1
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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2
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Guasp P, Reiche C, Sethna Z, Balachandran VP. RNA vaccines for cancer: Principles to practice. Cancer Cell 2024:S1535-6108(24)00168-5. [PMID: 38848720 DOI: 10.1016/j.ccell.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
Abstract
Vaccines are the most impactful medicines to improve health. Though potent against pathogens, vaccines for cancer remain an unfulfilled promise. However, recent advances in RNA technology coupled with scientific and clinical breakthroughs have spurred rapid discovery and potent delivery of tumor antigens at speed and scale, transforming cancer vaccines into a tantalizing prospect. Yet, despite being at a pivotal juncture, with several randomized clinical trials maturing in upcoming years, several critical questions remain: which antigens, tumors, platforms, and hosts can trigger potent immunity with clinical impact? Here, we address these questions with a principled framework of cancer vaccination from antigen detection to delivery. With this framework, we outline features of emergent RNA technology that enable rapid, robust, real-time vaccination with somatic mutation-derived neoantigens-an emerging "ideal" antigen class-and highlight latent features that have sparked the belief that RNA could realize the enduring vision for vaccines against cancer.
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Affiliation(s)
- Pablo Guasp
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlotte Reiche
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zachary Sethna
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Vinod P Balachandran
- Immuno-Oncology Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Hepatopancreatobiliary Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Levin N, Kim SP, Marquardt CA, Vale NR, Yu Z, Sindiri S, Gartner JJ, Parkhurst M, Krishna S, Lowery FJ, Zacharakis N, Levy L, Prickett TD, Benzine T, Ray S, Masi RV, Gasmi B, Li Y, Islam R, Bera A, Goff SL, Robbins PF, Rosenberg SA. Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes. J Immunother Cancer 2024; 12:e008645. [PMID: 38816232 PMCID: PMC11141192 DOI: 10.1136/jitc-2023-008645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND Tumor-infiltrating lymphocytes (TILs) targeting neoantigens can effectively treat a selected set of metastatic solid cancers. However, harnessing TILs for cancer treatments remains challenging because neoantigen-reactive T cells are often rare and exhausted, and ex vivo expansion can further reduce their frequencies. This complicates the identification of neoantigen-reactive T-cell receptors (TCRs) and the development of TIL products with high reactivity for patient treatment. METHODS We tested whether TILs could be in vitro stimulated against neoantigens to achieve selective expansion of neoantigen-reactive TILs. Given their prevalence, mutant p53 or RAS were studied as models of human neoantigens. An in vitro stimulation method, termed "NeoExpand", was developed to provide neoantigen-specific stimulation to TILs. 25 consecutive patient TILs from tumors harboring p53 or RAS mutations were subjected to NeoExpand. RESULTS We show that neoantigenic stimulation achieved selective expansion of neoantigen-reactive TILs and broadened the neoantigen-reactive CD4+ and CD8+ TIL clonal repertoire. This allowed the effective isolation of novel neoantigen-reactive TCRs. Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. Furthermore, neoantigenic stimulation improved the in vivo antitumor efficacy of TILs relative to the conventional OKT3-induced rapid TIL expansion in p53-mutated or KRAS-mutated xenograft mouse models. CONCLUSIONS Taken together, neoantigenic stimulation of TILs selectively expands neoantigen-reactive TILs by frequencies and by their clonal repertoire. NeoExpand led to improved phenotypes and functions of neoantigen-reactive TILs. Our data warrant its clinical evaluation. TRIAL REGISTRATION NUMBER NCT00068003, NCT01174121, and NCT03412877.
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Affiliation(s)
- Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sanghyun P Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Charles A Marquardt
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Maria Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Tiffany Benzine
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Robert V Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Yong Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Rafiqul Islam
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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4
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Delek FSP, Tunçer ŞB, Ödemiş DA, Erciyas SK, Erdoğan ÖŞ, Saip P, Yazıcı H. miR-3653-3p Expression in PBMCs: Unveiling the Diagnostic Potential for Ovarian Cancer. Biochem Genet 2024:10.1007/s10528-024-10819-0. [PMID: 38705961 DOI: 10.1007/s10528-024-10819-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
Ovarian cancer is typically diagnosed at an advanced stage, recurs early and often, and currently lacks effective treatment. Therefore, overall survival and progression-free survival are relatively short for this disease. Sensitive and specific biomarkers for early diagnosis and follow-up for effective treatment of the disease are currently lacking. MicroRNA (miRNA/miR) expression studies are widely used in cancer research. Disruption or malfunction of miRNAs, a class of noncoding small RNAs, has been implicated in cancer progression in several publications. Of note, the expression of a series of miRNAs is known to differ in ovarian cancer. In cancer research, it is crucial to analyze expression patterns in both cancer patients and healthy individuals to identify cancer-specific biological markers and to understand their role in cancer. In the present study, the expression levels of miR-3653-3p in the peripheral blood mononuclear cells (PBMCs) of 150 patients with high-risk ovarian cancer were determined, including those with a family history of cancer or an early-age diagnosis of ovarian cancer, as well as 100 healthy individuals. The results were then compared between the two groups. The expression level of miR-3653-3p in the PBMCs of patients with ovarian cancer was determined to be 9.49-fold higher than that in the healthy control group, and this result was statistically significant (P < 0.001). In addition, receiver-operating characteristic curve analysis of PBMC showed statistical significance of miR-3653-3p in discriminating ovarian cancer patients from healthy subjects (P < 0.001). These results suggest that miR-3653-3p detected in peripheral blood may be used as a non-invasive biomarker for ovarian cancer.
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Affiliation(s)
- Fatma Seher Pektopal Delek
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
- Division of Cancer Genetics, Department of Basic Oncology, Institute of Health Sciences, Istanbul University, Vezneciler-Fatih, 32416, Istanbul, Türkiye
| | - Şeref Buğra Tunçer
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Demet Akdeniz Ödemiş
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Seda Kılıç Erciyas
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Özge Şükrüoğlu Erdoğan
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Pınar Saip
- Department of Clinical Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye
| | - Hülya Yazıcı
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Çapa-Fatih, 34093, Istanbul, Türkiye.
- Department of Medical Biology and Genetics, Faculty of Medicine, Istanbul Arel University, Cevizlibağ-Zeytinburnu, 34010, Istanbul, Türkiye.
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5
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Sotirov S, Dimitrov I. Tumor-Derived Antigenic Peptides as Potential Cancer Vaccines. Int J Mol Sci 2024; 25:4934. [PMID: 38732150 PMCID: PMC11084719 DOI: 10.3390/ijms25094934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Peptide antigens derived from tumors have been observed to elicit protective immune responses, categorized as either tumor-associated antigens (TAAs) or tumor-specific antigens (TSAs). Subunit cancer vaccines incorporating these antigens have shown promise in inducing protective immune responses, leading to cancer prevention or eradication. Over recent years, peptide-based cancer vaccines have gained popularity as a treatment modality and are often combined with other forms of cancer therapy. Several clinical trials have explored the safety and efficacy of peptide-based cancer vaccines, with promising outcomes. Advancements in techniques such as whole-exome sequencing, next-generation sequencing, and in silico methods have facilitated the identification of antigens, making it increasingly feasible. Furthermore, the development of novel delivery methods and a deeper understanding of tumor immune evasion mechanisms have heightened the interest in these vaccines among researchers. This article provides an overview of novel insights regarding advancements in the field of peptide-based vaccines as a promising therapeutic avenue for cancer treatment. It summarizes existing computational methods for tumor neoantigen prediction, ongoing clinical trials involving peptide-based cancer vaccines, and recent studies on human vaccination experiments.
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Affiliation(s)
| | - Ivan Dimitrov
- Drug Design and Bioinformatics Lab, Faculty of Pharmacy, Medical University of Sofia, 2, Dunav Str., 1000 Sofia, Bulgaria;
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6
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Shao W, Yao Y, Yang L, Li X, Ge T, Zheng Y, Zhu Q, Ge S, Gu X, Jia R, Song X, Zhuang A. Novel insights into TCR-T cell therapy in solid neoplasms: optimizing adoptive immunotherapy. Exp Hematol Oncol 2024; 13:37. [PMID: 38570883 PMCID: PMC10988985 DOI: 10.1186/s40164-024-00504-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/21/2024] [Indexed: 04/05/2024] Open
Abstract
Adoptive immunotherapy in the T cell landscape exhibits efficacy in cancer treatment. Over the past few decades, genetically modified T cells, particularly chimeric antigen receptor T cells, have enabled remarkable strides in the treatment of hematological malignancies. Besides, extensive exploration of multiple antigens for the treatment of solid tumors has led to clinical interest in the potential of T cells expressing the engineered T cell receptor (TCR). TCR-T cells possess the capacity to recognize intracellular antigen families and maintain the intrinsic properties of TCRs in terms of affinity to target epitopes and signal transduction. Recent research has provided critical insight into their capability and therapeutic targets for multiple refractory solid tumors, but also exposes some challenges for durable efficacy. In this review, we describe the screening and identification of available tumor antigens, and the acquisition and optimization of TCRs for TCR-T cell therapy. Furthermore, we summarize the complete flow from laboratory to clinical applications of TCR-T cells. Last, we emerge future prospects for improving therapeutic efficacy in cancer world with combination therapies or TCR-T derived products. In conclusion, this review depicts our current understanding of TCR-T cell therapy in solid neoplasms, and provides new perspectives for expanding its clinical applications and improving therapeutic efficacy.
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Affiliation(s)
- Weihuan Shao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yiran Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Ludi Yang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiaoran Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Tongxin Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Yue Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Qiuyi Zhu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Xin Song
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
| | - Ai Zhuang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, 639 Zhi Zao Ju Road, Shanghai Ninth People's Hospital, Shanghai, 200011, People's Republic of China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, People's Republic of China.
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7
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Shafer P, Leung WK, Woods M, Choi JM, Rodriguez-Plata CM, Maknojia A, Mosquera A, Somes LK, Joubert J, Manliguez A, Ranjan R, Burt B, Lee HS, Zhang B, Fuqua S, Rooney C, Leen AM, Hoyos V. Incongruity between T cell receptor recognition of breast cancer hotspot mutations ESR1 Y537S and D538G following exogenous peptide loading versus endogenous antigen processing. Cytotherapy 2024; 26:266-275. [PMID: 38231165 PMCID: PMC10922969 DOI: 10.1016/j.jcyt.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/28/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
T cell receptor engineered T cell (TCR T) therapies have shown recent efficacy against certain types of solid metastatic cancers. However, to extend TCR T therapies to treat more patients across additional cancer types, new TCRs recognizing cancer-specific antigen targets are needed. Driver mutations in AKT1, ESR1, PIK3CA, and TP53 are common in patients with metastatic breast cancer (MBC) and if immunogenic could serve as ideal tumor-specific targets for TCR T therapy to treat this disease. Through IFN-γ ELISpot screening of in vitro expanded neopeptide-stimulated T cell lines from healthy donors and MBC patients, we identified reactivity towards 11 of 13 of the mutations. To identify neopeptide-specific TCRs, we then performed single-cell RNA sequencing of one of the T cell lines following neopeptide stimulation. Here, we identified an ESR1 Y537S specific T cell clone, clonotype 16, and an ESR1 Y537S/D538G dual-specific T cell clone, clonotype 21, which were HLA-B*40:02 and HLA-C*01:02 restricted, respectively. TCR Ts expressing these TCRs recognized and killed target cells pulsed with ESR1 neopeptides with minimal activity against ESR1 WT peptide. However, these TCRs failed to recognize target cells expressing endogenous mutant ESR1. To investigate the basis of this lack of recognition we performed immunopeptidomics analysis of a mutant-overexpressing lymphoblastoid cell line and found that the ESR1 Y537S neopeptide was not endogenously processed, despite binding to HLA-B*40:02 when exogenously pulsed onto the target cell. These results indicate that stimulation of T cells that likely derive from the naïve repertoire with pulsed minimal peptides may lead to the expansion of clones that recognize non-processed peptides, and highlights the importance of using methods that selectively expand T cells with specificity for antigens that are efficiently processed and presented.
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Affiliation(s)
- Paul Shafer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Wingchi K Leung
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Mae Woods
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Jong Min Choi
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Carlos M Rodriguez-Plata
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Arushana Maknojia
- Division of Infectious Disease, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Andres Mosquera
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Lauren K Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Jarrett Joubert
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Anthony Manliguez
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Rashi Ranjan
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Bryan Burt
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Hyun-Sung Lee
- Systems Onco-Immunology Laboratory, David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Bing Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Suzanne Fuqua
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Cliona Rooney
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Ann M Leen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA
| | - Valentina Hoyos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas, USA.
