1
|
Yu Z, Shi J, Fang Y, Zhao Y, Xu A, Li N. Developing innovative strategies of tumor‑infiltrating lymphocyte therapy for tumor treatment. Oncol Rep 2024; 51:85. [PMID: 38666543 PMCID: PMC11082634 DOI: 10.3892/or.2024.8744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/15/2024] [Indexed: 05/04/2024] Open
Abstract
Cancer is the main cause of global mortality, and thus far, effective therapeutic strategies for cancer treatment are in high demand. Adoptive transfer of tumor‑infiltrating lymphocytes (TILs) represents a promising avenue in immunotherapy for the management of malignancies. The clinical safety and efficacy of TIL‑based therapy have been established through numerous rigorous clinical trials. However, the efficacy of TIL infusion in inducing an anti‑tumor response is limited to a subset of clinical patients with cancer. Therefore, there is an urgent need to develop innovative strategies aimed at enhancing the effectiveness of TIL‑based therapy. In the present review, the developmental history of TIL‑based therapy was systematically summarized and analyzed, while also presenting a unique perspective on enhancing the multi‑dimensional anti‑tumor capabilities of TILs. The insight and conclusions presented in this review may contribute to improving the efficacy of TIL‑based therapy and expediting its development.
Collapse
Affiliation(s)
- Zhongjie Yu
- R&D, Qingdao Sino-cell Biomedicine Co., Ltd., Qingdao, Shandong 266000, P.R. China
| | - Jianhua Shi
- Phase I Clinical Research Center Affiliated, Linyi Tumor Hospital, Linyi, Shandong 276000, P.R. China
| | - Yuan Fang
- Clinical Trials Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Yi Zhao
- R&D, Qingdao Sino-cell Biomedicine Co., Ltd., Qingdao, Shandong 266000, P.R. China
| | - Aotian Xu
- R&D, Qingdao Sino-cell Biomedicine Co., Ltd., Qingdao, Shandong 266000, P.R. China
| | - Ning Li
- Clinical Trials Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| |
Collapse
|
2
|
Yi L, Xu Z, Ma T, Wang C, Wei P, Xiao B, Zhang H, Che N, Liu Z, Han Y. T-cell subsets and cytokines are indicative of neoadjuvant chemoimmunotherapy responses in NSCLC. Cancer Immunol Immunother 2024; 73:99. [PMID: 38619623 PMCID: PMC11018727 DOI: 10.1007/s00262-024-03687-5] [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: 08/24/2023] [Accepted: 03/19/2024] [Indexed: 04/16/2024]
Abstract
PURPOSE Neoadjuvant PD-1 blockade combined with chemotherapy is a promising treatment for resectable non-small cell lung cancer (NSCLC), yet the immunological mechanisms contributing to tumor regression and biomarkers corresponding to different pathological responses remain unclear. METHODS Using dynamic and paired blood samples from NSCLC patients receiving neoadjuvant chemoimmunotherapy, we analyzed the frequencies of CD8 + T-cell and Treg subsets and their dynamic changes during neoadjuvant treatment through flow cytometry. Cytokine profiles and function-related gene expression of CD8 + T cells and Tregs were analyzed through flow cytometry and mRNA-seq. Infiltrating T-cell subsets in resected tissues from patients with different pathological responses were analyzed through multiplex immunofluorescence. RESULTS Forty-two NSCLC patients receiving neoadjuvant chemoimmunotherapy were enrolled and then underwent surgical resection and pathological evaluation. Nineteen patients had pCR (45%), 7 patients had MPR (17%), and 16 patients had non-MPR (38%). In patients with pCR, the frequencies of CD137 + CD8 + T cells (P = 0.0475), PD-1 + Ki-67 + CD8 + T cells (P = 0.0261) and Tregs (P = 0.0317) were significantly different from those of non-pCR patients before treatment. pCR patients usually had low frequencies of CD137 + CD8 + T cells, PD-1 + Ki-67 + CD8 + T cells and Tregs, and their AUCs were higher than that of tissue PD-L1 expression. Neoadjuvant chemoimmunotherapy markedly improved CD8 + T-cell proliferation and activation, especially in pCR patients, as the frequencies of CD137 + CD8 + (P = 0.0136) and Ki-67 + CD8 + (P = 0.0391) T cells were significantly increased. The blood levels of cytokines such as IL-2 (P = 0.0391) and CXCL10 (P = 0.0195) were also significantly increased in the pCR group, which is consistent with the high density of activated cytotoxic T cells at the tumor site (P < 0.0001). CONCLUSION Neoadjuvant chemoimmunotherapy drives CD8 + T cells toward a proliferative and active profile. The frequencies of CD137 + CD8 + T cells, PD-1 + Ki-67 + CD8 + T cells and Tregs at baseline might predict the response to neoadjuvant chemoimmunotherapy in NSCLC patients. The increase in IL-2 and CXCL10 might reflect the chemotaxis and enrichment of cytotoxic T cells at the tumor site and a better response to neoadjuvant chemoimmunotherapy.
Collapse
Affiliation(s)
- Ling Yi
- Department of Central Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Ziwei Xu
- Department of Minimally Invasive Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Tianyu Ma
- Department of Thoracic Surgery II, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Chong Wang
- Department of Minimally Invasive Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Panjian Wei
- Department of Central Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Bo Xiao
- Department of Minimally Invasive Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Hongtao Zhang
- Department of Central Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.
| | - Nanying Che
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.
| | - Zhidong Liu
- Department of Thoracic Surgery II, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.
| | - Yi Han
- Department of Minimally Invasive Surgery, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China.
| |
Collapse
|
3
|
Shen L, Yang J, Zuo C, Xu J, Ma L, He Q, Zhou X, Ding X, Wei L, Jiang S, Ma L, Zhang B, Yang Y, Dong B, Wan L, Ding X, Zhu M, Sun Z, Wang P, Song X, Zhang Y. Circular mRNA-based TCR-T offers a safe and effective therapeutic strategy for treatment of cytomegalovirus infection. Mol Ther 2024; 32:168-184. [PMID: 37974400 PMCID: PMC10787193 DOI: 10.1016/j.ymthe.2023.11.017] [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: 07/03/2023] [Revised: 10/27/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023] Open
Abstract
Circular mRNA (cmRNA) is particular useful due to its high resistance to degradation by exonucleases, resulting in greater stability and protein expression compared to linear mRNA. T cell receptor (TCR)-engineered T cells (TCR-T) represent a promising means of treating viral infections and cancer. This study aimed to evaluate the feasibility and efficacy of cmRNA in antigen-specific-TCR discovery and TCR-T therapy. Using human cytomegalovirus (CMV) pp65 antigen as a model, we found that the expansion of pp65-responsive T cells was induced more effectively by monocyte-derived dendritic cells transfected with pp65-encoding cmRNA compared with linear mRNA. Subsequently, we developed cmRNA-transduced pp65-TCR-T (cm-pp65-TCR-T) that specifically targets the CMV-pp65 epitope. Our results showed that pp65-TCR could be expressed on primary T cells for more than 7 days. Moreover, both in vitro killing and in vivo CDX models demonstrated that cm-pp65-TCR-T cells specifically and persistently kill pp65-and HLA-expressing tumor cells, significantly prolonging the survival of mice. Collectively, our results demonstrated that cmRNA can be used as a more effective technical approach for antigen-specific TCR isolation and identification, and cm-pp65-TCR-T may provide a safe, non-viral, non-integrated therapeutic approach for controlling CMV infection, particularly in patients who have undergone allogeneic hematopoietic stem cell transplantation.
Collapse
Affiliation(s)
- Lianghua Shen
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China
| | - Jiali Yang
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China
| | - Chijian Zuo
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China.
| | - Jian Xu
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China
| | - Ling Ma
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China
| | - Qiaomei He
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Xiao Zhou
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Xiaodan Ding
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Lixiang Wei
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China
| | - Suqin Jiang
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China
| | - Luanluan Ma
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China
| | - Benjia Zhang
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China
| | - Yuqin Yang
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Baoxia Dong
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Liping Wan
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China
| | - Xueying Ding
- Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China
| | - Ming Zhu
- KuaiXu Biotechnologies Co., Ltd, Shanghai 201315, China
| | - Zhenhua Sun
- Suzhou CureMed Biopharma Technology Co., Ltd, Suzhou 215125, China.
| | - Pengran Wang
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China.
| | - Xianmin Song
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China.
| | - Yan Zhang
- Department of Hematology, Shanghai General Hospital, Shanghai JiaoTong University School of Medicine, Shanghai 201620, China; Engineering Technology Research Center of Cell Therapy and Clinical Translation, Science and Technology Committee of Shanghai Municipality, Shanghai 200080, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Zemanek T, Nova Z, Nicodemou A. Tumor-Infiltrating Lymphocytes and Adoptive Cell Therapy: State of the Art in Colorectal, Breast and Lung Cancer. Physiol Res 2023; 72:S209-S224. [PMID: 37888965 PMCID: PMC10669950 DOI: 10.33549/physiolres.935155] [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: 05/02/2023] [Accepted: 06/07/2023] [Indexed: 12/01/2023] Open
Abstract
Our knowledge of tumor-infiltrating lymphocytes (TILs) is dramatically expanding. These cells have proven prognostic and therapeutic value for many cancer outcomes and potential to treat also disseminated breast, colorectal, or lung cancer. However, the therapeutical outcome of TILs is negatively affected by tumor mutational burden and neoantigens. On the other hand, it can be improved in combination with checkpoint blockade therapy. This knowledge and rapid detection techniques alongside gene editing allow us to classify and modify T cells in many ways. Hence, to tailor them precisely to the patient´s needs as to program T cell receptors to recognize specific tumor-associated neoantigens and to insert them into lymphocytes or to select tumor neoantigen-specific T cells, for the development of vaccines that recognize tumor-specific antigens in tumors or metastases. Further studies and clinical trials in the field are needed for an even better-detailed understanding of TILs interactions and aiming in the fight against multiple cancers.
