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Huang KCY, Ke TW, Lai CY, Hong WZ, Chang HY, Lee CY, Wu CH, Chiang SF, Liang JA, Chen JY, Yang PC, Chen WTL, Chuang EY, Chao KSC. Inhibition of DNMTs increases neoantigen-reactive T-cell toxicity against microsatellite-stable colorectal cancer in combination with radiotherapy. Biomed Pharmacother 2024; 177:116958. [PMID: 38917760 DOI: 10.1016/j.biopha.2024.116958] [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: 02/14/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/27/2024] Open
Abstract
The therapeutic efficacy of immunotherapy is limited in the majority of colorectal cancer patients due to the low mutational and neoantigen burdens in this immunogenically "cold" microsatellite stability-colorectal cancer (MSS-CRC) cohort. Here, we showed that DNA methyltransferase (DNMT) inhibition upregulated neoantigen-bearing gene expression in MSS-CRC, resulting in increased neoantigen presentation by MHC class I in tumor cells and leading to increased neoantigen-specific T-cell activation in combination with radiotherapy. The cytotoxicity of neoantigen-reactive T cells (NRTs) to DNMTi-treated cancer cells was highly cytotoxic, and these cells secreted high IFNγ levels targeting MSS-CRC cells after ex vivo expansion of NRTs with DNMTi-treated tumor antigens. Moreover, the therapeutic efficacy of NRTs further increased when NRTs were combined with radiotherapy in vivo. Administration of DNMTi-augmented NRTs and radiotherapy achieved an ∼50 % complete response and extended survival time in an immunocompetent MSS-CRC animal model. Moreover, remarkably, splenocytes from these mice exhibited neoantigen-specific T-cell responses, indicating that radiotherapy in combination with DNMTi-augmented NRTs prolonged and increased neoantigen-specific T-cell toxicity in MSS-CRC patients. In addition, these DNMTi-augmented NRTs markedly increase the therapeutic efficacy of cancer vaccines and immune checkpoint inhibitors (ICIs). These data suggest that a combination of radiotherapy and epi-immunotherapeutic agents improves the function of ex vivo-expanded neoantigen-reactive T cells and increases the tumor-specific cytotoxic effector population to enhance therapeutic efficacy in MSS-CRC.
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Affiliation(s)
- Kevin Chih-Yang Huang
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taiwan; Translation Research Core, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung 40402, Taiwan.
| | - Tao-Wei Ke
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan; Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Chia-Ying Lai
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Wei-Ze Hong
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Hsin-Yu Chang
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Chien-Yueh Lee
- Innovation Frontier Institute of Research for Science and Technology, National Taipei University of Technology, Taipei 106344, Taiwan; Department of Electrical Engineering, National Taipei University of Technology, Taipei 106344, Taiwan
| | - Chia-Hsin Wu
- Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Bioinformatics and Biostatistics Core, Centers of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Shu-Fen Chiang
- Lab of Precision Medicine, Feng-Yuan Hospital, Taichung 42055, Taiwan
| | - Ji-An Liang
- Department of Radiation Oncology, School of Medicine, China Medical University, Taichung 40402, Taiwan; Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Jhen-Yu Chen
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taiwan; Translation Research Core, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - Pei-Chen Yang
- Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan
| | - William Tzu-Liang Chen
- Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Department of Surgery, School of Medicine, China Medical University, Taichung 40402, Taiwan; Department of Colorectal Surgery, China Medical University HsinChu Hospital, China Medical University, Hsinchu 302, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan; Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
| | - K S Clifford Chao
- Center of Proton therapy and Science, China Medical University Hospital, China Medical University, Taichung 40402, Taiwan; Department of Radiation Oncology, School of Medicine, China Medical University, Taichung 40402, Taiwan; Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan.
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Kumai T, Shinomiya H, Shibata H, Takahashi H, Kishikawa T, Okada R, Fujieda S, Sakashita M. Translational research in head and neck cancer: Molecular and immunological updates. Auris Nasus Larynx 2024; 51:391-400. [PMID: 37640594 DOI: 10.1016/j.anl.2023.08.006] [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: 06/19/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis. Each year, approximately 880,000 patients are newly diagnosed with HNSCC worldwide, and 450,000 patients with HNSCC die. Risk factors for developing HNSCC have been identified, with cigarette smoking, alcohol consumption, and viral infections being the major factors. Owing to the prevalence of human papillomavirus infection, the number of HNSCC cases is increasing considerably. Surgery and chemoradiotherapy are the primary treatments for HNSCC. With advancements in tumor biology, patients are eligible for novel treatment modalities, namely targeted therapies, immunotherapy, and photoimmunotherapy. Because this area of research has rapidly progressed, clinicians should understand the basic biology of HNSCC to choose an appropriate therapy in the upcoming era of personalized medicine. This review summarized recent developments in tumor biology, focusing on epidemiology, genetic/epigenetic factors, the tumor microenvironment, microbiota, immunity, and photoimmunotherapy in HNSCC, as well as how these findings can be translated into clinical settings.
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Affiliation(s)
- Takumi Kumai
- Department of Otolaryngology-Head and Neck Surgery, Asahikawa Medical University, Midorigaoka-Higashi 2-1-1-1, Asahikawa 078-8510, Japan.
| | - Hirotaka Shinomiya
- Department of Otolaryngology-Head and Neck Surgery, Kobe University Graduate School of Medicine, Kobe, Japan.
| | - Hirofumi Shibata
- Department of Otolaryngology-Head and Neck Surgery, Gifu University Graduate School of Medicine, Gifu, Japan.
| | - Hideaki Takahashi
- Department of Otorhinolaryngology, Head and Neck Surgery, School of Medicine, Yokohama City University, Yokohama, Japan.
| | - Toshihiro Kishikawa
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan.
| | - Ryuhei Okada
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Shigeharu Fujieda
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medical Sciences, University of Fukui, Fukui, Japan.
| | - Masafumi Sakashita
- Department of Otorhinolaryngology-Head and Neck Surgery, Faculty of Medical Sciences, University of Fukui, Fukui, Japan.
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3
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Luo LZ, Li S, Wei C, Ma J, Qian LM, Chen YX, Wang SX, Zhao Q. Unveiling the interplay between mutational signatures and tumor microenvironment: a pan-cancer analysis. Front Immunol 2023; 14:1186357. [PMID: 37283742 PMCID: PMC10239828 DOI: 10.3389/fimmu.2023.1186357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/04/2023] [Indexed: 06/08/2023] Open
Abstract
Background While recent studies have separately explored mutational signatures and the tumor microenvironment (TME), there is limited research on the associations of both factors in a pan-cancer context. Materials and methods We performed a pan-cancer analysis of over 8,000 tumor samples from The Cancer Genome Atlas (TCGA) project. Machine learning methods were employed to systematically explore the relationship between mutational signatures and TME and develop a risk score based on TME-associated mutational signatures to predict patient survival outcomes. We also constructed an interaction model to explore how mutational signatures and TME interact and influence cancer prognosis. Results Our analysis revealed a varied association between mutational signatures and TME, with the Clock-like signature showing the most widespread influence. Risk scores based on mutational signatures mainly induced by Clock-like and AID/APOBEC activity exhibited strong pan-cancer survival stratification ability. We also propose a novel approach to predict transcriptome decomposed infiltration levels using genome-derived mutational signatures as an alternative approach for exploring TME cell types when transcriptome data are unavailable. Our comprehensive analysis revealed that certain mutational signatures and their interaction with immune cells significantly impact clinical outcomes in particular cancer types. For instance, T cell infiltration levels only served as a prognostic biomarker in melanoma patients with high ultraviolet radiation exposure, breast cancer patients with high homologous recombination deficiency signature, and lung adenocarcinoma patients with high tobacco-associated mutational signature. Conclusion Our study comprehensively explains the complex interplay between mutational signatures and immune infiltration in cancer. The results highlight the importance of considering both mutational signatures and immune phenotypes in cancer research and their significant implications for developing personalized cancer treatments and more effective immunotherapy.
