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Vallacchi V, Vergani E, Cossa M, Gargiuli C, Busico A, Devecchi A, Dugo M, Bergamaschi L, De Cecco L, Cavalieri S, Valeri B, Tamborini E, Gallino G, Del Vecchio M, Santinami M, Sensi M, Rivoltini L, Di Guardo L, Rodolfo M. Multistep tumor genetic evolution and changes in immunogenicity trigger immune-mediated disease eradication in stage IV melanoma: lessons from a single case. J Immunother Cancer 2024; 12:e007612. [PMID: 38177075 PMCID: PMC10773440 DOI: 10.1136/jitc-2023-007612] [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: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Durable remissions are observed in 10%-20% of treated patients with advanced metastatic melanoma but the factors associated with long-term complete clinical responses are largely unknown. Here, we report the molecular characteristics of tumor evolution during disease progression along a 9-year clinical course in a patient with advanced disseminated melanoma who received different treatments, including trametinib, ipilimumab, radiation, vemurafenib, surgical tumor debulking and a second ipilimumab course, ultimately achieving complete long-term disease remission.Longitudinal analyses of therapies-resistant metastatic tumors revealed the effects of different treatments on tumor's microenvironment and immunogenicity, ultimately creating a milieu favorable to immunotherapy response. Monitoring of the temporal dynamics of T cells by analysis of the T cell receptor (TCR) repertoire in the tumor and peripheral blood during disease evolution indicated that T-cell clones with common TCR rearrangements, present at low levels at baseline, were maintained and expanded after immunotherapy, and that TCR diversity increased. Analysis of genetic, molecular, and cellular components of the tumor depicted a multistep process in which treatment with kinase inhibitors strongly conditioned the immune microenvironment creating an inflamed milieu converting cold into hot tumors, while ipilimumab impacted and increased the TCR repertoire, a requirement for tumor rejection.Since the optimal sequencing of treatment with antibodies targeting immune checkpoints and kinase inhibitors for advanced melanoma is still clinically debated, this case indicates that immunotherapy success is possible even after progression on targeted therapy.
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Affiliation(s)
- Viviana Vallacchi
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elisabetta Vergani
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mara Cossa
- Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara Gargiuli
- Applied Research and Technology Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Devecchi
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Medical Oncology, San Raffaele Hospital, Milan, Italy
| | - Laura Bergamaschi
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Integrated Biology of Rare Tumors, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Stefano Cavalieri
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
| | - Barbara Valeri
- Pathology Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Tamborini
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Michele Del Vecchio
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Mario Santinami
- Melanoma Surgery, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marialuisa Sensi
- Applied Research and Technology Development Department, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Licia Rivoltini
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Lorenza Di Guardo
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Monica Rodolfo
- Department of Experimental Oncology, Unit of Translational Immunology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Kim T, Lim H, Jun S, Park J, Lee D, Lee JH, Lee JY, Bang D. Globally shared TCR repertoires within the tumor-infiltrating lymphocytes of patients with metastatic gynecologic cancer. Sci Rep 2023; 13:20485. [PMID: 37993659 PMCID: PMC10665396 DOI: 10.1038/s41598-023-47740-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 11/17/2023] [Indexed: 11/24/2023] Open
Abstract
Gynecologic cancer, including ovarian cancer and endometrial cancer, is characterized by morphological and molecular heterogeneity. Germline and somatic testing are available for patients to screen for pathogenic variants in genes such as BRCA1/2. Tissue expression levels of immunogenomic markers such as PD-L1 are also being used in clinical research. The basic therapeutic approach to gynecologic cancer combines surgery with chemotherapy. Immunotherapy, while not yet a mainstream treatment for gynecologic cancers, is advancing, with Dostarlimab recently receiving approval as a treatment for endometrial cancer. The goal remains to harness stimulated immune cells in the bloodstream to eradicate multiple metastases, a feat currently deemed challenging in a typical clinical setting. For the discovery of novel immunotherapy-based tumor targets, tumor-infiltrating lymphocytes (TILs) give a key insight on tumor-related immune activities by providing T cell receptor (TCR) sequences. Understanding the TCR repertoires of TILs in metastatic tissues and the circulation is important from an immunotherapy standpoint, as a subset of T cells in the blood have the potential to help kill tumor cells. To explore the relationship between distant tissue biopsy regions and blood circulation, we investigated the TCR beta chain (TCRβ) in bulk tumor and matched blood samples from 39 patients with gynecologic cancer. We found that the TCR clones of TILs at different tumor sites were globally shared within patients and had high overlap with the TCR clones in peripheral blood.