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8
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Sun W, Hughes EP, Kim H, Perovanovic J, Charley KR, Perkins B, Du J, Ibarra A, Syage AR, Hale JS, Williams MA, Tantin D. OCA-B/Pou2af1 is sufficient to promote CD4 + T cell memory and prospectively identifies memory precursors. Proc Natl Acad Sci U S A 2024; 121:e2309153121. [PMID: 38386711 PMCID: PMC10907311 DOI: 10.1073/pnas.2309153121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/12/2024] [Indexed: 02/24/2024] Open
Abstract
The molecular mechanisms leading to the establishment of immunological memory are inadequately understood, limiting the development of effective vaccines and durable antitumor immune therapies. Here, we show that ectopic OCA-B expression is sufficient to improve antiviral memory recall responses, while having minimal effects on primary effector responses. At peak viral response, short-lived effector T cell populations are expanded but show increased Gadd45b and Socs2 expression, while memory precursor effector cells show increased expression of Bcl2, Il7r, and Tcf7 on a per-cell basis. Using an OCA-B mCherry reporter mouse line, we observe high OCA-B expression in CD4+ central memory T cells. We show that early in viral infection, endogenously elevated OCA-B expression prospectively identifies memory precursor cells with increased survival capability and memory recall potential. Cumulatively, the results demonstrate that OCA-B is both necessary and sufficient to promote CD4 T cell memory in vivo and can be used to prospectively identify memory precursor cells.
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Affiliation(s)
- Wenxiang Sun
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Erik P Hughes
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Heejoo Kim
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Jelena Perovanovic
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Krystal R Charley
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Bryant Perkins
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Junhong Du
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Andrea Ibarra
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Amber R Syage
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - J Scott Hale
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Matthew A Williams
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112
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9
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Pant S, Wainberg ZA, Weekes CD, Furqan M, Kasi PM, Devoe CE, Leal AD, Chung V, Basturk O, VanWyk H, Tavares AM, Seenappa LM, Perry JR, Kheoh T, McNeil LK, Welkowsky E, DeMuth PC, Haqq CM, O'Reilly EM. Lymph-node-targeted, mKRAS-specific amphiphile vaccine in pancreatic and colorectal cancer: the phase 1 AMPLIFY-201 trial. Nat Med 2024; 30:531-542. [PMID: 38195752 PMCID: PMC10878978 DOI: 10.1038/s41591-023-02760-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/11/2023] [Indexed: 01/11/2024]
Abstract
Pancreatic and colorectal cancers are often KRAS mutated and are incurable when tumor DNA or protein persists or recurs after curative intent therapy. Cancer vaccine ELI-002 2P enhances lymph node delivery and immune response using amphiphile (Amph) modification of G12D and G12R mutant KRAS (mKRAS) peptides (Amph-Peptides-2P) together with CpG oligonucleotide adjuvant (Amph-CpG-7909). We treated 25 patients (20 pancreatic and five colorectal) who were positive for minimal residual mKRAS disease (ctDNA and/or serum tumor antigen) after locoregional treatment in a phase 1 study of fixed-dose Amph-Peptides-2P and ascending-dose Amph-CpG-7909; study enrollment is complete with patient follow-up ongoing. Primary endpoints included safety and recommended phase 2 dose (RP2D). The secondary endpoint was tumor biomarker response (longitudinal ctDNA or tumor antigen), with exploratory endpoints including immunogenicity and relapse-free survival (RFS). No dose-limiting toxicities were observed, and the RP2D was 10.0 mg of Amph-CpG-7909. Direct ex vivo mKRAS-specific T cell responses were observed in 21 of 25 patients (84%; 59% both CD4+ and CD8+); tumor biomarker responses were observed in 21 of 25 patients (84%); biomarker clearance was observed in six of 25 patients (24%; three pancreatic and three colorectal); and the median RFS was 16.33 months. Efficacy correlated with T cell responses above or below the median fold increase over baseline (12.75-fold): median tumor biomarker reduction was -76.0% versus -10.2% (P < 0.0014), and the median RFS was not reached versus 4.01 months (hazard ratio = 0.14; P = 0.0167). ELI-002 2P was safe and induced considerable T cell responses in patients with immunotherapy-recalcitrant KRAS-mutated tumors. ClinicalTrials.gov identifier: NCT04853017 .
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Affiliation(s)
- Shubham Pant
- The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Zev A Wainberg
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | - Alexis D Leal
- University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Olca Basturk
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
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10
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Meyer M, Parpoulas C, Barthélémy T, Becker JP, Charoentong P, Lyu Y, Börsig S, Bulbuc N, Tessmer C, Weinacht L, Ibberson D, Schmidt P, Pipkorn R, Eichmüller SB, Steinberger P, Lindner K, Poschke I, Platten M, Fröhling S, Riemer AB, Hassel JC, Roberti MP, Jäger D, Zörnig I, Momburg F. MediMer: a versatile do-it-yourself peptide-receptive MHC class I multimer platform for tumor neoantigen-specific T cell detection. Front Immunol 2024; 14:1294565. [PMID: 38239352 PMCID: PMC10794645 DOI: 10.3389/fimmu.2023.1294565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/28/2023] [Indexed: 01/22/2024] Open
Abstract
Peptide-loaded MHC class I (pMHC-I) multimers have revolutionized our capabilities to monitor disease-associated T cell responses with high sensitivity and specificity. To improve the discovery of T cell receptors (TCR) targeting neoantigens of individual tumor patients with recombinant MHC molecules, we developed a peptide-loadable MHC class I platform termed MediMer. MediMers are based on soluble disulfide-stabilized β2-microglobulin/heavy chain ectodomain single-chain dimers (dsSCD) that can be easily produced in large quantities in eukaryotic cells and tailored to individual patients' HLA allotypes with only little hands-on time. Upon transient expression in CHO-S cells together with ER-targeted BirA biotin ligase, biotinylated dsSCD are purified from the cell supernatant and are ready to use. We show that CHO-produced dsSCD are free of endogenous peptide ligands. Empty dsSCD from more than 30 different HLA-A,B,C allotypes, that were produced and validated so far, can be loaded with synthetic peptides matching the known binding criteria of the respective allotypes, and stored at low temperature without loss of binding activity. We demonstrate the usability of peptide-loaded dsSCD multimers for the detection of human antigen-specific T cells with comparable sensitivities as multimers generated with peptide-tethered β2m-HLA heavy chain single-chain trimers (SCT) and wild-type peptide-MHC-I complexes prior formed in small-scale refolding reactions. Using allotype-specific, fluorophore-labeled competitor peptides, we present a novel dsSCD-based peptide binding assay capable of interrogating large libraries of in silico predicted neoepitope peptides by flow cytometry in a high-throughput and rapid format. We discovered rare T cell populations with specificity for tumor neoepitopes and epitopes from shared tumor-associated antigens in peripheral blood of a melanoma patient including a so far unreported HLA-C*08:02-restricted NY-ESO-1-specific CD8+ T cell population. Two representative TCR of this T cell population, which could be of potential value for a broader spectrum of patients, were identified by dsSCD-guided single-cell sequencing and were validated by cognate pMHC-I multimer staining and functional responses to autologous peptide-pulsed antigen presenting cells. By deploying the technically accessible dsSCD MHC-I MediMer platform, we hope to significantly improve success rates for the discovery of personalized neoepitope-specific TCR in the future by being able to also cover rare HLA allotypes.
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Affiliation(s)
- Marten Meyer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Christina Parpoulas
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Titouan Barthélémy
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jonas P. Becker
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Pornpimol Charoentong
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- Center for Quantitative Analysis of Molecular and Cellular Biosystems (Bioquant), Heidelberg University, Heidelberg, Germany
| | - Yanhong Lyu
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Selina Börsig
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Nadja Bulbuc
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Tessmer
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
| | - Lisa Weinacht
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, Heidelberg University, Heidelberg, Germany
| | - Patrick Schmidt
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
- GMP and T Cell Therapy, DKFZ, Heidelberg, Germany
| | | | | | - Peter Steinberger
- Division of Immune Receptors and T Cell Activation, Center for Pathophysiology, Infectiology, Medical University of Vienna, Vienna, Austria
| | - Katharina Lindner
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Isabel Poschke
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
| | - Michael Platten
- Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, DKFZ, Heidelberg, Germany
- Immune Monitoring Unit, NCT Heidelberg and DKFZ, Heidelberg, Germany
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Department of Neurology, Medical Faculty Mannheim, Mannheim Center for Translational Neuroscience (MCTN), Heidelberg University, Mannheim, Germany
- DKFZ Hector Cancer Institute at the University Medical Center, Mannheim, Germany
- Helmholtz Institute for Translational Oncology, Mainz (HI-TRON Mainz), Mainz, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), DKFZ, Core Center, Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, Heidelberg, Germany
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Angelika B. Riemer
- Division of Immunotherapy and Immunoprevention, DKFZ, Heidelberg, Germany
- German Center for Infection Research (DZIF) Partner Site Heidelberg, Heidelberg, Germany
| | - Jessica C. Hassel
- Section of DermatoOncology, Department of Dermatology and NCT, Heidelberg University Hospital, Heidelberg, Germany
| | - Maria Paula Roberti
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Dirk Jäger
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Inka Zörnig
- Clinical Cooperation Unit Applied Tumor Immunity, DKFZ, Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
| | - Frank Momburg
- Antigen Presentation and T/NK Cell Activation Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg University Hospital, Heidelberg, Germany
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11
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Sun L, Wan AH, Yan S, Liu R, Li J, Zhou Z, Wu R, Chen D, Bu X, Ou J, Li K, Lu X, Wan G, Ke Z. A multidimensional platform of patient-derived tumors identifies drug susceptibilities for clinical lenvatinib resistance. Acta Pharm Sin B 2024; 14:223-240. [PMID: 38261805 PMCID: PMC10793100 DOI: 10.1016/j.apsb.2023.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 01/25/2024] Open
Abstract
Lenvatinib, a second-generation multi-receptor tyrosine kinase inhibitor approved by the FDA for first-line treatment of advanced liver cancer, facing limitations due to drug resistance. Here, we applied a multidimensional, high-throughput screening platform comprising patient-derived resistant liver tumor cells (PDCs), organoids (PDOs), and xenografts (PDXs) to identify drug susceptibilities for conquering lenvatinib resistance in clinically relevant settings. Expansion and passaging of PDCs and PDOs from resistant patient liver tumors retained functional fidelity to lenvatinib treatment, expediting drug repurposing screens. Pharmacological screening identified romidepsin, YM155, apitolisib, NVP-TAE684 and dasatinib as potential antitumor agents in lenvatinib-resistant PDC and PDO models. Notably, romidepsin treatment enhanced antitumor response in syngeneic mouse models by triggering immunogenic tumor cell death and blocking the EGFR signaling pathway. A combination of romidepsin and immunotherapy achieved robust and synergistic antitumor effects against lenvatinib resistance in humanized immunocompetent PDX models. Collectively, our findings suggest that patient-derived liver cancer models effectively recapitulate lenvatinib resistance observed in clinical settings and expedite drug discovery for advanced liver cancer, providing a feasible multidimensional platform for personalized medicine.