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Affiliation(s)
- Li-Zhi Luo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Sheng Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Chen Wei
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Jiao Ma
- School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Li-Mei Qian
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Yan-Xing Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Shi-Xiang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
| | - Qi Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Sun Yat-Sen University, Guangzhou, China
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4
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Identification of T Cell Receptors Targeting a Neoantigen Derived from Recurrently Mutated FGFR3. Cancers (Basel) 2023; 15:cancers15041031. [PMID: 36831375 PMCID: PMC9953830 DOI: 10.3390/cancers15041031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Immunotherapies, including immune checkpoint blockades, play a critically important role in cancer treatments. For immunotherapies, neoantigens, which are generated by somatic mutations in cancer cells, are thought to be good targets due to their tumor specificity. Because neoantigens are unique in individual cancers, it is challenging to develop personalized immunotherapy targeting neoantigens. In this study, we screened "shared neoantigens", which are specific types of neoantigens derived from mutations observed commonly in a subset of cancer patients. Using exome sequencing data in the Cancer Genome Atlas (TCGA), we predicted shared neoantigen peptides and performed in vitro screening of shared neoantigen-reactive CD8+ T cells using peripheral blood from healthy donors. We examined the functional activity of neoantigen-specific T cell receptors (TCRs) by generating TCR-engineered T cells. Among the predicted shared neoantigens from TCGA data, we found that the mutated FGFR3Y373C peptide induced antigen-specific CD8+ T cells from the donor with HLA-A*02:06 via an ELISPOT assay. Subsequently, we obtained FGFR3Y373C-specific CD8+ T cell clones and identified two different sets of TCRs specifically reactive to FGFR3Y373C. We found that the TCR-engineered T cells expressing FGFR3Y373C-specific TCRs recognized the mutated FGFR3Y373C peptide but not the corresponding wild-type peptide. These two FGFR3Y373C-specific TCR-engineered T cells showed cytotoxic activity against mutated FGFR3Y373C-loaded cells. These results imply the possibility of strategies of immunotherapies targeting shared neoantigens, including cancer vaccines and TCR-engineered T cell therapies.
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5
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Sun M, Qi S, Wu M, Xia W, Xiong H. Calreticulin as a prognostic biomarker and correlated with immune infiltrate in kidney renal clear cell carcinoma. Front Genet 2022; 13:909556. [PMID: 36338983 PMCID: PMC9633671 DOI: 10.3389/fgene.2022.909556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 10/05/2022] [Indexed: 01/29/2024] Open
Abstract
Background: Calreticulin (CALR) has been investigated in several malignant diseases and is associated with immune-cell infiltration. However, the prognostic value of CALR in kidney renal clear cell carcinoma (KIRC) is still unknown. Methods: Based on the computational analysis, data from 530 KIRC cases and 72 normal kidney samples from The Cancer Genome Atlas (TGCA-KIRC) database were analyzed in this study. The expression of CALR mRNA in pan-cancer and immune infiltrates was analyzed using the Tumor Immune Estimation Resource (TIMER) database. The CALR protein expression was obtained from the UALCAN and Human Protein Atlas (HPA) databases. Survival, functional, and statistical analyses were conducted using R software. Results: The CALR expression was higher in KIRC cases than in normal kidneys. A high CALR expression was correlated with TNM stage, pathological stage, and histological grade. Kaplan-Meier survival analysis showed that a high CALR expression was associated with poor overall survival, disease-specific survival, and progression-free interval. Gene set enrichment analysis (GSEA) indicated that CALR was enriched in IL-6 and IL-2 signaling, interferon signaling, TNF signaling, inflammatory response, apoptosis, and the p53 pathway. CALR is correlated with immune-infiltrating cells. A significant correlation was observed between CALR expression and immunomodulators. Conclusion: We identified CALR as a prognostic biomarker of KIRC. Meanwhile, the CALR expression associated with immune infiltration indicated that CALR might be a potential immunotherapy target for patients with KIRC.
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Affiliation(s)
| | | | | | | | - Hao Xiong
- Department of Hematology and Oncology, Wuhan Children’s Hospital, Tongji Medical College, HUST, Wuhan, China
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6
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Neoantigens and their clinical applications in human gastrointestinal cancers. World J Surg Oncol 2022; 20:321. [PMID: 36171610 PMCID: PMC9520945 DOI: 10.1186/s12957-022-02776-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 09/16/2022] [Indexed: 12/24/2022] Open
Abstract
Background Tumor-specific neoantigens are ideal targets for cancer immunotherapy. As research findings have proved, neoantigen-specific T cell activity is immunotherapy’s most important determinant. Main text There is sufficient evidence showing the role of neoantigens in clinically successful immunotherapy, providing a justification for targeting. Because of the significance of the pre-existing anti-tumor immune response for the immune checkpoint inhibitor, it is believed that personalized neoantigen-based therapy may be an imperative approach for cancer therapy. Thus, intensive attention is given to strategies targeting neoantigens for the significant impact with other immunotherapies, such as the immune checkpoint inhibitor. Today, several algorithms are designed and optimized based on Next-Generation Sequencing and public databases, including dbPepNeo, TANTIGEN 2.0, Cancer Antigenic Peptide Database, NEPdb, and CEDAR databases for predicting neoantigens in silico that stimulates the development of T cell therapies, cancer vaccine, and other ongoing immunotherapy approaches. Conclusions In this review, we deliberated the current developments in understanding and recognition of the immunogenicity of newly found gastrointestinal neoantigens as well as their functions in immunotherapies and cancer detection. We also described how neoantigens are being developed and how they might be used in the treatment of GI malignancies.
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7
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Chow DT, Rardin MJ. Identification and Mitigation of Defensins in the Immunopurification of Peptide MHC-I Antigens from Lung Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1590-1597. [PMID: 34645265 DOI: 10.1021/jasms.1c00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The class I major histocompatibility (MHC-I) complex is a set of diverse cell surface receptors encoded by the human leukocyte antigen gene complex. These receptors present intracellular antigens to cytotoxic T cells providing information on the state and health of cells. Changes in the immunopeptidome during cancer may provide novel targets for therapeutic intervention. To understand how the tumor immunopeptidome is altered, we developed a mass spectrometry (MS) based platform for isolating and identifying MHC-I peptide antigens in lung tumors. In the course of our work, we encountered several large unknown peptide contaminants which had not been previously reported. To understand the source of these major contaminants, we isolated them using offline fractionation and identified them by liquid chromatography-tandem mass spectrometry (LC-MS/MS) as members of the host defense protein family known as the defensins. To mitigate their detrimental effects, we modified our "Original" data-dependent acquisition (DDA) MS method to narrowly target the MHC-I peptides based on their physical properties including charge state and molecular weight ("z state" DDA), evaluated field asymmetric ion mobility spectrometry to attempt gas-phase separation prior to MS analysis, and developed an immunodepletion approach using defensin specific antibodies. This modified approach improves peptide identification and reduces the impact of defensin contamination in lung tissue samples.
