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Shin SC, Vickman RE, Filimon B, Yang Y, Hu Z, Mangold KA, Prabhakar BS, Schreiber H, Xu W. The safety and efficacy of systemic delivery of a new liver-de-targeted TGFβ signaling inhibiting adenovirus in an immunocompetent triple negative mouse mammary tumor model. Cancer Gene Ther 2024; 31:574-585. [PMID: 38267626 PMCID: PMC11016465 DOI: 10.1038/s41417-024-00735-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Aberrant TGFβ signaling is linked to metastasis and tumor immune escape of many cancers including metastatic triple negative breast cancer (mTNBC). Previously, we have found that oncolytic adenoviruses expressing a TGFβ signaling inhibitory protein (sTGFβRIIFc) induced immune activation in a mouse TNBC (4T1) immunocompetent subcutaneous model with intratumoral injection. Systemic administration of adenoviruses can be a superior route to treat mTNBC but faces the challenges of increased toxicity and viral clearance. Thus, we created a liver-de-targeted sTGFβRIIFc- and LyP-1 peptide-expressing adenovirus (mHAdLyp.sT) with enhanced breast cancer cell tropism. Its safety and immune response features were profiled in the 4T1 model. Our data showed that the systemic administration of mHAdLyp.sT resulted in reduced hepatic and systemic toxicity. mHAdLyp.sT was also effective in increasing Th1 cytokines and anti-tumor cell populations by cytokine analysis, spleen/tumor qRT-PCR, and flow cytometry. We further tested the therapeutic effects of mHAdLyp.sT alone and in combination with immune checkpoint inhibitors (ICIs). mHAdLyp.sT alone and with all ICI combinations elicited significant inhibition of lung metastasis by histological analysis. When mHAdLyp.sT was combined with both anti-PD-1 and anti-CTLA-4 antibodies, primary 4T1 tumor growth was also significantly inhibited. We are confident in advancing this new treatment option for mTNBC.
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Affiliation(s)
- Soon Cheon Shin
- Cancer Gene Therapy Program, Department of Medicine, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA
| | - Renee E Vickman
- Center for Personalized Cancer Care, Department of Surgery, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA
| | - Beniamin Filimon
- Cancer Gene Therapy Program, Department of Medicine, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA
| | - Yuefeng Yang
- Cancer Gene Therapy Program, Department of Medicine, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA
- Department of Experimental Medical Science and Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zebin Hu
- Cancer Gene Therapy Program, Department of Medicine, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA
- National Institutes for Food and Drug Control, Beijing, China
| | - Kathy A Mangold
- Department of Pathology and Laboratory Medicine, NorthShore University HealthSystem, Endeavor Health Medical Group, Evanston, IL, USA
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Bellur S Prabhakar
- Department of Microbiology and Immunology, University of Illinois College of Medicine, Chicago, IL, USA
| | - Hans Schreiber
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Weidong Xu
- Cancer Gene Therapy Program, Department of Medicine, NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine, Endeavor Health Medical Group, Evanston, IL, USA.
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2
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Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
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Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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3
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Bardwell B, Bay J, Colburn Z. The clinical applications of immunosequencing. Curr Res Transl Med 2024; 72:103439. [PMID: 38447267 DOI: 10.1016/j.retram.2024.103439] [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: 11/23/2022] [Revised: 03/20/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Technological advances in high-throughput sequencing have opened the door for the interrogation of adaptive immune responses at unprecedented scale. It is now possible to determine the sequences of antibodies or T-cell receptors produced by individual B and T cells in a sample. This capability, termed immunosequencing, has transformed the study of both infectious and non-infectious diseases by allowing the tracking of dynamic changes in B and T cell clonal populations over time. This has improved our understanding of the pathology of cancers, autoimmune diseases, and infectious diseases. However, to date there has been only limited clinical adoption of the technology. Advances over the last decade and on the horizon that reduce costs and improve interpretability could enable widespread clinical use. Many clinical applications have been proposed and, while most are still undergoing research and development, some methods relying on immunosequencing data have been implemented, the most widespread of which is the detection of measurable residual disease. Here, we review the diagnostic, prognostic, and therapeutic applications of immunosequencing for both infectious and non-infectious diseases.
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Affiliation(s)
- B Bardwell
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - J Bay
- Department of Medicine, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - Z Colburn
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA.