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Affiliation(s)
- Lei Sun
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Arabella H. Wan
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shijia Yan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ruonian Liu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiarui Li
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhuolong Zhou
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Ruirui Wu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Dongshi Chen
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xianzhang Bu
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jingxing Ou
- Department of Hepatic Surgery and Liver Transplantation Center, Third Affiliated Hospital, Organ Transplantation Institute, Sun Yat-sen University, Organ Transplantation Research Center of Guangdong Province, Guangdong Province Engineering Laboratory for Transplantation Medicine, Guangzhou 510630, China
- Guangdong Provincial Key Laboratory of Liver Disease Research, Guangzhou 510630, China
| | - Kai Li
- Department of Ultrasound, Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Xiongbin Lu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN 46202, USA
| | - Guohui Wan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (Cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zunfu Ke
- Department of Pathology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
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12
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [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] [Indexed: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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13
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Yossef R, Krishna S, Sindiri S, Lowery FJ, Copeland AR, Gartner JJ, Parkhurst MR, Parikh NB, Hitscherich KJ, Levi ST, Chatani PD, Zacharakis N, Levin N, Vale NR, Nah SK, Dinerman A, Hill VK, Ray S, Bera A, Levy L, Jia L, Kelly MC, Goff SL, Robbins PF, Rosenberg SA. Phenotypic signatures of circulating neoantigen-reactive CD8 + T cells in patients with metastatic cancers. Cancer Cell 2023; 41:2154-2165.e5. [PMID: 38039963 PMCID: PMC10843665 DOI: 10.1016/j.ccell.2023.11.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 08/07/2023] [Accepted: 11/07/2023] [Indexed: 12/03/2023]
Abstract
Circulating T cells from peripheral blood (PBL) can provide a rich and noninvasive source for antitumor T cells. By single-cell transcriptomic profiling of 36 neoantigen-specific T cell clones from 6 metastatic cancer patients, we report the transcriptional and cell surface signatures of antitumor PBL-derived CD8+ T cells (NeoTCRPBL). Comparison of tumor-infiltrating lymphocyte (TIL)- and PBL-neoantigen-specific T cells revealed that NeoTCRPBL T cells are low in frequency and display less-dysfunctional memory phenotypes relative to their TIL counterparts. Analysis of 100 antitumor TCR clonotypes indicates that most NeoTCRPBL populations target the same neoantigens as TILs. However, NeoTCRPBL TCR repertoire is only partially shared with TIL. Prediction and testing of NeoTCRPBL signature-derived TCRs from PBL of 6 prospective patients demonstrate high enrichment of clonotypes targeting tumor mutations, a viral oncogene, and patient-derived tumor. Thus, the NeoTCRPBL signature provides an alternative source for identifying antitumor T cells from PBL of cancer patients, enabling immune monitoring and immunotherapies.
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Affiliation(s)
- Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aaron Dinerman
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lior Levy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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14
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Klebanoff CA, Chandran SS, Baker BM, Quezada SA, Ribas A. T cell receptor therapeutics: immunological targeting of the intracellular cancer proteome. Nat Rev Drug Discov 2023; 22:996-1017. [PMID: 37891435 PMCID: PMC10947610 DOI: 10.1038/s41573-023-00809-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2023] [Indexed: 10/29/2023]
Abstract
The T cell receptor (TCR) complex is a naturally occurring antigen sensor that detects, amplifies and coordinates cellular immune responses to epitopes derived from cell surface and intracellular proteins. Thus, TCRs enable the targeting of proteins selectively expressed by cancer cells, including neoantigens, cancer germline antigens and viral oncoproteins. As such, TCRs have provided the basis for an emerging class of oncology therapeutics. Herein, we review the current cancer treatment landscape using TCRs and TCR-like molecules. This includes adoptive cell transfer of T cells expressing endogenous or engineered TCRs, TCR bispecific engagers and antibodies specific for human leukocyte antigen (HLA)-bound peptides (TCR mimics). We discuss the unique complexities associated with the clinical development of these therapeutics, such as HLA restriction, TCR retrieval, potency assessment and the potential for cross-reactivity. In addition, we highlight emerging clinical data that establish the antitumour potential of TCR-based therapies, including tumour-infiltrating lymphocytes, for the treatment of diverse human malignancies. Finally, we explore the future of TCR therapeutics, including emerging genome editing methods to safely enhance potency and strategies to streamline patient identification.
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Affiliation(s)
- Christopher A Klebanoff
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA.
| | - Smita S Chandran
- Memorial Sloan Kettering Cancer Center (MSKCC), Human Oncology and Pathogenesis Program, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
- Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, ID, USA
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, ID, USA
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Achilles Therapeutics, London, UK
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles (UCLA), Los Angeles, CA, USA
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15
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Pang Z, Lu MM, Zhang Y, Gao Y, Bai JJ, Gu JY, Xie L, Wu WZ. Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges. Biomark Res 2023; 11:104. [PMID: 38037114 PMCID: PMC10690996 DOI: 10.1186/s40364-023-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Adoptive cell therapy using T cell receptor-engineered T cells (TCR-T) is a promising approach for cancer therapy with an expectation of no significant side effects. In the human body, mature T cells are armed with an incredible diversity of T cell receptors (TCRs) that theoretically react to the variety of random mutations generated by tumor cells. The outcomes, however, of current clinical trials using TCR-T cell therapies are not very successful especially involving solid tumors. The therapy still faces numerous challenges in the efficient screening of tumor-specific antigens and their cognate TCRs. In this review, we first introduce TCR structure-based antigen recognition and signaling, then describe recent advances in neoantigens and their specific TCR screening technologies, and finally summarize ongoing clinical trials of TCR-T therapies against neoantigens. More importantly, we also present the current challenges of TCR-T cell-based immunotherapies, e.g., the safety of viral vectors, the mismatch of T cell receptor, the impediment of suppressive tumor microenvironment. Finally, we highlight new insights and directions for personalized TCR-T therapy.
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Affiliation(s)
- Zhi Pang
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Man-Man Lu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yu Zhang
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan Gao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Jin-Jin Bai
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jian-Ying Gu
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lu Xie
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
| | - Wei-Zhong Wu
- Liver Cancer Institute, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Clinical Center for Biotherapy, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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16
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Drake KA, Talantov D, Tong GJ, Lin JT, Verheijden S, Katz S, Leung JM, Yuen B, Krishna V, Wu MJ, Sutherland AM, Short SA, Kheradpour P, Mumbach MR, Franz KM, Trifonov V, Lucas MV, Merson J, Kim CC. Multi-omic profiling reveals early immunological indicators for identifying COVID-19 Progressors. Clin Immunol 2023; 256:109808. [PMID: 37852344 DOI: 10.1016/j.clim.2023.109808] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/25/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
We sought to better understand the immune response during the immediate post-diagnosis phase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by identifying molecular associations with longitudinal disease outcomes. Multi-omic analyses identified differences in immune cell composition, cytokine levels, and cell subset-specific transcriptomic and epigenomic signatures between individuals on a more serious disease trajectory (Progressors) as compared to those on a milder course (Non-progressors). Higher levels of multiple cytokines were observed in Progressors, with IL-6 showing the largest difference. Blood monocyte cell subsets were also skewed, showing a comparative decrease in non-classical CD14-CD16+ and intermediate CD14+CD16+ monocytes. In lymphocytes, the CD8+ T effector memory cells displayed a gene expression signature consistent with stronger T cell activation in Progressors. These early stage observations could serve as the basis for the development of prognostic biomarkers of disease risk and interventional strategies to improve the management of severe COVID-19. BACKGROUND: Much of the literature on immune response post-SARS-CoV-2 infection has been in the acute and post-acute phases of infection. TRANSLATIONAL SIGNIFICANCE: We found differences at early time points of infection in approximately 160 participants. We compared multi-omic signatures in immune cells between individuals progressing to needing more significant medical intervention and non-progressors. We observed widespread evidence of a state of increased inflammation associated with progression, supported by a range of epigenomic, transcriptomic, and proteomic signatures. The signatures we identified support other findings at later time points and serve as the basis for prognostic biomarker development or to inform interventional strategies.
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Affiliation(s)
- Katherine A Drake
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Dimitri Talantov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Gary J Tong
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Jack T Lin
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Samuel Katz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Benjamin Yuen
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vinod Krishna
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Michelle J Wu
- Verily Life Sciences, South San Francisco, CA, United States of America
| | | | - Sarah A Short
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Pouya Kheradpour
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Maxwell R Mumbach
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Kate M Franz
- Verily Life Sciences, South San Francisco, CA, United States of America
| | - Vladimir Trifonov
- Janssen Research & Development, LLC, San Diego, CA, United States of America
| | - Molly V Lucas
- Janssen Research & Development, LLC, NJ, United States of America
| | - James Merson
- Janssen Research & Development, LLC, San Francisco, CA, United States of America
| | - Charles C Kim
- Verily Life Sciences, South San Francisco, CA, United States of America.
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17
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Chen G, Kong D, Lin Y. Neo-Antigen-Reactive T Cells Immunotherapy for Colorectal Cancer: A More Personalized Cancer Therapy Approach. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2200186. [PMID: 37970536 PMCID: PMC10632666 DOI: 10.1002/gch2.202200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/09/2023] [Indexed: 11/17/2023]
Abstract
Colorectal cancer (CRC) is the second most common malignancy in women and the third most frequent cancer in men. Evidence has revealed that the survival of patients with metastatic CRC is very low, between one and three years. Neoantigens are known proteins encoded by mutations in tumor cells. It is theorized that recognizing neoantigens by T cells leads to T cell activation and further antitumor responses. Neoantigen-reactive T cells (NRTs) are designed against the mentioned neoantigens expressed by tumor cells. NRTs selectively kill tumor cells without damage to non-cancerous cells. Identifying patient-specific and high immunogen neoantigens is important in NRT immunotherapy of patients with CRC. However, the main challenges are the side effects and preparation of NRTs, as well as the effectiveness of these cells in vivo. This review summarized the properties of neoantigens as well as the preparation and therapeutic outcomes of NRTs for the treatment of CRC.
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Affiliation(s)
- Guan‐Liang Chen
- Department of Gastroenterology SurgeryAffiliated Hospital of Shaoxing UniversityShaoxing312000China
| | - De‐Xia Kong
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
| | - Yan Lin
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
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18
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Ye Y, Shen Y, Wang J, Li D, Zhu Y, Zhao Z, Pan Y, Wang Y, Liu X, Wan J. SIGANEO: Similarity network with GAN enhancement for immunogenic neoepitope prediction. Comput Struct Biotechnol J 2023; 21:5538-5543. [PMID: 38034402 PMCID: PMC10681954 DOI: 10.1016/j.csbj.2023.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/02/2023] Open
Abstract
Target selection of the personalized cancer neoantigen vaccine, which is highly dependent on computational prediction algorithms, is crucial for its clinical efficacy. Due to the limited number of experimentally validated immunogenic neoepitopes as well as the complexity of neoantigens in eliciting T cell response, the accuracy of neoepitope immunogenicity prediction methods requires persistent efforts for improvement. We present a deep learning framework for neoepitope immunogenicity prediction - SIGANEO by integrating GAN-like network with similarity network to address issues of missing values and limited data concerning neoantigen prediction. This framework exhibits superior performance over competing machine-learning-based neoantigen prediction algorithms over an independent test dataset from TESLA consortium. Particularly for the clinical setting of neoantigen vaccine where only the top 10 and 20 predictions are selected for vaccine production, SIGANEO achieves significantly better accuracy for predicting experimentally validated neoepitopes. Our work demonstrates that deep learning techniques can greatly boost the accuracy of target identification for cancer neoantigen vaccine.
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Affiliation(s)
- Yilin Ye
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yiming Shen
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Jian Wang
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Dong Li
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yu Zhu
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Zhao Zhao
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Youdong Pan
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Yi Wang
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
| | - Xing Liu
- The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ji Wan
- Shenzhen Neocura Biotechnology Co. Ltd., Shenzhen 518055, China
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19
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Jayaraman S, Montagne JM, Nirschl TR, Marcisak E, Johnson J, Huff A, Hsiao MH, Nauroth J, Heumann T, Zarif JC, Jaffee EM, Azad N, Fertig EJ, Zaidi N, Larman HB. Barcoding intracellular reverse transcription enables high-throughput phenotype-coupled T cell receptor analyses. CELL REPORTS METHODS 2023; 3:100600. [PMID: 37776855 PMCID: PMC10626196 DOI: 10.1016/j.crmeth.2023.100600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/23/2023] [Accepted: 09/07/2023] [Indexed: 10/02/2023]
Abstract
Assays linking cellular phenotypes with T cell or B cell antigen receptor sequences are crucial for characterizing adaptive immune responses. Existing methodologies are limited by low sample throughput and high cost. Here, we present INtraCEllular Reverse Transcription with Sorting and sequencing (INCERTS), an approach that combines molecular indexing of receptor repertoires within intact cells and fluorescence-activated cell sorting (FACS). We demonstrate that INCERTS enables efficient processing of millions of cells from pooled human peripheral blood mononuclear cell (PBMC) samples while retaining robust association between T cell receptor (TCR) sequences and cellular phenotypes. We used INCERTS to discover antigen-specific TCRs from patients with cancer immunized with a novel mutant KRAS peptide vaccine. After ex vivo stimulation, 28 uniquely barcoded samples were pooled prior to FACS into peptide-reactive and non-reactive CD4+ and CD8+ populations. Combining complementary patient-matched single-cell RNA sequencing (scRNA-seq) data enabled retrieval of full-length, paired TCR alpha and beta chain sequences for future validation of therapeutic utility.