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Affiliation(s)
- David T Chow
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Amgen Research, Discovery Attribute Sciences Amgen, South San Francisco, California 94080, United States
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8
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Jiang J, Xia M, Zhang L, Chen X, Zhao Y, Zeng C, Yang H, Liang P, Li G, Li N, Qi H, Wei T, Ren L. Rapid generation of genetically engineered T cells for the treatment of virus-related cancers. Cancer Sci 2022; 113:3686-3697. [PMID: 35950597 DOI: 10.1111/cas.15528] [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: 06/24/2022] [Revised: 07/31/2022] [Accepted: 08/04/2022] [Indexed: 11/28/2022] Open
Abstract
Adoptive transfer of T cell receptor (TCR) engineered T cells targeting viral epitopes represents a promising approach for treating virus-related cancers. However, efficient identification of epitopes for T cells and corresponding TCR remains challenging. Here, we report a workflow permitting rapid generation of human papillomavirus (HPV)-specific TCR-T cells. Six epitopes of viral proteins belonged to HPV16 or HPV18 were predicted of high affinity to A11:01 according to bioinformatic analysis. Subsequently, cytotoxic T cells (CTLs) induction were performed with these six antigen peptides separately, and antigen-specific T cells were sorted by FACS. TCR clonotypes of these virus-specific T cells were determined by next-generation sequencing. To improve the efficiency of TCRαβ pairs validation, a lentiviral vector library containing 116 TCR constructs was generated, which was consisted of predominant TCRs according to TCR repoertire analysis. Later, TCR library transduced T cells were simulated with peptide pool-pulsed antigen presenting cells, then CD137-positive cells were sorted and subjected to TCR repoertire analysis. The top-hit TCRs and corresponding antigen peptides were deduced and validated. Through this workflow, a TCR targeting the E692-101 of HPV16 was identified. This HPV16-specific TCR-T cells showed high activities to HPV16-positive human cervical cancer cells in vitro and efficiently repressed tumor growth in murine model. This study provides a HPV16-specific TCR fitted to HLA-A11:01 population, and exemplifies an efficient approach which can be applied in large-scale screen of virus-specific TCRs, further encouraging researchers to exploit the therapeutic potential of TCR-T cell technique in treating virus-related cancers.
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Affiliation(s)
- Jinxing Jiang
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Ming Xia
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Lijie Zhang
- Department of Gynecology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Xi Chen
- RootPath, Inc. 65 Grove Street, Suite 203, 02472, Watertown, MA, USA
| | - Yue Zhao
- RootPath, Inc. 65 Grove Street, Suite 203, 02472, Watertown, MA, USA
| | - Chenquan Zeng
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Haiyan Yang
- RootPath, Inc. 65 Grove Street, Suite 203, 02472, Watertown, MA, USA
| | - Peng Liang
- RootPath, Inc. 65 Grove Street, Suite 203, 02472, Watertown, MA, USA
| | - Guanghe Li
- Department of Pharmacy, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Ning Li
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Hui Qi
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Teng Wei
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Lili Ren
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
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Lu M, Xu L, Jian X, Tan X, Zhao J, Liu Z, Zhang Y, Liu C, Chen L, Lin Y, Xie L. dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition. Front Immunol 2022; 13:855976. [PMID: 35493528 PMCID: PMC9043652 DOI: 10.3389/fimmu.2022.855976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/17/2022] [Indexed: 12/04/2022] Open
Abstract
Neoantigens are widely reported to induce T-cell response and lead to tumor regression, indicating a promising potential to immunotherapy. Previously, we constructed an open-access database, i.e., dbPepNeo, providing a systematic resource for human tumor neoantigens to storage and query. In order to expand data volume and application scope, we updated dbPepNeo to version 2.0 (http://www.biostatistics.online/dbPepNeo2). Here, we provide about 801 high-confidence (HC) neoantigens (increased by 170%) and 842,289 low-confidence (LC) HLA immunopeptidomes (increased by 107%). Notably, 55 class II HC neoantigens and 630 neoantigen-reactive T-cell receptor-β (TCRβ) sequences were firstly included. Besides, two new analytical tools are developed, DeepCNN-Ineo and BLASTdb. DeepCNN-Ineo predicts the immunogenicity of class I neoantigens, and BLASTdb performs local alignments to look for sequence similarities in dbPepNeo2.0. Meanwhile, the web features and interface have been greatly improved and enhanced.
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Affiliation(s)
- Manman Lu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Linfeng Xu
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xingxing Jian
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoxiu Tan
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Jingjing Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhenhao Liu
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Yu Zhang
- Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Chunyu Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Lanming Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yong Lin
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lu Xie
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.,Bioinformatics Center, National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, China
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10
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Tumor RNA transfected DCs derived from iPS cells elicit cytotoxicity against cancer cells induced from colorectal cancer patients in vitro. Sci Rep 2022; 12:3295. [PMID: 35228610 PMCID: PMC8885822 DOI: 10.1038/s41598-022-07305-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/04/2022] [Indexed: 12/11/2022] Open
Abstract
Significant efficacy of induced pluripotent stem cells (iPSCs) in generating DCs for cancer vaccine therapy was suggested in our previous studies. In clinical application of DC vaccine therapy, however, few DC vaccine systems have shown strong clinical response. To enhance immunogenicity in the DC vaccine, we transfected patient-derived iPSDCs with in vitro transcriptional RNA (ivtRNA), which was obtained from tumors of three patients with colorectal cancer. We investigated iPSDCs-ivtRNA which were induced by transfecting ivtRNA obtained from tumors of three colorectal cancer patients, and examined its antitumor effect. Moreover, we analyzed neoantigens expressed in colorectal cancer cells and examined whether iPSDCs-ivtRNA induced cytotoxic T lymphocytes (CTLs) against the predicted neoantigens. CTLs activated by iPSDCs-ivtRNA exhibited cytotoxic activity against the tumor spheroids in all three patients with colorectal cancer. Whole-exome sequencing revealed 1251 nonsynonymous mutations and 2155 neoantigens (IC50 < 500 nM) were predicted. For IFN-γ ELISPOT assay, these candidate neoantigens were further prioritised and 12 candidates were synthesized. IFN-γ ELISPOT assay revealed that the CTLs induced by iPSDCs-ivtRNA responded to one of the candidate neoantigens. In vitro CTLs obtained by transfecting tumor-derived RNA into iPSDCs derived from three patients with colorectal cancer showed potent tumor-specific killing effect.