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Huuhtanen J, Adnan-Awad S, Theodoropoulos J, Forstén S, Warfvinge R, Dufva O, Bouhlal J, Dhapola P, Duàn H, Laajala E, Kasanen T, Klievink J, Ilander M, Jaatinen T, Olsson-Strömberg U, Hjorth-Hansen H, Burchert A, Karlsson G, Kreutzman A, Lähdesmäki H, Mustjoki S. Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation. Leukemia 2024; 38:109-125. [PMID: 37919606 PMCID: PMC10776410 DOI: 10.1038/s41375-023-02074-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Immunological control of residual leukemia cells is thought to occur in patients with chronic myeloid leukemia (CML) that maintain treatment-free remission (TFR) following tyrosine kinase inhibitor (TKI) discontinuation. To study this, we analyzed 55 single-cell RNA and T cell receptor (TCR) sequenced samples (scRNA+TCRαβ-seq) from patients with CML (n = 13, N = 25), other cancers (n = 28), and healthy (n = 7). The high number and active phenotype of natural killer (NK) cells in CML separated them from healthy and other cancers. Most NK cells in CML belonged to the active CD56dim cluster with high expression of GZMA/B, PRF1, CCL3/4, and IFNG, with interactions with leukemic cells via inhibitory LGALS9-TIM3 and PVR-TIGIT interactions. Accordingly, upregulation of LGALS9 was observed in CML target cells and TIM3 in NK cells when co-cultured together. Additionally, we created a classifier to identify TCRs targeting leukemia-associated antigen PR1 and quantified anti-PR1 T cells in 90 CML and 786 healthy TCRβ-sequenced samples. Anti-PR1 T cells were more prevalent in CML, enriched in bone marrow samples, and enriched in the mature, cytotoxic CD8 + TEMRA cluster, especially in a patient maintaining TFR. Our results highlight the role of NK cells and anti-PR1 T cells in anti-leukemic immune responses in CML.
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Affiliation(s)
- Jani Huuhtanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- Department of Computer Science, Aalto University, Espoo, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Shady Adnan-Awad
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Jason Theodoropoulos
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Sofia Forstén
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Rebecca Warfvinge
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Olli Dufva
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jonas Bouhlal
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Parashar Dhapola
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Hanna Duàn
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Essi Laajala
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Tiina Kasanen
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Jay Klievink
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mette Ilander
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Taina Jaatinen
- Histocompatibility Testing Laboratory, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Ulla Olsson-Strömberg
- Department of Medical Sciences, Uppsala University and Hematology Section, Uppsala University Hospital, Uppsala, Sweden
| | - Henrik Hjorth-Hansen
- Department of Hematology, St. Olavs Hospital, Trondheim, Norway
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Andreas Burchert
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, and University Medical Center Giessen and Marburg, Marburg, Germany
| | - Göran Karlsson
- Division of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Anna Kreutzman
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
| | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, Espoo, Finland
| | - Satu Mustjoki
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland.
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland.
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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5
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Guo F, Yuan X, Cao J, Zhao X, Wang Y, Liu W, Liu B, Zeng Q. RNA-Seq and Immune Repertoire Analysis of Normal and Hepatocellular Carcinoma Relapse After Liver Transplantation. Int J Gen Med 2023; 16:4329-4341. [PMID: 37781272 PMCID: PMC10541230 DOI: 10.2147/ijgm.s421016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/08/2023] [Indexed: 10/03/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) relapse is the main reason for the poor prognosis of HCC after Liver transplantation (LT). This study aimed to explore the molecular mechanisms and immune repertoire profiles of HCC relapse. Material and Methods RNA-seq of blood samples from patients with normal (n=12) and HCC relapse (n=6) after LT was performed to identify differentially expressed genes (DEGs) and key signalling pathways. The DEGs and immune genes were further analyzed by bioinformatics. TRUST4 was used to analyze the differences in the immune repertoire between the two groups. Another 11 blood samples from patients with HCC who had received LT were collected for RT-qPCR verification of key genes. Results A total of 131 upregulated and 157 downregulated genes were identified using RNA-seq, and GO enrichment analysis revealed that the top 15 pathways were immune-related. The PPI network identified 10 key genes. Immune infiltration analysis revealed a significant difference in the five immune cell types between the two groups. A total of 83 intersecting genes were obtained by intersecting DEGs and immune genes. 6 key genes, including MX1, ISG15, OAS1, PRF1, SPP1, and THBS1 were obtained according to the intersection of DEGs, PPI network top 10 genes and immune intersecting genes. Immune repertoire analysis showed that the usage frequency of variable (V) and joining (J) genes in the normal group was higher than that in the relapse group. RT-qPCR validation showed that the expression levels of key genes were consistent with the RNA-seq results. Conclusion Our study identified key pathways and genes that could help determine whether transplant recipients are more prone to HCC relapse. Immune repertoire analysis revealed a difference in the usage frequency of VJ genes between the normal and relapse groups, providing a research direction for immunotherapy in patients with HCC relapse after liver transplantation.