Collapse
Affiliation(s)
- T Zemanek
- Lambda Life, Bratislava, Slovak Republic.
| | | | | |
Collapse
|
6
|
Aldea M, Friboulet L, Apcher S, Jaulin F, Mosele F, Sourisseau T, Soria JC, Nikolaev S, André F. Precision medicine in the era of multi-omics: can the data tsunami guide rational treatment decision? ESMO Open 2023; 8:101642. [PMID: 37769400 PMCID: PMC10539962 DOI: 10.1016/j.esmoop.2023.101642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 09/30/2023] Open
Abstract
Precision medicine for cancer is rapidly moving to an approach that integrates multiple dimensions of the biology in order to model mechanisms of cancer progression in each patient. The discovery of multiple drivers per tumor challenges medical decision that faces several treatment options. Drug sensitivity depends on the actionability of the target, its clonal or subclonal origin and coexisting genomic alterations. Sequencing has revealed a large diversity of drivers emerging at treatment failure, which are potential targets for clinical trials or drug repurposing. To effectively prioritize therapies, it is essential to rank genomic alterations based on their proven actionability. Moving beyond primary drivers, the future of precision medicine necessitates acknowledging the intricate spatial and temporal heterogeneity inherent in cancer. The advent of abundant complex biological data will make artificial intelligence algorithms indispensable for thorough analysis. Here, we will discuss the advancements brought by the use of high-throughput genomics, the advantages and limitations of precision medicine studies and future perspectives in this field.
Collapse
Affiliation(s)
- M Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif.
| | | | - S Apcher
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Jaulin
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif
| | | | - J-C Soria
- Paris Saclay University, Orsay; Drug Development Department, Gustave Roussy, Villejuif, France
| | - S Nikolaev
- PRISM, INSERM, Gustave Roussy, Villejuif
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif; PRISM, INSERM, Gustave Roussy, Villejuif; Paris Saclay University, Orsay
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Fast E, Dhar M, Chen B. TAPIR: a T-cell receptor language model for predicting rare and novel targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557285. [PMID: 37745475 PMCID: PMC10515850 DOI: 10.1101/2023.09.12.557285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
T-cell receptors (TCRs) are involved in most human diseases, but linking their sequences with their targets remains an unsolved grand challenge in the field. In this study, we present TAPIR (T-cell receptor and Peptide Interaction Recognizer), a T-cell receptor (TCR) language model that predicts TCR-target interactions, with a focus on novel and rare targets. TAPIR employs deep convolutional neural network (CNN) encoders to process TCR and target sequences across flexible representations (e.g., beta-chain only, unknown MHC allele, etc.) and learns patterns of interactivity via several training tasks. This flexibility allows TAPIR to train on more than 50k either paired (alpha and beta chain) or unpaired TCRs (just alpha or beta chain) from public and proprietary databases against 1933 unique targets. TAPIR demonstrates state-of-the-art performance when predicting TCR interactivity against common benchmark targets and is the first method to demonstrate strong performance when predicting TCR interactivity against novel targets, where no examples are provided in training. TAPIR is also capable of predicting TCR interaction against MHC alleles in the absence of target information. Leveraging these capabilities, we apply TAPIR to cancer patient TCR repertoires and identify and validate a novel and potent anti-cancer T-cell receptor against a shared cancer neoantigen target (PIK3CA H1047L). We further show how TAPIR, when extended with a generative neural network, is capable of directly designing T-cell receptor sequences that interact with a target of interest.
Collapse
Affiliation(s)
- Ethan Fast
- Vcreate, Inc., Menlo Park, CA, 94025, USA
| | | | | |
Collapse
|
9
|
Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
Collapse
Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
| |
Collapse
|
10
|
Ahmed R, Lozano LE, Anastasio A, Lofek S, Mastelic-Gavillet B, Navarro Rodrigo B, Nguyen S, Dartiguenave F, Rodrigues-Dias SC, Cesson V, Valério M, Roth B, Kandalaft LE, Redchenko I, Hill AVS, Harari A, Romero P, Derré L, Viganó S. Phenotype and Reactivity of Lymphocytes Expanded from Benign Prostate Hyperplasic Tissues and Prostate Cancer. Cancers (Basel) 2023; 15:3114. [PMID: 37370724 DOI: 10.3390/cancers15123114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Benign prostate hyperplasia (BPH) is a frequent condition in aging men, which affects life quality, causing principally lower urinary tract symptoms. Epidemiologic studies suggest that BPH may raise the risk of developing prostate cancer (PCa), most likely promoting a chronic inflammatory environment. Studies aiming at elucidating the link and risk factors that connect BPH and PCa are urgently needed to develop prevention strategies. The BPH microenvironment, similar to the PCa one, increases immune infiltration of the prostate, but, in contrast to PCa, immunosuppression may not be established yet. In this study, we found that prostate-infiltrating lymphocytes (PILs) expanded from hyperplastic prostate tissue recognized tumor-associated antigens (TAA) and autologous tissue, regardless of the presence of tumor cells. PILs expanded from BPH samples of patients with PCa, however, seem to respond more strongly to autologous tissue. Phenotypic characterization of the infiltrating PILs revealed a trend towards better expanding CD4+ T cells in infiltrates derived from PCa, but no significant differences were found. These findings suggest that T cell tolerance is compromised in BPH-affected prostates, likely due to qualitative or quantitative alterations of the antigenic landscape. Our data support the hypothesis that BPH increases the risk of PCa and may pave the way for new personalized preventive vaccine strategies for these patients.
Collapse
Affiliation(s)
- Ritaparna Ahmed
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Leyder Elena Lozano
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Amandine Anastasio
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Sebastien Lofek
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Beatris Mastelic-Gavillet
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Sylvain Nguyen
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Florence Dartiguenave
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Sonia-Cristina Rodrigues-Dias
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Valérie Cesson
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Massimo Valério
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Beat Roth
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Lana Elias Kandalaft
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Irina Redchenko
- Nuffield Department of Medicine, The Jenner Institute, Oxford University, Oxford OX3 7BN, UK
| | | | - Alexandre Harari
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Pedro Romero
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Laurent Derré
- Urology Research Unit and Urology Biobank, Department of Urology, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| | - Selena Viganó
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University Hospital of Lausanne, CH-1011 Lausanne, Switzerland
| |
Collapse
|
11
|
Islam SR, Maeda T, Tamaoki N, Good ML, Kishton RJ, Paria BC, Yu Z, Bosch-Marce M, Bedanova NM, Liu C, Kruhlak MJ, Restifo NP, Vizcardo R. Reprogramming of Tumor-reactive Tumor-infiltrating Lymphocytes to Human-induced Pluripotent Stem Cells. CANCER RESEARCH COMMUNICATIONS 2023; 3:917-932. [PMID: 37377887 PMCID: PMC10211394 DOI: 10.1158/2767-9764.crc-22-0265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 03/01/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023]
Abstract
UNLABELLED Tumor-infiltrating lymphocytes (TIL) that can recognize and kill tumor cells have curative potential in subsets of patients treated with adoptive cell transfer (ACT). However, lack of TIL therapeutic efficacy in many patients may be due in large part to a paucity of tumor-reactive T cells in TIL and the exhausted and terminally differentiated status of those tumor-reactive T cells. We sought to reprogram exhausted TIL that possess T-cell receptors (TCR) specific for tumor antigens into induced pluripotent stem cells (iPSC) to rejuvenate them for more potent ACT. We first attempted to reprogram tumor neoantigen-specific TIL by αCD3 Ab prestimulation which resulted in failure of establishing tumor-reactive TIL-iPSCs, instead, T cell-derived iPSCs from bystander T cells were established. To selectively activate and enrich tumor-reactive T cells from the heterogenous TIL population, CD8+ PD-1+ 4-1BB+ TIL population were isolated after coculture with autologous tumor cells, followed by direct reprogramming into iPSCs. TCR sequencing analysis of the resulting iPSC clones revealed that reprogrammed TIL-iPSCs encoded TCRs that were identical to the pre-identified tumor-reactive TCRs found in minimally cultured TIL. Moreover, reprogrammed TIL-iPSCs contained rare tumor antigen-specific TCRs, which were not detectable by TCR sequencing of the starting cell population. Thus, reprogramming of PD-1+ 4-1BB+ TIL after coculture with autologous tumor cells selectively generates tumor antigen-specific TIL-iPSCs, and is a distinctive method to enrich and identify tumor antigen-specific TCRs of low frequency from TIL. SIGNIFICANCE Reprogramming of TIL into iPSC holds great promise for the future treatment of cancer due to their rejuvenated nature and the retention of tumor-specific TCRs. One limitation is the lack of selective and efficient methods for reprogramming tumor-specific T cells from polyclonal TIL. Here we addressed this limitation and present a method to efficiently reprogram TIL into iPSC colonies carrying diverse tumor antigen reactive TCR recombination.
Collapse
Affiliation(s)
- S.M. Rafiqul Islam
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Takuya Maeda
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Naritaka Tamaoki
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Meghan L. Good
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Rigel J. Kishton
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | | | - Zhiya Yu
- Surgery Branch, NCI, NIH, Bethesda, Maryland
| | | | | | - Chengyu Liu
- Transgenic Core, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, Maryland
| | | | - Nicholas P. Restifo
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| | - Raul Vizcardo
- Surgery Branch, NCI, NIH, Bethesda, Maryland
- Center for Cell-Based Therapy, NCI, NIH, Bethesda, Maryland
| |
Collapse
|
12
|
Huang R, Zhao B, Hu S, Zhang Q, Su X, Zhang W. Adoptive neoantigen-reactive T cell therapy: improvement strategies and current clinical researches. Biomark Res 2023; 11:41. [PMID: 37062844 PMCID: PMC10108522 DOI: 10.1186/s40364-023-00478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
Neoantigens generated by non-synonymous mutations of tumor genes can induce activation of neoantigen-reactive T (NRT) cells which have the ability to resist the growth of tumors expressing specific neoantigens. Immunotherapy based on NRT cells has made preeminent achievements in melanoma and other solid tumors. The process of manufacturing NRT cells includes identification of neoantigens, preparation of neoantigen expression vectors or peptides, induction and activation of NRT cells, and analysis of functions and phenotypes. Numerous improvement strategies have been proposed to enhance the potency of NRT cells by engineering TCR, promoting infiltration of T cells and overcoming immunosuppressive factors in the tumor microenvironment. In this review, we outline the improvement of the preparation and the function assessment of NRT cells, and discuss the current status of clinical trials related to NRT cell immunotherapy.
Collapse
Affiliation(s)
- Ruichen Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Bi Zhao
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Shi Hu
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Qian Zhang
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Xiaoping Su
- School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325000, People's Republic of China.