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11
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Greenbaum U, Dumbrava EI, Biter AB, Haymaker CL, Hong DS. Engineered T-cell Receptor T Cells for Cancer Immunotherapy. Cancer Immunol Res 2021; 9:1252-1261. [PMID: 34728535 DOI: 10.1158/2326-6066.cir-21-0269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/03/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022]
Abstract
Engineering immune cells to target cancer is a rapidly advancing technology. The first commercial products, chimeric-antigen receptor (CAR) T cells, are now approved for hematologic malignancies. However, solid tumors pose a greater challenge for cellular therapy, in part because suitable cancer-specific antigens are more difficult to identify and surrounding healthy tissues are harder to avoid. In addition, impaired trafficking of immune cells to solid tumors, the harsh immune-inhibitory microenvironment, and variable antigen density and presentation help tumors evade immune cells targeting cancer-specific antigens. To overcome these obstacles, T cells are being engineered to express defined T-cell receptors (TCR). Given that TCRs target intracellular peptides expressed on tumor MHC molecules, this provides an expanded pool of potential targetable tumor-specific antigens relative to the cell-surface antigens that are targeted by CAR T cells. The affinity of TCR T cells can be tuned to allow for better tumor recognition, even with varying levels of antigen presentation on the tumor and surrounding healthy tissue. Further enhancements to TCR T cells include improved platforms that enable more robust cell expansion and persistence; coadministration of small molecules that enhance tumor recognition and immune activation; and coexpression of cytokine-producing moieties, activating coreceptors, or mediators that relieve checkpoint blockade. Early-phase clinical trials pose logistical challenges involving production, large-scale manufacturing, and more. The challenges and obstacles to successful TCR T-cell therapy, and ways to overcome these and improve anticancer activity and efficacy, are discussed herein.
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Affiliation(s)
- Uri Greenbaum
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ecaterina I Dumbrava
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amadeo B Biter
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara L Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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12
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Kverneland AH, Chamberlain CA, Borch TH, Nielsen M, Mørk SK, Kjeldsen JW, Lorentzen CL, Jørgensen LP, Riis LB, Yde CW, Met Ö, Donia M, Marie Svane I. Adoptive cell therapy with tumor-infiltrating lymphocytes supported by checkpoint inhibition across multiple solid cancer types. J Immunother Cancer 2021; 9:jitc-2021-003499. [PMID: 34607899 PMCID: PMC8491427 DOI: 10.1136/jitc-2021-003499] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2021] [Indexed: 02/01/2023] Open
Abstract
Background Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TILs) has shown remarkable results in malignant melanoma (MM), while studies on the potential in other cancer diagnoses are sparse. Further, the prospect of using checkpoint inhibitors (CPIs) to support TIL production and therapy remains to be explored. Study design TIL-based ACT with CPIs was evaluated in a clinical phase I/II trial. Ipilimumab (3 mg/kg) was administered prior to tumor resection and nivolumab (3 mg/kg, every 2 weeks ×4) in relation to TIL infusion. Preconditioning chemotherapy was given before TIL infusion and followed by low-dose (2 10e6 international units (UI) ×1 subcutaneous for 14 days) interleukin-2 stimulation. Results Twenty-five patients covering 10 different cancer diagnoses were treated with in vitro expanded TILs. Expansion of TILs was successful in 97% of recruited patients. Five patients had sizeable tumor regressions of 30%–63%, including two confirmed partial responses in patients with head-and-neck cancer and cholangiocarcinoma. Safety and feasibility were comparable to MM trials of ACT with the addition of expected CPI toxicity. In an exploratory analysis, tumor mutational burden and expression of the alpha-integrin CD103 (p=0.025) were associated with increased disease control. In vitro tumor reactivity was seen in both patients with an objective response and was associated with regressions in tumor size (p=0.028). Conclusion High success rates of TIL expansion were demonstrated across multiple solid cancers. TIL ACTs were found feasible, independent of previous therapy. Tumor regressions after ACT combined with CPIs were demonstrated in several cancer types supported by in vitro antitumor reactivity of the TILs. Trial registration numbers NCT03296137, and EudraCT No. 2017-002323-25.
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Affiliation(s)
- Anders Handrup Kverneland
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Christopher Aled Chamberlain
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Troels Holz Borch
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Morten Nielsen
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Sofie Kirial Mørk
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Julie Westerlin Kjeldsen
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Cathrine Lund Lorentzen
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Lise Pyndt Jørgensen
- Department of Pathology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Christina Westmose Yde
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Glostrup, Denmark
| | - Özcan Met
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Marco Donia
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark.,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Inge Marie Svane
- Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark .,National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
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13
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Bräunlein E, Lupoli G, Füchsl F, Abualrous ET, de Andrade Krätzig N, Gosmann D, Wietbrock L, Lange S, Engleitner T, Lan H, Audehm S, Effenberger M, Boxberg M, Steiger K, Chang Y, Yu K, Atay C, Bassermann F, Weichert W, Busch DH, Rad R, Freund C, Antes I, Krackhardt AM. Functional analysis of peripheral and intratumoral neoantigen-specific TCRs identified in a patient with melanoma. J Immunother Cancer 2021; 9:jitc-2021-002754. [PMID: 34518289 PMCID: PMC8438848 DOI: 10.1136/jitc-2021-002754] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background Neoantigens derived from somatic mutations correlate with therapeutic responses mediated by treatment with immune checkpoint inhibitors. Neoantigens are therefore highly attractive targets for the development of therapeutic approaches in personalized medicine, although many aspects of their quality and associated immune responses are not yet well understood. In a case study of metastatic malignant melanoma, we aimed to perform an in-depth characterization of neoantigens and respective T-cell responses in the context of immune checkpoint modulation. Methods Three neoantigens, which we identified either by immunopeptidomics or in silico prediction, were investigated using binding affinity analyses and structural simulations. We isolated seven T-cell receptors (TCRs) from the patient’s immune repertoire recognizing these antigens. TCRs were compared in vitro by multiparametric analyses including functional avidity, multicytokine secretion, and cross-reactivity screenings. A xenograft mouse model served to study in vivo functionality of selected TCRs. We investigated the patient’s TCR repertoire in blood and different tumor-related tissues over 3 years using TCR beta deep sequencing. Results Selected mutated peptide ligands with proven immunogenicity showed similar binding affinities to the human leukocyte antigen complex and comparable disparity to their wild-type counterparts in molecular dynamic simulations. Nevertheless, isolated TCRs recognizing these antigens demonstrated distinct patterns in functionality and frequency. TCRs with lower functional avidity showed at least equal antitumor immune responses in vivo. Moreover, they occurred at high frequencies and particularly demonstrated long-term persistence within tumor tissues, lymph nodes and various blood samples associated with a reduced activation pattern on primary in vitro stimulation. Conclusions We performed a so far unique fine characterization of neoantigen-specific T-cell responses revealing defined reactivity patterns of neoantigen-specific TCRs. Our data highlight qualitative differences of these TCRs associated with function and longevity of respective T cells. Such features need to be considered for further optimization of neoantigen targeting including adoptive T-cell therapies using TCR-transgenic T cells.