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Affiliation(s)
- Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Janelle M Montagne
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas R Nirschl
- Pathobiology Graduate Program, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Emily Marcisak
- Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jeanette Johnson
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Immunology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amanda Huff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Julie Nauroth
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thatcher Heumann
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Hematology Oncology, Vanderbilt-Ingram Comprehensive Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jelani C Zarif
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins Medicine Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21205, USA
| | - Elizabeth M Jaffee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nilo Azad
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Division of Quantitative Sciences, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Neeha Zaidi
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Convergence Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg Kimmel Immunology Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA.
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20
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Lu D, Chen Y, Jiang M, Wang J, Li Y, Ma K, Sun W, Zheng X, Qi J, Jin W, Chen Y, Chai Y, Zhang CWH, Liang H, Tan S, Gao GF. KRAS G12V neoantigen specific T cell receptor for adoptive T cell therapy against tumors. Nat Commun 2023; 14:6389. [PMID: 37828002 PMCID: PMC10570350 DOI: 10.1038/s41467-023-42010-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 09/27/2023] [Indexed: 10/14/2023] Open
Abstract
KRAS mutations are broadly recognized as promising targets for tumor therapy. T cell receptors (TCRs) can specifically recognize KRAS mutant neoantigens presented by human lymphocyte antigen (HLA) and mediate T cell responses to eliminate tumor cells. In the present study, we identify two TCRs specific for the 9-mer KRAS-G12V mutant neoantigen in the context of HLA-A*11:01. The TCR-T cells are constructed and display cytokine secretion and cytotoxicity upon co-culturing with varied tumor cells expressing the KRAS-G12V mutation. Moreover, 1-2C TCR-T cells show anti-tumor activity in preclinical models in female mice. The 9-mer KRAS-G12V mutant peptide exhibits a distinct conformation from the 9-mer wildtype peptide and its 10-mer counterparts. Specific recognition of the G12V mutant by TCR depends both on distinct conformation from wildtype peptide and on direct interaction with residues from TCRs. Our study reveals the mechanisms of presentation and TCR recognition of KRAS-G12V mutant peptide and describes TCRs with therapeutic potency for tumor immunotherapy.
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Affiliation(s)
- Dan Lu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Department of Immunology, Beijing Children's Hospital, Capital Medical University, National Centre for Children's Health, Beijing, China
| | - Yuan Chen
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, China
| | - Min Jiang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Yiting Li
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Keke Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China
| | - Wenqiao Sun
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xing Zheng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenjing Jin
- YKimmu (Beijing) Biotechnology Co., Ltd, Beijing, China
| | - Yu Chen
- YKimmu (Beijing) Biotechnology Co., Ltd, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | | | - Hao Liang
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, China
| | - Shuguang Tan
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Shenzhen Children's Hospital, Shenzhen, Guangdong, China.
- Beijing Life Science Academy, Beijing, China.
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China.
- Beijing Life Science Academy, Beijing, China.
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21
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Zhang Z, Chen X, Li B, Xia T, Wu X, Wu C. Helicobacter pylori induces urease subunit B-specific CD8 + T cell responses in infected individuals via cytosolic pathway of cross-presentation. Helicobacter 2023; 28:e13005. [PMID: 37382428 DOI: 10.1111/hel.13005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/04/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Urease subunit B (UreB), a conserved and key virulence factor of Helicobacter pylori (H. pylori), can induce the host CD4+ T cell immune responses to provide protection, but less is known regarding CD8+ T cell responses. The characteristics of H. pylori-specific CD8+ T cell responses and the mechanism underlying antigen processing and presentation pathways remain unclear. This study was focus on protective antigen recombinant UreB (rUreb) to detect specific CD8+ T cell responses in vitro and elucidate the mechanism of UreB antigen processing and presentation. METHODS The peripheral blood mononuclear cells (PBMCs) collected from H. pylori-infected individuals were stimulated with rUreB in vitro to detect specific CD8+ T cell responses after co-culture with rUreB-pulsed autologous hMDCs. Through blocking assay, we investigated the potential pathway of UreB antigen processing and presentation via the cytosolic pathway or vacuolar pathway. The cytokines production of UreB specific CD8+ T cell were evaluated as well. RESULTS We demonstrated UreB can induce specific CD8+ T cell immune responses in H. pylori infected individuals. Importantly, we characterized that UreB were mainly processed by proteasome instead of lysosomal proteases and presented through cytosolic pathway of cross-presentation, which requires endoplasmic reticulum-Golgi transport and newly synthesized MHC-I molecules, to induce functional-specific CD8+ T cell (IFN-γ + TNF-α + Grz A+ Grz B+) responses. CONCLUSIONS These results suggest that H. pylori UreB induces specific CD8+ T cell responses through cytosolic pathway of cross-presentation in infected individuals.
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Affiliation(s)
- Zelin Zhang
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xingchi Chen
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Bin Li
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Tingting Xia
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiaobin Wu
- Department of Gastrointestinal Surgery, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Chao Wu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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22
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Hall MS, Teer JK, Yu X, Branthoover H, Snedal S, Rodriguez-Valentin M, Nagle L, Scott E, Schachner B, Innamarato P, Hall AM, Blauvelt J, Rich CJ, Richards AD, Ceccarelli J, Langer TJ, Yoder SJ, Beatty MS, Cox CA, Messina JL, Abate-Daga D, Mule JJ, Mullinax JE, Sarnaik AA, Pilon-Thomas S. Neoantigen-specific CD4 + tumor-infiltrating lymphocytes are potent effectors identified within adoptive cell therapy products for metastatic melanoma patients. J Immunother Cancer 2023; 11:e007288. [PMID: 37802604 PMCID: PMC10565316 DOI: 10.1136/jitc-2023-007288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/13/2023] [Indexed: 10/10/2023] Open
Abstract
BACKGROUND Adoptive cell therapy (ACT) with tumor-infiltrating lymphocytes (TILs) is a promising immunotherapeutic approach for patients with advanced solid tumors. While numerous advances have been made, the contribution of neoantigen-specific CD4+T cells within TIL infusion products remains underexplored and therefore offers a significant opportunity for progress. METHODS We analyzed infused TIL products from metastatic melanoma patients previously treated with ACT for the presence of neoantigen-specific T cells. TILs were enriched on reactivity to neoantigen peptides derived and prioritized from patient sample-directed mutanome analysis. Enriched TILs were further investigated to establish the clonal neoantigen response with respect to function, transcriptomics, and persistence following ACT. RESULTS We discovered that neoantigen-specific TIL clones were predominantly CD4+ T cells and were present in both therapeutic responders and non-responders. CD4+ TIL demonstrated an effector T cell response with cytotoxicity toward autologous tumor in a major histocompatibility complex class II-dependent manner. These results were validated by paired TCR and single cell RNA sequencing, which elucidated transcriptomic profiles distinct to neoantigen-specific CD4+ TIL. CONCLUSIONS Despite methods which often focus on CD8+T cells, our study supports the importance of prospective identification of neoantigen-specific CD4+ T cells within TIL products as they are a potent source of tumor-specific effectors. We further advocate for the inclusion of neoantigen-specific CD4+ TIL in future ACT protocols as a strategy to improve antitumor immunity.
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Affiliation(s)
- MacLean S Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Cancer Biology PhD Program, University of South Florida, Tampa, Florida, USA
| | - Jamie K Teer
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Holly Branthoover
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Sebastian Snedal
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - Luz Nagle
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ellen Scott
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Ben Schachner
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Patrick Innamarato
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Amy M Hall
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jamie Blauvelt
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Carolyn J Rich
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Allison D Richards
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | | | - T J Langer
- Turnstone Biologics, Inc, San Diego, California, USA
| | - Sean J Yoder
- Molecular Genomics Core, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Matthew S Beatty
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Cheryl A Cox
- Cell Therapies Core Facility, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Jane L Messina
- Department of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Daniel Abate-Daga
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - James J Mule
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - John E Mullinax
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Sarcoma, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Amod A Sarnaik
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
- Department of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Shari Pilon-Thomas
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
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23
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O'Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. J Immunother Cancer 2023; 11:e006889. [PMID: 37775115 PMCID: PMC10546156 DOI: 10.1136/jitc-2023-006889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2023] [Indexed: 10/01/2023] Open
Abstract
BACKGROUND Certain phosphorylated peptides are differentially presented by major histocompatibility complex (MHC) molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their non-phosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, HLA-A*11:01, HLA-C*07:01, and HLA-C*07:02. METHODS We isolated peptide-MHC complexes by immunoprecipitation from 11 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics data sets to assemble a curated set of phosphopeptides presented by 96 samples spanning 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. RESULTS We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their non-phosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B-pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and HLA-A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the non-phosphorylated peptide was co-presented, HLA-A*03:01 or HLA-C*07:01 phosphopeptides were repeatedly non-immunogenic, requiring use of allogeneic T cells to induce phosphopeptide-specific T cells. CONCLUSIONS Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Martin G Klatt
- Department of Hematology, Oncology and Tumor Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany
- German Cancer Research Center, Heidelberg, Baden-Württemberg, Germany
- Berlin Institute of Health at Charité -Universitätsmedizin Berlin, BIH Biomedical 13 Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Jessica Urraca
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - David A Scheinberg
- Department of Pediatrics, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Weill Cornell Medicine, New York, New York, USA
| | - Richard J O'Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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24
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Brightman SE, Becker A, Thota RR, Naradikian MS, Chihab L, Zavala KS, Ramamoorthy Premlal AL, Griswold RQ, Dolina JS, Cohen EEW, Miller AM, Peters B, Schoenberger SP. Neoantigen-specific stem cell memory-like CD4 + T cells mediate CD8 + T cell-dependent immunotherapy of MHC class II-negative solid tumors. Nat Immunol 2023; 24:1345-1357. [PMID: 37400675 PMCID: PMC10382322 DOI: 10.1038/s41590-023-01543-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023]
Abstract
CD4+ T cells play key roles in a range of immune responses, either as direct effectors or through accessory cells, including CD8+ T lymphocytes. In cancer, neoantigen (NeoAg)-specific CD8+ T cells capable of direct tumor recognition have been extensively studied, whereas the role of NeoAg-specific CD4+ T cells is less well understood. We have characterized the murine CD4+ T cell response against a validated NeoAg (CLTCH129>Q) expressed by the MHC-II-deficient squamous cell carcinoma tumor model (SCC VII) at the level of single T cell receptor (TCR) clonotypes and in the setting of adoptive immunotherapy. We find that the natural CLTCH129>Q-specific repertoire is diverse and contains TCRs with distinct avidities as measured by tetramer-binding assays and CD4 dependence. Despite these differences, CD4+ T cells expressing high or moderate avidity TCRs undergo comparable in vivo proliferation to cross-presented antigen from growing tumors and drive similar levels of therapeutic immunity that is dependent on CD8+ T cells and CD40L signaling. Adoptive cellular therapy (ACT) with NeoAg-specific CD4+ T cells is most effective when TCR-engineered cells are differentiated ex vivo with IL-7 and IL-15 rather than IL-2 and this was associated with both increased expansion as well as the acquisition and stable maintenance of a T stem cell memory (TSCM)-like phenotype in tumor-draining lymph nodes (tdLNs). ACT with TSCM-like CD4+ T cells results in lower PD-1 expression by CD8+ T cells in the tumor microenvironment and an increased frequency of PD-1+CD8+ T cells in tdLNs. These findings illuminate the role of NeoAg-specific CD4+ T cells in mediating antitumor immunity via providing help to CD8+ T cells and highlight their therapeutic potential in ACT.
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Affiliation(s)
- Spencer E Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angelica Becker
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Rukman R Thota
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Martin S Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Leila Chihab
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Karla Soria Zavala
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Ryan Q Griswold
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joseph S Dolina
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ezra E W Cohen
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Aaron M Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stephen P Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA.