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China.
| |
Collapse
|
13
|
Melero I, Sanmamed MF, Glez-Vaz J, Luri-Rey C, Wang J, Chen L. CD137 (4-1BB)-Based Cancer Immunotherapy on Its 25th Anniversary. Cancer Discov 2023; 13:552-569. [PMID: 36576322 DOI: 10.1158/2159-8290.cd-22-1029] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/28/2022] [Accepted: 11/21/2022] [Indexed: 12/29/2022]
Abstract
Twenty-five years ago, we reported that agonist anti-CD137 monoclonal antibodies eradicated transplanted mouse tumors because of enhanced CD8+ T-cell antitumor immunity. Mouse models indicated that anti-CD137 agonist antibodies synergized with various other therapies. In the clinic, the agonist antibody urelumab showed evidence for single-agent activity against melanoma and non-Hodgkin lymphoma but caused severe liver inflammation in a fraction of the patients. CD137's signaling domain is included in approved chimeric antigen receptors conferring persistence and efficacy. A new wave of CD137 agonists targeting tumors, mainly based on bispecific constructs, are in early-phase trials and are showing promising safety and clinical activity. SIGNIFICANCE CD137 (4-1BB) is a costimulatory receptor of T and natural killer lymphocytes whose activity can be exploited in cancer immunotherapy strategies as discovered 25 years ago. Following initial attempts that met unacceptable toxicity, new waves of constructs acting agonistically on CD137 are being developed in patients, offering signs of clinical and pharmacodynamic activity with tolerable safety profiles.
Collapse
Affiliation(s)
- Ignacio Melero
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Departments of Immunology-Immunotherapy and Oncology, Clínica Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Miguel F Sanmamed
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Departments of Immunology-Immunotherapy and Oncology, Clínica Universidad de Navarra, Pamplona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Javier Glez-Vaz
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Carlos Luri-Rey
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - Jun Wang
- Department of Pathology, New York University Grossman School of Medicine, New York, New York
| | - Lieping Chen
- Department of Immunobiology, Yale University, New Haven, Connecticut
| |
Collapse
|
14
|
Baulu E, Gardet C, Chuvin N, Depil S. TCR-engineered T cell therapy in solid tumors: State of the art and perspectives. SCIENCE ADVANCES 2023; 9:eadf3700. [PMID: 36791198 PMCID: PMC9931212 DOI: 10.1126/sciadv.adf3700] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/06/2023] [Indexed: 05/25/2023]
Abstract
T cell engineering has changed the landscape of cancer immunotherapy. Chimeric antigen receptor T cells have demonstrated a remarkable efficacy in the treatment of B cell malignancies in hematology. However, their clinical impact on solid tumors has been modest so far. T cells expressing an engineered T cell receptor (TCR-T cells) represent a promising therapeutic alternative. The target repertoire is not limited to membrane proteins, and intrinsic features of TCRs such as high antigen sensitivity and near-to-physiological signaling may improve tumor cell detection and killing while improving T cell persistence. In this review, we present the clinical results obtained with TCR-T cells targeting different tumor antigen families. We detail the different methods that have been developed to identify and optimize a TCR candidate. We also discuss the challenges of TCR-T cell therapies, including toxicity assessment and resistance mechanisms. Last, we share some perspectives and highlight future directions in the field.
Collapse
Affiliation(s)
- Estelle Baulu
- Centre de Recherche en Cancérologie de Lyon, Lyon, France
- ErVaccine Technologies, Lyon, France
| | - Célia Gardet
- Centre de Recherche en Cancérologie de Lyon, Lyon, France
| | | | - Stéphane Depil
- Centre de Recherche en Cancérologie de Lyon, Lyon, France
- ErVaccine Technologies, Lyon, France
- Centre Léon Bérard, Lyon, France
- Université Claude Bernard Lyon 1, Lyon, France
| |
Collapse
|
15
|
Marin I, Boix O, Garcia-Garijo A, Sirois I, Caballe A, Zarzuela E, Ruano I, Attolini CSO, Prats N, López-Domínguez JA, Kovatcheva M, Garralda E, Muñoz J, Caron E, Abad M, Gros A, Pietrocola F, Serrano M. Cellular Senescence Is Immunogenic and Promotes Antitumor Immunity. Cancer Discov 2023. [PMID: 36302218 DOI: 10.1101/2022.06.05.494912] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
UNLABELLED Cellular senescence is a stress response that activates innate immune cells, but little is known about its interplay with the adaptive immune system. Here, we show that senescent cells combine several features that render them highly efficient in activating dendritic cells (DC) and antigen-specific CD8 T cells. This includes the release of alarmins, activation of IFN signaling, enhanced MHC class I machinery, and presentation of senescence-associated self-peptides that can activate CD8 T cells. In the context of cancer, immunization with senescent cancer cells elicits strong antitumor protection mediated by DCs and CD8 T cells. Interestingly, this protection is superior to immunization with cancer cells undergoing immunogenic cell death. Finally, the induction of senescence in human primary cancer cells also augments their ability to activate autologous antigen-specific tumor-infiltrating CD8 lymphocytes. Our study indicates that senescent cancer cells can be exploited to develop efficient and protective CD8-dependent antitumor immune responses. SIGNIFICANCE Our study shows that senescent cells are endowed with a high immunogenic potential-superior to the gold standard of immunogenic cell death. We harness these properties of senescent cells to trigger efficient and protective CD8-dependent antitumor immune responses. See related article by Chen et al., p. 432. This article is highlighted in the In This Issue feature, p. 247.
Collapse
Affiliation(s)
- Ines Marin
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga Boix
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Adrià Caballe
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Irene Ruano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Neus Prats
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - José A López-Domínguez
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Kovatcheva
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Javier Muñoz
- Spanish National Cancer Research Center, Madrid, Spain
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - María Abad
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Alena Gros
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Federico Pietrocola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| |
Collapse
|
16
|
Marin I, Boix O, Garcia-Garijo A, Sirois I, Caballe A, Zarzuela E, Ruano I, Attolini CSO, Prats N, López-Domínguez JA, Kovatcheva M, Garralda E, Muñoz J, Caron E, Abad M, Gros A, Pietrocola F, Serrano M. Cellular Senescence Is Immunogenic and Promotes Antitumor Immunity. Cancer Discov 2023; 13:410-431. [PMID: 36302218 PMCID: PMC7614152 DOI: 10.1158/2159-8290.cd-22-0523] [Citation(s) in RCA: 82] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/31/2022] [Accepted: 10/24/2022] [Indexed: 02/07/2023]
Abstract
Cellular senescence is a stress response that activates innate immune cells, but little is known about its interplay with the adaptive immune system. Here, we show that senescent cells combine several features that render them highly efficient in activating dendritic cells (DC) and antigen-specific CD8 T cells. This includes the release of alarmins, activation of IFN signaling, enhanced MHC class I machinery, and presentation of senescence-associated self-peptides that can activate CD8 T cells. In the context of cancer, immunization with senescent cancer cells elicits strong antitumor protection mediated by DCs and CD8 T cells. Interestingly, this protection is superior to immunization with cancer cells undergoing immunogenic cell death. Finally, the induction of senescence in human primary cancer cells also augments their ability to activate autologous antigen-specific tumor-infiltrating CD8 lymphocytes. Our study indicates that senescent cancer cells can be exploited to develop efficient and protective CD8-dependent antitumor immune responses. SIGNIFICANCE Our study shows that senescent cells are endowed with a high immunogenic potential-superior to the gold standard of immunogenic cell death. We harness these properties of senescent cells to trigger efficient and protective CD8-dependent antitumor immune responses. See related article by Chen et al., p. 432. This article is highlighted in the In This Issue feature, p. 247.
Collapse
Affiliation(s)
- Ines Marin
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Olga Boix
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | | | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Adrià Caballe
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Irene Ruano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Neus Prats
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - José A López-Domínguez
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Kovatcheva
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
| | | | - Javier Muñoz
- Spanish National Cancer Research Center, Madrid, Spain
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - María Abad
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Alena Gros
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Federico Pietrocola
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Manuel Serrano
- Institute for Research in Biomedicine (IRB), Barcelona Institute of Science and Technology, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| |
Collapse
|
17
|
Baek GW, Yun SO, Park MY, Kang HJ. Generation of antigen-specific T lymphocytes targeting Wilms tumor 1 using activated B cells. Hum Immunol 2023; 84:106-112. [PMID: 36379724 DOI: 10.1016/j.humimm.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
In order to develop a therapeutic target for T cells, it is necessary to amplify T cells and increase activity through antigen-presenting cells (APCs) expressing an intracellular cancer antigen. Although dendritic cells are frequently used as APCs, producing dendritic cells is costly and time-consuming. In addition, as dendritic cells are attached cells, they are not suitable for mass production for use as immune cell therapy. On the other hand, B cells are non-adherent floating cells, and thus can easily be cultured in suspension systems. As such, B cells can be considered as suitable substance cells for the development of immune cell therapeutics.B cells lack the antigen-presenting ability of dendritic cells. Therefore, to use B cells as APCs, we previously reported a technology that can be used which simply and effectively produces anti-viral T cells in vitro by activating B cells with α-galactosylceramide (α-GalCer). To apply this technology to anti-cancer treatment, Wilms tumor 1, the most representative cancer antigen expressed in various cancers, was selected. Wilms tumor 1 (WT1) was used to produce anti-cancer (anti-WT1) T cells using active B cells as APCs, and their respective activities were investigated.
Collapse
Affiliation(s)
- Gyung Won Baek
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun Ok Yun
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Mi Young Park
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyoung Jin Kang
- Department of Pediatrics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
| |
Collapse
|
18
|
Gfeller D, Schmidt J, Croce G, Guillaume P, Bobisse S, Genolet R, Queiroz L, Cesbron J, Racle J, Harari A. Improved predictions of antigen presentation and TCR recognition with MixMHCpred2.2 and PRIME2.0 reveal potent SARS-CoV-2 CD8 + T-cell epitopes. Cell Syst 2023; 14:72-83.e5. [PMID: 36603583 PMCID: PMC9811684 DOI: 10.1016/j.cels.2022.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/06/2023]
Abstract
The recognition of pathogen or cancer-specific epitopes by CD8+ T cells is crucial for the clearance of infections and the response to cancer immunotherapy. This process requires epitopes to be presented on class I human leukocyte antigen (HLA-I) molecules and recognized by the T-cell receptor (TCR). Machine learning models capturing these two aspects of immune recognition are key to improve epitope predictions. Here, we assembled a high-quality dataset of naturally presented HLA-I ligands and experimentally verified neo-epitopes. We then integrated these data in a refined computational framework to predict antigen presentation (MixMHCpred2.2) and TCR recognition (PRIME2.0). The depth of our training data and the algorithmic developments resulted in improved predictions of HLA-I ligands and neo-epitopes. Prospectively applying our tools to SARS-CoV-2 proteins revealed several epitopes. TCR sequencing identified a monoclonal response in effector/memory CD8+ T cells against one of these epitopes and cross-reactivity with the homologous peptides from other coronaviruses.