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Affiliation(s)
- Eva Bräunlein
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Gaia Lupoli
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Franziska Füchsl
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Esam T Abualrous
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Dario Gosmann
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Lukas Wietbrock
- TUM School of Life Sciences and Center for Integrated Protein Science Munich, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Sebastian Lange
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Huan Lan
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Stefan Audehm
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Manuel Effenberger
- Institute for Medical Microbiology Immunology and Hygiene, Technische Universität München, München, Germany
| | - Melanie Boxberg
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,MRI-TUM-Biobank at the Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Core Facility Experimental Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Yinshui Chang
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Kai Yu
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Cigdem Atay
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Florian Bassermann
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,MRI-TUM-Biobank at the Institute of Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Core Facility Experimental Pathology, School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology Immunology and Hygiene, Technische Universität München, München, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
| | - Christian Freund
- Laboratory of Protein Biochemistry, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Iris Antes
- TUM School of Life Sciences and Center for Integrated Protein Science Munich, Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - Angela M Krackhardt
- Klinik und Poliklinik für Innere Medizin III, Klinikum rechts der Isar der Technischen Universität München, München, Germany .,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Klinikum rechts der Isar der Technischen Universität München, München, Germany.,German Cancer Consortium (DKTK), partner-site Munich, and German Cancer Research Center (DKFZ) Heidelberg, Heidelberg, Germany
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14
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Srivastava RM, Purohit TA, Chan TA. Diverse Neoantigens and the Development of Cancer Therapies. Semin Radiat Oncol 2021; 30:113-128. [PMID: 32381291 DOI: 10.1016/j.semradonc.2019.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer is the manifestation of uncontrolled cellular growth and immune escape mechanisms. Unrestrained tumor growth can be associated with incidental errors in the genome during replication and genotoxic agents can alter the structure and sequence of our DNA. Among all genetic aberrations in cancer, only limited number of mutations can produce immunogenic antigens which have the potential to bind human leukocyte antigen class I or human leukocyte antigen class II, and help activate the adaptive immune system. These neoantigens can be recognized by CD8+ and CD4+ neoantigen-specific T lymphocytes. Recently, several immune checkpoint targeting drugs have been approved for clinical use. Primarily, these drugs expand and facilitate the cytotoxic activity of neoantigen-specific T cells to eradicate tumors. Differential drug response across cancers could be attributed, at least in part, to differences in the 'tumor antigen landscape' and 'antigen presentation pathway' in patients. Although tumor mutational burden correlates with response to immune checkpoint inhibitors in many cancer types and has evolved as a broad biomarker, a comprehensive understanding of the neoantigen landscape and the function of cognate T cell responses is lacking and is needed for improved patient selection criteria and neoantigen vaccine design. Here, we review cancer neoantigens, their implications for antitumor responses, the dynamics of neoantigen-specific T cells, and the advancement of neoantigen-based therapy in proposed clinical trials.
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Affiliation(s)
- Raghvendra M Srivastava
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tanaya A Purohit
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY.
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15
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Kiyotani K, Toyoshima Y, Nakamura Y. Personalized immunotherapy in cancer precision medicine. Cancer Biol Med 2021; 18:j.issn.2095-3941.2021.0032. [PMID: 34369137 PMCID: PMC8610159 DOI: 10.20892/j.issn.2095-3941.2021.0032] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/30/2021] [Indexed: 11/25/2022] Open
Abstract
With the significant advances in cancer genomics using next-generation sequencing technologies, genomic and molecular profiling-based precision medicine is used as a part of routine clinical test for guiding and selecting the most appropriate treatments for individual cancer patients. Although many molecular-targeted therapies for a number of actionable genomic alterations have been developed, the clinical application of such information is still limited to a small proportion of cancer patients. In this review, we summarize the current status of personalized drug selection based on genomic and molecular profiling and highlight the challenges how we can further utilize the individual genomic information. Cancer immunotherapies, including immune checkpoint inhibitors, would be one of the potential approaches to apply the results of genomic sequencing most effectively. Highly cancer-specific antigens derived from somatic mutations, the so-called neoantigens, occurring in individual cancers have been in focus recently. Cancer immunotherapies, which target neoantigens, could lead to a precise treatment for cancer patients, despite the challenge in accurately predicting neoantigens that can induce cytotoxic T cells in individual patients. Precise prediction of neoantigens should accelerate the development of personalized immunotherapy including cancer vaccines and T-cell receptor-engineered T-cell therapy for a broader range of cancer patients.
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Affiliation(s)
- Kazuma Kiyotani
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Yujiro Toyoshima
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Yusuke Nakamura
- Project for Immunogenomics, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
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16
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Shide K. Calreticulin mutations in myeloproliferative neoplasms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 365:179-226. [PMID: 34756244 DOI: 10.1016/bs.ircmb.2021.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Calreticulin (CALR) is a chaperone present in the endoplasmic reticulum, which is involved in the quality control of N-glycosylated proteins and storage of calcium ions. In 2013, the C-terminal mutation in CALR was identified in half of the patients with essential thrombocythemia and primary myelofibrosis who did not have a JAK2 or MPL mutation. The results of 8 years of intensive research are changing the clinical practice associated with treating myeloproliferative neoplasms (MPNs). The presence or absence of CALR mutations and their mutation types already provide important information for diagnosis and treatment decision making. In addition, the interaction with the thrombopoietin receptor MPL, which is the main mechanism of transformation by CALR mutation, and the expression of the mutant protein on the cell surface have a great potential as targets for molecular-targeted drugs and immunotherapy. This chapter presents recent findings on the clinical significance of the CALR mutation and the molecular basis by which this mutation drives MPNs.
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Affiliation(s)
- Kotaro Shide
- Division of Haematology, Diabetes, and Endocrinology, Department of Internal Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
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17
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Immunogenomics in personalized cancer treatments. J Hum Genet 2021; 66:901-907. [PMID: 34193979 DOI: 10.1038/s10038-021-00950-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/29/2021] [Accepted: 06/09/2021] [Indexed: 12/30/2022]
Abstract
Recent advances in next-generation sequencing technologies have led to significant improvements in cancer genomic research and cancer treatment. Through the use of comprehensive cancer genome data, precision medicine has become more of a reality; albeit, at present, only ~10-15% of patients can benefit from current genomic testing practices. Improvements in cancer genome analyses have contributed to a better understanding of antitumor immunity and have provided solutions for targeting highly cancer-specific neoantigens generated from somatic mutations in individual patients. Since then, numerous studies have demonstrated the importance of neoantigens and neoantigen-reactive T cells in the tumor microenvironment and how their presence influences the beneficial responses associated with various cancer immunotherapies, including immune checkpoint inhibitor therapy. Indeed, cancer immunotherapies that explicitly target neoantigens specific to individual cancer patients would lead to the ultimate form of cancer precision medicine. For this to be realized, several issues would need to be overcome, including the accurate prediction and selection of neoantigens that can induce cytotoxic T cells in individual patients. The precise prediction of target neoantigens will likely accelerate the development of personalized immunotherapy including cancer vaccines and T-cell receptor-engineered T-cell therapy for patients with cancer.