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Affiliation(s)
- Fansheng Guo
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Xiaoye Yuan
- Department of Gerontology, Hebei General Hospital, Shijiazhuang, 050000, People’s Republic of China
| | - Jinglin Cao
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Xin Zhao
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Yang Wang
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Wenpeng Liu
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Baowang Liu
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
| | - Qiang Zeng
- Department of Hepatobiliary Surgery, the Third Hospital of Hebei Medical University, Shijiazhuang, 050000, People’s Republic of China
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6
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Xu W, Shin SC, Vickman R, Filimon B, Yang Y, Hu Z, Mangold K, Prabhakar B, Schreiber H. The Safety and Efficacy of Systemic Delivery of a New Liver-de-targeted TGFβ Signaling Inhibiting Adenovirus in an Immunocompetent Triple Negative Mouse Mammary Tumor Model. RESEARCH SQUARE 2023:rs.3.rs-3317863. [PMID: 37790556 PMCID: PMC10543255 DOI: 10.21203/rs.3.rs-3317863/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Aberrant TGFβ signaling is linked to metastasis and tumor immune escape of many cancers including metastatic triple negative breast cancer (mTNBC). Previously, we have found that oncolytic adenoviruses expressing a TGFβ signaling inhibitory protein (sTGFβRIIFc) induced immune activation in a mouse TNBC (4T1) immunocompetent subcutaneous model with intratumoral injection. Systemic administration of adenoviruses can be a superior route to treat mTNBC but faces the challenges of increased toxicity and viral clearance. Thus, we created a liver-de-targeted sTGFβRIIFc- and LyP-1 peptide-expressing adenovirus (mHAdLyp.sT) with enhanced breast cancer cell tropism. Its safety and immune response features were profiled in the 4T1 model. Our data showed that the systemic administration of mHAdLyp.sT resulted in reduced hepatic and systemic toxicity. mHAdLyp.sT was also effective in increasing Th1 cytokines and anti-tumor cell populations by cytokine analysis, spleen/tumor qRT-PCR, and flow cytometry. We further tested the therapeutic effects of mHAdLyp.sT alone and in combination with immune checkpoint inhibitors (ICIs). mHAdLyp.sT alone and with all ICI combinations elicited significant inhibition of lung metastasis by histological analysis. When mHAdLyp.sT was combined with both anti-PD-1 and anti-CTLA-4 antibodies, primary 4T1 tumor growth was also significantly inhibited. We are confident in advancing this new treatment option for mTNBC.
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Affiliation(s)
- Weidong Xu
- NorthShore University HealthSystem, an Academic Affiliate of the University of Chicago Pritzker School of Medicine
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Haraguchi M, Kiyotani K, Tate T, Sakata S, Sagawa R, Takagi S, Nagayama S, Takeuchi K, Takahashi K, Katayama R. Spatiotemporal commonality of the TCR repertoire in a T-cell memory murine model and in metastatic human colorectal cancer. Cancer Immunol Immunother 2023; 72:2971-2989. [PMID: 37270735 DOI: 10.1007/s00262-023-03473-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have shown superior clinical responses and significantly prolong overall survival (OS) for many types of cancer. However, some patients exhibit long-term OS, whereas others do not respond to ICI therapy at all. To develop more effective and long-lasting ICI therapy, understanding the host immune response to tumors and the development of biomarkers are imperative. In this study, we established an MC38 immunological memory mouse model by administering an anti-PD-L1 antibody and evaluating the detailed characteristics of the immune microenvironment including the T cell receptor (TCR) repertoire. In addition, we found that the memory mouse can be established by surgical resection of residual tumor following anti-PD-L1 antibody treatment with a success rate of > 40%. In this model, specific depletion of CD8 T cells revealed that they were responsible for the rejection of reinoculated MC38 cells. Analysis of the tumor microenvironment (TME) of memory mice using RNA-seq and flow cytometry revealed that memory mice had a quick and robust immune response to MC38 cells compared with naïve mice. A TCR repertoire analysis indicated that T cells with a specific TCR repertoire were expanded in the TME, systemically distributed, and preserved in the host for a long time period. We also identified shared TCR clonotypes between serially resected tumors in patients with colorectal cancer (CRC). Our results suggest that memory T cells are widely preserved in patients with CRC, and the MC38 memory model is potentially useful for the analysis of systemic memory T-cell behavior.
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Affiliation(s)
- Mizuki Haraguchi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Kazuma Kiyotani
- Immunopharmacogenomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Tomohiro Tate
- Immunopharmacogenomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Seiji Sakata
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ray Sagawa
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan
| | - Satoshi Nagayama
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Gastroenterological Surgery, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Surgery, Uji-Tokushukai Medical Center, Kyoto, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Pathology, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31, Ariake, Koto-Ku, Tokyo, 135-8550, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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8
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Su J, Zhou L, Zhang Z, Xiao X, Qin Y, Zhou X, Huang T. The components of tumor microenvironment as biomarker for immunotherapy in metastatic renal cell carcinoma. Front Immunol 2023; 14:1146738. [PMID: 37350955 PMCID: PMC10282412 DOI: 10.3389/fimmu.2023.1146738] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/26/2023] [Indexed: 06/24/2023] Open
Abstract
Substantial improvement in prognosis among metastatic renal cell carcinoma (mRCC) patients has been achieved, owing to the rapid development and utilization of immunotherapy. In particular, immune checkpoint inhibitors (ICIs) have been considered the backbone of systemic therapy for patients with mRCC alongside multi-targeted tyrosine kinase inhibitors (TKIs) in the latest clinical practice guidelines. However, controversies and challenges in optimal individualized treatment regarding immunotherapy remains still About 2/3 of the patients presented non-response or acquired resistance to ICIs. Besides, immune-related toxicities, namely immune-related adverse events, are still elusive and life-threatening. Thus, reliable biomarkers to predict immunotherapeutic outcomes for mRCC patients are needed urgently. Tumor microenvironment (TME), consisting of immune cells, vasculature, signaling molecules, and extracellular matrix and regulates tumor immune surveillance and immunological evasion through complex interplay, plays a critical role in tumor immune escape and consequently manipulates the efficacy of immunotherapy. Various studied have identified the different TME components are significantly associated with the outcome of mRCC patients receiving immunotherapy, making them potential valuable biomarkers in therapeutic guidance. The present review aims to summarize the latest evidence on the associations between the components of TME including immune cells, cytokines and extracellular matrix, and the therapeutic responses among mRCC patients with ICI-based treatment. We further discuss the feasibility and limitation of these components as biomarkers.
