Li D, Lv D, Yu J, Ma Y, Jiang T, Ding N, Liu Z, Li Y, Xu J. MHC-I-presented non-canonical antigens expand the cancer immunotherapy targets in acute myeloid leukemia. Sci Data 2024; 11:831. [PMID: 39090129 PMCID: PMC11294462 DOI: 10.1038/s41597-024-03660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Identification of tumor neoantigens is indispensable for the development of cancer immunotherapies. However, we are still lacking knowledge about the potential neoantigens derived from sequences outside protein-coding regions. Here, we comprehensively characterized the immunopeptidome landscape by integrating multi-omics data in acute myeloid leukemia (AML). Both canonical and non-canonical MHC-associated peptides (MAPs) in AML were identified. We found that the quality and characteristics of ncMAPs are comparable or superior to cMAPs, suggesting ncMAPs are indispensable sources for tumor neoantigens. We further proposed a computational framework to prioritize the neoantigens by integrating additional transcriptome and immunopeptidome in normal tissues. Notably, 6 of prioritized 13 neoantigens were derived from ncMAPs. The expressions of corresponding source genes are highly related to infiltrations of immune cells. Finally, a risk model was developed, which exhibited good performance for clinical prognosis in AML. Our findings expand potential cancer immunotherapy targets and provide in-depth insights into AML treatment, laying a new foundation for precision therapies in AML.
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Affiliation(s)
- Yangyang Cai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Donghao Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Jiaxin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Yingying Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Tiantongfei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China
| | - Zhigang Liu
- Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Guangzhou, China.
| | - Yongsheng Li
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150081, China.
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang Province, 150001, China.
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6
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Su Z, Wu Y, Cao K, Du J, Cao L, Wu Z, Wu X, Wang X, Song Y, Wang X, Duan H. APEX-pHLA: A novel method for accurate prediction of the binding between exogenous short peptides and HLA class I molecules. Methods 2024; 228:38-47. [PMID: 38772499 DOI: 10.1016/j.ymeth.2024.05.013] [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: 01/27/2024] [Revised: 04/28/2024] [Accepted: 05/18/2024] [Indexed: 05/23/2024] Open
Abstract
Human leukocyte antigen (HLA) molecules play critically significant role within the realm of immunotherapy due to their capacities to recognize and bind exogenous antigens such as peptides, subsequently delivering them to immune cells. Predicting the binding between peptides and HLA molecules (pHLA) can expedite the screening of immunogenic peptides and facilitate vaccine design. However, traditional experimental methods are time-consuming and inefficient. In this study, an efficient method based on deep learning was developed for predicting peptide-HLA binding, which treated peptide sequences as linguistic entities. It combined the architectures of textCNN and BiLSTM to create a deep neural network model called APEX-pHLA. This model operated without limitations related to HLA class I allele variants and peptide segment lengths, enabling efficient encoding of sequence features for both HLA and peptide segments. On the independent test set, the model achieved Accuracy, ROC_AUC, F1, and MCC is 0.9449, 0.9850, 0.9453, and 0.8899, respectively. Similarly, on an external test set, the results were 0.9803, 0.9574, 0.8835, and 0.7863, respectively. These findings outperformed fifteen methods previously reported in the literature. The accurate prediction capability of the APEX-pHLA model in peptide-HLA binding might provide valuable insights for future HLA vaccine design.
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Affiliation(s)
- Zhihao Su
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Yejian Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Kaiqiang Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Jie Du
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Lujing Cao
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Zhipeng Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xinyi Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Xinqiao Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Ying Song
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Xudong Wang
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
| | - Hongliang Duan
- Faculty of Applied Sciences, Macao Polytechnic University, Macao 999078, China.
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7
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Liu T, Yao W, Sun W, Yuan Y, Liu C, Liu X, Wang X, Jiang H. Components, Formulations, Deliveries, and Combinations of Tumor Vaccines. ACS NANO 2024; 18:18801-18833. [PMID: 38979917 DOI: 10.1021/acsnano.4c05065] [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: 07/10/2024]
Abstract
Tumor vaccines, an important part of immunotherapy, prevent cancer or kill existing tumor cells by activating or restoring the body's own immune system. Currently, various formulations of tumor vaccines have been developed, including cell vaccines, tumor cell membrane vaccines, tumor DNA vaccines, tumor mRNA vaccines, tumor polypeptide vaccines, virus-vectored tumor vaccines, and tumor-in-situ vaccines. There are also multiple delivery systems for tumor vaccines, such as liposomes, cell membrane vesicles, viruses, exosomes, and emulsions. In addition, to decrease the risk of tumor immune escape and immune tolerance that may exist with a single tumor vaccine, combination therapy of tumor vaccines with radiotherapy, chemotherapy, immune checkpoint inhibitors, cytokines, CAR-T therapy, or photoimmunotherapy is an effective strategy. Given the critical role of tumor vaccines in immunotherapy, here, we look back to the history of tumor vaccines, and we discuss the antigens, adjuvants, formulations, delivery systems, mechanisms, combination therapy, and future directions of tumor vaccines.
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Affiliation(s)
- Tengfei Liu
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenyan Yao
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wenyu Sun
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Yihan Yuan
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chen Liu
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, Jiangsu Key Laboratory for Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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8
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Liu B, Zhou H, Tan L, Siu KTH, Guan XY. Exploring treatment options in cancer: Tumor treatment strategies. Signal Transduct Target Ther 2024; 9:175. [PMID: 39013849 PMCID: PMC11252281 DOI: 10.1038/s41392-024-01856-7] [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: 01/23/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 07/18/2024] Open
Abstract
Traditional therapeutic approaches such as chemotherapy and radiation therapy have burdened cancer patients with onerous physical and psychological challenges. Encouragingly, the landscape of tumor treatment has undergone a comprehensive and remarkable transformation. Emerging as fervently pursued modalities are small molecule targeted agents, antibody-drug conjugates (ADCs), cell-based therapies, and gene therapy. These cutting-edge treatment modalities not only afford personalized and precise tumor targeting, but also provide patients with enhanced therapeutic comfort and the potential to impede disease progression. Nonetheless, it is acknowledged that these therapeutic strategies still harbour untapped potential for further advancement. Gaining a comprehensive understanding of the merits and limitations of these treatment modalities holds the promise of offering novel perspectives for clinical practice and foundational research endeavours. In this review, we discussed the different treatment modalities, including small molecule targeted drugs, peptide drugs, antibody drugs, cell therapy, and gene therapy. It will provide a detailed explanation of each method, addressing their status of development, clinical challenges, and potential solutions. The aim is to assist clinicians and researchers in gaining a deeper understanding of these diverse treatment options, enabling them to carry out effective treatment and advance their research more efficiently.
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Affiliation(s)
- Beilei Liu
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China
| | - Hongyu Zhou
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Licheng Tan
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Kin To Hugo Siu
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
- Department of Clinical Oncology, The University of Hong Kong, Hong Kong, China.
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, China.
- MOE Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, China.
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9
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Culliford R, Lawrence SED, Mills C, Tippu Z, Chubb D, Cornish AJ, Browning L, Kinnersley B, Bentham R, Sud A, Pallikonda H, Frangou A, Gruber AJ, Litchfield K, Wedge D, Larkin J, Turajlic S, Houlston RS. Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma. Nat Commun 2024; 15:5935. [PMID: 39009593 PMCID: PMC11250826 DOI: 10.1038/s41467-024-49692-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/17/2024] [Indexed: 07/17/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing for a detailed description of the somatic mutational landscape of ccRCC. We identify candidate driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for therapeutic interventions. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The observations that higher T-cell infiltration is associated with better overall survival and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients.
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Affiliation(s)
- Richard Culliford
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Samuel E D Lawrence
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Zayd Tippu
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Alex J Cornish
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Robert Bentham
- Department of Oncology, University College London Cancer Institute, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Husayn Pallikonda
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Anna Frangou
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
- Algebraic Systems Biology, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Algebraic Systems Biology, Centre for Systems Biology Dresden, Dresden, Germany
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Samra Turajlic
- Renal and Skin Units, The Royal Marsden NHS Foundation Trust, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
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10
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Jurczak S, Druchok M. Cancer Immunotherapies Ignited by a Thorough Machine Learning-Based Selection of Neoantigens. Adv Biol (Weinh) 2024:e2400114. [PMID: 38971967 DOI: 10.1002/adbi.202400114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/02/2024] [Indexed: 07/08/2024]
Abstract
Identification of neoantigens, derived from somatic DNA alterations, emerges as a promising strategy for cancer immunotherapies. However, not all somatic mutations result in immunogenicity, hence, efficient tools to predict the immunogenicity of neoepitopes are needed. A pipeline is presented that provides a comprehensive solution for the identification of neoepitopes based on genomic sequencing data. The pipeline consists of a data pre-processing step and three machine learning predictive steps. The pre-processing step analyzes genomic data for different types of alterations, produces a list of all possible antigens, and determines the human leukocyte antigen (HLA) type and T-cell receptor (TCR) repertoire. The first predictive step performs a classification into antigens and neoantigens, selecting neoantigens for further consideration. The next step predicts the strength of binding between neoantigens and available major histocompatibility complexes of class I (MHC-I). The third step is engaged to predict the likelihood of inducing an immune response. Neoepitopes satisfying all three predictive stages are assumed to be potent candidates to ensure immunogenicity. The predictive pipeline is used in two regimes: selecting neoantigens from patients' sequencing data and generating novel neoantigen candidates. Two different techniques - Monte Carlo and Reinforcement Learning - are implemented to facilitate the generative regime.