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18
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Wei T, Leisegang M, Xia M, Kiyotani K, Li N, Zeng C, Deng C, Jiang J, Harada M, Agrawal N, Li L, Qi H, Nakamura Y, Ren L. Generation of neoantigen-specific T cells for adoptive cell transfer for treating head and neck squamous cell carcinoma. Oncoimmunology 2021; 10:1929726. [PMID: 34104546 PMCID: PMC8158031 DOI: 10.1080/2162402x.2021.1929726] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Adoptive cell therapy using TCR-engineered T cells (TCR-T cells) represents a promising strategy for treating relapsed and metastatic cancers. We previously established methods to identify neoantigen-specific TCRs based on patients’ PBMCs. However, in clinical practice isolation of PBMCs from advanced-stage cancer patients proves to be difficult. In this study, we substituted blood-derived T cells for tumor-infiltrating lymphocytes (TILs) and used an HLA-matched cell line of antigen-presenting cells (APCs) to replace autologous dendritic cells. Somatic mutations were determined in head and neck squamous cell carcinoma resected from two patients. HLA-A*02:01-restricted neoantigen libraries were constructed and transferred into HLA-matched APCs for stimulation of patient TILs. TCRs were isolated from reactive TIL cultures and functionality was tested using TCR- T cells in vitro and in vivo. To exemplify the screening approach, we identified the targeted neoantigen leading to recognition of the minigene construct that stimulated the strongest TIL response. Neoantigen peptides were used to load MHC-tetramers for T cell isolation and a TCR was identified targeting the KIAA1429D1358E mutation. TCR-T cells were activated, exhibited cytotoxicity, and secreted cytokines in a dose-dependent manner, and only when stimulated with the mutant peptide. Furthermore, comparable to a neoantigen-specific TCR that was isolated from the patient’s PBMCs, KIAA1429D1358E-specific TCR T cells destroyed human tumors in mice. The established protocol provides the required flexibility to methods striving to identify neoantigen-specific TCRs. By using an MHC-matched APC cell line and neoantigen-encoding minigene libraries, autologous TILs can be stimulated and screened when patient PBMCs and/or tumor material are not available anymore. Abbreviations: Head and neck squamous cell carcinoma (HNSCC); adoptive T cell therapy (ACT); T cell receptor (TCR); tumor-infiltrating lymphocytes (TIL); cytotoxic T lymphocyte (CTL); peripheral blood mononuclear cell (PBMC); dendritic cell (DC); antigen-presenting cells (APC)
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Affiliation(s)
- Teng Wei
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China.,Institute of Clinical Oncology, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - Matthias Leisegang
- Institute of Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany.,David and Etta Jonas Center for Cellular Therapy, the University of Chicago, Chicago, IL, USA.,German Cancer Consortium (DKTK), Partner Site Berlin, Berlin, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ming Xia
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Kazuma Kiyotani
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ning Li
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Chenquan Zeng
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Chunyan Deng
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Jinxing Jiang
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Makiko Harada
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Nishant Agrawal
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Liangping Li
- Institute of Clinical Oncology, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - Hui Qi
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
| | - Yusuke Nakamura
- Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Lili Ren
- Cytotherapy Laboratory, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; the First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Guangdong, China
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19
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Centuori SM, Caulin C, Bauman JE. Precision and Immunoprevention Strategies for Tobacco-Related Head and Neck Cancer Chemoprevention. Curr Treat Options Oncol 2021; 22:52. [PMID: 33991232 PMCID: PMC8122210 DOI: 10.1007/s11864-021-00848-x] [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] [Accepted: 03/16/2021] [Indexed: 12/02/2022]
Abstract
OPINION STATEMENT To date, there is no FDA-approved chemoprevention approach for tobacco-related HNSCC. Effective chemoprevention approaches validated in sufficiently powered randomized trials are needed to reduce the incidence and improve survival. In this review, we recap the challenges encountered in past chemoprevention trials and discuss emerging approaches, with major focus on green chemoprevention, precision prevention, and immunoprevention. As our current depth of knowledge expands in the arena of cancer immunotherapy, the field of immunoprevention is primed for new discoveries and successes in cancer prevention.
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Affiliation(s)
- Sara M. Centuori
- Department of Medicine, University of Arizona, 1515 N. Campbell Ave, PO Box 245024, Tucson, AZ 85724-5024 USA
- University of Arizona Cancer Center, 1515 N. Campbell Ave, Tucson, AZ 85724 USA
| | - Carlos Caulin
- University of Arizona Cancer Center, 1515 N. Campbell Ave, Tucson, AZ 85724 USA
- Department of Otolaryngology-Head and Neck Surgery, University of Arizona, 1515 N. Campbell Ave, Tucson, AZ 85724 USA
| | - Julie E. Bauman
- Department of Medicine, University of Arizona, 1515 N. Campbell Ave, PO Box 245024, Tucson, AZ 85724-5024 USA
- University of Arizona Cancer Center, 1515 N. Campbell Ave, Tucson, AZ 85724 USA
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Tumor Heterogeneity: A Great Barrier in the Age of Cancer Immunotherapy. Cancers (Basel) 2021; 13:cancers13040806. [PMID: 33671881 PMCID: PMC7918981 DOI: 10.3390/cancers13040806] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/17/2022] Open
Abstract
Throughout the history of oncology research, tumor heterogeneity has been a major hurdle for the successful treatment of cancer. As a result of aberrant changes in the tumor microenvironment such as high mutational burden, hypoxic conditions and abnormal vasculature, several malignant subpopulations often exist within a single tumor mass. Therapeutic intervention can also increase selective pressure towards subpopulations with acquired resistance. This phenomenon is often the cause of relapse in previously responsive patients, drastically changing the expected outcome of therapy. In the case of cancer immunotherapy, tumor heterogeneity is a substantial barrier as acquired resistance often takes the form of antigen escape and immunosuppression. In an effort to combat intrinsic resistance mechanisms, therapies are often combined as a multi-pronged approach to target multiple pathways simultaneously. These multi-therapy regimens have long been a mainstay of clinical oncology with chemotherapy cocktails but are more recently being investigated in the emerging landscape of immunotherapy. Furthermore, as high throughput technology becomes more affordable and accessible, researchers continue to deepen their understanding of the factors that influence tumor heterogeneity and shape the TME over the course of treatment regimens. In this review, we will investigate the factors that give rise to tumor heterogeneity and the impact it has on the field of immunotherapy. We will discuss how tumor heterogeneity causes resistance to various treatments and review the strategies currently being employed to overcome this challenging clinical hurdle. Finally, we will outline areas of research that should be prioritized to gain a better understanding of tumor heterogeneity and develop appropriate solutions.
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21
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Jones HF, Molvi Z, Klatt MG, Dao T, Scheinberg DA. Empirical and Rational Design of T Cell Receptor-Based Immunotherapies. Front Immunol 2021; 11:585385. [PMID: 33569049 PMCID: PMC7868419 DOI: 10.3389/fimmu.2020.585385] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/04/2020] [Indexed: 01/04/2023] Open
Abstract
The use of T cells reactive with intracellular tumor-associated or tumor-specific antigens has been a promising strategy for cancer immunotherapies in the past three decades, but the approach has been constrained by a limited understanding of the T cell receptor's (TCR) complex functions and specificities. Newer TCR and T cell-based approaches are in development, including engineered adoptive T cells with enhanced TCR affinities, TCR mimic antibodies, and T cell-redirecting bispecific agents. These new therapeutic modalities are exciting opportunities by which TCR recognition can be further exploited for therapeutic benefit. In this review we summarize the development of TCR-based therapeutic strategies and focus on balancing efficacy and potency versus specificity, and hence, possible toxicity, of these powerful therapeutic modalities.
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Affiliation(s)
- Heather F. Jones
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, New York, NY, United States
| | - Zaki Molvi
- Weill Cornell Medicine, New York, NY, United States
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martin G. Klatt
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - David A. Scheinberg
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, New York, NY, United States
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22
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Kast F, Klein C, Umaña P, Gros A, Gasser S. Advances in identification and selection of personalized neoantigen/T-cell pairs for autologous adoptive T cell therapies. Oncoimmunology 2021; 10:1869389. [PMID: 33520408 PMCID: PMC7808433 DOI: 10.1080/2162402x.2020.1869389] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Based on the success of tumor-infiltrating lymphocytes (TIL)-based therapies, personalized adoptive cell therapies (ACT) targeting neoantigens have the potential to become a disruptive technology and lead to highly effective treatments for cancer patients for whom no other options exist. ACT of TIL, peripheral blood or gene-engineered peripheral blood lymphocytes (PBLs) targeting neoantigens is a highly personalized intervention that requires three discrete steps: i) Identification of suitable personal targets (neoantigens), ii) selection of T cells or their T cell receptors (TCRs) that are specific for the identified neoantigens and iii) expansion of the selected T cell population or generation of sufficient number of TCR modified T cells. In this review, we provide an introduction into challenges and approaches to identify neoantigens and to select the Adoptive Cell Therapy, ACT, Neoantigen, T cell, Cancer respective neoantigen-reactive T cells for use in ACT.