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Affiliation(s)
- Jiaming Su
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Lu Zhou
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Zhe Zhang
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, China
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
| | - Xue Xiao
- Department of Otorhinolaryngology and Head and Neck Surgery, First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | | | - Xiaoying Zhou
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
- Life Science Institute, Guangxi Medical University, Nanning, China
| | - Tingting Huang
- Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor (Guangxi Medical University), Ministry of Education, Nanning, China
- Department of Radiation Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, China
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9
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Bao X, Zhong Y, Yang C, Chen Y, Han Y, Lin X, Huang C, Wang K, Liu Z, Li C. T-Cell Repertoire Analysis in the Conjunctiva of Murine Dry Eye Model. Invest Ophthalmol Vis Sci 2023; 64:14. [PMID: 36877515 PMCID: PMC10007900 DOI: 10.1167/iovs.64.3.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Purpose Dry eye is closely related to the activation and proliferation of immune cells, especially T cells. However, the determination of the preferential T-cell clonotypes is technically challenging. This study aimed to investigate the characterization of T-cell receptor (TCR) repertoire in the conjunctiva during dry eye. Methods A desiccating stress animal model was established using C57/BL6 mice (8-10 weeks, female). After 7 days of stress stimulation, the slit-lamp image and Oregon-green-dextran staining were used to evaluate the ocular surface injury. Periodic acid-Schiff staining was used to measure the number of goblet cells. Flow cytometry was used to detect the activation and proliferation of T cells in the conjunctiva and cervical lymph nodes. Next-generation sequencing was used to detect the αβ TCR repertoire of the conjunctiva. Results The αβ TCR diversity increased significantly in the dry eye group, including the higher CDR3 amino acid length, marked gene usage on TCR V and J gene segments, extensive V(D)J recombination, and distinct CDR3 aa motifs. More important, several T-cell clonotypes were uniquely identified in dry eye. Furthermore, these perturbed rearrangements were reversed after glucocorticoid administration. Conclusions A comprehensive analysis of the αβ TCR repertoire in the conjunctiva of the dry eye mouse model was performed. Data in this study contributed significantly to the research on dry eye pathogenesis by demonstrating the TCR gene distribution and disease-specific TCR signatures. This study further provided some potential predictive T-cell biomarkers for future studies.
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Affiliation(s)
- Xiaorui Bao
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Yanlin Zhong
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Chunyan Yang
- School of Life Science, Xiamen University, Xiamen, Fujian, China
| | - Yujie Chen
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Yi Han
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Xiang Lin
- Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Caihong Huang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
| | - Kejia Wang
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zuguo Liu
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China.,The First Affiliated Hospital of University of South China, Hengyang, Hunan, China
| | - Cheng Li
- Fujian Provincial Key Laboratory of Ophthalmology and Visual Science, Eye Institute & Affiliated Xiamen Eye Center, School of Medicine, Xiamen University, Xiamen, Fujian, China.,Department of Ophthalmology, Xiang'an Hospital of Xiamen University, Xiamen, Fujian, China
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10
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Wang H, Yin X, Fang T, Lou S, Han B, Gao J, Wang Y, Zhang D, Wang X, Lu Z, Wu J, Zhang J, Wang Y, Zhang Y, Xue Y. Development and Validation of an Age-Related Gastric Cancer-Specific Immune Index. J Inflamm Res 2022; 15:6393-6407. [DOI: 10.2147/jir.s388792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
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11
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Wang M, Gao P, Ren L, Duan J, Yang S, Wang H, Wang H, Sun J, Gao X, Li B, Li S, Su W. Profiling the peripheral blood T cell receptor repertoires of gastric cancer patients. Front Immunol 2022; 13:848113. [PMID: 35967453 PMCID: PMC9367216 DOI: 10.3389/fimmu.2022.848113] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer driven by somatic mutations may express neoantigens that can trigger T-cell immune responses. Since T-cell receptor (TCR) repertoires play critical roles in anti-tumor immune responses for oncology, next-generation sequencing (NGS) was used to profile the hypervariable complementarity-determining region 3 (CDR3) of the TCR-beta chain in peripheral blood samples from 68 gastric cancer patients and 49 healthy controls. We found that most hyper-expanded CDR3 are individual-specific, and the gene usage of TRBV3-1 is more frequent in the tumor group regardless of tumor stage than in the healthy control group. We identified 374 hyper-expanded tumor-specific CDR3, which may play a vital role in anti-tumor immune responses. The patients with stage IV gastric cancer have higher EBV-specific CDR3 abundance than the control. In conclusion, analysis of the peripheral blood TCR repertoires may provide the biomarker for gastric cancer prognosis and guide future immunotherapy.