Collapse
Affiliation(s)
- David Gfeller
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland,Corresponding author
| | - Julien Schmidt
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Giancarlo Croce
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Philippe Guillaume
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Sara Bobisse
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Raphael Genolet
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Lise Queiroz
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Cesbron
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Julien Racle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University of Lausanne, Lausanne, Switzerland,Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| | - Alexandre Harari
- Agora Cancer Research Centre, 1011 Lausanne, Switzerland,Department of Oncology, Ludwig Institute for Cancer Research Lausanne, University Hospital of Lausanne, Lausanne, Switzerland,Swiss Cancer Center Leman (SCCL), Lausanne, Switzerland
| |
Collapse
|
19
|
Palomero J, Panisello C, Lozano-Rabella M, Tirtakasuma R, Díaz-Gómez J, Grases D, Pasamar H, Arregui L, Dorca Duch E, Guerra Fernández E, Vivancos A, de Andrea CE, Melero I, Ponce J, Vidal A, Piulats JM, Matias-Guiu X, Gros A. Biomarkers of tumor-reactive CD4 + and CD8 + TILs associate with improved prognosis in endometrial cancer. J Immunother Cancer 2022; 10:jitc-2022-005443. [PMID: 36581331 PMCID: PMC9806064 DOI: 10.1136/jitc-2022-005443] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Despite the growing interest in immunotherapeutic interventions for endometrial cancer (EC), the prevalence, phenotype, specificity and prognostic value of tumor infiltrating lymphocytes (TILs) in this tumor type remains unclear. METHODS To better understand the role of TILs in EC, we analyzed the phenotypic traits of CD8+ and CD4+ EC-resident T cells from 47 primary tumors by high-dimensional flow cytometry. In addition, CD8+ and CD4+ TIL subpopulations were isolated based on the differential expression of programmed cell death protein-1 (PD-1) (negative, dim and high) and CD39 (positive or negative) by fluorescence activated cell sorting (FACS), expanded in vitro, and screened for autologous tumor recognition. We further investigated whether phenotypic markers preferentially expressed on CD8+ and CD4+ tumor-reactive TIL subsets were associated with the four distinct molecular subtypes of EC, tumor mutational burden and patient survival. RESULTS We found that CD8+TILs expressing high levels of PD-1 (PD-1hi) co-expressed CD39, TIM-3, HLA-DR and CXCL13, as compared with TILs lacking or displaying intermediate levels of PD-1 expression (PD-1- and PD-1dim, respectively). Autologous tumor reactivity of sorted and in vitro expanded CD8+ TILs demonstrated that the CD8+PD-1dimCD39+ and PD-1hiCD39+ T cell subsets both contained tumor-reactive TILs and that a higher level of PD-1 expression was associated with increased CD39 and a superior frequency of tumor reactivity. With respect to CD4+ T conventional (Tconv) TILs, co-expression of inhibitory and activation markers was more apparent on PD-1hi compared with PD-1- or PD-1dim T cells, and in fact, it was the CD4+PD-1hi subpopulation that accumulated the antitumor T cells irrespective of CD39 expression. Most importantly, detection of CD8+PD-1hiCD39+ and CD4+PD-1hi tumor-reactive T-cell subsets, but also markers specifically expressed by these subpopulations of TILs, that is, PD-1hi, CD39, CXCL13 and CD103 by CD8+ TILs and PD-1hi and CXCL13 by CD4+ Tconv TILs, correlated with prolonged survival of patients with EC. CONCLUSIONS Our results demonstrate that EC are frequently infiltrated by tumor-reactive TILs, and that expression of PD-1hi and CD39 or PD-1hi can be used to select and expand CD8+ and CD4+ tumor-reactive TILs, respectively. In addition, biomarkers preferentially expressed on tumor-reactive TILs, rather than the frequency of CD3+, CD8+ and CD4+ lymphocytes, hold prognostic value suggesting their protective role in antitumor immunity.
Collapse
Affiliation(s)
- Jara Palomero
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carla Panisello
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Maria Lozano-Rabella
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Ricky Tirtakasuma
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Judit Díaz-Gómez
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Daniela Grases
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Helena Pasamar
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Laura Arregui
- HUB-ICO-IDIBELL Biobank, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Spain
| | - Eduard Dorca Duch
- Pathology, Bellvitge University Hospital, IDIBELL, L'Hospitalet de Llobregat, Spain
| | | | - Ana Vivancos
- Cancer Genomics, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - Carlos E de Andrea
- Pathology, Clinica Universidad de Navarra, Pamplona, Spain,Centro de Investigación Biomedica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ignacio Melero
- Centro de Investigación Biomedica en Red de Cáncer (CIBERONC), Madrid, Spain,Program of Immunology and Immunotherapy, CIMA Universidad de Navarra, Pamplona, Spain,Navarra Institute for Health Research IDISNA, Pamplona, Spain
| | - Jordi Ponce
- Department of Gynaecology, Bellvitge University Hospital, L'Hospitalet de Llobregat, Spain
| | - August Vidal
- Pathology, Bellvitge University Hospital, IDIBELL, L'Hospitalet de Llobregat, Spain,Centro de Investigación Biomedica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Josep Maria Piulats
- Medical Oncology, Catalan Institute of Oncology (ICO), IDIBELL-OncoBell, L'Hospitalet de Llobregat, Spain
| | - Xavier Matias-Guiu
- Pathology, Bellvitge University Hospital, IDIBELL, L'Hospitalet de Llobregat, Spain,Centro de Investigación Biomedica en Red de Cáncer (CIBERONC), Madrid, Spain,Pathology, Arnau de Vilanova University Hospital, University of LLeida, IRBLLEIDA, Lleida, Spain
| | - Alena Gros
- Tumor Immunology and Immunotherapy, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| |
Collapse
|
20
|
Agrafiotis AC, Siozopoulou V, Hendriks JMH, Pauwels P, Koljenovic S, Van Schil PE. Tumor Microenvironment in Thymic Epithelial Tumors: A Narrative Review. Cancers (Basel) 2022; 14:cancers14246082. [PMID: 36551568 PMCID: PMC9775621 DOI: 10.3390/cancers14246082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The tumor microenvironment (TME) is a complex and constantly changing entity. The TME consists of stromal cells, fibroblasts, endothelial cells, and innate and adaptive immune cells. Cancer development and progression occurs through this interplay between the tumor and the adjacent stroma. Cancer cells are capable of modifying their microenvironment by secreting various message-carrying molecules, such as cytokines, chemokines, and other factors. This action causes a reprogramming of the neighboring cells, which are enabled to play a crucial role in tumor survival and progression. The study of TME has many clinical implications in terms of cancer therapeutics because many new drugs, such as antibodies, kinase inhibitors, and liposome formulations that can encapsulate anti-cancer drugs, can be developed. Although chemotherapy is considered the standard of treatment for advanced disease, recent research has brought to light immunotherapy as a possible systemic alternative. However, the complex structure and function of the thymus hinders its routine use in clinical practice. The aim of this review paper is to discuss the recent advances in the investigation of the unique characteristics of the TME of thymic epithelial tumors that could possibly lead to the development of novel promising therapies.
Collapse
Affiliation(s)
- Apostolos C. Agrafiotis
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
| | - Vasiliki Siozopoulou
- Laboratory of Pathology, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
| | - Jeroen M. H. Hendriks
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
| | - Patrick Pauwels
- Laboratory of Pathology, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
| | - Senada Koljenovic
- Laboratory of Pathology, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
| | - Paul E. Van Schil
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, University of Antwerp, B-2650 Edegem, Belgium
- Correspondence:
| |
Collapse
|
21
|
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.
Collapse
|
22
|
Ge W, Dong Y, Deng Y, Chen L, Chen J, Liu M, Wu J, Wang W, Ma X. Potential biomarkers: Identifying powerful tumor specific T cells in adoptive cellular therapy. Front Immunol 2022; 13:1003626. [PMID: 36451828 PMCID: PMC9702804 DOI: 10.3389/fimmu.2022.1003626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/27/2022] [Indexed: 12/01/2023] Open
Abstract
Tumor-specific T cells (TSTs) are essential components for the success of personalized tumor-infiltrating lymphocyte (TIL)-based adoptive cellular therapy (ACT). Therefore, the selection of a common biomarker for screening TSTs in different tumor types, followed by ex vivo expansion to clinical number levels can generate the greatest therapeutic effect. However, studies on shared biomarkers for TSTs have not been realized yet. The present review summarizes the similarities and differences of a number of biomarkers for TSTs in several tumor types studied in the last 5 years, and the advantages of combining biomarkers. In addition, the review discusses the possible shortcomings of current biomarkers and highlights strategies to identify TSTs accurately using intercellular interactions. Finally, the development of TSTs in personalized TIL-based ACT for broader clinical applications is explored.
Collapse
Affiliation(s)
- Wu Ge
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yuqian Dong
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yao Deng
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lujuan Chen
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Juan Chen
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Muqi Liu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Jianmin Wu
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Wei Wang
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoqian Ma
- Cell Transplantation and Gene Therapy Institute, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, The Third Xiangya Hospital of Central South University, Changsha, China
| |
Collapse
|
23
|
Ji F, Chen L, Chen Z, Luo B, Wang Y, Lan X. TCR repertoire and transcriptional signatures of circulating tumour-associated T cells facilitate effective non-invasive cancer detection. Clin Transl Med 2022; 12:e853. [PMID: 36134717 PMCID: PMC9494610 DOI: 10.1002/ctm2.853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/11/2022] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Fansen Ji
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Tsinghua University, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
| | - Lin Chen
- School of Medicine, Tsinghua University, Beijing, China.,General Surgery Department, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Zhizhuo Chen
- School of Life Science, Tsinghua University, Beijing, China
| | - Bin Luo
- General Surgery Department, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
| | - Yongwang Wang
- Department of Anesthesiology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xun Lan
- Tsinghua-Peking Center for Life Sciences, MOE Key Laboratory of Tsinghua University, Beijing, China.,School of Medicine, Tsinghua University, Beijing, China
| |
Collapse
|
24
|
Ma Y, Liu F, Li B, Peng K, Zhou H, Xu Y, Qiao D, Deng L, Tian G, Nielsen M, Wang M. Identification and assessment of TCR-T cells targeting an epitope conserved in SARS-CoV-2 variants for the treatment of COVID-19. Int Immunopharmacol 2022; 112:109283. [PMID: 36201943 PMCID: PMC9515335 DOI: 10.1016/j.intimp.2022.109283] [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: 07/27/2022] [Revised: 09/09/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022]
Abstract
Background Coronavirus disease 2019 (COVID-19) continues to be a major global public health challenge, with the emergence of variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Current vaccines or monoclonal antibodies may not well be protect against infection with new SARS-CoV-2 variants. Unlike antibody-based treatment, T cell-based therapies such as TCR-T cells can target epitopes that are highly conserved across different SARS-CoV-2 variants. Reportedly, T cell-based immunity alone can restrict SARS-CoV-2 replication. Methods In this study, we identified two TCRs targeting the RNA-dependent RNA polymerase (RdRp) protein in CD8 + T cells. Functional evaluation by transducing these TCRs into CD8 + or CD4 + T cells confirmed their specificity. Results Combinations of inflammatory and anti-inflammatory cytokines secreted by CD8 + and CD4 + T cells can help control COVID-19 in patients. Moreover, the targeted epitope is highly conserved in all emerged SARS-CoV-2 variants, including the Omicron. It is also conserved in the seven coronaviruses that infect humans and more broadly in the subfamily Coronavirinae. Conclusions The pan-genera coverage of mutant epitopes from the Coronavirinae subfamily by the two TCRs highlights the unique strengths of TCR-T cell therapies in controlling the ongoing pandemic and in preparing for the next coronavirus outbreak.