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Affiliation(s)
- Florian Kast
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Christian Klein
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Pablo Umaña
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
| | - Alena Gros
- Vall d'Hebron Institute of Oncology, Cellex Center, Barcelona, Spain
| | - Stephan Gasser
- Roche Pharma Research & Early Development, Roche Innovation Center Zurich, Schlieren, Switzerland
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Welters MJP, Santegoets SJ, van der Burg SH. The Tumor Microenvironment and Immunotherapy of Oropharyngeal Squamous Cell Carcinoma. Front Oncol 2020; 10:545385. [PMID: 33425717 PMCID: PMC7793705 DOI: 10.3389/fonc.2020.545385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022] Open
Abstract
Oropharyngeal squamous cell carcinoma (OPSCC) develops as a consequence of several mutations in the tumor suppressor pathways or after a progressive infection with high risk human papillomavirus (HPV). The dismal side effects of the current standard of care and the clear involvement of the immune system has led to a surge in clinical trials that aim to reinforce the tumor-specific immune response as a new treatment option. In this review, we have focused on the most recent literature to discuss the new findings and insights on the role of different immune cells in the context of OPSCC and its etiology. We then applied this knowledge to describe potential biomarkers and analyzed the rationale and outcomes of earlier and ongoing immunotherapy trials. Finally, we describe new developments that are still at the preclinical phase and provide an outlook on what the near future may bring, now that several new and exciting techniques to study the immune system at the single cell level are being exploited.
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Affiliation(s)
- Marij J P Welters
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Saskia J Santegoets
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
| | - Sjoerd H van der Burg
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, Netherlands
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24
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Wu W, Chen Y, Huang L, Li W, Tao C, Shen H. Point mutation screening of tumor neoantigens and peptide-induced specific cytotoxic T lymphocytes using The Cancer Genome Atlas database. Oncol Lett 2020; 20:123. [PMID: 32934692 PMCID: PMC7471748 DOI: 10.3892/ol.2020.11986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/18/2020] [Indexed: 12/30/2022] Open
Abstract
The aim of the present study was to use The Cancer Genome Atlas (TCGA) database to identify tumor neoantigens, combined with a bioinformatics analysis to design and analyze antigen epitope peptides. Epitopes were screened using immunogenicity tests to identify the ideal epitope peptides to target tumor neoantigens, which can specifically activate the immune response of T cells. The high-frequency mutation loci (top 10) of colorectal, lung and liver cancer genes were screened using TCGA database. The antigenic epitope peptides with high affinity for major histocompatibility complex molecules were selected and synthesized using computer prediction algorithms, and were subsequently detected using flow cytometry. The cytotoxicity of specific cytotoxic T lymphocytes (CTLs) on peptide-loaded T2 cells was initially verified using interferon IFN-γ detection and a calcein-acetoxymethyl (Cal-AM) release assay. Tumor cell lines expressing point mutations in KRAS, TP53 and CTNNB1 genes were constructed respectively, and the cytotoxicity of peptide-induced specific CTLs on wild-type and mutant tumor cells was verified using a Cal-AM release assay and carboxyfluorescein succinimidyl ester-propidium iodide staining. The high-frequency gene mutation loci of KRAS proto-oncogene (KRAS) G12V, tumor protein p53 (TP53) R158L and catenin β1 (CTNNB1) K335I were identified in TCGA database. A total of 3 groups of wild-type and mutant peptides were screened using a peptide prediction algorithm. The CTNNB1 group had a strong affinity for the human leukocyte antigen-A2 molecule, as determined using flow cytometry. The IFN-γ secretion of specific CTLs in the CTNNB1 group was the highest, followed by the TP53 and the KRAS groups. The killing rate of mutant peptide-induced specific CTLs on peptide-loaded T2 cells in the CTNNB1 group was higher compared with that observed in the other groups. The killing rate of specific CTLs induced by mutant peptides present on tumor cells was higher compared with that induced by wild-type peptides. However, when compared with the TP53 and KRAS groups, specific CTLs induced by mutant peptides in the CTNNB1 group had more potent cytotoxicity towards mutant and wild-type tumor cells. In conclusion, point mutant tumor neoantigens screened in the three groups improved the cytotoxicity of specific T cells, and the mutant peptides in the CTNNB1 group were more prominent, indicating that they may activate the cellular immune response more readily.
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Affiliation(s)
- Wanwen Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Ying Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Lan Huang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Wenjian Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Changli Tao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Han Shen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
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25
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Xu P, Luo H, Kong Y, Lai WF, Cui L, Zhu X. Cancer neoantigen: Boosting immunotherapy. Biomed Pharmacother 2020; 131:110640. [PMID: 32836075 DOI: 10.1016/j.biopha.2020.110640] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 12/21/2022] Open
Abstract
Tumor neoantigen has a high degree of immunogenicity. As one of the emerging methods of tumor immunotherapy, the vaccine developed against it has served to clinical trials of various solid tumors, especially in the treatment of melanoma. Currently, a variety of immunotherapy methods have been applied to the treatment of the tumor. However, other therapeutic methods have the disadvantages of low specificity and prominent side effects. Treatments require tumor antigen with higher immunogenicity as the target of immune attack. This review will recommend the identification of neoantigen, the influencing factors of neoantigen, and the application of personalized vaccines for neoantigen in metastatic tumors such as malignant melanoma.
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Affiliation(s)
- Peijia Xu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, 524023, China
| | - Haiqing Luo
- Cancer Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524023, China
| | - Ying Kong
- Department of Clinical Laboratory, Hubei No. 3 People's Hospital of Jianghan University, Wuhan, 430033, China
| | - Wing-Fu Lai
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, China; School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen, China.
| | - Liao Cui
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
| | - Xiao Zhu
- Guangdong Key Laboratory for Research and Development of Natural Drugs, The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, 524023, China; The Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China; The Key Lab of Zhanjiang for R&D Marine Microbial Resources in the Beibu Gulf Rim, Guangdong Medical University, Zhanjiang, 524023, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhanjiang), Zhanjiang, 524023, China.
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26
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Abstract
Calreticulin (CALR) is an endoplasmic reticulum (ER)-resident protein involved in a spectrum of cellular processes. In healthy cells, CALR operates as a chaperone and Ca2+ buffer to assist correct protein folding within the ER. Besides favoring the maintenance of cellular proteostasis, these cell-intrinsic CALR functions support Ca2+-dependent processes, such as adhesion and integrin signaling, and ensure normal antigen presentation on MHC Class I molecules. Moreover, cancer cells succumbing to immunogenic cell death (ICD) expose CALR on their surface, which promotes the uptake of cell corpses by professional phagocytes and ultimately supports the initiation of anticancer immunity. Thus, loss-of-function CALR mutations promote oncogenesis not only as they impair cellular homeostasis in healthy cells, but also as they compromise natural and therapy-driven immunosurveillance. However, the prognostic impact of total or membrane-exposed CALR levels appears to vary considerably with cancer type. For instance, while genetic CALR defects promote pre-neoplastic myeloproliferation, patients with myeloproliferative neoplasms bearing CALR mutations often experience improved overall survival as compared to patients bearing wild-type CALR. Here, we discuss the context-dependent impact of CALR on malignant transformation, tumor progression and response to cancer therapy.