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25
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Koya T, Yoshida K, Togi M, Niida Y, Togi S, Ura H, Mizuta S, Kato T, Yamada S, Shibata T, Liu YC, Yuan SS, Wu DC, Kobayashi H, Utsugisawa T, Kanno H, Shimodaira S. Clinical Trial on the Safety and Tolerability of Personalized Cancer Vaccines Using Human Platelet Lysate-Induced Antigen-Presenting Cells. Cancers (Basel) 2023; 15:3627. [PMID: 37509288 PMCID: PMC10377585 DOI: 10.3390/cancers15143627] [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: 05/27/2023] [Revised: 06/27/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Research and development of personalized cancer vaccines as precision medicine are ongoing. We predicted human leukocyte antigen (HLA)-compatible cancer antigen candidate peptides based on patient-specific cancer genomic profiles and performed a Phase I clinical trial for the safety and tolerability of cancer vaccines with human platelet lysate-induced antigen-presenting cells (HPL-APCs) from peripheral monocytes. Among the five enrolled patients, two patients completed six doses per course (2-3 × 107 cells per dose), and an interim analysis was performed based on the immune response. An immune response was detected by enzyme-linked immunosorbent spot (ELISpot) assays to HLA-A*33:03-matched KRASWT, HLA-DRB1*09:01-compliant KRASWT or G12D, or HLA-A*31:01-matched SMAD4WT, and HLA-DRB1*04:01-matched SMAD4G365D peptides in two completed cases, respectively. Moreover, SMAD4WT-specific CD8+ effector memory T cells were amplified. However, an attenuation of the acquired immune response was observed 6 months after one course of cancer vaccination as the disease progressed. This study confirmed the safety and tolerability of HPL-APCs in advanced and recurrent cancers refractory to standard therapy and is the first clinical report to demonstrate the immunoinducibility of personalized cancer vaccines using HPL-APCs. Phase II clinical trials to determine immune responses with optimized adjuvant drugs and continued administration are expected to demonstrate efficacy.
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Affiliation(s)
- Terutsugu Koya
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Kenichi Yoshida
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Misa Togi
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
| | - Yo Niida
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Sumihito Togi
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Hiroki Ura
- Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Shuichi Mizuta
- Department of Hematology and Immunology, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Tomohisa Kato
- Division of Stem Cell Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Sohsuke Yamada
- Department of Pathology and Laboratory Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Takeo Shibata
- Department of Obstetrics and Gynecology, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
| | - Yi-Chang Liu
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyng-Shiou Yuan
- Office of Research & Development, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Deng-Chyang Wu
- Internal Medicine, School of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hirohito Kobayashi
- Division of Transfusion and Cell Therapy, Tokyo Women's Medical University, Adachi Medical Center, Adachi 123-8558, Tokyo, Japan
| | - Taiju Utsugisawa
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
| | - Hitoshi Kanno
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
| | - Shigetaka Shimodaira
- Department of Regenerative Medicine, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Center for Regenerative Medicine, Kanazawa Medical University Hospital, Kahoku 920-0293, Ishikawa, Japan
- Division of Stem Cell Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University, Kahoku 920-0293, Ishikawa, Japan
- Department of Transfusion Medicine and Cell Processing, Tokyo Women's Medical University, Shinjuku 162-8666, Tokyo, Japan
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26
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Li D, Chen C, Li J, Yue J, Ding Y, Wang H, Liang Z, Zhang L, Qiu S, Liu G, Gao Y, Huang Y, Li D, Zhang R, Liu W, Wen X, Li B, Zhang X, Zhang X, Xu RH. A pilot study of lymphodepletion intensity for peripheral blood mononuclear cell-derived neoantigen-specific CD8 + T cell therapy in patients with advanced solid tumors. Nat Commun 2023; 14:3447. [PMID: 37301885 PMCID: PMC10257664 DOI: 10.1038/s41467-023-39225-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Currently, the optimal lymphodepletion intensity for peripheral blood mononuclear cell-derived neoantigen-specific CD8 + T cell (Neo-T) therapy has yet to be determined. We report a single-arm, open-label and non-randomized phase 1 study (NCT02959905) of Neo-T therapy with lymphodepletion at various dose intensity in patients with locally advanced or metastatic solid tumors that are refractory to standard therapies. The primary end point is safety and the secondary end points are disease control rate (DCR), progression-free survival (PFS), overall survival (OS). Results show that the treatment is well tolerated with lymphopenia being the most common adverse event in the highest-intensity lymphodepletion groups. Neo-T infusion-related adverse events are only grade 1-2 in the no lymphodepletion group. The median PFS is 7.1 months (95% CI:3.7-9.8), the median OS is 16.8 months (95% CI: 11.9-31.7), and the DCR is 66.7% (6/9) among all groups. Three patients achieve partial response, two of them are in the no lymphodepletion group. In the group without lymphodepletion pretreatment, one patient refractory to prior anti-PD1 therapy shows partial response to Neo-T therapy. Neoantigen specific TCRs are examined in two patients and show delayed expansion after lymphodepletion treatment. In summary, Neo-T therapy without lymphodepletion could be a safe and promising regimen for advanced solid tumors.
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Affiliation(s)
- Dandan Li
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Thoracic Surgery, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, 518035, China
| | - Jingjing Li
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China
| | | | - Ya Ding
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China
| | | | | | - Le Zhang
- BGI-Shenzhen, Shenzhen, 518083, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Si Qiu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Geng Liu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Gao
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Dongli Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Rong Zhang
- Department of Radiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Liu
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China
| | - Xizhi Wen
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China
| | - Bo Li
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xiaoshi Zhang
- Biotherapy Center, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China.
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China.
| | - Xi Zhang
- BGI-Shenzhen, Shenzhen, 518083, China.
| | - Rui-Hua Xu
- State Key Laboratory of Oncology in South China, 510060, Guangzhou, China.
- Collaborative Innovation Center for Cancer Medicine, 510060, Guangzhou, China.
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, 510060, Guangzhou, China.
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27
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Brown TJ, Reiss KA, O'Hara MH. Advancements in Systemic Therapy for Pancreatic Cancer. Am Soc Clin Oncol Educ Book 2023; 43:e397082. [PMID: 37192430 DOI: 10.1200/edbk_397082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Outcomes for patients with advanced pancreatic cancer have improved in the past 12 years, mainly because of progress made in systemic therapies. New treatment strategies for advanced pancreatic cancer include switch maintenance with cytotoxic therapies, induction maintenance, and the utilization of targeted agents for patients with actionable variants, as well as ongoing development of cytotoxic regimens, such as NALIRIFOX. The activity of immunotherapy has been disappointing to date, but novel combinations and identifying appropriate patient populations may further unlock its potential.
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Affiliation(s)
- Timothy J Brown
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA
| | - Kim A Reiss
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA
| | - Mark H O'Hara
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA
- Penn Center for Cancer Care Innovation, University of Pennsylvania, Philadelphia, PA
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28
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Millar DG, Yang SYC, Sayad A, Zhao Q, Nguyen LT, Warner K, Sangster AG, Nakatsugawa M, Murata K, Wang BX, Shaw P, Clarke B, Bernardini MQ, Pugh T, Thibault P, Hirano N, Perreault C, Ohashi PS. Identification of antigenic epitopes recognized by tumor infiltrating lymphocytes in high grade serous ovarian cancer by multi-omics profiling of the auto-antigen repertoire. Cancer Immunol Immunother 2023:10.1007/s00262-023-03413-7. [PMID: 36943460 DOI: 10.1007/s00262-023-03413-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Immunotherapeutic strategies aimed at enhancing tumor cell killing by tumor-specific T cells hold great potential for reducing tumor burden and prolonging survival of cancer patients. Although many potential tumor antigens have been described, identifying relevant targets when designing anti-cancer vaccines or targeted cell therapies remains a challenge. To identify novel, potentially immunogenic candidate tumor antigens, we performed integrated tumor transcriptomic, seromic, and proteomic analyses of high grade serous ovarian cancer (HGSC) patient tumor samples. We identified tumor neo-antigens and over-expressed antigens using whole exome and RNA sequencing and examined these in relation to patient-matched auto-antibody repertoires. Focusing on MHC class I epitopes recognized by CD8+ T cells, HLA-binding epitopes were identified or predicted from the highly expressed, mutated, or auto-antibody target antigen, or MHC-associated peptides (MAPs). Recognition of candidate antigenic peptides was assessed within the tumor-infiltrating T lymphocyte (TIL) population expanded from each patient. Known tumor-associated antigens (TAA) and cancer/testis antigens (CTA) were commonly found in the auto-antibody and MAP repertoires and CD8+ TILs recognizing epitopes from these antigens were detected, although neither expression level nor the presence of auto-antibodies correlated with TIL recognition. Auto-antibodies against tumor-mutated antigens were found in most patients, however, no TIL recognition of the highest predicted affinity neo-epitopes was detected. Using high expression level, auto-antibody recognition, and epitope prediction algorithms, we identified epitopes in 5 novel antigens (MOB1A, SOCS3, TUBB, PRKAR1A, CCDC6) recognized by HGSC patient TILs. Furthermore, selection of epitopes from the MAP repertoire identified 5 additional targets commonly recognized by multiple patient TILs. We find that the repertoire of TIL specificities includes recognition of highly expressed and immunogenic self-antigens that are processed and presented by tumors. These results indicate an ongoing autoimmune response against a range of self-antigens targeted by HGSC TILs.
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Affiliation(s)
- Douglas G Millar
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - S Y Cindy Yang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Azin Sayad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Qingchuan Zhao
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Linh T Nguyen
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kathrin Warner
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ami G Sangster
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Munehide Nakatsugawa
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Kenji Murata
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Ben X Wang
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Patricia Shaw
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Blaise Clarke
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Marcus Q Bernardini
- Division of Gynecologic Oncology, Cancer Clinical Research Unit (CCRU), Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Trevor Pugh
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Naoto Hirano
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Claude Perreault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
| | - Pamela S Ohashi
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada.
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
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29
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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30
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Molvi Z, Klatt MG, Dao T, Urraca J, Scheinberg DA, O’Reilly RJ. The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.08.527552. [PMID: 36798179 PMCID: PMC9934604 DOI: 10.1101/2023.02.08.527552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Background Certain phosphorylated peptides are differentially presented by MHC molecules on cancer cells characterized by aberrant phosphorylation. Phosphopeptides presented in complex with the human leukocyte antigen HLA-A*02:01 provide a stability advantage over their nonphosphorylated counterparts. This stability is thought to contribute to enhanced immunogenicity. Whether tumor-associated phosphopeptides presented by other common alleles exhibit immunogenicity and structural characteristics similar to those presented by A*02:01 is unclear. Therefore, we determined the identity, structural features, and immunogenicity of phosphopeptides presented by the prevalent alleles HLA-A*03:01, -A*11:01, -C*07:01, and - C*07:02. Methods We isolated peptide-MHC complexes by immunoprecipitation from 10 healthy and neoplastic tissue samples using mass spectrometry, and then combined the resulting data with public immunopeptidomics datasets to assemble a curated set of phosphopeptides presented by 20 distinct healthy and neoplastic tissue types. We determined the biochemical features of selected phosphopeptides by in vitro binding assays and in silico docking, and their immunogenicity by analyzing healthy donor T cells for phosphopeptide-specific multimer binding and cytokine production. Results We identified a subset of phosphopeptides presented by HLA-A*03:01, A*11:01, C*07:01 and C*07:02 on multiple tumor types, particularly lymphomas and leukemias, but not healthy tissues. These phosphopeptides are products of genes essential to lymphoma and leukemia survival. The presented phosphopeptides generally exhibited similar or worse binding to A*03:01 than their nonphosphorylated counterparts. HLA-C*07:01 generally presented phosphopeptides but not their unmodified counterparts. Phosphopeptide binding to HLA-C*07:01 was dependent on B- pocket interactions that were absent in HLA-C*07:02. While HLA-A*02:01 and -A*11:01 phosphopeptide-specific T cells could be readily detected in an autologous setting even when the nonphosphorylated peptide was co-presented, HLA-A*03:01 or -C*07:01 phosphopeptides were repeatedly nonimmunogenic, requiring use of allogeneic T cells to induce phosphopeptide- specific T cells. Conclusions Phosphopeptides presented by multiple alleles that are differentially expressed on tumors constitute tumor-specific antigens that could be targeted for cancer immunotherapy, but the immunogenicity of such phosphopeptides is not a general feature. In particular, phosphopeptides presented by HLA-A*02:01 and A*11:01 exhibit consistent immunogenicity, while phosphopeptides presented by HLA-A*03:01 and C*07:01, although appropriately presented, are not immunogenic. Thus, to address an expanded patient population, phosphopeptide-targeted immunotherapies should be wary of allele-specific differences. What is already known on this topic - Phosphorylated peptides presented by the common HLA alleles A*02:01 and B*07:02 are differentially expressed by multiple tumor types, exhibit structural fitness due to phosphorylation, and are targets of healthy donor T cell surveillance, but it is not clear, however, whether such features apply to phosphopeptides presented by other common HLA alleles. What this study adds - We investigated the tumor presentation, binding, structural features, and immunogenicity of phosphopeptides to the prevalent alleles A*03:01, A*11:01, C*07:01, and C*07:02, selected on the basis of their presentation by malignant cells but not normal cells. We found tumor antigens derived from genetic dependencies in lymphomas and leukemias that bind HLA-A3, -A11, -C7 molecules. While we could detect circulating T cell responses in healthy individuals to A*02:01 and A*11:01 phosphopeptides, we did not find such responses to A*03:01 or C*07:01 phosphopeptides, except when utilizing allogeneic donor T cells, indicating that these phosphopeptides may not be immunogenic in an autologous setting but can still be targeted by other means. How this study might affect research, practice or policy - An expanded patient population expressing alleles other than A*02:01 can be addressed through the development of immunotherapies specific for phosphopeptides profiled in the present work, provided the nuances we describe between alleles are taken into consideration.