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Affiliation(s)
- Mengyao Wang
- Department of Computer Science, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | | | - Laifeng Ren
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jingjing Duan
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Silu Yang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Haina Wang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Hongxia Wang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Junning Sun
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | | | - Bo Li
- BGI-Shenzhen, Shenzhen, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- *Correspondence: Wen Su, ; Shuaicheng Li,
| | - Wen Su
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Wen Su, ; Shuaicheng Li,
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12
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Song L, Ouyang Z, Cohen D, Cao Y, Altreuter J, Bai G, Hu X, Livak KJ, Li H, Tang M, Li B, Shirley Liu X. Comprehensive Characterizations of Immune Receptor Repertoire in Tumors and Cancer Immunotherapy Studies. Cancer Immunol Res 2022; 10:788-799. [PMID: 35605261 PMCID: PMC9299271 DOI: 10.1158/2326-6066.cir-21-0965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/17/2022] [Accepted: 05/20/2022] [Indexed: 01/03/2023]
Abstract
We applied our computational algorithm TRUST4 to assemble immune receptor (T-cell receptor/B-cell receptor) repertoires from approximately 12,000 RNA sequencing samples from The Cancer Genome Atlas and seven immunotherapy studies. From over 35 million assembled complete complementary-determining region 3 sequences, we observed that the expression of CCL5 and MZB1 is the most positively correlated genes with T-cell clonal expansion and B-cell clonal expansion, respectively. We analyzed amino acid evolution during B-cell receptor somatic hypermutation and identified tyrosine as the preferred residue. We found that IgG1+IgG3 antibodies together with FcRn were associated with complement-dependent cytotoxicity and antibody-dependent cellular cytotoxicity or phagocytosis. In addition to B-cell infiltration, we discovered that B-cell clonal expansion and IgG1+IgG3 antibodies are also correlated with better patient outcomes. Finally, we created a website, VisualizIRR, for users to interactively explore and visualize the immune repertoires in this study. See related Spotlight by Liu and Han, p. 786.
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Affiliation(s)
- Li Song
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhangyi Ouyang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Experimental Hematology and Biochemistry, Beijing Institute of Radiation Medicine, Beijing, China
| | - David Cohen
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Yang Cao
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Jennifer Altreuter
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gali Bai
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Xihao Hu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Current affiliation: GV20 Therapeutics, Cambridge, MA, USA
| | - Kenneth J. Livak
- Department of Medical, Dana-Farber Cancer Institute, Boston, MA, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Heng Li
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bo Li
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - X. Shirley Liu
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, USA
- Current affiliation: GV20 Therapeutics, Cambridge, MA, USA
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13
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Liu M, Goo J, Liu Y, Sun W, Wu MC, Hsu L, He Q. TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes. BMC Bioinformatics 2022; 23:152. [PMID: 35484495 PMCID: PMC9052542 DOI: 10.1186/s12859-022-04690-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background T cell receptors (TCRs) play critical roles in adaptive immune responses, and recent advances in genome technology have made it possible to examine the T cell receptor (TCR) repertoire at the individual sequence level. The analysis of the TCR repertoire with respect to clinical phenotypes can yield novel insights into the etiology and progression of immune-mediated diseases. However, methods for association analysis of the TCR repertoire have not been well developed. Methods We introduce an analysis tool, TCR-L, for evaluating the association between the TCR repertoire and disease outcomes. Our approach is developed under a mixed effect modeling, where the fixed effect represents features that can be explicitly extracted from TCR sequences while the random effect represents features that are hidden in TCR sequences and are difficult to be extracted. Statistical tests are developed to examine the two types of effects independently, and then the p values are combined. Results Simulation studies demonstrate that (1) the proposed approach can control the type I error well; and (2) the power of the proposed approach is greater than approaches that consider fixed effect only or random effect only. The analysis of real data from a skin cutaneous melanoma study identifies an association between the TCR repertoire and the short/long-term survival of patients. Conclusion The TCR-L can accommodate features that can be extracted as well as features that are hidden in TCR sequences. TCR-L provides a powerful approach for identifying association between TCR repertoire and disease outcomes.
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Affiliation(s)
- Meiling Liu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Juna Goo
- Department of Mathematics, Boise State University, Boise, USA
| | - Yang Liu
- Department of Mathematics and Statistics, Wright State University, Dayton, USA
| | - Wei Sun
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - Qianchuan He
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA.