Collapse
|
25
|
Tumor Infiltrating Lymphocyte (TIL) Therapy for Solid Tumor Treatment: Progressions and Challenges. Cancers (Basel) 2022; 14:cancers14174160. [PMID: 36077696 PMCID: PMC9455018 DOI: 10.3390/cancers14174160] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 12/15/2022] Open
Abstract
Over the past decade, immunotherapy, especially cell-based immunotherapy, has provided new strategies for cancer therapy. Recent clinical studies demonstrated that adopting cell transfer of tumor-infiltrating lymphocytes (TILs) for advanced solid tumors showed good efficacy. TIL therapy is a type of cell-based immunotherapy using the patient’s own immune cells from the microenvironment of the solid tumor to kill tumor cells. In this review, we provide a comprehensive summary of the current strategies and challenges in TIL isolation and generation. Moreover, the current clinical experience of TIL therapy is summarized and discussed, with an emphasis on lymphodepletion regimen, the use of interleukin-2, and related toxicity. Furthermore, we highlight the clinical trials where TIL therapy is used independently and in combination with other types of therapy for solid cancers. Finally, the limitations, future potential, and directions of TIL therapy for solid tumor treatment are also discussed.
Collapse
|
26
|
Abstract
The protocol describes the procedure of antigen-specific T cell generation and TCR identification for the use in adoptive T cell therapy. We describe two paths of generating antigen-specific T cells, first, T cell stimulation with autologous dendritic cells pulsed with antigen peptide, second, in vivo T cell stimulation with peptide or DNA by gene gun application in a suitable mouse model followed by in vitro enrichment of peptide-reactive T cells. Peptide-stimulated T cells are sorted by fluorescence-activated cell sorting for CD107α or IFNγ expression and subsequently isolated RNA is used in a 5' rapid amplification of cDNA ends (RACE )-PCR specific for TCR for TCR chain identification. After retroviral cloning, it is re-expressed on human T cells to test its applicability in adoptive T cell therapy.
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Development of Cancer Immunotherapies. Cancer Treat Res 2022; 183:1-48. [PMID: 35551655 DOI: 10.1007/978-3-030-96376-7_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cancer immunotherapy, or the utilization of components of the immune system to target and eliminate cancer, has become a highly active area of research in the past several decades and a common treatment strategy for several cancer types. The concept of harnessing the immune system for this purpose originated over 100 years ago when a physician by the name of William Coley successfully treated several of his cancer patients with a combination of live and attenuated bacteria, later known as "Coley's Toxins", after observing a subset of prior patients enter remission following their diagnosis with the common bacterial infection, erysipelas. However, it was not until late in the twentieth century that cancer immunotherapies were developed for widespread use, thereby transforming the treatment landscape of numerous cancer types. Pivotal studies elucidating molecular and cellular functions of immune cells, such as the discovery of IL-2 and production of monoclonal antibodies, fostered the development of novel techniques for studying the immune system and ultimately the development and approval of several cancer immunotherapies by the United States Food and Drug Association in the 1980s and 1990s, including the tuberculosis vaccine-Bacillus Calmette-Guérin, IL-2, and the CD20-targeting monoclonal antibody. Approval of the first therapeutic cancer vaccine, Sipuleucel-T, for the treatment of metastatic castration-resistant prostate cancer and the groundbreaking success and approval of immune checkpoint inhibitors and chimeric antigen receptor T cell therapy in the last decade, have driven an explosion of interest in and pursuit of novel cancer immunotherapy strategies. A broad range of modalities ranging from antibodies to adoptive T cell therapies is under investigation for the generalized treatment of a broad spectrum of cancers as well as personalized medicine. This chapter will focus on the recent advances, current strategies, and future outlook of immunotherapy development for the treatment of cancer.
Collapse
|
29
|
Hanada KI, Zhao C, Gil-Hoyos R, Gartner JJ, Chow-Parmer C, Lowery FJ, Krishna S, Prickett TD, Kivitz S, Parkhurst MR, Wong N, Rae Z, Kelly MC, Goff SL, Robbins PF, Rosenberg SA, Yang JC. A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers. Cancer Cell 2022; 40:479-493.e6. [PMID: 35452604 PMCID: PMC9196205 DOI: 10.1016/j.ccell.2022.03.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 02/08/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023]
Abstract
A common theme across multiple successful immunotherapies for cancer is the recognition of tumor-specific mutations (neoantigens) by T cells. The rapid discovery of such antigen responses could lead to improved therapies through the adoptive transfer of T cells engineered to express neoantigen-reactive T cell receptors (TCRs). Here, through CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) and TCR-seq of non-small cell lung cancer (NSCLC) tumor-infiltrating lymphocytes (TILs), we develop a neoantigen-reactive T cell signature based on clonotype frequency and CD39 protein and CXCL13 mRNA expression. Screening of TCRs selected by the signature allows us to identify neoantigen-reactive TCRs with a success rate of 45% for CD8+ and 66% for CD4+ T cells. Because of the small number of samples analyzed (4 patients), generalizability remains to be tested. However, this approach can enable the quick identification of neoantigen-reactive TCRs and expedite the engineering of personalized neoantigen-reactive T cells for therapy.
Collapse
Affiliation(s)
- Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Chihao Zhao
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raul Gil-Hoyos
- 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
| | - Christopher Chow-Parmer
- 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
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott Kivitz
- 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
| | - Nathan Wong
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Frederick, MD 21701, USA
| | - Zachary Rae
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, 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
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Kiessling A, Ramanathan K, Nilsson OB, Notari L, Renken S, Kiessling R, Grönlund H, Wickström SL. Generation of Tumor-Specific Cytotoxic T Cells From Blood via In Vitro Expansion Using Autologous Dendritic Cells Pulsed With Neoantigen-Coupled Microbeads. Front Oncol 2022; 12:866763. [PMID: 35433456 PMCID: PMC9009257 DOI: 10.3389/fonc.2022.866763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
For the past decade, adoptive cell therapy including tumor-infiltrating lymphocytes, genetically modified cytotoxic lymphocytes expressing a chimeric antigen receptor, or a novel T-cell receptor has revolutionized the treatment of many cancers. Progress within exome sequencing and neoantigen prediction technologies provides opportunities for further development of personalized immunotherapies. In this study, we present a novel strategy to deliver in silico predicted neoantigens to autologous dendritic cells (DCs) using paramagnetic beads (EpiTCer beads). DCs pulsed with EpiTCer beads are superior in enriching for healthy donor and patient blood-derived tumor-specific CD8+ T cells compared to DC loaded with whole-tumor lysate or 9mer neoantigen peptides. A dose-dependent effect was observed, with higher EpiTCer bead per DC being favorable. We concluded that CD8+ T cells enriched by DC loaded with EpiTCer beads are tumor specific with limited tumor cross-reactivity and low recognition of autologous non-activated monocytes or CD8+ T cells. Furthermore, tumor specificity and recognition were improved and preserved after additional expansion using our Good Manufacturing Process (GMP)-compatible rapid expansion protocol. Phenotypic analysis of patient-derived EpiTCer DC expanded CD8+ T cells revealed efficient maturation, with high frequencies of central memory and effector memory T cells, similar to those observed in autologous expanded tumor-infiltrating lymphocytes. These results indicate that DC pulsed with EpiTCer beads enrich for a T-cell population with high capacity of tumor recognition and elimination, which are features needed for a T-cell product to be used for personalized adoptive cell therapy.
Collapse
Affiliation(s)
- Adela Kiessling
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ola B. Nilsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- NEOGAP Therapeutics AB, Stockholm, Sweden
| | - Luigi Notari
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- NEOGAP Therapeutics AB, Stockholm, Sweden
| | - Stefanie Renken
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Kiessling
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Theme Cancer, Patient Area Head and Neck, Lung and Skin, Karolinska University Hospital, Stockholm, Sweden
| | - Hans Grönlund
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- NEOGAP Therapeutics AB, Stockholm, Sweden
| | - Stina L. Wickström
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- NEOGAP Therapeutics AB, Stockholm, Sweden
- Theme Cancer, Patient Area Head and Neck, Lung and Skin, Karolinska University Hospital, Stockholm, Sweden
- *Correspondence: Stina L. Wickström,
| |
Collapse
|
32
|
Genetic Modification of T Cells for the Immunotherapy of Cancer. Vaccines (Basel) 2022; 10:vaccines10030457. [PMID: 35335089 PMCID: PMC8949949 DOI: 10.3390/vaccines10030457] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/05/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
Immunotherapy is a beneficial treatment approach for multiple cancers, however, current therapies are effective only in a small subset of patients. Adoptive cell transfer (ACT) is a facet of immunotherapy where T cells targeting the tumor cells are transferred to the patient with several primary forms, utilizing unmodified or modified T cells: tumor-infiltrating lymphocytes (TIL), genetically modified T cell receptor transduced T cells, and chimeric antigen receptor (CAR) transduced T cells. Many clinical trials are underway investigating the efficacy and safety of these different subsets of ACT, as well as trials that combine one of these subsets with another type of immunotherapy. The main challenges existing with ACT are improving clinical responses and decreasing adverse events. Current research focuses on identifying novel tumor targeting T cell receptors, improving safety and efficacy, and investigating ACT in combination with other immunotherapies.