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Affiliation(s)
- Zaki Molvi
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Martin G. Klatt
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité- University Medicine Berlin, Berlin, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Berlin Institute of Health at Charité –Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Clinician Scientist Program, Berlin, Germany
| | - Tao Dao
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jessica Urraca
- Department of Pediatrics, 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, NY, NY, USA
| | - Richard J. O’Reilly
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Weill Cornell Medicine, NY, NY, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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Vivekanandhan S, Bahr D, Kothari A, Ashary MA, Baksh M, Gabriel E. Immunotherapies in rare cancers. Mol Cancer 2023; 22:23. [PMID: 36726126 PMCID: PMC9890725 DOI: 10.1186/s12943-023-01720-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 01/10/2023] [Indexed: 02/03/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, placing a significant burden on healthcare systems as well as the global economy. Rare cancers comprise a group of about 200 cancers that individually occur at extremely low frequencies. In the United States (US), their frequency is approximately 15 cases per 100,000 people, and it is even lower in Europe with approximately 6 cases per 100,000 people. However, combined their frequency of occurrence is much higher than any singular cancer. Cancer treatment and management has tremendously improved in the last decade, particularly with the administration of immune-based therapies. The four most prevalent immune-based therapies are (1) the use of immune-checkpoint inhibitors, (2) macrophage therapy, (3) Chimeric Antigen Receptor (CAR) T cell therapy, and (4) neoantigen-based therapies. In our review, we discuss these various aproaches and their implementation in the treatment of a variety of rare cancers. Furthermore, we discuss their limitations and potential strategies to overcome them to enhance the therapeutic efficacy of these approaches. Finally, our article presents the future directions and other additional immune therapies that may be incorporated into the treatment of rare cancers.
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Affiliation(s)
- Sneha Vivekanandhan
- grid.417467.70000 0004 0443 9942Department of Immunology, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Deborah Bahr
- grid.417467.70000 0004 0443 9942Department of Immunology, Mayo Clinic, Jacksonville, FL 32224 USA
| | - Ashish Kothari
- grid.413618.90000 0004 1767 6103Department of Microbiology, All India Institute of Medical Sciences, Rishikesh, 249203 India
| | - Mohammed Ali Ashary
- grid.417467.70000 0004 0443 9942Department of Surgery, Division of Surgical Oncology, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
| | - Mizba Baksh
- grid.417467.70000 0004 0443 9942Department of Surgery, Division of Surgical Oncology, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL 32224 USA
| | - Emmanuel Gabriel
- Department of Surgery, Division of Surgical Oncology, Mayo Clinic, 4500 San Pablo Rd, Jacksonville, FL, 32224, USA.
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32
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Martinov T, Greenberg PD. Targeting Driver Oncogenes and Other Public Neoantigens Using T Cell Receptor-Based Cellular Therapy. ANNUAL REVIEW OF CANCER BIOLOGY 2023; 7:331-351. [PMID: 37655310 PMCID: PMC10470615 DOI: 10.1146/annurev-cancerbio-061521-082114] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
T cell reactivity to tumor-specific neoantigens can drive endogenous and therapeutically induced antitumor immunity. However, most tumor-specific neoantigens are unique to each patient (private) and targeting them requires personalized therapy. A smaller subset of neoantigens includes epitopes that span recurrent mutation hotspots, translocations, or gene fusions in oncogenic drivers and tumor suppressors, as well as epitopes that arise from viral oncogenic proteins. Such antigens are likely to be shared across patients (public), uniformly expressed within a tumor, and required for cancer cell survival and fitness. Although a limited number of these public neoantigens are naturally immunogenic, recent studies affirm their clinical utility. In this review, we highlight efforts to target mutant KRAS, mutant p53, and epitopes derived from oncogenic viruses using T cells engineered with off-the-shelf T cell receptors. We also discuss the challenges and strategies to achieving more effective T cell therapies, particularly in the context of solid tumors.
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Affiliation(s)
- Tijana Martinov
- Program in Immunology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Philip D Greenberg
- Program in Immunology and Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Immunology Department, University of Washington, Seattle, Washington, USA
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Brightman SE, Naradikian MS, Thota RR, Becker A, Montero L, Bahmanof M, Premlal ALR, Greenbaum JA, Peters B, Cohen EE, Miller AM, Schoenberger SP. Tumor cells fail to present MHC-II-restricted epitopes derived from oncogenes to CD4+ T cells. JCI Insight 2023; 8:165570. [PMID: 36512410 PMCID: PMC9977289 DOI: 10.1172/jci.insight.165570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
CD4+ T cells play a critical role in antitumor immunity via recognition of peptide antigens presented on MHC class II (MHC-II). Although some solid cancers can be induced to express MHC-II, the extent to which this enables direct recognition by tumor-specific CD4+ T cells is unclear. We isolated and characterized T cell antigen receptors (TCRs) from naturally primed CD4+ T cells specific for 2 oncoproteins, HPV-16 E6 and the activating KRASG12V mutation, from patients with head and neck squamous cell carcinoma and pancreatic ductal adenocarcinoma, respectively, and determined their ability to recognize autologous or human leukocyte antigen-matched antigen-expressing tumor cells. We found in both cases that the TCRs were capable of recognizing peptide-loaded target cells expressing the relevant MHC-II or B cell antigen-presenting cells (APCs) when the antigens were endogenously expressed and directed to the endosomal pathway but failed to recognize tumor cells expressing the source protein even after induction of surface MHC-II expression by IFN-γ or transduction with CIITA. These results suggest that priming and functional recognition of both a nuclear (E6) and a membrane-associated (KRAS) oncoprotein are predominantly confined to crosspresenting APCs rather than via direct recognition of tumor cells induced to express MHC-II.
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Affiliation(s)
- Spencer E. Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Biomedical Sciences Program, School of Medicine, UCSD, La Jolla, California, USA
| | - Martin S. Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA.,Novartis, San Diego, California, USA
| | - Rukman R. Thota
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Angelica Becker
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,IconOVir Bio, San Diego, California, USA
| | - Leslie Montero
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Milad Bahmanof
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | | | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA.,Department of Medicine, UCSD, La Jolla, California, USA
| | - Ezra E.W. Cohen
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA
| | - Aaron M. Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA
| | - Stephen P. Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
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Golan T, Raitses-Gurevich M, Beller T, Carroll J, Brody JR. Strategies for the Management of Patients with Pancreatic Cancer with PARP Inhibitors. Cancer Treat Res 2023; 186:125-142. [PMID: 37978134 DOI: 10.1007/978-3-031-30065-3_8] [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] [Indexed: 11/19/2023]
Abstract
A subset of patients with pancreatic adenocarcinomas (PDAC) harbor mutations that are exploitable in the context of DNA-damage response and repair (DDR) inhibitory strategies. Between 8-18% of PDACs harbor specific mutations in the DDR pathway such as BRCA1/2 mutations, and a higher prevalence exists in high-risk populations (e.g., Ashkenazi Jews). Herein, we will review the current trials and data on the treatment of PDAC patients who harbor such mutations and who appear sensitive to platinum and/or poly ADP ribose polymerase inhibitor (PARPi) based therapies due to a concept known as synthetic lethality. Although this current best-in-class precision treatment shows clinical promise, the specter of resistance limits the extent of therapeutic responses. We therefore also evaluate promising pre-clinical and clinical approaches in the pipeline that may either work with existing therapies to break resistance or work separately with combination therapies against this subset of PDACs.
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Affiliation(s)
- Talia Golan
- Cancer Center, Chaim Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Maria Raitses-Gurevich
- Cancer Center, Chaim Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tamar Beller
- Cancer Center, Chaim Sheba Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - James Carroll
- Department of Surgery, Brenden Colson Center for Pancreatic Care, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
| | - Jonathan R Brody
- Department of Surgery, Brenden Colson Center for Pancreatic Care, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
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35
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Bannoura SF, Khan HY, Azmi AS. KRAS G12D targeted therapies for pancreatic cancer: Has the fortress been conquered? Front Oncol 2022; 12:1013902. [PMID: 36531078 PMCID: PMC9749787 DOI: 10.3389/fonc.2022.1013902] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/08/2022] [Indexed: 08/17/2023] Open
Abstract
KRAS mutations are among the most commonly occurring mutations in cancer. After being deemed undruggable for decades, KRAS G12C specific inhibitors showed that small molecule inhibitors can be developed against this notorious target. At the same time, there is still no agent that could target KRAS G12D which is the most common KRAS mutation and is found in the majority of KRAS-mutated pancreatic tumors. Nevertheless, significant progress is now being made in the G12D space with the development of several compounds that can bind to and inhibit KRAS G12D, most notably MRTX1133. Exciting advances in this field also include an immunotherapeutic approach that uses adoptive T-cell transfer to specifically target G12D in pancreatic cancer. In this mini-review, we discuss recent advances in KRAS G12D targeting and the potential for further clinical development of the various approaches.
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Affiliation(s)
- Sahar F. Bannoura
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Karmanos Cancer Institute, Detroit, MI, United States
| | - Husain Yar Khan
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
| | - Asfar S. Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States
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36
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Expansion of KRAS hotspot mutations reactive T cells from human pancreatic tumors using autologous T cells as the antigen-presenting cells. Cancer Immunol Immunother 2022; 72:1301-1313. [PMID: 36436020 DOI: 10.1007/s00262-022-03335-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/18/2022] [Indexed: 11/28/2022]
Abstract
Adoptive cell therapy (ACT) with expanded tumor-infiltrating lymphocytes (TIL) or TCR gene-modified T cells (TCR-T) that recognize mutant KRAS neo-antigens can mediate tumor regression in patients with advanced pancreatic ductal adenocarcinoma (PDAC) (Tran et al in N Engl J Med, 375:2255-2262, 2016; Leidner et al in N Engl J Med, 386:2112-2119, 2022). The mutant KRAS-targeted ACT holds great potential to achieve durable clinical responses for PDAC, which has had no meaningful improvement over 40 years. However, the wide application of mutant KRAS-centric ACT is currently limited by the rarity of TIL that recognize the mutant KRAS. In addition, PDAC is generally recognized as a poorly immunogenic tumor, and TILs in PDAC are less abundant than in immunogenic tumors such as melanoma. To increase the success rate of TIL production, we adopted a well-utilized K562-based artificial APC (aAPC) that expresses 4-1BBL as the costimulatory molecules to enhance the TIL production from PDCA. However, stimulation with K562-based aAPC led to a rapid loss of specificity to mutant KRAS. To selectively expand neo-antigen-specific T cells, particularly mKRAS, from the TILs, we used tandem mini gene-modified autologous T cells (TMG-T) as the novel aAPC. Using this modified IVS protocol, we successfully generated TIL cultures specifically reactive to mKRAS (G12V). We believe that autologous TMG-T cells provide a reliable source of autologous APC to expand a rare population of neoantigen-specific T cells in TILs.