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14
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Wu M, Pan W, Jia C, He Z, Zhao M, Tang C, Chang C, Li S, Wu H, Lu Q. Systemic lupus erythematosus patients contain B cell receptor repertoires sensitive to immunosuppressive drugs. Eur J Immunol 2022; 52:669-680. [PMID: 35092307 DOI: 10.1002/eji.202149596] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/30/2021] [Accepted: 01/03/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Meiyu Wu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Wenjing Pan
- Nanjing ARP Biotechnology Co., Ltd Nanjing China
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices Hunan University of Technology Zhuzhou China
| | - Chen Jia
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Zhenghao He
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Ming Zhao
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Congli Tang
- Nanjing ARP Biotechnology Co., Ltd Nanjing China
| | - Christopher Chang
- Christopher Chang Division of Rheumatology Allergy and Clinical Immunology University of California at Davis School of Medicine Davis California USA
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices Hunan University of Technology Zhuzhou China
| | - Haijing Wu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
| | - Qianjin Lu
- Hunan Key Laboratory of Medical Epigenomics Department of Dermatology Second Xiangya Hospital Central South University Changsha China
- Institute of Dermatology Chinese Academy of Medical Sciences and Peking Union Medical College Nanjing China
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15
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Chan JTH, Kadri S, Köllner B, Rebl A, Korytář T. RNA-Seq of Single Fish Cells – Seeking Out the Leukocytes Mediating Immunity in Teleost Fishes. Front Immunol 2022; 13:798712. [PMID: 35140719 PMCID: PMC8818700 DOI: 10.3389/fimmu.2022.798712] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/03/2022] [Indexed: 01/01/2023] Open
Abstract
The immune system is a complex and sophisticated biological system, spanning multiple levels of complexity, from the molecular level to that of tissue. Our current understanding of its function and complexity, of the heterogeneity of leukocytes, is a result of decades of concentrated efforts to delineate cellular markers using conventional methods of antibody screening and antigen identification. In mammalian models, this led to in-depth understanding of individual leukocyte subsets, their phenotypes, and their roles in health and disease. The field was further propelled forward by the development of single-cell (sc) RNA-seq technologies, offering an even broader and more integrated view of how cells work together to generate a particular response. Consequently, the adoption of scRNA-seq revealed the unexpected plasticity and heterogeneity of leukocyte populations and shifted several long-standing paradigms of immunology. This review article highlights the unprecedented opportunities offered by scRNA-seq technology to unveil the individual contributions of leukocyte subsets and their crosstalk in generating the overall immune responses in bony fishes. Single-cell transcriptomics allow identifying unseen relationships, and formulating novel hypotheses tailored for teleost species, without the need to rely on the limited number of fish-specific antibodies and pre-selected markers. Several recent studies on single-cell transcriptomes of fish have already identified previously unnoticed expression signatures and provided astonishing insights into the diversity of teleost leukocytes and the evolution of vertebrate immunity. Without a doubt, scRNA-seq in tandem with bioinformatics tools and state-of-the-art methods, will facilitate studying the teleost immune system by not only defining key markers, but also teaching us about lymphoid tissue organization, development/differentiation, cell-cell interactions, antigen receptor repertoires, states of health and disease, all across time and space in fishes. These advances will invite more researchers to develop the tools necessary to explore the immunology of fishes, which remain non-conventional animal models from which we have much to learn.
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Affiliation(s)
- Justin T. H. Chan
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
| | - Safwen Kadri
- Helmholtz Zentrum München, Institute of Lung Biology and Disease, Regenerative Biology and Medicine, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Bernd Köllner
- Institute of Immunology, Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald, Germany
| | - Alexander Rebl
- Institute of Genome Biology, Research Institute for Farm Animal Biology, Dummerstorf, Germany
- *Correspondence: Alexander Rebl, ; Tomáš Korytář,
| | - Tomáš Korytář
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Fisheries and Protection of Waters, University of South Bohemia, České Budějovice, Czechia
- *Correspondence: Alexander Rebl, ; Tomáš Korytář,
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16
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Hirschhorn D, Betof Warner A, Maniyar R, Chow A, Mangarin LM, Cohen AD, Hamadene L, Rizzuto GA, Budhu S, Suek N, Liu C, Houghton AN, Merghoub T, Wolchok JD. Cyclophosphamide enhances the antitumor potency of GITR engagement by increasing oligoclonal cytotoxic T cell fitness. JCI Insight 2021; 6:151035. [PMID: 34676831 PMCID: PMC8564916 DOI: 10.1172/jci.insight.151035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2021] [Indexed: 01/22/2023] Open
Abstract
Only a subset of cancer patients responds to checkpoint blockade inhibition in the clinic. Strategies to overcome resistance are promising areas of investigation. Targeting glucocorticoid-induced tumor necrosis factor receptor-related protein (GITR) has shown efficacy in preclinical models, but GITR engagement is ineffective in controlling advanced, poorly immunogenic tumors, such as B16 melanoma, and has not yielded benefit in clinical trials. The alkylating agent cyclophosphamide (CTX) depletes regulatory T cells (Tregs), expands tumor-specific effector T cells (Teffs) via homeostatic proliferation, and induces immunogenic cell death. GITR agonism has an inhibitory effect on Tregs and activates Teffs. We therefore hypothesized that CTX and GITR agonism would promote effective antitumor immunity. Here we show that the combination of CTX and GITR agonism controlled tumor growth in clinically relevant mouse models. Mechanistically, we show that the combination therapy caused tumor cell death, clonal expansion of highly active CD8+ T cells, and depletion of Tregs by activation-induced cell death. Control of tumor growth was associated with the presence of an expanded population of highly activated, tumor-infiltrating, oligoclonal CD8+ T cells that led to a diminished TCR repertoire. Our studies show that the combination of CTX and GITR agonism is a rational chemoimmunotherapeutic approach that warrants further clinical investigation.