Collapse
|
33
|
Terada K, Kondo K, Ishigaki H, Nagashima A, Satooka H, Nagano S, Masuda K, Kawamura T, Hirata T, Ogasawara K, Itoh Y, Kawamoto H, Agata Y. Isolation of TCR genes with tumor-killing activity from tumor-infiltrating and circulating lymphocytes in a tumor rejection cynomolgus macaque model. Mol Ther Oncolytics 2022; 24:77-86. [PMID: 35024435 PMCID: PMC8717465 DOI: 10.1016/j.omto.2021.12.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/04/2021] [Indexed: 11/24/2022] Open
Abstract
To develop effective adoptive cell transfer therapy using T cell receptor (TCR)-engineered T cells, it is critical to isolate tumor-reactive TCRs that have potent anti-tumor activity. In humans, tumor-infiltrating lymphocytes (TILs) have been reported to contain CD8+PD-1+ T cells that express tumor-reactive TCRs. Characterization of tumor reactivity of TILs from non-human primate tumors could improve anti-tumor activity of TCR-engineered T cells in preclinical research. In this study, we sought to isolate TCR genes from CD8+PD-1+ T cells among TILs in a cynomolgus macaque model of tumor transplantation in which the tumors were infiltrated with CD8+ T cells and were eventually rejected. We analyzed the repertoire of TCRα and β pairs obtained from single CD8+PD-1+ T cells in TILs and circulating lymphocytes and identified multiple TCR pairs with high frequency, suggesting that T cells expressing these recurrent TCRs were clonally expanded in response to tumor cells. We further showed that the recurrent TCRs exhibited cytotoxic activity to tumor cells in vitro and potent anti-tumor activity in mice transplanted with tumor cells. These results imply that this tumor transplantation macaque model recapitulates key features of human TILs and can serve as a platform toward preclinical studies of non-human primate tumor models.
Collapse
|
34
|
Lowery FJ, Krishna S, Yossef R, Parikh NB, Chatani PD, Zacharakis N, Parkhurst MR, Levin N, Sindiri S, Sachs A, Hitscherich KJ, Yu Z, Vale NR, Lu YC, Zheng Z, Jia L, Gartner JJ, Hill VK, Copeland AR, Nah SK, Masi RV, Gasmi B, Kivitz S, Paria BC, Florentin M, Kim SP, Hanada KI, Li YF, Ngo LT, Ray S, Shindorf ML, Levi ST, Shepherd R, Toy C, Parikh AY, Prickett TD, Kelly MC, Beyer R, Goff SL, Yang JC, Robbins PF, Rosenberg SA. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science 2022; 375:877-884. [PMID: 35113651 PMCID: PMC8996692 DOI: 10.1126/science.abl5447] [Citation(s) in RCA: 162] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen-specific TCR clonotypes (NeoTCRs) from 10 metastatic human tumors to their single-cell transcriptomes, we identified signatures of CD8+ and CD4+ neoantigen-reactive tumor-infiltrating lymphocytes (TILs). Neoantigen-specific TILs exhibited tumor-specific expansion with dysfunctional phenotypes, distinct from blood-emigrant bystanders and regulatory TILs. Prospective prediction and testing of 73 NeoTCR signature-derived clonotypes demonstrated that half of the tested TCRs recognized tumor antigens or autologous tumors. NeoTCR signatures identified TCRs that target driver neoantigens and nonmutated viral or tumor-associated antigens, suggesting a common metastatic TIL exhaustion program. NeoTCR signatures delineate the landscape of TILs across metastatic tumors, enabling successful TCR prediction based purely on TIL transcriptomic states for use in cancer immunotherapy.
Collapse
Affiliation(s)
- Frank J. Lowery
- 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
| | - Rami Yossef
- 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
| | - 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
| | - Maria R. Parkhurst
- 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
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abraham Sachs
- 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
| | - Zhiya Yu
- 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
| | - Yong-Chen Lu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhili Zheng
- 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
| | - Jared J. Gartner
- 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
| | - Amy R. Copeland
- 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
| | - Robert V. Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott Kivitz
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Biman C. Paria
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Florentin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanghyun P. Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ken-ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong F. Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lien T. Ngo
- 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
| | - Mackenzie L. Shindorf
- 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
| | - Ryan Shepherd
- Vector Production Facility, Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Chris Toy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anup Y. Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd D. Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, 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
| | - Rachel Beyer
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie L. Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C. Yang
- 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
| |
Collapse
|
35
|
Characterizing cell interactions at scale with made-to-order droplet ensembles (MODEs). Proc Natl Acad Sci U S A 2022; 119:2110867119. [PMID: 35074872 PMCID: PMC8812558 DOI: 10.1073/pnas.2110867119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/22/2023] Open
Abstract
The study of specific cell–cell interactions at scale would be a significant advancement in single-cell biology with clear utility in immuno-oncology. Our development of Droplet Assembly provides a tool for such studies by extending the benefits of single-cell droplet microfluidics to high-order cell analyses. This technology allows for the construction, sorting, and downstream processing of cell–cell interactions and is compatible with single-cell genomic readouts. Cell–cell interactions are important to numerous biological systems, including tissue microenvironments, the immune system, and cancer. However, current methods for studying cell combinations and interactions are limited in scalability, allowing just hundreds to thousands of multicell assays per experiment; this limited throughput makes it difficult to characterize interactions at biologically relevant scales. Here, we describe a paradigm in cell interaction profiling that allows accurate grouping of cells and characterization of their interactions for tens to hundreds of thousands of combinations. Our approach leverages high-throughput droplet microfluidics to construct multicellular combinations in a deterministic process that allows inclusion of programmed reagent mixtures and beads. The combination droplets are compatible with common manipulation and measurement techniques, including imaging, barcode-based genomics, and sorting. We demonstrate the approach by using it to enrich for chimeric antigen receptor (CAR)-T cells that activate upon incubation with target cells, a bottleneck in the therapeutic T cell engineering pipeline. The speed and control of our approach should enable valuable cell interaction studies.
Collapse
|
36
|
Zur RT, Adler G, Shamalov K, Tal Y, Ankri C, Cohen CJ. Adoptive T-cell Immunotherapy: Perfecting Self-Defenses. EXPERIENTIA SUPPLEMENTUM (2012) 2022; 113:253-294. [PMID: 35165867 DOI: 10.1007/978-3-030-91311-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
As an important part of the immune system, T lymphocytes exhibit undoubtedly an important role in targeting and eradicating cancer. However, despite these characteristics, their natural antitumor response may be insufficient. Numerous clinical trials in terminally ill cancer patients testing the design of novel and efficient immunotherapeutic approaches based on the adoptive transfer of autologous tumor-specific T lymphocytes have shown encouraging results. Moreover, this also led to the approval of engineered T-cell therapies in patients. Herein, we will expand on the development and the use of such strategies using tumor-infiltrating lymphocytes or genetically engineered T-cells. We will also comment on the requirements and potential hurdles encountered when elaborating and implementing such treatments as well as the exciting prospects for this kind of emerging personalized medicine therapy.
Collapse
Affiliation(s)
- Raphaëlle Toledano Zur
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Galit Adler
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Katerina Shamalov
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Yair Tal
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Chen Ankri
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Cyrille J Cohen
- Laboratory of Tumor Immunology and Immunotherapy, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
| |
Collapse
|
37
|
Arnaud M, Chiffelle J, Genolet R, Navarro Rodrigo B, Perez MAS, Huber F, Magnin M, Nguyen-Ngoc T, Guillaume P, Baumgaertner P, Chong C, Stevenson BJ, Gfeller D, Irving M, Speiser DE, Schmidt J, Zoete V, Kandalaft LE, Bassani-Sternberg M, Bobisse S, Coukos G, Harari A. Sensitive identification of neoantigens and cognate TCRs in human solid tumors. Nat Biotechnol 2022; 40:656-660. [PMID: 34782741 PMCID: PMC9110298 DOI: 10.1038/s41587-021-01072-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 08/20/2021] [Indexed: 12/18/2022]
Abstract
The identification of patient-specific tumor antigens is complicated by the low frequency of T cells specific for each tumor antigen. Here we describe NeoScreen, a method that enables the sensitive identification of rare tumor (neo)antigens and of cognate T cell receptors (TCRs) expressed by tumor-infiltrating lymphocytes. T cells transduced with tumor antigen-specific TCRs identified by NeoScreen mediate regression of established tumors in patient-derived xenograft mice.
Collapse
Affiliation(s)
- Marion Arnaud
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Raphael Genolet
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Blanca Navarro Rodrigo
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Marta A. S. Perez
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Florian Huber
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Morgane Magnin
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Tu Nguyen-Ngoc
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Philippe Guillaume
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Petra Baumgaertner
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Chloe Chong
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Brian J. Stevenson
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Gfeller
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Melita Irving
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniel E. Speiser
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Julien Schmidt
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Vincent Zoete
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lana E. Kandalaft
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Michal Bassani-Sternberg
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sara Bobisse
- grid.9851.50000 0001 2165 4204Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland ,grid.9851.50000 0001 2165 4204Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - George Coukos
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland. .,Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. .,Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
| | - Alexandre Harari
- Ludwig Institute for Cancer Research, Lausanne Branch - University of Lausanne (UNIL), Lausanne, Switzerland. .,Centre des Thérapies Expérimentales (CTE), Department of Oncology - Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland. .,Department of Oncology - University of Lausanne (UNIL) and Lausanne University Hospital (CHUV), Lausanne, Switzerland.
| |
Collapse
|
38
|
Eiva MA, Omran DK, Chacon JA, Powell DJ. Systematic analysis of CD39, CD103, CD137, and PD-1 as biomarkers for naturally occurring tumor antigen-specific TILs. Eur J Immunol 2022; 52:96-108. [PMID: 34505280 PMCID: PMC8755575 DOI: 10.1002/eji.202149329] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/07/2021] [Accepted: 09/10/2021] [Indexed: 01/03/2023]
Abstract
The detection of tumor-specific T cells in solid tumors is integral to interrogate endogenous antitumor responses and to advance downstream therapeutic applications. Multiple biomarkers are reported to identify endogenous tumor-specific tumor-infiltrating lymphocytes (TILs), namely CD137, PD-1, CD103, and CD39; however, a direct comparison of these molecules has yet to be performed. We evaluated these biomarkers in primary human ovarian tumor samples using single-cell mass cytometry to compare their relative phenotypic profiles, and examined their response to autologous tumor cells ex vivo. PD-1+ , CD103+ , and CD39+ TILs all contain a CD137+ cell subset, while CD137+ TILs highly co-express the aforementioned markers. CD137+ TILs exhibit the highest expression of cytotoxic effector molecules compared to PD-1+ , CD103+ , or CD39+ TILs. Removal of CD137+ cells from PD-1+ , CD103+ , or CD39+ TILs diminish their IFN-γ secretion in response to autologous tumor cell stimulation, while CD137+ TILs maintain high HLA-dependent IFN-γ secretion. CD137+ TILs exhibited an exhausted phenotype but with CD28 co-expression, suggesting possible receptiveness to reinvigoration via immune checkpoint blockade. Together, our findings demonstrate that the antitumor abilities of PD-1+ , CD103+ , and CD39+ TILs are mainly derived from a subset of CD137-expressing TILs, implicating CD137 as a more selective biomarker for naturally occurring tumor-specific TILs.