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37
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Zhou W, Yu J, Li Y, Wang K. Neoantigen-specific TCR-T cell-based immunotherapy for acute myeloid leukemia. Exp Hematol Oncol 2022; 11:100. [PMID: 36384590 PMCID: PMC9667632 DOI: 10.1186/s40164-022-00353-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/26/2022] [Indexed: 11/17/2022] Open
Abstract
Neoantigens derived from non-synonymous somatic mutations are restricted to malignant cells and are thus considered ideal targets for T cell receptor (TCR)-based immunotherapy. Adoptive transfer of T cells bearing neoantigen-specific TCRs exhibits the ability to preferentially target tumor cells while remaining harmless to normal cells. High-avidity TCRs specific for neoantigens expressed on AML cells have been identified in vitro and verified using xenograft mouse models. Preclinical studies of these neoantigen-specific TCR-T cells are underway and offer great promise as safe and effective therapies. Additionally, TCR-based immunotherapies targeting tumor-associated antigens are used in early-phase clinical trials for the treatment of AML and show encouraging anti-leukemic effects. These clinical experiences support the application of TCR-T cells that are specifically designed to recognize neoantigens. In this review, we will provide a detailed profile of verified neoantigens in AML, describe the strategies to identify neoantigen-specific TCRs, and discuss the potential of neoantigen-specific T-cell-based immunotherapy in AML.
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38
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Huang Y, Liu J, Zhu X. Mutations in lysine methyltransferase 2C and PEG3 are associated with tumor mutation burden, prognosis, and antitumor immunity in pancreatic adenocarcinoma patients. Digit Health 2022; 8:20552076221133699. [PMID: 36312851 PMCID: PMC9597037 DOI: 10.1177/20552076221133699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 09/30/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND As a common cancer-related death worldwide, pancreatic adenocarcinoma (PAAD) has significantly increased mortality in recent years. In recent years, tumor mutation burden (TMB) has been regarded as the most popular biomarker for PAAD immunotherapy. However, it remains unclear which gene mutations affect TMB and immune response in pancreatic adenocarcinoma. METHODS The somatic mutation images of PAAD samples were downloaded from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Based on the expression data of the TCGA and IGCC cohorts, various bioinformatics algorithms are used for evaluating the prognostic value and functional annotation of some frequently somatically mutated genes. Furthermore, the correlation between gene mutation and tumor immunity was also evaluated. RESULTS The results showed that lysine methyltransferase 2C (KMT2C) and paternally expressed 3 (PEG3) are frequently mutated genes in PAAD. Patients with KMT2C and PEG3 mutations have higher TMB severity and a lousy prognosis. In addition, the mutations of KMT2C and PEG3 genes positively regulate the metabolic and protein-related pathways in PAAD. Meanwhile, significant differences in the composition of the immune cells were observed for KMT2C and PEG3 mutations PAAD patients, for providing additional guidelines for antitumor treatments in various KMT2C and PEG3 mutation states in PAAD. CONCLUSION This study reveals that KMT2C and PEG3 mutation may serve as biomarkers for predicting prognosis and guiding anti-PAAD immunotherapy for PAAD patients.
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Affiliation(s)
- Yili Huang
- The Third Clinical Medical College, Henan University of Traditional Chinese
Medicine, Zhengzhou, Henan Province, People's Republic of China,Department of Radiotherapy, Henan Cancer Hospital, Zhengzhou, Henan Province, People's Republic of China,Xiaole Zhu, Pancreas Center, Jiangsu Province Hospital, 300
Guangzhou Road, Nanjing 210029, Jiangsu Province, People's Republic of China.
Jinsong Liu, Department of
Radiotherapy, Henan Cancer Hospital, 127 Dongming Road, Zhengzhou 450003, Henan
Province, People's Republic of China.
| | - Jinsong Liu
- The Third Clinical Medical College, Henan University of Traditional Chinese
Medicine, Zhengzhou, Henan Province, People's Republic of China,Department of Radiotherapy, Henan Cancer Hospital, Zhengzhou, Henan Province, People's Republic of China
| | - Xiaole Zhu
- Pancreas Center, Jiangsu Province Hospital,
Nanjing, Jiangsu Province, People's Republic of China
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Nagel R, Pataskar A, Champagne J, Agami R. Boosting Antitumor Immunity with an Expanded Neoepitope Landscape. Cancer Res 2022; 82:3637-3649. [PMID: 35904353 PMCID: PMC9574376 DOI: 10.1158/0008-5472.can-22-1525] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 01/07/2023]
Abstract
Immune-checkpoint blockade therapy has been successfully applied to many cancers, particularly tumors that harbor a high mutational burden and consequently express a high abundance of neoantigens. However, novel approaches are needed to improve the efficacy of immunotherapy for treating tumors that lack a high load of classic genetically derived neoantigens. Recent discoveries of broad classes of nongenetically encoded and inducible neoepitopes open up new avenues for therapeutic development to enhance sensitivity to immunotherapies. In this review, we discuss recent work on neoantigen discovery, with an emphasis on novel classes of noncanonical neoepitopes.
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Affiliation(s)
- Remco Nagel
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Abhijeet Pataskar
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Julien Champagne
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Reuven Agami
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands.,Erasmus MC, Rotterdam University, Rotterdam, the Netherlands.,Corresponding Author: Reuven Agami, Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands. Phone: 3102-0512-2079; E-mail:
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40
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Awad MM, Govindan R, Balogh KN, Spigel DR, Garon EB, Bushway ME, Poran A, Sheen JH, Kohler V, Esaulova E, Srouji J, Ramesh S, Vyasamneni R, Karki B, Sciuto TE, Sethi H, Dong JZ, Moles MA, Manson K, Rooney MS, Khondker ZS, DeMario M, Gaynor RB, Srinivasan L. Personalized neoantigen vaccine NEO-PV-01 with chemotherapy and anti-PD-1 as first-line treatment for non-squamous non-small cell lung cancer. Cancer Cell 2022; 40:1010-1026.e11. [PMID: 36027916 DOI: 10.1016/j.ccell.2022.08.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/06/2022] [Accepted: 08/02/2022] [Indexed: 12/13/2022]
Abstract
Neoantigens arising from mutations in tumor DNA provide targets for immune-based therapy. Here, we report the clinical and immune data from a Phase Ib clinical trial of a personalized neoantigen-vaccine NEO-PV-01 in combination with pemetrexed, carboplatin, and pembrolizumab as first-line therapy for advanced non-squamous non-small cell lung cancer (NSCLC). This analysis of 38 patients treated with the regimen demonstrated no treatment-related serious adverse events. Multiple parameters including baseline tumor immune infiltration and on-treatment circulating tumor DNA levels were highly correlated with clinical response. De novo neoantigen-specific CD4+ and CD8+ T cell responses were observed post-vaccination. Epitope spread to non-vaccinating neoantigens, including responses to KRAS G12C and G12V mutations, were detected post-vaccination. Neoantigen-specific CD4+ T cells generated post-vaccination revealed effector and cytotoxic phenotypes with increased CD4+ T cell infiltration in the post-vaccine tumor biopsy. Collectively, these data support the safety and immunogenicity of this regimen in advanced non-squamous NSCLC.
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Affiliation(s)
- Mark M Awad
- Dana Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Edward B Garon
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | - Binisha Karki
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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Therapeutic high affinity T cell receptor targeting a KRASG12D cancer neoantigen. Nat Commun 2022; 13:5333. [PMID: 36088370 PMCID: PMC9464187 DOI: 10.1038/s41467-022-32811-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
Neoantigens derived from somatic mutations are specific to cancer cells and are ideal targets for cancer immunotherapy. KRAS is the most frequently mutated oncogene and drives the pathogenesis of several cancers. Here we show the identification and development of an affinity-enhanced T cell receptor (TCR) that recognizes a peptide derived from the most common KRAS mutant, KRASG12D, presented in the context of HLA-A*11:01. The affinity of the engineered TCR is increased by over one million-fold yet fully able to distinguish KRASG12D over KRASWT. While crystal structures reveal few discernible differences in TCR interactions with KRASWT versus KRASG12D, thermodynamic analysis and molecular dynamics simulations reveal that TCR specificity is driven by differences in indirect electrostatic interactions. The affinity enhanced TCR, fused to a humanized anti-CD3 scFv, enables selective killing of cancer cells expressing KRASG12D. Our work thus reveals a molecular mechanism that drives TCR selectivity and describes a soluble bispecific molecule with therapeutic potential against cancers harboring a common shared neoantigen. Cancers often harbor mutations in genes encoding important regulatory proteins, but therapeutic targeting of these molecules proves difficult due to their high structural similarity to their non-mutated counterpart. Here authors show the engineering of T cell engaging bispecific protein able to selectively target cancer cells with a high-frequency mutation in the KRAS oncogene.
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Khanniche A, Yang Y, Zhang J, Liu S, Xia L, Duan H, Yao Y, Zhao B, Zhao GP, Hu C, Wang Y, Lu S. Early-like differentiation status of systemic PD-1 +CD8 + T cells predicts PD-1 blockade outcome in non-small cell lung cancer. Clin Transl Immunology 2022; 11:e1406. [PMID: 35910005 PMCID: PMC9327560 DOI: 10.1002/cti2.1406] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/24/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Objectives Despite remarkable advances in the treatment of non‐small cell lung cancer (NSCLC) with anti‐programmed death (PD)‐1 therapy; only a fraction of patients derives durable clinical benefit. In this study, we investigated whether the differentiation status of systemic CD8+ T cells predicts the outcome of PD‐1 blockade in NSCLC. Methods We carried out a prospective study on a total of 77 NSCLC patients receiving anti‐PD‐1 blockers, among which 47 patients were assigned as a discovery cohort and 30 patients as a validation cohort. Peripheral blood samples were obtained at baseline and upon multiple therapy cycles and analyzed by multi‐parameter flow cytometry. Results We found that a higher baseline ratio of PD‐1+ early effector memory CD8+ T cells (CD28+CD27−CD45RO+, TEEM) to PD‐1+ effector CD8+ T cells (CD28−CD27−CD45RO−, TE) delineated responders to PD‐1 blockade from progressors and was associated with prolonged progression‐free survival (PFS) and durable clinical benefit. Moreover, PD‐1+CD8 TEEM cells exhibited early responses after anti‐PD‐1 therapy and was the major fraction of cycling PD‐1+Ki67+CD8+ T cells to expand specifically with positive impact on PFS. Conclusion These findings provide insights into how the baseline differentiation status of the peripheral immune system determines responses to PD‐1‐targeted therapies.
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Affiliation(s)
- Asma Khanniche
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China.,Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Yi Yang
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China
| | - Jie Zhang
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China
| | - Shiqing Liu
- Department of Respiratory Medicine, Xiangya Lung Cancer Center, Xiangya Hospital Central South University Changsha China
| | - Liliang Xia
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China
| | - Huangqi Duan
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yaxian Yao
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China
| | - Bingrong Zhao
- Department of Respiratory Medicine, Xiangya Lung Cancer Center, Xiangya Hospital Central South University Changsha China
| | - Guo-Ping Zhao
- Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China
| | - Chengping Hu
- Department of Respiratory Medicine, Xiangya Lung Cancer Center, Xiangya Hospital Central South University Changsha China
| | - Ying Wang
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Shun Lu
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital Shanghai Jiao Tong University Shanghai China
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Neoantigens in precision cancer immunotherapy: from identification to clinical applications. Chin Med J (Engl) 2022; 135:1285-1298. [PMID: 35838545 PMCID: PMC9433083 DOI: 10.1097/cm9.0000000000002181] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunotherapies targeting cancer neoantigens are safe, effective, and precise. Neoantigens can be identified mainly by genomic techniques such as next-generation sequencing and high-throughput single-cell sequencing; proteomic techniques such as mass spectrometry; and bioinformatics tools based on high-throughput sequencing data, mass spectrometry data, and biological databases. Neoantigen-related therapies are widely used in clinical practice and include neoantigen vaccines, neoantigen-specific CD8+ and CD4+ T cells, and neoantigen-pulsed dendritic cells. In addition, neoantigens can be used as biomarkers to assess immunotherapy response, resistance, and prognosis. Therapies based on neoantigens are an important and promising branch of cancer immunotherapy. Unremitting efforts are needed to unravel the comprehensive role of neoantigens in anti-tumor immunity and to extend their clinical application. This review aimed to summarize the progress in neoantigen research and to discuss its opportunities and challenges in precision cancer immunotherapy.
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Abstract
ABSTRACT The holy grail of cancer therapeutics is the destruction of cancer cells while avoiding harm to normal cells. Cancer is unique from normal tissues because of the presence of somatic mutations that accumulate during tumorigenesis. Some nonsynonymous mutations can give rise to mutated peptide antigens (hereafter referred to as neoantigens) that can be specifically recognized by T cells. Thus, the immunological targeting of neoantigens represents a safe and promising strategy to treat patients with cancer. This article reviews the clinical application of adoptive cell therapy targeting neoantigens in patients with epithelial cancers.