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Affiliation(s)
- Taehoon Kim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Hyeonseob Lim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Soyeong Jun
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Junsik Park
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Dongin Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
- Department of Biomedical Science and Technology, Kyung Hee Medical Science Research Institute, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul, 02447, Korea
| | - Jung-Yun Lee
- Department of Obstetrics and Gynecology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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Pospiech M, Tamizharasan M, Wei YC, Kumar AMS, Lou M, Milstein J, Alachkar H. Features of the TCR repertoire associate with patients' clinical and molecular characteristics in acute myeloid leukemia. Front Immunol 2023; 14:1236514. [PMID: 37928542 PMCID: PMC10620936 DOI: 10.3389/fimmu.2023.1236514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023] Open
Abstract
Background Allogeneic hematopoietic stem cell transplant remains the most effective strategy for patients with high-risk acute myeloid leukemia (AML). Leukemia-specific neoantigens presented by the major histocompatibility complexes (MHCs) are recognized by the T cell receptors (TCR) triggering the graft-versus-leukemia effect. A unique TCR signature is generated by a complex V(D)J rearrangement process to form TCR capable of binding to the peptide-MHC. The generated TCR repertoire undergoes dynamic changes with disease progression and treatment. Method Here we applied two different computational tools (TRUST4 and MIXCR) to extract the TCR sequences from RNA-seq data from The Cancer Genome Atlas (TCGA) and examine the association between features of the TCR repertoire in adult patients with AML and their clinical and molecular characteristics. Results We found that only ~30% of identified TCR CDR3s were shared by the two computational tools. Yet, patterns of TCR associations with patients' clinical and molecular characteristics based on data obtained from either tool were similar. The numbers of unique TCR clones were highly correlated with patients' white blood cell counts, bone marrow blast percentage, and peripheral blood blast percentage. Multivariable regressions of TCRA and TCRB median normalized number of unique clones with mutational status of AML patients using TRUST4 showed significant association of TCRA or TCRB with WT1 mutations, WBC count, %BM blast, and sex (adjusted in TCRB model). We observed a correlation between TCRA/B number of unique clones and the expression of T cells inhibitory signal genes (TIGIT, LAG3, CTLA-4) and foxp3, but not IL2RA, CD69 and TNFRSF9 suggestive of exhausted T cell phenotypes in AML. Conclusion Benchmarking of computational tools is needed to increase the accuracy of the identified clones. The utilization of RNA-seq data enables identification of highly abundant TCRs and correlating these clones with patients' clinical and molecular characteristics. This study further supports the value of high-resolution TCR-Seq analyses to characterize the TCR repertoire in patients.
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Affiliation(s)
- Mateusz Pospiech
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Mukund Tamizharasan
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Yu-Chun Wei
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Advaith Maya Sanjeev Kumar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Department of Computer Science, University of Southern California, Los Angeles, CA, United States
| | - Mimi Lou
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
| | - Joshua Milstein
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Houda Alachkar
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA, United States
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, United States
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Vandoren R, Gielis S, Laukens K, Meysman P. Identification of TCR repertoire patterns linked with anti-cancer immunotherapy. Methods Cell Biol 2023; 183:115-142. [PMID: 38548409 DOI: 10.1016/bs.mcb.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
The highly diverse T cell receptor (TCR) repertoire is a crucial component of the adaptive immune system that aids in the protection against a wide variety of pathogens. This TCR repertoire, comprising the collection of all TCRs in an individual, is a valuable source of information on both recent and ongoing T cell activation. Cancer cells, like pathogens, have the ability to trigger an adaptive immune response. However, because cancer cells use a variety of strategies to escape immune responses, this is often insufficient to completely eradicate them. As a result, immunotherapy is a promising treatment option for cancer patients. This treatment is expected to increase T cell activation and subsequently alter the TCR repertoire composition in these patients. Monitoring TCR repertoires before and after immunotherapy can therefore provide additional insight into T cell responses and might identify cancer-associated TCR sequences. Here we present a computational strategy to identify those changes in the TCR repertoire that occur after treatment with immunotherapy. Since this method allows the identification of TCR patterns that might be treatment-associated, it can help future research by revealing those patterns that are related with response. This TCR analysis workflow is illustrated using public data from three different cancer patients who received anti-PD-1 treatment.
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Affiliation(s)
- Romi Vandoren
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Sofie Gielis
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Kris Laukens
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium
| | - Pieter Meysman
- Adrem Data Lab, Department of Computer Science, University of Antwerp, Antwerp, Belgium; Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing (AUDACIS), University of Antwerp, Antwerp, Belgium.