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The Quest for the Best: How TCR Affinity, Avidity, and Functional Avidity Affect TCR-Engineered T-Cell Antitumor Responses. Cells 2020; 9:cells9071720. [PMID: 32708366 PMCID: PMC7408146 DOI: 10.3390/cells9071720] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Over the past decades, adoptive transfer of T cells has revolutionized cancer immunotherapy. In particular, T-cell receptor (TCR) engineering of T cells has marked important milestones in developing more precise and personalized cancer immunotherapies. However, to get the most benefit out of this approach, understanding the role that TCR affinity, avidity, and functional avidity play on how TCRs and T cells function in the context of tumor-associated antigen (TAA) recognition is vital to keep generating improved adoptive T-cell therapies. Aside from TCR-related parameters, other critical factors that govern T-cell activation are the effect of TCR co-receptors on TCR–peptide-major histocompatibility complex (pMHC) stabilization and TCR signaling, tumor epitope density, and TCR expression levels in TCR-engineered T cells. In this review, we describe the key aspects governing TCR specificity, T-cell activation, and how these concepts can be applied to cancer-specific TCR redirection of T cells.
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28
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Recurrent Neoantigens in Colorectal Cancer as Potential Immunotherapy Targets. BIOMED RESEARCH INTERNATIONAL 2020; 2020:2861240. [PMID: 32733937 PMCID: PMC7383341 DOI: 10.1155/2020/2861240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/26/2020] [Accepted: 06/02/2020] [Indexed: 12/24/2022]
Abstract
This study was aimed at investigating the mutations in colorectal cancer (CRC) for recurrent neoantigen identification. A total of 1779 samples with whole exome sequencing (WES) data were obtained from 7 published CRC cohorts. Common HLA genotypes were used to predict the probability of neoantigens at high-frequency mutants in the dataset. Based on the WES data, we not only obtained the most comprehensive CRC mutation landscape so far but also found 1550 mutations which could be identified in at least 5 patients, including KRAS G12D (8%), KRAS G12V (5.8%), PIK3CA E545K (3.5%), PIK3CA H1047R (2.5%), and BMPR2 N583Tfs∗44 (2.8%). These mutations can also be recognized by multiple common HLA molecules in Chinese and TCGA cohort as potential "public" neoantigens. Many of these mutations also have high mutation rates in metastatic pan-cancers, suggesting their value as therapeutic targets in different cancer types. Overall, our analysis provides recurrent neoantigens as potential cancer immunotherapy targets.
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Protecting Tumors by Preventing Human Papilloma Virus Antigen Presentation: Insights from Emerging Bioinformatics Algorithms. Cancers (Basel) 2019; 11:cancers11101543. [PMID: 31614809 PMCID: PMC6826432 DOI: 10.3390/cancers11101543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022] Open
Abstract
Recent developments in bioinformatics technologies have led to advances in our understanding of how oncogenic viruses such as the human papilloma virus drive cancer progression and evade the host immune system. Here, we focus our review on understanding how these emerging bioinformatics technologies influence our understanding of how human papilloma virus (HPV) drives immune escape in cancers of the head and neck, and how these new informatics approaches may be generally applicable to other virally driven cancers. Indeed, these tools enable researchers to put existing data from genome wide association studies, in which high risk alleles have been identified, in the context of our current understanding of cellular processes regulating neoantigen presentation. In the future, these new bioinformatics approaches are highly likely to influence precision medicine-based decision making for the use of immunotherapies in virally driven cancers.
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Jiang T, Shi T, Zhang H, Hu J, Song Y, Wei J, Ren S, Zhou C. Tumor neoantigens: from basic research to clinical applications. J Hematol Oncol 2019; 12:93. [PMID: 31492199 PMCID: PMC6731555 DOI: 10.1186/s13045-019-0787-5] [Citation(s) in RCA: 233] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 08/29/2019] [Indexed: 12/20/2022] Open
Abstract
Tumor neoantigen is the truly foreign protein and entirely absent from normal human organs/tissues. It could be specifically recognized by neoantigen-specific T cell receptors (TCRs) in the context of major histocompatibility complexes (MHCs) molecules. Emerging evidence has suggested that neoantigens play a critical role in tumor-specific T cell-mediated antitumor immune response and successful cancer immunotherapies. From a theoretical perspective, neoantigen is an ideal immunotherapy target because they are distinguished from germline and could be recognized as non-self by the host immune system. Neoantigen-based therapeutic personalized vaccines and adoptive T cell transfer have shown promising preliminary results. Furthermore, recent studies suggested the significant role of neoantigen in immune escape, immunoediting, and sensitivity to immune checkpoint inhibitors. In this review, we systematically summarize the recent advances of understanding and identification of tumor-specific neoantigens and its role on current cancer immunotherapies. We also discuss the ongoing development of strategies based on neoantigens and its future clinical applications.
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Affiliation(s)
- Tao Jiang
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, No. 507, Zheng Min Road, Shanghai, 200433, China
| | - Tao Shi
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, No. 321, Zhongshan Road, Nanjing, 210008, China
| | | | - Jie Hu
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary Medicine, Shanghai Respiratory Research Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jia Wei
- The Comprehensive Cancer Centre of Drum Tower Hospital, Medical School of Nanjing University, No. 321, Zhongshan Road, Nanjing, 210008, China.
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, No. 507, Zheng Min Road, Shanghai, 200433, China.
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital & Thoracic Cancer Institute, Tongji University School of Medicine, No. 507, Zheng Min Road, Shanghai, 200433, China.
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Parameters for Optoperforation-Induced Killing of Cancer Cells Using Gold Nanoparticles Functionalized With the C-terminal Fragment of Clostridium Perfringens Enterotoxin. Int J Mol Sci 2019; 20:ijms20174248. [PMID: 31480250 PMCID: PMC6747448 DOI: 10.3390/ijms20174248] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/11/2022] Open
Abstract
Recently, we used a recombinant produced C-terminus (D194-F319) of the Clostridium perfringens enterotoxin (C-CPE) to functionalize gold nanoparticles (AuNPs) for a subsequent specific killing of claudin expressing tumor cells using the gold nanoparticle-mediated laser perforation (GNOME-LP) technique. For a future in vivo application, it will be crucial to know the physical parameters and the biological mechanisms inducing cell death for a rational adaptation of the system to real time situation. Regarding the AuNP functionalization, we observed that a relationship of 2.5 × 10−11 AuNP/mL to 20 µg/mL C-CPE maximized the killing efficiency. Regardingphysical parameters, a laser fluence up to 30 mJ/cm2 increased the killing efficiency. Independent from the applied laser fluence, the maximal killing efficiency was achieved at a scanning velocity of 5 mm/s. In 3D matrigel culture system, the GNOME-LP/C-CPE-AuNP completely destroyed spheroids composed of Caco-2 cells and reduced OE-33 cell spheroid formation. At the biology level, GNOME-LP/C-CPE-AuNP-treated cells bound annexin V and showed reduced mitochondria activity. However, an increased caspase-3/7 activity in the cells was not found. Similarly, DNA analysis revealed no apoptosis-related DNA ladder. The results suggest that the GNOME-LP/C-CPE-AuNP treatment induced necrotic than apoptotic reaction in tumor cells.
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