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Leidner R, Sanjuan Silva N, Huang H, Sprott D, Zheng C, Shih YP, Leung A, Payne R, Sutcliffe K, Cramer J, Rosenberg SA, Fox BA, Urba WJ, Tran E. Neoantigen T-Cell Receptor Gene Therapy in Pancreatic Cancer. N Engl J Med 2022; 386:2112-2119. [PMID: 35648703 PMCID: PMC9531755 DOI: 10.1056/nejmoa2119662] [Citation(s) in RCA: 207] [Impact Index Per Article: 103.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A patient with progressive metastatic pancreatic cancer was treated with a single infusion of 16.2×109 autologous T cells that had been genetically engineered to clonally express two allogeneic HLA-C*08:02-restricted T-cell receptors (TCRs) targeting mutant KRAS G12D expressed by the tumors. The patient had regression of visceral metastases (overall partial response of 72% according to the Response Evaluation Criteria in Solid Tumors, version 1.1); the response was ongoing at 6 months. The engineered T cells constituted more than 2% of all the circulating peripheral-blood T cells 6 months after the cell transfer. In this patient, TCR gene therapy targeting the KRAS G12D driver mutation mediated the objective regression of metastatic pancreatic cancer. (Funded by the Providence Portland Medical Foundation.).
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Affiliation(s)
- Rom Leidner
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Nelson Sanjuan Silva
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Huayu Huang
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - David Sprott
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Chunhong Zheng
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Yi-Ping Shih
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Amy Leung
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Roxanne Payne
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Kim Sutcliffe
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Julie Cramer
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Steven A Rosenberg
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Bernard A Fox
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Walter J Urba
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
| | - Eric Tran
- From the Earle A. Chiles Research Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., B.A.F., W.J.U., E.T.), Providence Cancer Institute (R.L., N.S.S., H.H., D.S., C.Z., Y.-P.S., A.L., R.P., K.S., J.C., B.A.F., W.J.U., E.T.), Portland, OR; and the Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD (S.A.R.)
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Diaz-Cano I, Paz-Ares L, Otano I. Adoptive tumor infiltrating lymphocyte transfer as personalized immunotherapy. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 370:163-192. [PMID: 35798505 DOI: 10.1016/bs.ircmb.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Cancer is a leading cause of death worldwide and, despite new targeted therapies and immunotherapies, a large group of patients fail to respond to therapy or progress after initial response, which brings the need for additional treatment options. Manipulating the immune system using a variety of approaches has been explored for the past years with successful results. Sustained progress has been made to understand the T cell-mediated anti-tumor responses counteracting the tumorigenesis process. The T-lymphocyte pool, especially its capacity for antigen-directed cytotoxicity, has become a central focus for engaging the immune system in defeating cancer. The adoptive cell transfer of autologous tumor-infiltrating lymphocytes has been used in humans for over 30 years to treat metastatic melanoma. In this review, we provide a brief history of ACT-TIL and discuss the current state of ACT-TIL clinical development in solid tumors. We also discuss how key advances in understanding genetic intratumor heterogeneity, to accurately identify neoantigens, and new strategies designed to overcome T-cell exhaustion and tumor immunosuppression have improved the efficacy of the TIL-therapy infusion. Characteristics of the TIL products will be discussed, as well as new strategies, including the selective expansion of specific fractions from the cell product or the genetic manipulation of T cells for improving the in-vivo survival and functionality. In summary, this review outlines the potential of ACT-TIL as a personalized approach for epithelial tumors and continued discoveries are making it increasingly more effective against other types of cancers.
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Affiliation(s)
- Ines Diaz-Cano
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Luis Paz-Ares
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain; Spanish Center for Biomedical Research Network in Oncology (CIBERONC), Madrid, Spain; Medicine and Physiology Department, School of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Itziar Otano
- H12O-CNIO Lung Cancer Clinical Research Unit, Health Research Institute Hospital 12 de Octubre/Spanish National Cancer Research Center (CNIO), Madrid, Spain; Spanish Center for Biomedical Research Network in Oncology (CIBERONC), Madrid, Spain.
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47
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Shafer P, Kelly LM, Hoyos V. Cancer Therapy With TCR-Engineered T Cells: Current Strategies, Challenges, and Prospects. Front Immunol 2022; 13:835762. [PMID: 35309357 PMCID: PMC8928448 DOI: 10.3389/fimmu.2022.835762] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/10/2022] [Indexed: 12/23/2022] Open
Abstract
To redirect T cells against tumor cells, T cells can be engineered ex vivo to express cancer-antigen specific T cell receptors (TCRs), generating products known as TCR-engineered T cells (TCR T). Unlike chimeric antigen receptors (CARs), TCRs recognize HLA-presented peptides derived from proteins of all cellular compartments. The use of TCR T cells for adoptive cellular therapies (ACT) has gained increased attention, especially as efforts to treat solid cancers with ACTs have intensified. In this review, we describe the differing mechanisms of T cell antigen recognition and signal transduction mediated through CARs and TCRs. We describe the classes of cancer antigens recognized by current TCR T therapies and discuss both classical and emerging pre-clinical strategies for antigen-specific TCR discovery, enhancement, and validation. Finally, we review the current landscape of clinical trials for TCR T therapy and discuss what these current results indicate for the development of future engineered TCR approaches.
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Affiliation(s)
- Paul Shafer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, United States.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Program in Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Lauren M Kelly
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, United States.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States.,Program in Cancer & Cell Biology, Baylor College of Medicine, Houston, TX, United States
| | - Valentina Hoyos
- Center for Cell and Gene Therapy, Baylor College of Medicine, Texas Children's Hospital and Houston Methodist Hospital, Houston, TX, United States.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, United States
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48
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Veatch JR, Lee SM, Shasha C, Singhi N, Szeto JL, Moshiri AS, Kim TS, Smythe K, Kong P, Fitzgibbon M, Jesernig B, Bhatia S, Tykodi SS, Hall ET, Byrd DR, Thompson JA, Pillarisetty VG, Duhen T, McGarry Houghton A, Newell E, Gottardo R, Riddell SR. Neoantigen-specific CD4 + T cells in human melanoma have diverse differentiation states and correlate with CD8 + T cell, macrophage, and B cell function. Cancer Cell 2022; 40:393-409.e9. [PMID: 35413271 PMCID: PMC9011147 DOI: 10.1016/j.ccell.2022.03.006] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 12/23/2021] [Accepted: 03/14/2022] [Indexed: 12/29/2022]
Abstract
CD4+ T cells that recognize tumor antigens are required for immune checkpoint inhibitor efficacy in murine models, but their contributions in human cancer are unclear. We used single-cell RNA sequencing and T cell receptor sequences to identify signatures and functional correlates of tumor-specific CD4+ T cells infiltrating human melanoma. Conventional CD4+ T cells that recognize tumor neoantigens express CXCL13 and are subdivided into clusters expressing memory and T follicular helper markers, and those expressing cytolytic markers, inhibitory receptors, and IFN-γ. The frequency of CXCL13+ CD4+ T cells in the tumor correlated with the transcriptional states of CD8+ T cells and macrophages, maturation of B cells, and patient survival. Similar correlations were observed in a breast cancer cohort. These results identify phenotypes and functional correlates of tumor-specific CD4+ T cells in melanoma and suggest the possibility of using such cells to modify the tumor microenvironment.
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Affiliation(s)
- Joshua R Veatch
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| | - Sylvia M Lee
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Carolyn Shasha
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Naina Singhi
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Julia L Szeto
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ata S Moshiri
- Department of Dermatology, University of Washington, Seattle, WA, USA
| | - Teresa S Kim
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - Kimberly Smythe
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul Kong
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Matthew Fitzgibbon
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Brenda Jesernig
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Shailender Bhatia
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Scott S Tykodi
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - Evan T Hall
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | - David R Byrd
- Department of Surgery, University of Washington, Seattle, WA, USA
| | - John A Thompson
- Department of Medical Oncology, University of Washington, Seattle, WA, USA
| | | | - Thomas Duhen
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | - A McGarry Houghton
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Evan Newell
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Raphael Gottardo
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stanley R Riddell
- Department of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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49
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Isolation of Neoantigen-Specific Human T Cell Receptors from Different Human and Murine Repertoires. Cancers (Basel) 2022; 14:cancers14071842. [PMID: 35406613 PMCID: PMC8998067 DOI: 10.3390/cancers14071842] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 01/24/2023] Open
Abstract
Simple Summary T cell-based immunotherapy has achieved remarkable clinical responses in patients with cancer. Neoepitope-specific T cells can specifically recognize mutated tumor cells and have led to tumor regression in mouse models and clinical studies. However, isolating neoepitope-specific T cell receptors (TCRs) from the patients’ own repertoire has shown limited success. Sourcing T cell repertoires, other than the patients’ own, has certain advantages: the availability of larger amounts of blood from healthy donors, circumventing tumor-related immunosuppression in patients, and including different donors to broaden the pool of specific T cells. Here, for the first time, a side-by-side comparison of three different TCR donor repertoires, including patients and HLA-matched allogenic healthy human repertoires, as well as repertoires of transgenic mice, is performed. Our results support recent studies that using not only healthy donor T cell repertoires, but also transgenic mice might be a viable strategy for isolating TCRs with known specificity directed against neoantigens for adoptive T cell therapy. Abstract (1) Background: Mutation-specific T cell receptor (TCR)-based adoptive T cell therapy represents a truly tumor-specific immunotherapeutic strategy. However, isolating neoepitope-specific TCRs remains a challenge. (2) Methods: We investigated, side by side, different TCR repertoires—patients’ peripheral lymphocytes (PBLs) and tumor-infiltrating lymphocytes (TILs), PBLs of healthy donors, and a humanized mouse model—to isolate neoepitope-specific TCRs against eight neoepitope candidates from a colon cancer and an ovarian cancer patient. Neoepitope candidates were used to stimulate T cells from different repertoires in vitro to generate neoepitope-specific T cells and isolate the specific TCRs. (3) Results: We isolated six TCRs from healthy donors, directed against four neoepitope candidates and one TCR from the murine T cell repertoire. Endogenous processing of one neoepitope, for which we isolated one TCR from both human and mouse-derived repertoires, could be shown. No neoepitope-specific TCR could be generated from the patients’ own repertoire. (4) Conclusion: Our data indicate that successful isolation of neoepitope-specific TCRs depends on various factors such as the heathy donor’s TCR repertoire or the presence of a tumor microenvironment allowing neoepitope-specific immune responses of the host. We show the advantage and feasibility of using healthy donor repertoires and humanized mouse TCR repertoires to generate mutation-specific TCRs with different specificities, especially in a setting when the availability of patient material is limited.
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50
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Lang F, Schrörs B, Löwer M, Türeci Ö, Sahin U. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat Rev Drug Discov 2022; 21:261-282. [PMID: 35105974 PMCID: PMC7612664 DOI: 10.1038/s41573-021-00387-y] [Citation(s) in RCA: 163] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 02/07/2023]
Abstract
Somatic mutations in cancer cells can generate tumour-specific neoepitopes, which are recognized by autologous T cells in the host. As neoepitopes are not subject to central immune tolerance and are not expressed in healthy tissues, they are attractive targets for therapeutic cancer vaccines. Because the vast majority of cancer mutations are unique to the individual patient, harnessing the full potential of this rich source of targets requires individualized treatment approaches. Many computational algorithms and machine-learning tools have been developed to identify mutations in sequence data, to prioritize those that are more likely to be recognized by T cells and to design tailored vaccines for every patient. In this Review, we fill the gaps between the understanding of basic mechanisms of T cell recognition of neoantigens and the computational approaches for discovery of somatic mutations and neoantigen prediction for cancer immunotherapy. We present a new classification of neoantigens, distinguishing between guarding, restrained and ignored neoantigens, based on how they confer proficient antitumour immunity in a given clinical context. Such context-based differentiation will contribute to a framework that connects neoantigen biology to the clinical setting and medical peculiarities of cancer, and will enable future neoantigen-based therapies to provide greater clinical benefit.
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Affiliation(s)
- Franziska Lang
- TRON Translational Oncology, Mainz, Germany
- Faculty of Biology, Johannes Gutenberg University Mainz, Mainz, Germany
| | | | | | | | - Ugur Sahin
- BioNTech, Mainz, Germany.
- University Medical Center, Johannes Gutenberg University, Mainz, Germany.
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