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Affiliation(s)
- Sebastian Jurczak
- SoftServe Inc., 11/13 Building B, Jaworska St., Wroclaw, 53-612, Poland
| | - Maksym Druchok
- SoftServe Inc., 2d Sadova St., Lviv, 79021, Ukraine
- Institute for Condensed Matter Physics, 1 Svientsitskii St., Lviv, 79011, Ukraine
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11
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Liang Y, Lv D, Liu K, Yang L, Shu H, Wen L, Lv C, Sun Q, Yin J, Liu H, Xu J, Liu Z, Ding N. MicroProteinDB: A database to provide knowledge on sequences, structures and function of ncRNA-derived microproteins. Comput Biol Med 2024; 177:108660. [PMID: 38820774 DOI: 10.1016/j.compbiomed.2024.108660] [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: 03/20/2024] [Revised: 05/08/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Omics-based technologies have revolutionized our comprehension of microproteins encoded by ncRNAs, revealing their abundant presence and pivotal roles within complex functional landscapes. Here, we developed MicroProteinDB (http://bio-bigdata.hrbmu.edu.cn/MicroProteinDB), which offers and visualizes the extensive knowledge to aid retrieval and analysis of computationally predicted and experimentally validated microproteins originating from various ncRNA types. Employing prediction algorithms grounded in diverse deep learning approaches, MicroProteinDB comprehensively documents the fundamental physicochemical properties, secondary and tertiary structures, interactions with functional proteins, family domains, and inter-species conservation of microproteins. With five major analytical modules, it will serve as a valuable knowledge for investigating ncRNA-derived microproteins.
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Affiliation(s)
- Yinan Liang
- The First Affiliated Hospital, Harbin Medical University, Harbin, 150001, China
| | - Dezhong Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Kefan Liu
- School of Interdisciplinary Medicine and Engineering, Harbin Medical University, Harbin, 150081, China
| | - Liting Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Huan Shu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Luan Wen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Chongwen Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qisen Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Jiaqi Yin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Hui Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| | - Zhigang Liu
- Affiliated Foshan Maternity&Child Healthcare Hospital, Southern Medical University, Guangzhou, 510000, China.
| | - Na Ding
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
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12
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Hao Q, Long Y, Yang Y, Deng Y, Ding Z, Yang L, Shu Y, Xu H. Development and Clinical Applications of Therapeutic Cancer Vaccines with Individualized and Shared Neoantigens. Vaccines (Basel) 2024; 12:717. [PMID: 39066355 PMCID: PMC11281709 DOI: 10.3390/vaccines12070717] [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: 05/29/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Neoantigens, presented as peptides on the surfaces of cancer cells, have recently been proposed as optimal targets for immunotherapy in clinical practice. The promising outcomes of neoantigen-based cancer vaccines have inspired enthusiasm for their broader clinical applications. However, the individualized tumor-specific antigens (TSA) entail considerable costs and time due to the variable immunogenicity and response rates of these neoantigens-based vaccines, influenced by factors such as neoantigen response, vaccine types, and combination therapy. Given the crucial role of neoantigen efficacy, a number of bioinformatics algorithms and pipelines have been developed to improve the accuracy rate of prediction through considering a series of factors involving in HLA-peptide-TCR complex formation, including peptide presentation, HLA-peptide affinity, and TCR recognition. On the other hand, shared neoantigens, originating from driver mutations at hot mutation spots (e.g., KRASG12D), offer a promising and ideal target for the development of therapeutic cancer vaccines. A series of clinical practices have established the efficacy of these vaccines in patients with distinct HLA haplotypes. Moreover, increasing evidence demonstrated that a combination of tumor associated antigens (TAAs) and neoantigens can also improve the prognosis, thus expand the repertoire of shared neoantigens for cancer vaccines. In this review, we provide an overview of the complex process involved in identifying personalized neoantigens, their clinical applications, advances in vaccine technology, and explore the therapeutic potential of shared neoantigen strategies.
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Affiliation(s)
- Qing Hao
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yuhang Long
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yi Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yiqi Deng
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Colorectal Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenyu Ding
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Li Yang
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
| | - Yang Shu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Gastric Cancer Center, Department of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, Department of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; (Q.H.); (Y.L.); (Y.Y.); (Y.D.); (Z.D.); (L.Y.)
- Institute of General Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
- Research Center of Clinical Laboratory Medicine, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
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13
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Bresser K, Nicolet BP, Jeko A, Wu W, Loayza-Puch F, Agami R, Heck AJR, Wolkers MC, Schumacher TN. Gene and protein sequence features augment HLA class I ligand predictions. Cell Rep 2024; 43:114325. [PMID: 38870014 DOI: 10.1016/j.celrep.2024.114325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/22/2024] [Accepted: 05/22/2024] [Indexed: 06/15/2024] Open
Abstract
The sensitivity of malignant tissues to T cell-based immunotherapies depends on the presence of targetable human leukocyte antigen (HLA) class I ligands. Peptide-intrinsic factors, such as HLA class I affinity and proteasomal processing, have been established as determinants of HLA ligand presentation. However, the role of gene and protein sequence features as determinants of epitope presentation has not been systematically evaluated. We perform HLA ligandome mass spectrometry to evaluate the contribution of 7,135 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turnover, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of such "hard-coded" sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as experimental measures of gene expression. Our study highlights the value of gene and protein features for HLA ligand predictions.
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Affiliation(s)
- Kaspar Bresser
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Benoit P Nicolet
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation lab, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Anita Jeko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Wei Wu
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Fabricio Loayza-Puch
- Translational Control and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, the Netherlands
| | - Monika C Wolkers
- Sanquin Blood Supply Foundation, Department of Research, T cell differentiation lab, Amsterdam, The Netherlands; Amsterdam UMC, University of Amsterdam, Landsteiner Laboratory, Amsterdam, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Ton N Schumacher
- Department of Molecular Oncology and Immunology, Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands; Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands.
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14
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Xia H, Hoang M, Schmidt E, Kiwala S, McMichael J, Skidmore ZL, Fisk B, Song JJ, Hundal J, Mooney T, Walker JR, Peter Goedegebuure S, Miller CA, Gillanders WE, Griffith OL, Griffith M. pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection. ARXIV 2024:arXiv:2406.06985v1. [PMID: 38947921 PMCID: PMC11213132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies are underway globally. Accurate identification and prioritization of neoantigens is highly relevant to designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address. Results We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select and export their neoantigen candidates. The tool allows users to visualize candidates across three different levels, including variant, transcript and peptide information. Conclusions pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings The application is available as part of the pVACtools pipeline at pvactools.org and as an online server at pvacview.org.
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Affiliation(s)
- Huiming Xia
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - My Hoang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Evelyn Schmidt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Bryan Fisk
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jonathan J Song
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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15
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Koncz B, Balogh GM, Manczinger M. A journey to your self: The vague definition of immune self and its practical implications. Proc Natl Acad Sci U S A 2024; 121:e2309674121. [PMID: 38722806 PMCID: PMC11161755 DOI: 10.1073/pnas.2309674121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2024] Open
Abstract
The identification of immunogenic peptides has become essential in an increasing number of fields in immunology, ranging from tumor immunotherapy to vaccine development. The nature of the adaptive immune response is shaped by the similarity between foreign and self-protein sequences, a concept extensively applied in numerous studies. Can we precisely define the degree of similarity to self? Furthermore, do we accurately define immune self? In the current work, we aim to unravel the conceptual and mechanistic vagueness hindering the assessment of self-similarity. Accordingly, we demonstrate the remarkably low consistency among commonly employed measures and highlight potential avenues for future research.
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Affiliation(s)
- Balázs Koncz
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Gergő Mihály Balogh
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
| | - Máté Manczinger
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Hungarian Research Network (HUN-REN) Biological Research Centre, Szeged6726, Hungary
- Hungarian Centre of Excellence for Molecular Medicine - Biological Research Centre (HCEMM-BRC) Systems Immunology Research Group, Szeged6726, Hungary
- Department of Dermatology and Allergology, University of Szeged, Szeged6720, Hungary
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16
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Bowen CM, Demarest K, Vilar E, Shah PD. Novel Cancer Prevention Strategies in Individuals With Hereditary Cancer Syndromes: Focus on BRCA1, BRCA2, and Lynch Syndrome. Am Soc Clin Oncol Educ Book 2024; 44:e433576. [PMID: 38913968 DOI: 10.1200/edbk_433576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Germline pathogenic variants (PVs) in the BRCA1 and BRCA2 genes confer elevated risks of breast, ovarian, and other cancers. Lynch syndrome (LS) is associated with increased risks of multiple cancer types including colorectal and uterine cancers. Current cancer risk mitigation strategies have focused on pharmacologic risk reduction, enhanced surveillance, and preventive surgeries. While these approaches can be effective, they stand to be improved on because of either limited efficacy or undesirable impact on quality of life. The current review summarizes ongoing investigational efforts in cancer risk prevention strategies for patients with germline PVs in BRCA1, BRCA2, or LS-associated genes. These efforts span radiation, surgery, and pharmacology including vaccine strategies. Understanding the molecular events involved in the premalignant to malignant transformation in high-risk individuals may ultimately contribute significantly to novel prevention strategies.
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Affiliation(s)
- Charles M Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Payal D Shah
- Perelman Center for Advanced Medicine, Abramson Cancer Center, Philadelphia, PA
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17
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Kim SH, Lee BR, Kim SM, Kim S, Kim MS, Kim J, Lee I, Kim HS, Nam GH, Kim IS, Song K, Choi Y, Lee DS, Park WY. The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex. Exp Mol Med 2024; 56:1461-1471. [PMID: 38866910 PMCID: PMC11263684 DOI: 10.1038/s12276-024-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Neoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUSpMHC and VACINUSTCR: VACINUSpMHC incorporates physical binding between peptides and MHCs (pMHCs), and VACINUSTCR integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs). We then validated our neoantigen prediction workflows both in vitro and in vivo in patients with hepatocellular carcinoma (HCC) and in a B16F10 mouse melanoma model. The predictive abilities of VACINUSpMHC and VACINUSTCR were confirmed in a validation cohort of 8 patients with HCC. Of a total of 118 neoantigen candidates predicted by VACINUSpMHC, 48 peptides were ultimately selected using VACINUSTCR. In vitro validation revealed that among the 48 predicted neoantigen candidates, 13 peptides were immunogenic. Assessment of the antitumor efficacy of the candidate neoepitopes using a VACINUSTCR in vivo mouse model suggested that vaccination with the predicted neoepitopes induced neoantigen-specific T cell responses and enabled the trafficking of neoantigen-specific CD8 + T cell clones into the tumor tissue, leading to tumor suppression. This study showed that the prediction of immunogenic neoantigens can be improved by integrating a tumor-reactive TIL TCR-pMHC ternary complex.