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Affiliation(s)
- Daniel Hirschhorn
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Allison Betof Warner
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Rachana Maniyar
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Andrew Chow
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Levi Mb Mangarin
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Adam D Cohen
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and
| | - Linda Hamadene
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Gabrielle A Rizzuto
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Sadna Budhu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Nathan Suek
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Cailian Liu
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Alan N Houghton
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA
| | - Taha Merghoub
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
| | - Jedd D Wolchok
- Swim Across America and Ludwig Collaborative Laboratory, Immunology Program, Parker Institute for Cancer Immunotherapy, and.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, New York, USA.,Weill Cornell Medical College, New York, New York, USA
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17
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Zhang Y, Chen T, Zeng H, Yang X, Xu Q, Zhang Y, Chen Y, Wang M, Zhu Y, Lan C, Wang Q, Tang H, Zhang Y, Wang C, Xie W, Ma C, Guan J, Guo S, Chen S, Yang W, Wei L, Ren J, Yu X, Zhang Z. RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database. Front Immunol 2021; 12:717496. [PMID: 34484220 PMCID: PMC8414647 DOI: 10.3389/fimmu.2021.717496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
The antibody repertoire is a critical component of the adaptive immune system and is believed to reflect an individual’s immune history and current immune status. Delineating the antibody repertoire has advanced our understanding of humoral immunity, facilitated antibody discovery, and showed great potential for improving the diagnosis and treatment of disease. However, no tool to date has effectively integrated big Rep-seq data and prior knowledge of functional antibodies to elucidate the remarkably diverse antibody repertoire. We developed a Rep-seq dataset Analysis Platform with an Integrated antibody Database (RAPID; https://rapid.zzhlab.org/), a free and web-based tool that allows researchers to process and analyse Rep-seq datasets. RAPID consolidates 521 WHO-recognized therapeutic antibodies, 88,059 antigen- or disease-specific antibodies, and 306 million clones extracted from 2,449 human IGH Rep-seq datasets generated from individuals with 29 different health conditions. RAPID also integrates a standardized Rep-seq dataset analysis pipeline to enable users to upload and analyse their datasets. In the process, users can also select set of existing repertoires for comparison. RAPID automatically annotates clones based on integrated therapeutic and known antibodies, and users can easily query antibodies or repertoires based on sequence or optional keywords. With its powerful analysis functions and rich set of antibody and antibody repertoire information, RAPID will benefit researchers in adaptive immune studies.
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Affiliation(s)
- Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tianjian Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huikun Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qingxian Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanxia Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Nephrology, Hainan General Hospital, Haikou, China.,Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Yan Zhu
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chunhong Lan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chengrui Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenxi Xie
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Cuiyu Ma
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Junjie Guan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Sen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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18
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Li W, Qu Y, Wen F, Yu R, He X, Jia H, Liu H, Yu H. Prognostic nutritional index and systemic immune-inflammation index are prognostic biomarkers for non-small-cell lung cancer brain metastases. Biomark Med 2021; 15:1071-1084. [PMID: 34397267 DOI: 10.2217/bmm-2020-0786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Aim: This research aimed to elucidate the prognosis values of prognostic nutritional index (PNI) and systemic immune-inflammation index (SII) and clinical characteristics in NSCLC patients with brain metastases (BM) underwent radiotherapy. Materials & methods: Cut-off points of hematological indicators were determined by receiver operating characteristic curve. Overall survival was evaluated by Kaplan-Meier method and Cox proportional hazards model. Results: We retrospectively analyzed 214 patients from January 2009 to December 2018. The result demonstrated the independent prognostic values of PNI (hazard ratio: 0.600; p = 0.004) and SII (hazard ratio: 1.486; p = 0.019). The remaining clinicopathologic factors, including brain radiotherapy modality, smoking history, numbers of brain metastases, intracranial symptoms and Radiation Therapy Oncology Group - recursive partitioning analysis, were independently related to survival (p < 0.05). Conclusion: PNI and SII could be critical prognostic indicators for NSCLC patients with BM.
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Affiliation(s)
- Wang Li
- Dalian Medical University, Dalian, Liaoning, 116044, PR China.,Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Yanli Qu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Fengyun Wen
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Ruoxi Yu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Xiaoyi He
- Dalian Medical University, Dalian, Liaoning, 116044, PR China
| | - Hongying Jia
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Hangyu Liu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
| | - Hong Yu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, no. 44 Xiaoheyan Road, Dadong District, Shenyang, Liaoning Province, 110042, PR China
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19
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Cannarile MA, Gomes B, Canamero M, Reis B, Byrd A, Charo J, Yadav M, Karanikas V. Biomarker Technologies to Support Early Clinical Immuno-oncology Development: Advances and Interpretation. Clin Cancer Res 2021; 27:4147-4159. [PMID: 33766813 DOI: 10.1158/1078-0432.ccr-20-2345] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/02/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022]
Abstract
Today, there is a huge effort to develop cancer immunotherapeutics capable of combating cancer cells as well as the biological environment in which they can grow, adapt, and survive. For such treatments to benefit more patients, there is a great need to dissect the complex interplays between tumor cells and the host's immune system. Monitoring mechanisms of resistance to immunotherapeutics can delineate the evolution of key players capable of driving an efficacious antitumor immune response. In doing so, simultaneous and systematic interrogation of multiple biomarkers beyond single biomarker approaches needs to be undertaken. Zooming into cell-to-cell interactions using technological advancements with unprecedented cellular resolution such as single-cell spatial transcriptomics, advanced tissue histology approaches, and new molecular immune profiling tools promises to provide a unique level of molecular granularity of the tumor environment and may support better decision-making during drug development. This review will focus on how such technological tools are applied in clinical settings, to inform the underlying tumor-immune biology of patients and offer a deeper understanding of cancer immune responsiveness to immuno-oncology treatments.