Collapse
Affiliation(s)
- Monika A. Eiva
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dalia K. Omran
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jessica A. Chacon
- Paul L Foster School of Medicine and Woody L. Hunt School of Dental Medicine, Texas Tech University Health Sciences Center, El Paso, Texas, USA
| | - Daniel J. Powell
- Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Center for Cellular Immunotherapies, Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania, USA,Department of Pathology and Laboratory Medicine, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
39
|
Gartner JJ, Parkhurst MR, Gros A, Tran E, Jafferji MS, Copeland A, Hanada KI, Zacharakis N, Lalani A, Krishna S, Sachs A, Prickett TD, Li YF, Florentin M, Kivitz S, Chatmon SC, Rosenberg SA, Robbins PF. A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types. NATURE CANCER 2021; 2:563-574. [PMID: 34927080 DOI: 10.1038/s43018-021-00197-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tumor neoepitopes presented by major histocompatibility complex (MHC) class I are recognized by tumor-infiltrating lymphocytes (TIL) and are targeted by adoptive T-cell therapies. Identifying which mutant neoepitopes from tumor cells are capable of recognition by T cells can assist in the development of tumor-specific, cell-based therapies and can shed light on antitumor responses. Here, we generate a ranking algorithm for class I candidate neoepitopes by using next-generation sequencing data and a dataset of 185 neoepitopes that are recognized by HLA class I-restricted TIL from individuals with metastatic cancer. Random forest model analysis showed that the inclusion of multiple factors impacting epitope presentation and recognition increased output sensitivity and specificity compared to the use of predicted HLA binding alone. The ranking score output provides a set of class I candidate neoantigens that may serve as therapeutic targets and provides a tool to facilitate in vitro and in vivo studies aimed at the development of more effective immunotherapies.
Collapse
Affiliation(s)
- Jared J Gartner
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria R Parkhurst
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alena Gros
- Vall d'Hebron Institute of Oncology (VHIO), Cellex Center, Barcelona, Spain
| | - Eric Tran
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, USA
| | | | - Amy Copeland
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ken-Ichi Hanada
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nikolaos Zacharakis
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Almin Lalani
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sri Krishna
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abraham Sachs
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Todd D Prickett
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yong F Li
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maria Florentin
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Scott Kivitz
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Samuel C Chatmon
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Steven A Rosenberg
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul F Robbins
- Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
40
|
Zhu Y, Qian Y, Li Z, Li Y, Li B. Neoantigen-reactive T cell: An emerging role in adoptive cellular immunotherapy. MedComm (Beijing) 2021; 2:207-220. [PMID: 34766142 PMCID: PMC8491202 DOI: 10.1002/mco2.41] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 01/06/2023] Open
Abstract
Adoptive cellular immunotherapy harnessing the intrinsic immune system for precise treatment has exhibited preliminary success against malignant tumors. As one of the emerging roles in adoptive cellular immunotherapy, neoantigen-reactive T cell (NRT) focuses on the antigens expressed only by tumor cells. It exclusively obliterates tumor and spares normal tissues, achieving more satisfying effects. However, the development of NRT immunotherapy remains in a relatively primitive stage. Current challenges include identification of NRTs and maintenance of adoptive cell efficacy in vivo. The possible side effects and other limitations of this treatment also hinder its application. Here, we present an overview of NRT immunotherapy and discuss the progress and challenges as well as the prospects in this promising field.
Collapse
Affiliation(s)
- Yicheng Zhu
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Youkun Qian
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Zhile Li
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Yangyang Li
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| | - Bin Li
- Department of Immunology and Microbiology, Shanghai Institute of Immunology Shanghai Jiao Tong University School of Medicine Shanghai China
| |
Collapse
|
41
|
Zhu WJ, Hu ZF, Yuan Z. Progress in research of tumor infiltrating lymphocytes in pancreatic cancer. Shijie Huaren Xiaohua Zazhi 2021; 29:1207-1214. [DOI: 10.11569/wcjd.v29.i21.1207] [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] [Indexed: 02/07/2023] Open
Abstract
The 5-year survival rate of pancreatic cancer is less than 5%, and the only available treatments, surgery, chemotherapy, and chemoradiation, have shown limited effectiveness. Therefore, alternative treatment strategies are urgently needed. In recent years, tumor infiltrating lymphocyte (TIL) therapy has shown promising successes in the treatment of some types of solid tumors because of its diverse TCR clonality, superior tumor-homing ability, and low off-target toxicity. The significant association between a high TIL density in pancreatic cancer tissue and a good clinical outcome and success of pancreatic cancer-specific TIL expansion ex vivo potentiates the rationality of the TIL therapy in pancreatic cancer. However, there are still many challenges ahead, such as neoantigen screening, rapid cell expansion, and low cytotoxicity. This article reviews the recent advances and limitations of TIL therapy in pancreatic cancer and discusses its future directions.
Collapse
Affiliation(s)
- Wen-Jun Zhu
- CAR-T (Shanghai) Cell Biotechnology Co., Ltd, Shanghai 200433, China
| | - Zhan-Fei Hu
- CAR-T (Shanghai) Cell Biotechnology Co., Ltd, Shanghai 200433, China
| | - Zhou Yuan
- The Sixth People's Hospital Affiliated to Shanghai Jiaotong University, Shanghai 200233, China
| |
Collapse
|
42
|
Draghi A, Chamberlain CA, Khan S, Papp K, Lauss M, Soraggi S, Radic HD, Presti M, Harbst K, Gokuldass A, Kverneland A, Nielsen M, Westergaard MCW, Andersen MH, Csabai I, Jönsson G, Szallasi Z, Svane IM, Donia M. Rapid Identification of the Tumor-Specific Reactive TIL Repertoire via Combined Detection of CD137, TNF, and IFNγ, Following Recognition of Autologous Tumor-Antigens. Front Immunol 2021; 12:705422. [PMID: 34707600 PMCID: PMC8543011 DOI: 10.3389/fimmu.2021.705422] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022] Open
Abstract
Detecting the entire repertoire of tumor-specific reactive tumor-infiltrating lymphocytes (TILs) is essential for investigating their immunological functions in the tumor microenvironment. Current in vitro assays identifying tumor-specific functional activation measure the upregulation of surface molecules, de novo production of antitumor cytokines, or mobilization of cytotoxic granules following recognition of tumor-antigens, yet there is no widely adopted standard method. Here we established an enhanced, yet simple, method for identifying simultaneously CD8+ and CD4+ tumor-specific reactive TILs in vitro, using a combination of widely known and available flow cytometry assays. By combining the detection of intracellular CD137 and de novo production of TNF and IFNγ after recognition of naturally-presented tumor antigens, we demonstrate that a larger fraction of tumor-specific and reactive CD8+ TILs can be detected in vitro compared to commonly used assays. This assay revealed multiple polyfunctionality-based clusters of both CD4+ and CD8+ tumor-specific reactive TILs. In situ, the combined detection of TNFRSF9, TNF, and IFNG identified most of the tumor-specific reactive TIL repertoire. In conclusion, we describe a straightforward method for efficient identification of the tumor-specific reactive TIL repertoire in vitro, which can be rapidly adopted in most cancer immunology laboratories.
Collapse
Affiliation(s)
- Arianna Draghi
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Christopher Aled Chamberlain
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Shawez Khan
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Krisztian Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Martin Lauss
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Samuele Soraggi
- Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
| | - Haja Dominike Radic
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Mario Presti
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Katja Harbst
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | - Aishwarya Gokuldass
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Anders Kverneland
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Morten Nielsen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | | | - Mads Hald Andersen
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Istvan Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Göran Jönsson
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden
- Lund University Cancer Centre, Lund University, Lund, Sweden
| | | | - Inge Marie Svane
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| | - Marco Donia
- National Center for Cancer Immune Therapy (CCIT-DK), Department of Oncology, Copenhagen University Hospital, Herlev, Denmark
| |
Collapse
|
43
|
Yang C, Zhang Z, Tang X, Zhang X, Chen Y, Hu T, Zhang H, Guan M, Zhang X, Wu Z. Pan-cancer analysis reveals homologous recombination deficiency score as a predictive marker for immunotherapy responders. Hum Cell 2021; 35:199-213. [PMID: 34628623 DOI: 10.1007/s13577-021-00630-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
The immune context of the tumor microenvironment (TME) is critical for effective immunotherapy. Nonetheless, DNA-based biomarkers for the immune-sensitive TME and the identification of immune checkpoint inhibitor (ICI) responders are under-explored. This study aims to comprehensively landscape the homologous recombination deficiency (HRD) score, an emerging hallmark for tumor genome instability that triggers immune responsiveness across major cancer types, and to unveil their link to the TME and immunotherapeutic response. The HRD-associated genomic scars were characterized in 9088 tumor samples across 32 cancer types from TCGA. We evaluated the HRD score's performance in classifying ICI responders using an independent breast cancer cohort (GSE87049) and 11 in vivo murine mammary tumor models treated with anti-PD1/CTLA4 regimen (GSE124821). This study revealed a broad association between HRD-high genotype and neoantigenesis in the major cancer types including bladder cancer, breast cancer, head and neck squamous carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian cancer, and sarcoma. Tumors with high HRD score bears increased leukocyte infiltration and lymphocyte fraction and demonstrated immune-sensitive microenvironment. The tumor immune dysfunction and exclusion (TIDE) model further confirmed HRD score-high genotype as a potential predictor for ICI immunotherapy responders in breast cancer. In conclusion, tumors with high HRD score exhibit an immune-sensitive TME. The HRD-high genotype is a promising marker for identifying ICI therapy responders among breast cancer patients.
Collapse
Affiliation(s)
- Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zijing Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yuming Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tingting Hu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Huating Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, 518002, China.