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MESH Headings
- Antigens, Neoplasm/immunology
- Animals
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Cell Line, Tumor
- Melanoma, Experimental/immunology
- Melanoma, Experimental/therapy
- Major Histocompatibility Complex/immunology
- Liver Neoplasms/immunology
- Liver Neoplasms/therapy
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/therapy
- CD8-Positive T-Lymphocytes/immunology
- Female
- Immunotherapy/methods
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Affiliation(s)
| | | | | | | | | | - Jaehyun Kim
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
| | - Inkyu Lee
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
| | | | - Gi-Hoon Nam
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, 02841, Korea
| | - In-San Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
- Chemical & Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | | | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, Korea.
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Geninus Inc., Seoul, 05836, Korea.
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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18
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Houlahan KE, Khan A, Greenwald NF, Vivas CS, West RB, Angelo M, Curtis C. Germline-mediated immunoediting sculpts breast cancer subtypes and metastatic proclivity. Science 2024; 384:eadh8697. [PMID: 38815010 DOI: 10.1126/science.adh8697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024]
Abstract
Tumors with the same diagnosis can have different molecular profiles and response to treatment. It remains unclear when and why these differences arise. Somatic genomic aberrations occur within the context of a highly variable germline genome. Interrogating 5870 breast cancer lesions, we demonstrated that germline-derived epitopes in recurrently amplified genes influence somatic evolution by mediating immunoediting. Individuals with a high germline-epitope burden in human epidermal growth factor receptor 2 (HER2/ERBB2) are less likely to develop HER2-positive breast cancer compared with other subtypes. The same holds true for recurrent amplicons defining three aggressive estrogen receptor (ER)-positive subgroups. Tumors that overcome such immune-mediated negative selection are more aggressive and demonstrate an "immune cold" phenotype. These data show that the germline genome plays a role in dictating somatic evolution.
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Affiliation(s)
- Kathleen E Houlahan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Aziz Khan
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Noah F Greenwald
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Robert B West
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Michael Angelo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Christina Curtis
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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19
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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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20
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Mørk SK, Skadborg SK, Albieri B, Draghi A, Bol K, Kadivar M, Westergaard MCW, Stoltenborg Granhøj J, Borch A, Petersen NV, Thuesen N, Rasmussen IS, Andreasen LV, Dohn RB, Yde CW, Noergaard N, Lorentzen T, Soerensen AB, Kleine-Kohlbrecher D, Jespersen A, Christensen D, Kringelum J, Donia M, Hadrup SR, Marie Svane I. Dose escalation study of a personalized peptide-based neoantigen vaccine (EVX-01) in patients with metastatic melanoma. J Immunother Cancer 2024; 12:e008817. [PMID: 38782542 PMCID: PMC11116868 DOI: 10.1136/jitc-2024-008817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Neoantigens can serve as targets for T cell-mediated antitumor immunity via personalized neopeptide vaccines. Interim data from our clinical study NCT03715985 showed that the personalized peptide-based neoantigen vaccine EVX-01, formulated in the liposomal adjuvant, CAF09b, was safe and able to elicit EVX-01-specific T cell responses in patients with metastatic melanoma. Here, we present results from the dose-escalation part of the study, evaluating the feasibility, safety, efficacy, and immunogenicity of EVX-01 in addition to anti-PD-1 therapy. METHODS Patients with metastatic melanoma on anti-PD-1 therapy were treated in three cohorts with increasing vaccine dosages (twofold and fourfold). Tumor-derived neoantigens were selected by the AI platform PIONEER and used in personalized therapeutic cancer peptide vaccines EVX-01. Vaccines were administered at 2-week intervals for a total of three intraperitoneal and three intramuscular injections. The study's primary endpoint was safety and tolerability. Additional endpoints were immunological responses, survival, and objective response rates. RESULTS Compared with the base dose level previously reported, no new vaccine-related serious adverse events were observed during dose escalation of EVX-01 in combination with an anti-PD-1 agent given according to local guidelines. Two patients at the third dose level (fourfold dose) developed grade 3 toxicity, most likely related to pembrolizumab. Overall, 8 out of the 12 patients had objective clinical responses (6 partial response (PR) and 2 CR), with all 4 patients at the highest dose level having a CR (1 CR, 3 PR). EVX-01 induced peptide-specific CD4+ and/or CD8+T cell responses in all treated patients, with CD4+T cells as the dominating responses. The magnitude of immune responses measured by IFN-γ ELISpot assay correlated with individual peptide doses. A significant correlation between the PIONEER quality score and induced T cell immunogenicity was detected, while better CRs correlated with both the number of immunogenic EVX-01 peptides and the PIONEER quality score. CONCLUSION Immunization with EVX-01-CAF09b in addition to anti-PD-1 therapy was shown to be safe and well tolerated and elicit vaccine neoantigen-specific CD4+and CD8+ T cell responses at all dose levels. In addition, objective tumor responses were observed in 67% of patients. The results encourage further assessment of the antitumor efficacy of EVX-01 in combination with anti-PD-1 therapy.
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Affiliation(s)
- Sofie Kirial Mørk
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | | | - Benedetta Albieri
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Arianna Draghi
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Kalijn Bol
- Medical Oncology, Radboudumc, Nijmegen, The Netherlands
| | - Mohammad Kadivar
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | - Joachim Stoltenborg Granhøj
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Annie Borch
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | | | | | | | | | - Rebecca Bach Dohn
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Nis Noergaard
- Department of Urology, Copenhagen University Hospital, Herlev, Denmark
| | - Torben Lorentzen
- Department of Gastroenterology, Copenhagen University Hospital, Herlev, Denmark
| | | | | | | | - Dennis Christensen
- Center for Vaccine Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marco Donia
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Inge Marie Svane
- Department of Oncology, Copenhagen University Hospital, National Center for Cancer Immune Therapy (CCIT-DK), Herlev, Denmark
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21
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Deng N, Sinha KM, Vilar E. MONET: a database for prediction of neoantigens derived from microsatellite loci. Front Immunol 2024; 15:1394593. [PMID: 38835776 PMCID: PMC11148240 DOI: 10.3389/fimmu.2024.1394593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/03/2024] [Indexed: 06/06/2024] Open
Abstract
Background Microsatellite instability (MSI) secondary to mismatch repair (MMR) deficiency is characterized by insertions and deletions (indels) in short DNA sequences across the genome. These indels can generate neoantigens, which are ideal targets for precision immune interception. However, current neoantigen databases lack information on neoantigens arising from coding microsatellites. To address this gap, we introduce The MicrOsatellite Neoantigen Discovery Tool (MONET). Method MONET identifies potential mutated tumor-specific neoantigens (neoAgs) by predicting frameshift mutations in coding microsatellite sequences of the human genome. Then MONET annotates these neoAgs with key features such as binding affinity, stability, expression, frequency, and potential pathogenicity using established algorithms, tools, and public databases. A user-friendly web interface (https://monet.mdanderson.org/) facilitates access to these predictions. Results MONET predicts over 4 million and 15 million Class I and Class II potential frameshift neoAgs, respectively. Compared to existing databases, MONET demonstrates superior coverage (>85% vs. <25%) using a set of experimentally validated neoAgs. Conclusion MONET is a freely available, user-friendly web tool that leverages publicly available resources to identify neoAgs derived from microsatellite loci. This systems biology approach empowers researchers in the field of precision immune interception.
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Affiliation(s)
- Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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22
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Omelchenko AA, Siwek JC, Chhibbar P, Arshad S, Nazarali I, Nazarali K, Rosengart A, Rahimikollu J, Tilstra J, Shlomchik MJ, Koes DR, Joglekar AV, Das J. Sliding Window INteraction Grammar (SWING): a generalized interaction language model for peptide and protein interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592062. [PMID: 38746274 PMCID: PMC11092674 DOI: 10.1101/2024.05.01.592062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The explosion of sequence data has allowed the rapid growth of protein language models (pLMs). pLMs have now been employed in many frameworks including variant-effect and peptide-specificity prediction. Traditionally, for protein-protein or peptide-protein interactions (PPIs), corresponding sequences are either co-embedded followed by post-hoc integration or the sequences are concatenated prior to embedding. Interestingly, no method utilizes a language representation of the interaction itself. We developed an interaction LM (iLM), which uses a novel language to represent interactions between protein/peptide sequences. Sliding Window Interaction Grammar (SWING) leverages differences in amino acid properties to generate an interaction vocabulary. This vocabulary is the input into a LM followed by a supervised prediction step where the LM's representations are used as features. SWING was first applied to predicting peptide:MHC (pMHC) interactions. SWING was not only successful at generating Class I and Class II models that have comparable prediction to state-of-the-art approaches, but the unique Mixed Class model was also successful at jointly predicting both classes. Further, the SWING model trained only on Class I alleles was predictive for Class II, a complex prediction task not attempted by any existing approach. For de novo data, using only Class I or Class II data, SWING also accurately predicted Class II pMHC interactions in murine models of SLE (MRL/lpr model) and T1D (NOD model), that were validated experimentally. To further evaluate SWING's generalizability, we tested its ability to predict the disruption of specific protein-protein interactions by missense mutations. Although modern methods like AlphaMissense and ESM1b can predict interfaces and variant effects/pathogenicity per mutation, they are unable to predict interaction-specific disruptions. SWING was successful at accurately predicting the impact of both Mendelian mutations and population variants on PPIs. This is the first generalizable approach that can accurately predict interaction-specific disruptions by missense mutations with only sequence information. Overall, SWING is a first-in-class generalizable zero-shot iLM that learns the language of PPIs.