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Arechaga-Ocampo E. Epigenetics as a determinant of radiation response in cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:145-190. [PMID: 38359968 DOI: 10.1016/bs.ircmb.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Radiation therapy is a cornerstone of modern cancer treatment. Treatment is based on depositing focal radiation to the tumor to inhibit cell growth, proliferation and metastasis, and to promote the death of cancer cells. In addition, radiation also affects non-tumor cells in the tumor microenvironmental (TME). Radiation resistance of the tumor cells is the most common cause of treatment failure, allowing survival of cancer cell and subsequent tumor growing. Molecular radioresistance comprises genetic and epigenetic characteristics inherent in cancer cells, or characteristics acquired after exposure to radiation. Furthermore, cancer stem cells (CSCs) and non-tumor cells into the TME as stromal and immune cells have a role in promoting and maintaining radioresistant tumor phenotypes. Different regulatory molecules and pathways distinctive of radiation resistance include DNA repair, survival signaling and cell death pathways. Epigenetic mechanisms are one of the most relevant events that occur after radiotherapy to regulate the expression and function of key genes and proteins in the differential radiation-response. This article reviews recent data on the main molecular mechanisms and signaling pathways related to the biological response to radiotherapy in cancer; highlighting the epigenetic control exerted by DNA methylation, histone marks, chromatin remodeling and m6A RNA methylation on gene expression and activation of signaling pathways related to radiation therapy response.
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Affiliation(s)
- Elena Arechaga-Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico.
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Ogura H, Gohda J, Lu X, Yamamoto M, Takesue Y, Son A, Doi S, Matsushita K, Isobe F, Fukuda Y, Huang TP, Ueno T, Mambo N, Murakami H, Kawaguchi Y, Inoue JI, Shirai K, Yamasaki S, Hirata JI, Ishido S. Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19. Nat Commun 2022; 13:7063. [PMID: 36526616 PMCID: PMC9758236 DOI: 10.1038/s41467-022-34655-1] [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: 07/04/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
Although the importance of virus-specific cytotoxic T lymphocytes (CTL) in virus clearance is evident in COVID-19, the characteristics of virus-specific CTLs related to disease severity have not been fully explored. Here we show that the phenotype of virus-specific CTLs against immunoprevalent epitopes in COVID-19 convalescents might differ according to the course of the disease. We establish a cellular screening method that uses artificial antigen presenting cells, expressing HLA-A*24:02, the costimulatory molecule 4-1BBL, SARS-CoV-2 structural proteins S, M, and N and non-structural proteins ORF3a and nsp6/ORF1a. The screen implicates SARS-CoV-2 M protein as a frequent target of IFNγ secreting CD8+ T cells, and identifies M198-206 as an immunoprevalent epitope in our cohort of HLA-A*24:02 positive convalescent COVID-19 patients recovering from mild, moderate and severe disease. Further exploration of M198-206-specific CD8+ T cells with single cell RNA sequencing reveals public TCRs in virus-specific CD8+ T cells, and shows an exhausted phenotype with less differentiated status in cells from the severe group compared to cells from the moderate group. In summary, this study describes a method to identify T cell epitopes, indicate that dysfunction of virus-specific CTLs might be an important determinant of clinical outcomes.
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Affiliation(s)
- Hideki Ogura
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
| | - Jin Gohda
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Xiuyuan Lu
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Mizuki Yamamoto
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshio Takesue
- grid.272264.70000 0000 9142 153XDepartment of Infection Control and Prevention, Hyogo Medical University, Hyogo, Japan ,Tokoname City Hospital, Aichi, Japan
| | - Aoi Son
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
| | - Sadayuki Doi
- grid.513274.60000 0004 0569 8532Kawanishi City Hospital, Hyogo, Japan
| | | | - Fumitaka Isobe
- Kyowa Marina Hospital/Wellhouse Nishinomiya, Hyogo, Japan
| | | | | | - Takamasa Ueno
- grid.274841.c0000 0001 0660 6749Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Naomi Mambo
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Hiromoto Murakami
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Yasushi Kawaguchi
- grid.26999.3d0000 0001 2151 536XResearch Center for Asian Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDivision of Molecular Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jun-ichiro Inoue
- grid.26999.3d0000 0001 2151 536XResearch Platform Office, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kunihiro Shirai
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Sho Yamasaki
- grid.136593.b0000 0004 0373 3971Laboratory of Molecular Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan ,grid.136593.b0000 0004 0373 3971Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan ,grid.177174.30000 0001 2242 4849Division of Molecular Design, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan ,grid.136304.30000 0004 0370 1101Division of Molecular Immunology, Medical Mycology Research Center, Chiba University, Chiba, Japan
| | - Jun-Ichi Hirata
- grid.272264.70000 0000 9142 153XDepartment of Emergency and Critical Care Medicine, Hyogo Medical University, Hyogo, Japan
| | - Satoshi Ishido
- grid.272264.70000 0000 9142 153XDepartment of Microbiology, Hyogo Medical University, Hyogo, Japan
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