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| |
Collapse
|
44
|
Tang Y, Zhang AXJ, Chen G, Wu Y, Gu W. Prognostic and therapeutic TILs of cervical cancer-Current advances and future perspectives. MOLECULAR THERAPY-ONCOLYTICS 2021; 22:410-430. [PMID: 34553029 PMCID: PMC8430272 DOI: 10.1016/j.omto.2021.07.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cervical cancer is a top lethal cancer for women worldwide. Although screening and vaccination programs are available in many countries, resulting in the decline of new cases, this is not true for developing countries where there are many new cases and related deaths. Cancer immunotherapy through adaptive cell therapy (ACT) has been applied in clinics, but now much attention is focused on autogenic tumor-infiltrating lymphocyte (TIL)-based therapy, which has shown more specificity and better ability to inhibit tumor growth. Data from melanoma and cervical cancers confirm that tumor-specific T cells in TILs can be expanded for more specific and effective ACT. Moreover, TILs are derived from individual patients and are ready to home back to kill tumor cells after patient infusion, aligning well with personalized and precision medicine. In addition to therapy, TIL cell types and numbers are good indicators of host immune response to the tumor, and thus they have significant values in prognosis. Because of the special relationship with human papillomavirus (HPV) infection, cervical cancer has some specialties in TIL-based prognosis and therapy. In this review, we summarize the recent advances in the prognostic significance of TILs and TIL-based therapy for cervical cancer and discuss related perspectives.
Collapse
Affiliation(s)
- Ying Tang
- Institute of Tumor, Guangzhou University of Chinese Medicine, Guangzhou, China.,Gillion ITM Research Institute, Guangzhou Hongkeyuan, Guangzhou, China
| | - Anne X J Zhang
- Gillion ITM Research Institute, Guangzhou Hongkeyuan, Guangzhou, China
| | - Guangyu Chen
- Gillion ITM Research Institute, Guangzhou Hongkeyuan, Guangzhou, China
| | - Yanheng Wu
- Gillion ITM Research Institute, Guangzhou Hongkeyuan, Guangzhou, China
| | - Wenyi Gu
- Gillion ITM Research Institute, Guangzhou Hongkeyuan, Guangzhou, China.,Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
45
|
Leem G, Park J, Jeon M, Kim ES, Kim SW, Lee YJ, Choi SJ, Choi B, Park S, Ju YS, Jung I, Kim S, Shin EC, Lee JY, Park SH. 4-1BB co-stimulation further enhances anti-PD-1-mediated reinvigoration of exhausted CD39 + CD8 T cells from primary and metastatic sites of epithelial ovarian cancers. J Immunother Cancer 2021; 8:jitc-2020-001650. [PMID: 33335029 PMCID: PMC7745695 DOI: 10.1136/jitc-2020-001650] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
Background Responses to immunotherapy vary between different cancer types and sites. Here, we aimed to investigate features of exhaustion and activation in tumor-infiltrating CD8 T cells at both the primary and metastatic sites in epithelial ovarian cancer. Methods Tumor tissues and peripheral blood were obtained from 65 patients with ovarian cancer. From these samples, we isolated tumor-infiltrating lymphocytes (TILs) and peripheral blood mononuclear cells. These cells were used for immunophenotype using multicolor flow cytometry, gene expression profile using RNA sequencing and ex vivo functional restoration assays. Results We found that CD39+ CD8 TILs were enriched with tumor-specific CD8 TILs, and that the activation status of these cells was determined by the differential programmed cell death protein 1 (PD-1) expression level. CD39+ CD8 TILs with high PD-1 expression (PD-1high) exhibited features of highly tumor-reactive and terminally exhausted phenotypes. Notably, PD-1high CD39+ CD8 TILs showed similar characteristics in terms of T-cell exhaustion and activation between the primary and metastatic sites. Among co-stimulatory receptors, 4-1BB was exclusively overexpressed in CD39+ CD8 TILs, especially on PD-1high cells, and 4-1BB-expressing cells displayed immunophenotypes indicating higher degrees of T-cell activation and proliferation, and less exhaustion, compared with cells not expressing 4-1BB. Importantly, 4-1BB agonistic antibodies further enhanced the anti-PD-1-mediated reinvigoration of exhausted CD8 TILs from both primary and metastatic sites. Conclusion Severely exhausted PD-1high CD39+ CD8 TILs displayed a distinctly heterogeneous exhaustion and activation status determined by differential 4-1BB expression levels, providing rationale and evidence for immunotherapies targeting co-stimulatory receptor 4-1BB in ovarian cancers.
Collapse
Affiliation(s)
- Galam Leem
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Junsik Park
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Minwoo Jeon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Eui-Soon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sang Wun Kim
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Jae Lee
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seong Jin Choi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Baekgyu Choi
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Sunghoon Kim
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jung Yun Lee
- Department of Obstetrics and Gynecology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| |
Collapse
|
46
|
Mösch A, Frishman D. TCRpair: prediction of functional pairing between HLA-A*02:01-restricted T cell receptor α and β chains. Bioinformatics 2021; 37:3938-3940. [PMID: 34487137 DOI: 10.1093/bioinformatics/btab573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/21/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
SUMMARY The ability of a T cell to recognize foreign peptides is defined by a single α and a single β hypervariable complementarity determining region (CDR3), which together form the T cell receptor (TCR) heterodimer. In ∼30%-35% of T cells, two α chains are expressed at the mRNA level but only one α chain is part of the functional TCR. This effect can also be observed for β chains, although it is less common. The identification of functional α/β chain pairs is instrumental in high-throughput characterization of therapeutic TCRs. TCRpair is the first method that predicts whether an α and β chain pair forms a functional, HLA-A*02:01 specific TCR without requiring the sequence of a recognized peptide. By taking additional amino acids flanking the CDR3 regions into account, TCRpair achieves an AUC of 0.71. AVAILABILITY TCRpair is implemented in Python using TensorFlow 2.0 and is freely available at https://www.github.com/amoesch/TCRpair. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Anja Mösch
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, 85354, Germany.,Medigene Immunotherapies GmbH, a subsidiary of Medigene AG, Planegg, 82152, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technical University of Munich, Freising, 85354, Germany.,Department of Bioinformatics, Peter the Great Saint Petersburg Polytechnic University, Petersburg, 195251, St Russia
| |
Collapse
|
47
|
Integrin-α V-mediated activation of TGF-β regulates anti-tumour CD8 T cell immunity and response to PD-1 blockade. Nat Commun 2021; 12:5209. [PMID: 34471106 PMCID: PMC8410945 DOI: 10.1038/s41467-021-25322-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 07/29/2021] [Indexed: 12/17/2022] Open
Abstract
TGF-β is secreted in the tumour microenvironment in a latent, inactive form bound to latency associated protein and activated by the integrin αV subunit. The activation of latent TGF-β by cancer-cell-expressed αV re-shapes the tumour microenvironment, and this could affect patient responses to PD-1-targeting therapy. Here we show, using multiplex immunofluorescence staining in cohorts of anti-PD-1 and anti-PD-L1-treated lung cancer patients, that decreased expression of cancer cell αV is associated with improved immunotherapy-related, progression-free survival, as well as with an increased density of CD8+CD103+ tumour-infiltrating lymphocytes. Mechanistically, tumour αV regulates CD8 T cell recruitment, induces CD103 expression on activated CD8+ T cells and promotes their differentiation to granzyme B-producing CD103+CD69+ resident memory T cells via autocrine TGF-β signalling. Thus, our work provides the underlying principle of targeting cancer cell αV for more efficient PD-1 checkpoint blockade therapy. Response to PD-1 checkpoint blockade is unpredictable in lung cancer patients. Here authors show in human lung and mouse tumour models that low or absent αV integrin expression leads to better tumour growth control by anti-PD-1 via reduced TGF-β activation and hence increased infiltration of anti-tumour CD8+ T cells.
Collapse
|
48
|
Verdon DJ, Jenkins MR. Identification and Targeting of Mutant Peptide Neoantigens in Cancer Immunotherapy. Cancers (Basel) 2021; 13:4245. [PMID: 34439399 PMCID: PMC8391927 DOI: 10.3390/cancers13164245] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 12/30/2022] Open
Abstract
In recent decades, adoptive cell transfer and checkpoint blockade therapies have revolutionized immunotherapeutic approaches to cancer treatment. Advances in whole exome/genome sequencing and bioinformatic detection of tumour-specific genetic variations and the amino acid sequence alterations they induce have revealed that T cell mediated anti-tumour immunity is substantially directed at mutated peptide sequences, and the identification and therapeutic targeting of patient-specific mutated peptide antigens now represents an exciting and rapidly progressing frontier of personalized medicine in the treatment of cancer. This review outlines the historical identification and validation of mutated peptide neoantigens as a target of the immune system, and the technical development of bioinformatic and experimental strategies for detecting, confirming and prioritizing both patient-specific or "private" and frequently occurring, shared "public" neoantigenic targets. Further, we examine the range of therapeutic modalities that have demonstrated preclinical and clinical anti-tumour efficacy through specifically targeting neoantigens, including adoptive T cell transfer, checkpoint blockade and neoantigen vaccination.
Collapse
Affiliation(s)
- Daniel J. Verdon
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
| | - Misty R. Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia;
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
- La Trobe Institute of Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
| |
Collapse
|
49
|
Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
Collapse
Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| |
Collapse
|
50
|
Arnaud M, Bobisse S, Chiffelle J, Harari A. The Promise of Personalized TCR-Based Cellular Immunotherapy for Cancer Patients. Front Immunol 2021; 12:701636. [PMID: 34394096 PMCID: PMC8363295 DOI: 10.3389/fimmu.2021.701636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
Mutation-derived neoantigens are now established as attractive targets for cancer immunotherapy. The field of adoptive T cell transfer (ACT) therapy was significantly reshaped by tumor neoantigens and is now moving towards the genetic engineering of T cells with neoantigen-specific T cell receptors (TCRs). Yet, the identification of neoantigen-reactive TCRs remains challenging and the process needs to be adapted to clinical timelines. In addition, the state of recipient T cells for TCR transduction is critical and can affect TCR-ACT efficacy. Here we provide an overview of the main strategies for TCR-engineering, describe the selection and expansion of optimal carrier cells for TCR-ACT and discuss the next-generation methods for rapid identification of relevant TCR candidates for gene transfer therapy.
Collapse
Affiliation(s)
- Marion Arnaud
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sara Bobisse
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Johanna Chiffelle
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Alexandre Harari
- Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland
- Center of Experimental Therapeutics, Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| |
Collapse
|