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Affiliation(s)
- Alisa A. Omelchenko
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jane C. Siwek
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Prabal Chhibbar
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Integrative systems biology PhD program, School of Medicine, University of Pittsburgh, PA, USA
| | - Sanya Arshad
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Iliyan Nazarali
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kiran Nazarali
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - AnnaElaine Rosengart
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Javad Rahimikollu
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
- The joint CMU-Pitt PhD program in computational biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jeremy Tilstra
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Rheumatology and Clinical Immunology, Department of Medicine, School of Medicine, University of Pittsburgh, PA, USA
| | - Mark J. Shlomchik
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David R. Koes
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Alok V. Joglekar
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
| | - Jishnu Das
- Center for Systems immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, PA, USA
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23
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Fuchs KJ, van de Meent M, Honders MW, Khatri I, Kester MGD, Koster EAS, Koutsoumpli G, de Ru AH, van Bergen CAM, van Veelen PA, ’t Hoen PAC, van Balen P, van den Akker EB, Veelken JH, Halkes CJM, Falkenburg JHF, Griffioen M. Expanding the repertoire reveals recurrent, cryptic, and hematopoietic HLA class I minor histocompatibility antigens. Blood 2024; 143:1856-1872. [PMID: 38427583 PMCID: PMC11076866 DOI: 10.1182/blood.2023022343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/03/2024] Open
Abstract
ABSTRACT Allogeneic stem cell transplantation (alloSCT) is a curative treatment for hematological malignancies. After HLA-matched alloSCT, antitumor immunity is caused by donor T cells recognizing polymorphic peptides, designated minor histocompatibility antigens (MiHAs), that are presented by HLA on malignant patient cells. However, T cells often target MiHAs on healthy nonhematopoietic tissues of patients, thereby inducing side effects known as graft-versus-host disease. Here, we aimed to identify the dominant repertoire of HLA-I-restricted MiHAs to enable strategies to predict, monitor or modulate immune responses after alloSCT. To systematically identify novel MiHAs by genome-wide association screening, T-cell clones were isolated from 39 transplanted patients and tested for reactivity against 191 Epstein-Barr virus transformed B cell lines of the 1000 Genomes Project. By discovering 81 new MiHAs, we more than doubled the antigen repertoire to 159 MiHAs and demonstrated that, despite many genetic differences between patients and donors, often the same MiHAs are targeted in multiple patients. Furthermore, we showed that one quarter of the antigens are cryptic, that is translated from unconventional open reading frames, for example long noncoding RNAs, showing that these antigen types are relevant targets in natural immune responses. Finally, using single cell RNA-seq data, we analyzed tissue expression of MiHA-encoding genes to explore their potential role in clinical outcome, and characterized 11 new hematopoietic-restricted MiHAs as potential targets for immunotherapy. In conclusion, we expanded the repertoire of HLA-I-restricted MiHAs and identified recurrent, cryptic and hematopoietic-restricted antigens, which are fundamental to predict, follow or manipulate immune responses to improve clinical outcome after alloSCT.
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Affiliation(s)
- Kyra J. Fuchs
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marian van de Meent
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Willy Honders
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Indu Khatri
- Department of Immunology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michel G. D. Kester
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eva A. S. Koster
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Georgia Koutsoumpli
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud H. de Ru
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Peter A. van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A. C. ’t Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter van Balen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B. van den Akker
- Center for Computational Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Hendrik Veelken
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Marieke Griffioen
- Department of Hematology, Leiden University Medical Center, Leiden, The Netherlands
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24
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Bolivar AM, Duzagac F, Deng N, Reyes-Uribe L, Chang K, Wu W, Bowen CM, Taggart MW, Thirumurthi S, Lynch PM, You YN, Rodriguez-Pascual J, Lipkin SM, Kopetz S, Scheet P, Lizee GA, Reuben A, Sinha KM, Vilar E. Genomic Landscape of Lynch Syndrome Colorectal Neoplasia Identifies Shared Mutated Neoantigens for Immunoprevention. Gastroenterology 2024; 166:787-801.e11. [PMID: 38244726 PMCID: PMC11034773 DOI: 10.1053/j.gastro.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/18/2023] [Accepted: 01/07/2024] [Indexed: 01/22/2024]
Abstract
BACKGROUND & AIMS Lynch syndrome (LS) carriers develop mismatch repair-deficient neoplasia with high neoantigen (neoAg) rates. No detailed information on targetable neoAgs from LS precancers exists, which is crucial for vaccine development and immune-interception strategies. We report a focused somatic mutation and frameshift-neoAg landscape of microsatellite loci from colorectal polyps without malignant potential (PWOMP), precancers, and early-stage cancers in LS carriers. METHODS We generated paired whole-exome and transcriptomic sequencing data from 8 colorectal PWOMP, 41 precancers, 8 advanced precancers, and 12 early-stage cancers of 43 LS carriers. A computational pipeline was developed to predict, rank, and prioritize the top 100 detected mutated neoAgs that were validated in vitro using ELISpot and tetramer assays. RESULTS Mutation calling revealed >10 mut/Mb in 83% of cancers, 63% of advanced precancers, and 20% of precancers. Cancers displayed an average of 616 MHC-I neoAgs/sample, 294 in advanced precancers, and 107 in precancers. No neoAgs were detected in PWOMP. A total of 65% of our top 100 predicted neoAgs were immunogenic in vitro, and were present in 92% of cancers, 50% of advanced precancers, and 29% of precancers. We observed increased levels of naïve CD8+ and memory CD4+ T cells in mismatch repair-deficient cancers and precancers via transcriptomics analysis. CONCLUSIONS Shared frameshift-neoAgs are generated within unstable microsatellite loci at initial stages of LS carcinogenesis and can induce T-cell responses, generating opportunities for vaccine development, targeting LS precancers and early-stage cancers.
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Affiliation(s)
- Ana M Bolivar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fahriye Duzagac
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nan Deng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laura Reyes-Uribe
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kyle Chang
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenhui Wu
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Charles M Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melissa W Taggart
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Selvi Thirumurthi
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick M Lynch
- Department of Gastroenterology, Hepatology and Nutrition, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Y Nancy You
- Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Colorectal Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Steven M Lipkin
- Division of Gastroenterology and Hepatology, Weill Cornell University, New York, New York
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gregory A Lizee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Krishna M Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas; Clinical Cancer Genetics Program, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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25
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Wang AF, Hsueh B, Choi BD, Gerstner ER, Dunn GP. Immunotherapy for Brain Tumors: Where We Have Been, and Where Do We Go From Here? Curr Treat Options Oncol 2024; 25:628-643. [PMID: 38649630 DOI: 10.1007/s11864-024-01200-9] [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] [Accepted: 03/18/2024] [Indexed: 04/25/2024]
Abstract
OPINION STATEMENT Immunotherapy for glioblastoma (GBM) remains an intensive area of investigation. Given the seismic impact of cancer immunotherapy across a range of malignancies, there is optimism that harnessing the power of immunity will influence GBM as well. However, despite several phase 3 studies, there are still no FDA-approved immunotherapies for GBM. Importantly, the field has learned a great deal from the randomized studies to date. Today, we are continuing to better understand the disease-specific features of the microenvironment in GBM-as well as the exploitable antigenic characteristic of the tumor cells themselves-that are informing the next generation of immune-based therapeutic strategies. The coming phase of next-generation immunotherapies is thus poised to bring us closer to treatments that will improve the lives of patients with GBM.
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Affiliation(s)
- Alexander F Wang
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Brian Hsueh
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth R Gerstner
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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26
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Bowen CM, Sinha KM, Vilar E. Current Trends in Vaccine Development for Hereditary Colorectal Cancer Syndromes. Clin Colon Rectal Surg 2024; 37:146-156. [PMID: 38606044 PMCID: PMC11006444 DOI: 10.1055/s-0043-1770383] [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: 04/13/2024]
Abstract
The coming of age for cancer treatment has experienced exponential growth in the last decade with the addition of immunotherapy as the fourth pillar to the fundamentals of cancer treatment-chemotherapy, surgery, and radiation-taking oncology to an astounding new frontier. In this time, rapid developments in computational biology coupled with immunology have led to the exploration of priming the host immune system through vaccination to prevent and treat certain subsets of cancer such as melanoma and hereditary colorectal cancer. By targeting the immune system through tumor-specific antigens-namely, neoantigens (neoAgs)-the future of cancer prevention may lie within arm's reach by employing neoAg vaccines as an immune-preventive modality for hereditary cancer syndromes like Lynch syndrome. In this review, we discuss the history, current trends, utilization, and future direction of neoAg-based vaccines in the setting of hereditary colorectal cancer.
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Affiliation(s)
- Charles M. Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Krishna M. Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Wong MK, Yee C. Polyomavirus-positive Merkel cell carcinoma: the beginning of the beginning. J Clin Invest 2024; 134:e179749. [PMID: 38618960 PMCID: PMC11014648 DOI: 10.1172/jci179749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive, fast-growing, highly metastatic neuroendocrine skin cancer. The Merkel cell polyomavirus (MCPyV) is an oncogenic driver in the majority of MCC tumors. In this issue of the JCI, Hansen and authors report on their tracking of CD8+ T cells reactive to MCPyV T antigen (T-Ag) in the peripheral blood of 26 patients with MCC who were undergoing frontline anti-programmed cell death protein-1 (anti-PD-1) immunotherapy. They discovered unique T cell epitopes and used the power of bar-coded tetramers to portray immune checkpoint inhibitor-induced immunogenicity as a predictor of clinical response. These findings provide the foundation for therapeutic possibilities for MCC, including vaccines and adoptive T cell- and T cell receptor-driven (TCR-driven) treatments.
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Ragone C, Cavalluzzo B, Mauriello A, Tagliamonte M, Buonaguro L. Lack of shared neoantigens in prevalent mutations in cancer. J Transl Med 2024; 22:344. [PMID: 38600547 PMCID: PMC11005154 DOI: 10.1186/s12967-024-05110-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
Tumors are mostly characterized by genetic instability, as result of mutations in surveillance mechanisms, such as DNA damage checkpoint, DNA repair machinery and mitotic checkpoint. Defect in one or more of these mechanisms causes additive accumulation of mutations. Some of these mutations are drivers of transformation and are positively selected during the evolution of the cancer, giving a growth advantage on the cancer cells. If such mutations would result in mutated neoantigens, these could be actionable targets for cancer vaccines and/or adoptive cell therapies. However, the results of the present analysis show, for the first time, that the most prevalent mutations identified in human cancers do not express mutated neoantigens. The hypothesis is that this is the result of the selection operated by the immune system in the very early stages of tumor development. At that stage, the tumor cells characterized by mutations giving rise to highly antigenic non-self-mutated neoantigens would be efficiently targeted and eliminated. Consequently, the outgrowing tumor cells cannot be controlled by the immune system, with an ultimate growth advantage to form large tumors embedded in an immunosuppressive tumor microenvironment (TME). The outcome of such a negative selection operated by the immune system is that the development of off-the-shelf vaccines, based on shared mutated neoantigens, does not seem to be at hand. This finding represents the first demonstration of the key role of the immune system on shaping the tumor antigen presentation and the implication in the development of antitumor immunological strategies.
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Affiliation(s)
- Concetta Ragone
- Lab of Innovative Immunological Models Unit, Istituto Nazionale Tumori, IRCCS - "Fondazione Pascale", Via Mariano Semmola, 52, 80131, Naples, Italy
| | - Beatrice Cavalluzzo
- Lab of Innovative Immunological Models Unit, Istituto Nazionale Tumori, IRCCS - "Fondazione Pascale", Via Mariano Semmola, 52, 80131, Naples, Italy
| | - Angela Mauriello
- Lab of Innovative Immunological Models Unit, Istituto Nazionale Tumori, IRCCS - "Fondazione Pascale", Via Mariano Semmola, 52, 80131, Naples, Italy
| | - Maria Tagliamonte
- Lab of Innovative Immunological Models Unit, Istituto Nazionale Tumori, IRCCS - "Fondazione Pascale", Via Mariano Semmola, 52, 80131, Naples, Italy.
| | - Luigi Buonaguro
- Lab of Innovative Immunological Models Unit, Istituto Nazionale Tumori, IRCCS - "Fondazione Pascale", Via Mariano Semmola, 52, 80131, Naples, Italy.
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Borch A, Carri I, Reynisson B, Alvarez HMG, Munk KK, Montemurro A, Kristensen NP, Tvingsholm SA, Holm JS, Heeke C, Moss KH, Hansen UK, Schaap-Johansen AL, Bagger FO, de Lima VAB, Rohrberg KS, Funt SA, Donia M, Svane IM, Lassen U, Barra C, Nielsen M, Hadrup SR. IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition. Front Immunol 2024; 15:1360281. [PMID: 38633261 PMCID: PMC11021644 DOI: 10.3389/fimmu.2024.1360281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024] Open
Abstract
Background Mutation-derived neoantigens are critical targets for tumor rejection in cancer immunotherapy, and better tools for neoepitope identification and prediction are needed to improve neoepitope targeting strategies. Computational tools have enabled the identification of patient-specific neoantigen candidates from sequencing data, but limited data availability has hindered their capacity to predict which of the many neoepitopes will most likely give rise to T cell recognition. Method To address this, we make use of experimentally validated T cell recognition towards 17,500 neoepitope candidates, with 467 being T cell recognized, across 70 cancer patients undergoing immunotherapy. Results We evaluated 27 neoepitope characteristics, and created a random forest model, IMPROVE, to predict neoepitope immunogenicity. The presence of hydrophobic and aromatic residues in the peptide binding core were the most important features for predicting neoepitope immunogenicity. Conclusion Overall, IMPROVE was found to significantly advance the identification of neoepitopes compared to other current methods.
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Affiliation(s)
- Annie Borch
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Ibel Carri
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Birkir Reynisson
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Heli M. Garcia Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Kamilla K. Munk
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Siri A. Tvingsholm
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jeppe Sejerø Holm
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Christina Heeke
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Keith Henry Moss
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Ulla Kring Hansen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | | | | | | | | | - Samuel A. Funt
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
| | - Marco Donia
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Copenhagen University Hospital, Herlev, Denmark
| | - Ulrik Lassen
- Department of Oncology, Phase 1 Unit, Rigshospitalet, Copenhagen, Denmark
| | - Carolina Barra
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Sine Reker Hadrup
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
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Ma W, Zhang J, Yao H. NeoMUST: an accurate and efficient multi-task learning model for neoantigen presentation. Life Sci Alliance 2024; 7:e202302255. [PMID: 38290755 PMCID: PMC10828515 DOI: 10.26508/lsa.202302255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
Accurate identification of neoantigens is important for advancing cancer immunotherapies. This study introduces Neoantigen MUlti-taSk Tower (NeoMUST), a model employing multi-task learning to effectively capture task-specific information across related tasks. Our results show that NeoMUST rivals existing algorithms in predicting the presentation of neoantigens via MHC-I molecules, while demonstrating a significantly shorter training time for enhanced computational efficiency. The use of multi-task learning enables NeoMUST to leverage shared knowledge and task dependencies, leading to improved performance metrics and a significant reduction in the training time. NeoMUST, implemented in Python, is freely accessible at the GitHub repository. Our model will facilitate neoantigen prediction and empower the development of effective cancer immunotherapeutic approaches.
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Affiliation(s)
- Wang Ma
- Fresh Wind Biotechnologies Inc. (Tianjin), Tianjin, China
| | - Jiawei Zhang
- Fresh Wind Biotechnologies Inc. (Tianjin), Tianjin, China
| | - Hui Yao
- Fresh Wind Biotechnologies USA Inc., Houston, TX, USA
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31
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Wu R, Sun F, Zhang W, Ren J, Liu GH. Targeting aging and age-related diseases with vaccines. NATURE AGING 2024; 4:464-482. [PMID: 38622408 DOI: 10.1038/s43587-024-00597-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/20/2024] [Indexed: 04/17/2024]
Abstract
Aging is a major risk factor for numerous chronic diseases. Vaccination offers a promising strategy to combat these age-related diseases by targeting specific antigens and inducing immune responses. Here, we provide a comprehensive overview of recent advances in vaccine-based interventions targeting these diseases, including Alzheimer's disease, type II diabetes, hypertension, abdominal aortic aneurysm, atherosclerosis, osteoarthritis, fibrosis and cancer, summarizing current approaches for identifying disease-associated antigens and inducing immune responses against these targets. Further, we reflect on the recent development of vaccines targeting senescent cells, as a strategy for more broadly targeting underlying causes of aging and associated pathologies. In addition to highlighting recent progress in these areas, we discuss important next steps to advance the therapeutic potential of these vaccines, including improving and robustly demonstrating efficacy in human clinical trials, as well as rigorously evaluating the safety and long-term effects of these vaccine strategies.
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Affiliation(s)
- Ruochen Wu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Weiqi Zhang
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China.
- Sino-Danish College, School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Aging Biomarker Consortium, Beijing, China.
| | - Jie Ren
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, China.
- Sino-Danish College, School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
- Aging Biomarker Consortium, Beijing, China.
- Key Laboratory of RNA Science and Engineering, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China.
| | - Guang-Hui Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China.
- Aging Biomarker Consortium, Beijing, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China.
- Advanced Innovation Center for Human Brain Protection, and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital, Capital Medical University, Beijing, China.
- Aging Translational Medicine Center, International Center for Aging and Cancer, Xuanwu Hospital, Capital Medical University, Beijing, China.
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32
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Lin Y, Ma J, Yuan H, Chen Z, Xu X, Jiang M, Zhu J, Meng W, Qiu W, Liu Y. Integrating Reinforcement Learning and Monte Carlo Tree Search for enhanced neoantigen vaccine design. Brief Bioinform 2024; 25:bbae247. [PMID: 38770719 PMCID: PMC11107383 DOI: 10.1093/bib/bbae247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Recent advances in cancer immunotherapy have highlighted the potential of neoantigen-based vaccines. However, the design of such vaccines is hindered by the possibility of weak binding affinity between the peptides and the patient's specific human leukocyte antigen (HLA) alleles, which may not elicit a robust adaptive immune response. Triggering cross-immunity by utilizing peptide mutations that have enhanced binding affinity to target HLA molecules, while preserving their homology with the original one, can be a promising avenue for neoantigen vaccine design. In this study, we introduced UltraMutate, a novel algorithm that combines Reinforcement Learning and Monte Carlo Tree Search, which identifies peptide mutations that not only exhibit enhanced binding affinities to target HLA molecules but also retains a high degree of homology with the original neoantigen. UltraMutate outperformed existing state-of-the-art methods in identifying affinity-enhancing mutations in an independent test set consisting of 3660 peptide-HLA pairs. UltraMutate further showed its applicability in the design of peptide vaccines for Human Papillomavirus and Human Cytomegalovirus, demonstrating its potential as a promising tool in the advancement of personalized immunotherapy.
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Affiliation(s)
- Yicheng Lin
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Jiakang Ma
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Haozhe Yuan
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Ziqiang Chen
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Xingyu Xu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Mengping Jiang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Jialiang Zhu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Weida Meng
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
| | - Wenqing Qiu
- Shanghai Xuhui Central Hospital, 366 North Longchuan Road, Shanghai, 200231, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Shanghai Xuhui Central Hospital, Fudan University, 131 DongAn Road, Shanghai, 200032, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, 131 DongAn Road, Shanghai, 200032, China
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Zhang W, Sun S, Zhu W, Meng D, Hu W, Yang S, Gao M, Yao P, Wang Y, Wang Q, Ji J. Birinapant Reshapes the Tumor Immunopeptidome and Enhances Antigen Presentation. Int J Mol Sci 2024; 25:3660. [PMID: 38612472 PMCID: PMC11011986 DOI: 10.3390/ijms25073660] [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: 02/05/2024] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Birinapant, an antagonist of the inhibitor of apoptosis proteins, upregulates MHCs in tumor cells and displays a better tumoricidal effect when used in combination with immune checkpoint inhibitors, indicating that Birinapant may affect the antigen presentation pathway; however, the mechanism remains elusive. Based on high-resolution mass spectrometry and in vitro and in vivo models, we adopted integrated genomics, proteomics, and immunopeptidomics strategies to study the mechanism underlying the regulation of tumor immunity by Birinapant from the perspective of antigen presentation. Firstly, in HT29 and MCF7 cells, Birinapant increased the number and abundance of immunopeptides and source proteins. Secondly, a greater number of cancer/testis antigen peptides with increased abundance and more neoantigens were identified following Birinapant treatment. Moreover, we demonstrate the existence and immunogenicity of a neoantigen derived from insertion/deletion mutation. Thirdly, in HT29 cell-derived xenograft models, Birinapant administration also reshaped the immunopeptidome, and the tumor exhibited better immunogenicity. These data suggest that Birinapant can reshape the tumor immunopeptidome with respect to quality and quantity, which improves the presentation of CTA peptides and neoantigens, thus enhancing the immunogenicity of tumor cells. Such changes may be vital to the effectiveness of combination therapy, which can be further transferred to the clinic or aid in the development of new immunotherapeutic strategies to improve the anti-tumor immune response.
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Affiliation(s)
- Weiyan Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Shenghuan Sun
- Bakar Computational Health Sciences Institute, University of California, San Francisco, CA 94143, USA;
| | - Wenyuan Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Delan Meng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Weiyi Hu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Siqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Mingjie Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Pengju Yao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Yuhao Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Qingsong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
| | - Jianguo Ji
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; (W.Z.)
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Sng CCT, Kallor AA, Simpson BS, Bedran G, Alfaro J, Litchfield K. Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy. Front Immunol 2024; 15:1347542. [PMID: 38558815 PMCID: PMC10978585 DOI: 10.3389/fimmu.2024.1347542] [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: 12/01/2023] [Accepted: 02/19/2024] [Indexed: 04/04/2024] Open
Abstract
Background Neoantigens, mutated tumour-specific antigens, are key targets of anti-tumour immunity during checkpoint inhibitor (CPI) treatment. Their identification is fundamental to designing neoantigen-directed therapy. Non-canonical neoantigens arising from the untranslated regions (UTR) of the genome are an overlooked source of immunogenic neoantigens. Here, we describe the landscape of UTR-derived neoantigens and release a computational tool, PrimeCUTR, to predict UTR neoantigens generated by start-gain and stop-loss mutations. Methods We applied PrimeCUTR to a whole genome sequencing dataset of pre-treatment tumour samples from CPI-treated patients (n = 341). Cancer immunopeptidomic datasets were interrogated to identify MHC class I presentation of UTR neoantigens. Results Start-gain neoantigens were predicted in 72.7% of patients, while stop-loss mutations were found in 19.3% of patients. While UTR neoantigens only accounted 2.6% of total predicted neoantigen burden, they contributed 12.4% of neoantigens with high dissimilarity to self-proteome. More start-gain neoantigens were found in CPI responders, but this relationship was not significant when correcting for tumour mutational burden. While most UTR neoantigens are private, we identified two recurrent start-gain mutations in melanoma. Using immunopeptidomic datasets, we identify two distinct MHC class I-presented UTR neoantigens: one from a recurrent start-gain mutation in melanoma, and one private to Jurkat cells. Conclusion PrimeCUTR is a novel tool which complements existing neoantigen discovery approaches and has potential to increase the detection yield of neoantigens in personalised therapeutics, particularly for neoantigens with high dissimilarity to self. Further studies are warranted to confirm the expression and immunogenicity of UTR neoantigens.
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Affiliation(s)
- Christopher C. T. Sng
- Cancer Research UK Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Ashwin Adrian Kallor
- International Center for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Benjamin S. Simpson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, London, United Kingdom
| | - Georges Bedran
- International Center for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Javier Alfaro
- International Center for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, United Kingdom
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, London, United Kingdom
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Zhang H, Lee S, Muthakana RR, Lu B, Boone DN, Lee D, Wang XS. Intragenic Rearrangement Burden Associates with Immune Cell Infiltration and Response to Immune Checkpoint Blockade in Cancer. Cancer Immunol Res 2024; 12:287-295. [PMID: 38345376 PMCID: PMC11107381 DOI: 10.1158/2326-6066.cir-22-0637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 02/27/2023] [Accepted: 12/21/2023] [Indexed: 03/06/2024]
Abstract
Immune checkpoint blockade (ICB) can induce durable cancer remission. However, only a small subset of patients gains benefits. While tumor mutation burden (TMB) differentiates responders from nonresponders in some cases, it is a weak predictor in tumor types with low mutation rates. Thus, there is an unmet need to discover a new class of genetic aberrations that predict ICB responses in these tumor types. Here, we report analyses of pan-cancer whole genomes which revealed that intragenic rearrangement (IGR) burden is significantly associated with immune infiltration in breast, ovarian, esophageal, and endometrial cancers, particularly with increased M1 macrophage and CD8+ T-cell signatures. Multivariate regression against spatially counted tumor-infiltrating lymphocytes in breast, endometrial, and ovarian cancers suggested that IGR burden is a more influential covariate than other genetic aberrations in these cancers. In the MEDI4736 trial evaluating durvalumab in esophageal adenocarcinoma, IGR burden correlated with patient benefits. In the IMVigor210 trial evaluating atezolizumab in urothelial carcinoma, IGR burden increased with platinum exposure and predicted patient benefit among TMB-low, platinum-exposed tumors. Altogether, we have demonstrated that IGR burden correlates with T-cell inflammation and predicts ICB benefit in TMB-low, IGR-dominant tumors, and in platinum-exposed tumors.
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Affiliation(s)
- Han Zhang
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Sanghoon Lee
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Renee R. Muthakana
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biological Sciences, University of
Pittsburgh, PA
| | - Binfeng Lu
- Center for Discovery and Innovation, Hackensack Meridian
Health
| | - David N Boone
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Biomedical Informatics, University of
Pittsburgh, Pittsburgh, PA
| | - Daniel Lee
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Medicine, University of Pittsburgh,
Pittsburgh, PA
| | - Xiao-Song Wang
- UPMC Hillman Cancer Center, University of Pittsburgh,
Pittsburgh, PA, 15213, U.S.A
- Department of Pathology, University of Pittsburgh,
Pittsburgh, PA
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Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024; 13:100030. [PMID: 38577265 PMCID: PMC10994007 DOI: 10.1016/j.immuno.2023.100030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
The cellular immune response comprises several processes, with the most notable ones being the binding of the peptide to the Major Histocompability Complex (MHC), the peptide-MHC (pMHC) presentation to the surface of the cell, and the recognition of the pMHC by the T-Cell Receptor. Identifying the most potent peptide targets for MHC binding, presentation and T-cell recognition is vital for developing peptide-based vaccines and T-cell-based immunotherapies. Data-driven tools that predict each of these steps have been developed, and the availability of mass spectrometry (MS) datasets has facilitated the development of accurate Machine Learning (ML) methods for class-I pMHC binding prediction. However, the accuracy of ML-based tools for pMHC kinetic stability prediction and peptide immunogenicity prediction is uncertain, as stability and immunogenicity datasets are not abundant. Here, we use transfer learning techniques to improve stability and immunogenicity predictions, by taking advantage of a large number of binding affinity and MS datasets. The resulting models, TLStab and TLImm, exhibit comparable or better performance than state-of-the-art approaches on different stability and immunogenicity test sets respectively. Our approach demonstrates the promise of learning from the task of peptide binding to improve predictions on downstream tasks. The source code of TLStab and TLImm is publicly available at https://github.com/KavrakiLab/TL-MHC.
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Affiliation(s)
- Romanos Fasoulis
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Mauricio Menegatti Rigo
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
| | - Dinler Amaral Antunes
- Department of Biology and Biochemistry, University of Houston, 4800 Calhoun Rd, Houston, 77004, TX, United States
| | - Georgios Paliouras
- Institute of Informatics and Telecommunications, NCSR Demokritos, Patr. Gregoriou E and 27 Neapoleos St, Athens, 15341, Greece
| | - Lydia E. Kavraki
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, United States
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37
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Wan YTR, Koşaloğlu‐Yalçın Z, Peters B, Nielsen M. A large-scale study of peptide features defining immunogenicity of cancer neo-epitopes. NAR Cancer 2024; 6:zcae002. [PMID: 38288446 PMCID: PMC10823584 DOI: 10.1093/narcan/zcae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 01/03/2024] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
Accurate prediction of immunogenicity for neo-epitopes arising from a cancer associated mutation is a crucial step in many bioinformatics pipelines that predict outcome of checkpoint blockade treatments or that aim to design personalised cancer immunotherapies and vaccines. In this study, we performed a comprehensive analysis of peptide features relevant for prediction of immunogenicity using the Cancer Epitope Database and Analysis Resource (CEDAR), a curated database of cancer epitopes with experimentally validated immunogenicity annotations from peer-reviewed publications. The developed model, ICERFIRE (ICore-based Ensemble Random Forest for neo-epitope Immunogenicity pREdiction), extracts the predicted ICORE from the full neo-epitope as input, i.e. the nested peptide with the highest predicted major histocompatibility complex (MHC) binding potential combined with its predicted likelihood of antigen presentation (%Rank). Key additional features integrated into the model include assessment of the BLOSUM mutation score of the neo-epitope, and antigen expression levels of the wild-type counterpart which is often reflecting a neo-epitope's abundance. We demonstrate improved and robust performance of ICERFIRE over existing immunogenicity and epitope prediction models, both in cross-validation and on external validation datasets.
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Affiliation(s)
- Yat-tsai Richie Wan
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, DK 28002, Denmark
| | - Zeynep Koşaloğlu‐Yalçın
- Center for Infectious Disease and Vaccine Research, La Jolla Institute of Immunology, La Jolla, CA 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute of Immunology, La Jolla, CA 92037, USA
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, DK 28002, Denmark
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38
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Katsikis PD, Ishii KJ, Schliehe C. Challenges in developing personalized neoantigen cancer vaccines. Nat Rev Immunol 2024; 24:213-227. [PMID: 37783860 DOI: 10.1038/s41577-023-00937-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2023] [Indexed: 10/04/2023]
Abstract
The recent success of cancer immunotherapies has highlighted the benefit of harnessing the immune system for cancer treatment. Vaccines have a long history of promoting immunity to pathogens and, consequently, vaccines targeting cancer neoantigens have been championed as a tool to direct and amplify immune responses against tumours while sparing healthy tissue. In recent years, extensive preclinical research and more than one hundred clinical trials have tested different strategies of neoantigen discovery and vaccine formulations. However, despite the enthusiasm for neoantigen vaccines, proof of unequivocal efficacy has remained beyond reach for the majority of clinical trials. In this Review, we focus on the key obstacles pertaining to vaccine design and tumour environment that remain to be overcome in order to unleash the true potential of neoantigen vaccines in cancer therapy.
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Affiliation(s)
- Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.
| | - Ken J Ishii
- Division of Vaccine Science, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
- International Vaccine Design Center (vDesC), The Institute of Medical Science, The University of Tokyo (IMSUT), Tokyo, Japan
| | - Christopher Schliehe
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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Srivastava PK. Cancer neoepitopes viewed through negative selection and peripheral tolerance: a new path to cancer vaccines. J Clin Invest 2024; 134:e176740. [PMID: 38426497 PMCID: PMC10904052 DOI: 10.1172/jci176740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
A proportion of somatic mutations in tumors create neoepitopes that can prime T cell responses that target the MHC I-neoepitope complexes on tumor cells, mediating tumor control or rejection. Despite the compelling centrality of neoepitopes to cancer immunity, we know remarkably little about what constitutes a neoepitope that can mediate tumor control in vivo and what distinguishes such a neoepitope from the vast majority of similar candidate neoepitopes that are inefficacious in vivo. Studies in mice as well as clinical trials have begun to reveal the unexpected paradoxes in this area. Because cancer neoepitopes straddle that ambiguous ground between self and non-self, some rules that are fundamental to immunology of frankly non-self antigens, such as viral or model antigens, do not appear to apply to neoepitopes. Because neoepitopes are so similar to self-epitopes, with only small changes that render them non-self, immune response to them is regulated at least partially the way immune response to self is regulated. Therefore, neoepitopes are viewed and understood here through the clarifying lens of negative thymic selection. Here, the emergent questions in the biology and clinical applications of neoepitopes are discussed critically and a mechanistic and testable framework that explains the complexity and translational potential of these wonderful antigens is proposed.
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40
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Miller AM, Koşaloğlu-Yalçın Z, Westernberg L, Montero L, Bahmanof M, Frentzen A, Lanka M, Logandha Ramamoorthy Premlal A, Seumois G, Greenbaum J, Brightman SE, Soria Zavala K, Thota RR, Naradikian MS, Makani SS, Lippman SM, Sette A, Cohen EEW, Peters B, Schoenberger SP. A functional identification platform reveals frequent, spontaneous neoantigen-specific T cell responses in patients with cancer. Sci Transl Med 2024; 16:eabj9905. [PMID: 38416845 DOI: 10.1126/scitranslmed.abj9905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
The clinical impact of tumor-specific neoantigens as both immunotherapeutic targets and biomarkers has been impeded by the lack of efficient methods for their identification and validation from routine samples. We have developed a platform that combines bioinformatic analysis of tumor exomes and transcriptional data with functional testing of autologous peripheral blood mononuclear cells (PBMCs) to simultaneously identify and validate neoantigens recognized by naturally primed CD4+ and CD8+ T cell responses across a range of tumor types and mutational burdens. The method features a human leukocyte antigen (HLA)-agnostic bioinformatic algorithm that prioritizes mutations recognized by patient PBMCs at a greater than 40% positive predictive value followed by a short-term in vitro functional assay, which allows interrogation of 50 to 75 expressed mutations from a single 50-ml blood sample. Neoantigens validated by this method include both driver and passenger mutations, and this method identified neoantigens that would not have been otherwise detected using an in silico prediction approach. These findings reveal an efficient approach to systematically validate clinically actionable neoantigens and the T cell receptors that recognize them and demonstrate that patients across a variety of human cancers have a diverse repertoire of neoantigen-specific T cells.
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Affiliation(s)
- Aaron M Miller
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Zeynep Koşaloğlu-Yalçın
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Luise Westernberg
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Leslie Montero
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Milad Bahmanof
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Angela Frentzen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Manasa Lanka
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | | | - Gregory Seumois
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Spencer E Brightman
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Karla Soria Zavala
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Rukman R Thota
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Martin S Naradikian
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Samir S Makani
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Scott M Lippman
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Ezra E W Cohen
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Stephen P Schoenberger
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
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41
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Terai M, Sato T. Individualised neoantigen cancer vaccine therapy. Lancet 2024; 403:590-591. [PMID: 38246193 DOI: 10.1016/s0140-6736(23)02463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 01/23/2024]
Affiliation(s)
- Mizue Terai
- Department of Medical Oncology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Takami Sato
- Department of Medical Oncology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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42
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Adams AC, Macy AM, Borden ES, Herrmann LM, Brambley CA, Ma T, Li X, Hughes A, Roe DJ, Mangold AR, Buetow KH, Wilson MA, Baker BM, Hastings KT. Distinct sets of molecular characteristics define tumor-rejecting neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.579546. [PMID: 38405868 PMCID: PMC10888839 DOI: 10.1101/2024.02.13.579546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Challenges in identifying tumor-rejecting neoantigens limit the efficacy of neoantigen vaccines to treat cancers, including cutaneous squamous cell carcinoma (cSCC). A minority of human cSCC tumors shared neoantigens, supporting the need for personalized vaccines. Using a UV-induced mouse cSCC model which recapitulated the mutational signature and driver mutations found in human disease, we found that CD8 T cells constrain cSCC. Two MHC class I neoantigens were identified that constrained cSCC growth. Compared to the wild-type peptides, one tumor-rejecting neoantigen exhibited improved MHC binding and the other had increased solvent accessibility of the mutated residue. Across known neoantigens that do not impact MHC binding, structural modeling of the peptide/MHC complexes indicated that increased solvent accessibility, which will facilitate TCR recognition of the neoantigen, distinguished tumor-rejecting from non-immunogenic neoantigens. This work reveals characteristics of tumor-rejecting neoantigens that may be of considerable importance in identifying optimal vaccine candidates in cSCC and other cancers.
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43
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Zhang X, Yu C, Zhou S, Zhang Y, Tian B, Bian Y, Wang W, Lin H, Wang LW. Risk model based on genes regulating the response of tumor cells to T-cell-mediated killing in esophageal squamous cell carcinoma. Aging (Albany NY) 2024; 16:2494-2516. [PMID: 38305770 PMCID: PMC10911339 DOI: 10.18632/aging.205495] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 02/03/2024]
Abstract
Immune checkpoint inhibitors (ICIs) represent a promising therapeutic approach for esophageal squamous cell carcinoma (ESCC). However, the subpopulations of ESCC patients expected to benefit from ICIs have not been clearly defined. The anti-tumor cytotoxic activity of T cells is an important pharmacological mechanism of ICIs. In this study, the prognostic value of the genes regulating tumor cells to T cell-mediated killing (referred to as GRTTKs) in ESCC was explored by using a comprehensive bioinformatics approach. Training and validation datasets were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), respectively. A prognostic risk scoring model was developed by integrating prognostic GRTTKs from TCGA and GEO datasets using a ridge regression algorithm. Patients with ESCC were divided into high- and low-risk groups based on eight GRTTKs (EIF4H, CDK2, TCEA1, SPTLC2, TMEM209, RGP1, EIF3D, and CAPZA3) to predict overall survival in the TCGA cohort. Using Kaplan-Meier curves, receiver operating characteristic curves, and C-index analysis, the high reliability of the prognostic risk-scoring model was certified. The model scores served as independent prognostic factors, and combining clinical staging with risk scoring improved the predictive value. Patients in the high-risk group exhibited abundant immune cell infiltration, including immune checkpoint expression, antigen presentation capability, immune cycle gene expression, and high tumor inflammation signature scores. The high-risk group exhibited a greater response to immunotherapy and neoadjuvant chemotherapy than the low-risk group. Drug sensitivity analysis demonstrated lower IC50 for AZD6244 and PD.0332991 in high-risk groups and lower IC50 for cisplatin, ATRA, QS11, and vinorelbine in the low-risk group. Furthermore, the differential expression of GRTTK-related signatures including CDK2, TCEA1, and TMEM209 were verified in ESCC tissues and paracancerous tissues. Overall, the novel GRTTK-based prognostic model can serve as indicators to predict the survival status and immunotherapy response of patients with ESCC, thereby providing guidance for the development of personalized treatment strategies.
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Affiliation(s)
- Xun Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Chuting Yu
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Siwei Zhou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Yanhui Zhang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Bo Tian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Yan Bian
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Wei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Han Lin
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
| | - Luo-Wei Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- National Clinical Research Center for Digestive Diseases, Shanghai, China
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44
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Moussion C, Delamarre L. Antigen cross-presentation by dendritic cells: A critical axis in cancer immunotherapy. Semin Immunol 2024; 71:101848. [PMID: 38035643 DOI: 10.1016/j.smim.2023.101848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023]
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells that play a key role in shaping adaptive immunity. DCs have a unique ability to sample their environment, capture and process exogenous antigens into peptides that are then loaded onto major histocompatibility complex class I molecules for presentation to CD8+ T cells. This process, called cross-presentation, is essential for initiating and regulating CD8+ T cell responses against tumors and intracellular pathogens. In this review, we will discuss the role of DCs in cancer immunity, the molecular mechanisms underlying antigen cross-presentation by DCs, the immunosuppressive factors that limit the efficiency of this process in cancer, and approaches to overcome DC dysfunction and therapeutically promote antitumoral immunity.
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Affiliation(s)
| | - Lélia Delamarre
- Cancer Immunology, Genentech, South San Francisco, CA 94080, USA.
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45
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Chuwdhury GS, Guo Y, Chiang CL, Lam KO, Kam NW, Liu Z, Dai W. ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction. Brief Bioinform 2024; 25:bbae024. [PMID: 38343325 PMCID: PMC10859690 DOI: 10.1093/bib/bbae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Neoantigens are derived from somatic mutations in the tumors but are absent in normal tissues. Emerging evidence suggests that neoantigens can stimulate tumor-specific T-cell-mediated antitumor immune responses, and therefore are potential immunotherapeutic targets. We developed ImmuneMirror as a stand-alone open-source pipeline and a web server incorporating a balanced random forest model for neoantigen prediction and prioritization. The prediction model was trained and tested using known immunogenic neopeptides collected from 19 published studies. The area under the curve of our trained model was 0.87 based on the testing data. We applied ImmuneMirror to the whole-exome sequencing and RNA sequencing data obtained from gastrointestinal tract cancers including 805 tumors from colorectal cancer (CRC), esophageal squamous cell carcinoma (ESCC) and hepatocellular carcinoma patients. We discovered a subgroup of microsatellite instability-high (MSI-H) CRC patients with a low neoantigen load but a high tumor mutation burden (> 10 mutations per Mbp). Although the efficacy of PD-1 blockade has been demonstrated in advanced MSI-H patients, almost half of such patients do not respond well. Our study identified a subset of MSI-H patients who may not benefit from this treatment with lower neoantigen load for major histocompatibility complex I (P < 0.0001) and II (P = 0.0008) molecules, respectively. Additionally, the neopeptide YMCNSSCMGV-TP53G245V, derived from a hotspot mutation restricted by HLA-A02, was identified as a potential actionable target in ESCC. This is so far the largest study to comprehensively evaluate neoantigen prediction models using experimentally validated neopeptides. Our results demonstrate the reliability and effectiveness of ImmuneMirror for neoantigen prediction.
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Affiliation(s)
- Gulam Sarwar Chuwdhury
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Yunshan Guo
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Chi-Leung Chiang
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Ka-On Lam
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
| | - Ngar-Woon Kam
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, Shatin, Hong Kong
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Wei Dai
- Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China
- University of Hong Kong-Shenzhen Hospital, Shenzhen, P. R. China
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46
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Li G, Mahajan S, Ma S, Jeffery ED, Zhang X, Bhattacharjee A, Venkatasubramanian M, Weirauch MT, Miraldi ER, Grimes HL, Sheynkman GM, Tilburgs T, Salomonis N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Sci Transl Med 2024; 16:eade2886. [PMID: 38232136 DOI: 10.1126/scitranslmed.ade2886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/13/2023] [Indexed: 01/19/2024]
Abstract
Immunotherapy has emerged as a crucial strategy to combat cancer by "reprogramming" a patient's own immune system. Although immunotherapy is typically reserved for patients with a high mutational burden, neoantigens produced from posttranscriptional regulation may provide an untapped reservoir of common immunogenic targets for new targeted therapies. To comprehensively define tumor-specific and likely immunogenic neoantigens from patient RNA-Seq, we developed Splicing Neo Antigen Finder (SNAF), an easy-to-use and open-source computational workflow to predict splicing-derived immunogenic MHC-bound peptides (T cell antigen) and unannotated transmembrane proteins with altered extracellular epitopes (B cell antigen). This workflow uses a highly accurate deep learning strategy for immunogenicity prediction (DeepImmuno) in conjunction with new algorithms to rank the tumor specificity of neoantigens (BayesTS) and to predict regulators of mis-splicing (RNA-SPRINT). T cell antigens from SNAF were frequently evidenced as HLA-presented peptides from mass spectrometry (MS) and predict response to immunotherapy in melanoma. Splicing neoantigen burden was attributed to coordinated splicing factor dysregulation. Shared splicing neoantigens were found in up to 90% of patients with melanoma, correlated to overall survival in multiple cancer cohorts, induced T cell reactivity, and were characterized by distinct cells of origin and amino acid preferences. In addition to T cell neoantigens, our B cell focused pipeline (SNAF-B) identified a new class of tumor-specific extracellular neoepitopes, which we termed ExNeoEpitopes. ExNeoEpitope full-length mRNA predictions were tumor specific and were validated using long-read isoform sequencing and in vitro transmembrane localization assays. Therefore, our systematic identification of splicing neoantigens revealed potential shared targets for therapy in heterogeneous cancers.
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Affiliation(s)
- Guangyuan Li
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Shweta Mahajan
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Siyuan Ma
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Erin D Jeffery
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Xuan Zhang
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Anukana Bhattacharjee
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Meenakshi Venkatasubramanian
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Emily R Miraldi
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Gloria M Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22903, USA
| | - Tamara Tilburgs
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Nathan Salomonis
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Biomedical Informatics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [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] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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Barajas A, Amengual-Rigo P, Pons-Grífols A, Ortiz R, Gracia Carmona O, Urrea V, de la Iglesia N, Blanco-Heredia J, Anjos-Souza C, Varela I, Trinité B, Tarrés-Freixas F, Rovirosa C, Lepore R, Vázquez M, de Mattos-Arruda L, Valencia A, Clotet B, Aguilar-Gurrieri C, Guallar V, Carrillo J, Blanco J. Virus-like particle-mediated delivery of structure-selected neoantigens demonstrates immunogenicity and antitumoral activity in mice. J Transl Med 2024; 22:14. [PMID: 38172991 PMCID: PMC10763263 DOI: 10.1186/s12967-023-04843-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Neoantigens are patient- and tumor-specific peptides that arise from somatic mutations. They stand as promising targets for personalized therapeutic cancer vaccines. The identification process for neoantigens has evolved with the use of next-generation sequencing technologies and bioinformatic tools in tumor genomics. However, in-silico strategies for selecting immunogenic neoantigens still have very low accuracy rates, since they mainly focus on predicting peptide binding to Major Histocompatibility Complex (MHC) molecules, which is key but not the sole determinant for immunogenicity. Moreover, the therapeutic potential of neoantigen-based vaccines may be enhanced using an optimal delivery platform that elicits robust de novo immune responses. METHODS We developed a novel neoantigen selection pipeline based on existing software combined with a novel prediction method, the Neoantigen Optimization Algorithm (NOAH), which takes into account structural features of the peptide/MHC-I interaction, as well as the interaction between the peptide/MHC-I complex and the TCR, in its prediction strategy. Moreover, to maximize neoantigens' therapeutic potential, neoantigen-based vaccines should be manufactured in an optimal delivery platform that elicits robust de novo immune responses and bypasses central and peripheral tolerance. RESULTS We generated a highly immunogenic vaccine platform based on engineered HIV-1 Gag-based Virus-Like Particles (VLPs) expressing a high copy number of each in silico selected neoantigen. We tested different neoantigen-loaded VLPs (neoVLPs) in a B16-F10 melanoma mouse model to evaluate their capability to generate new immunogenic specificities. NeoVLPs were used in in vivo immunogenicity and tumor challenge experiments. CONCLUSIONS Our results indicate the relevance of incorporating other immunogenic determinants beyond the binding of neoantigens to MHC-I. Thus, neoVLPs loaded with neoantigens enhancing the interaction with the TCR can promote the generation of de novo antitumor-specific immune responses, resulting in a delay in tumor growth. Vaccination with the neoVLP platform is a robust alternative to current therapeutic vaccine approaches and a promising candidate for future personalized immunotherapy.
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Affiliation(s)
- Ana Barajas
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | | | - Anna Pons-Grífols
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- Univeritat Autónoma de Barcelona (UAB), Cerdanyola, Spain
| | - Raquel Ortiz
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- Univeritat Autónoma de Barcelona (UAB), Cerdanyola, Spain
| | | | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | - Nuria de la Iglesia
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | - Juan Blanco-Heredia
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | - Carla Anjos-Souza
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | - Ismael Varela
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | - Benjamin Trinité
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | | | - Carla Rovirosa
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
| | | | | | | | | | - Bonaventura Clotet
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Infectious Diseases Department, Germans Trias I Pujol Hospital, Badalona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Julià Blanco
- IrsiCaixa AIDS Research Institute, Crta del Canyet S/N., 08916, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
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49
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Wongklaew P, Sriswasdi S, Chuangsuwanich E. MHCSeqNet2-improved peptide-class I MHC binding prediction for alleles with low data. Bioinformatics 2024; 40:btad780. [PMID: 38152987 PMCID: PMC10783953 DOI: 10.1093/bioinformatics/btad780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 12/14/2023] [Accepted: 12/27/2023] [Indexed: 12/29/2023] Open
Abstract
MOTIVATION The binding of a peptide antigen to a Class I major histocompatibility complex (MHC) protein is part of a key process that lets the immune system recognize an infected cell or a cancer cell. This mechanism enabled the development of peptide-based vaccines that can activate the patient's immune response to treat cancers. Hence, the ability of accurately predict peptide-MHC binding is an essential component for prioritizing the best peptides for each patient. However, peptide-MHC binding experimental data for many MHC alleles are still lacking, which limited the accuracy of existing prediction models. RESULTS In this study, we presented an improved version of MHCSeqNet that utilized sub-word-level peptide features, a 3D structure embedding for MHC alleles, and an expanded training dataset to achieve better generalizability on MHC alleles with small amounts of data. Visualization of MHC allele embeddings confirms that the model was able to group alleles with similar binding specificity, including those with no peptide ligand in the training dataset. Furthermore, an external evaluation suggests that MHCSeqNet2 can improve the prioritization of T cell epitopes for MHC alleles with small amount of training data. AVAILABILITY AND IMPLEMENTATION The source code and installation instruction for MHCSeqNet2 are available at https://github.com/cmb-chula/MHCSeqNet2.
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Affiliation(s)
- Patiphan Wongklaew
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
| | - Sira Sriswasdi
- Center of Excellence in Computational Molecular Biology, Division of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
- Center for Artificial Intelligence in Medicine, Division of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ekapol Chuangsuwanich
- Department of Computer Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand
- Center of Excellence in Computational Molecular Biology, Division of Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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