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Affiliation(s)
- Michael A Cannarile
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bruno Gomes
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | - Marta Canamero
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Munich, Munich, Germany
| | - Bernhard Reis
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Basel, Basel, Switzerland
| | | | - Jehad Charo
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland
| | | | - Vaios Karanikas
- F. Hoffmann-La Roche AG, Pharmaceutical Research and Early Development Oncology, Roche Innovation Center Zurich, Zurich, Switzerland.
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20
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Sheng J, Wang H, Liu X, Deng Y, Yu Y, Xu P, Shou J, Pan H, Li H, Zhou X, Han W, Sun T, Pan H, Fang Y. Deep Sequencing of T-Cell Receptors for Monitoring Peripheral CD8 + T Cells in Chinese Advanced Non-Small-Cell Lung Cancer Patients Treated With the Anti-PD-L1 Antibody. Front Mol Biosci 2021; 8:679130. [PMID: 34307450 PMCID: PMC8299707 DOI: 10.3389/fmolb.2021.679130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/08/2021] [Indexed: 12/29/2022] Open
Abstract
Background: Atezolizumab, a high-affinity engineered human anti-PD-L1 antibody, has produced a clinical benefit for patients with advanced non-small-cell lung cancer (NSCLC). However, associated with T-cell regulation, the immunomodulatory effect of PD-L1 blockade and its biomarker in peripheral immunity remains elusive. Methods: In a prospective cohort with 12 Chinese advanced NSCLC patients who received atezolizumab 1,200 mg every 3 weeks as a second-line treatment, blood samples were obtained before and 6 weeks after atezolizumab initiation, and when disease progression was confirmed. Patients were classified into a response or progression group according to response evaluation criteria in solid tumors (RECIST) 1.1. Fresh peripheral blood mononuclear cells (PBMCs) from patients were stained with antihuman CD3, CD8, and PD-1 antibodies for flow cytometry analysis. T-cell receptor (TCR)-β chains of CD8+ T cells were analyzed by next-generation sequencing (NGS) at the deep level. Diversity, clonality, and similarity of TCR have been calculated before and after treatment in both groups. Results: Clonal expansion with high PD-1 expression was detected in all patients' peripheral CD8+ T cells before the treatment of atezolizumab. Unlike the progression group, the diversity of TCR repertoire and singletons in the TCRβ pool increased over time with atezolizumab administration, and the TCR repertoire dynamically changes in the response group. The percentage of CD8+ PD-1high terminal exhausted T cells declined in the response group after the PD-L1 blockade. Two patterns of TCR changes among patients who received PD-L1-targeted immunotherapy were observed. Conclusions: Deep sequencing of the T-cell receptors confirmed the existence of CD8+ PD-1high T cells with an exhaustion phenotype in Chinese NSCLC patients. Our study demonstrated that efficient anti-PD-L1 therapy could reshape the TCR repertoire for antitumor patients. Furthermore, singleton frequency may help us select patients who are sensitive to anti-PD-L1 immunotherapy.
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Affiliation(s)
- Jin Sheng
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Huadi Wang
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Xiao Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, United States
| | - Yunyun Deng
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Yingying Yu
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Pengfei Xu
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China
| | - Jiawei Shou
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hong Pan
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Hongsen Li
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Xiaoyun Zhou
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Weidong Han
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Laboratory of Cancer Biology, Institute of Clinical Science, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Tao Sun
- Hangzhou ImmuQuad Biotechnologies, LLC, Hangzhou, China.,Zhejiang-California International Nano-Systems Institute, Zhejiang University, Hangzhou, China
| | - Hongming Pan
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Yong Fang
- Department of Medical Oncology, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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21
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Christley S, Ostmeyer J, Quirk L, Zhang W, Sirak B, Giuliano AR, Zhang S, Monson N, Tiro J, Lucas E, Cowell LG. T Cell Receptor Repertoires Acquired via Routine Pap Testing May Help Refine Cervical Cancer and Precancer Risk Estimates. Front Immunol 2021; 12:624230. [PMID: 33868241 PMCID: PMC8050337 DOI: 10.3389/fimmu.2021.624230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
Cervical cancer is the fourth most common cancer and fourth leading cause of cancer death among women worldwide. In low Human Development Index settings, it ranks second. Screening and surveillance involve the cytology-based Papanicolaou (Pap) test and testing for high-risk human papillomavirus (hrHPV). The Pap test has low sensitivity to detect precursor lesions, while a single hrHPV test cannot distinguish a persistent infection from one that the immune system will naturally clear. Furthermore, among women who are hrHPV-positive and progress to high-grade cervical lesions, testing cannot identify the ~20% who would progress to cancer if not treated. Thus, reliable detection and treatment of cancers and precancers requires routine screening followed by frequent surveillance among those with past abnormal or positive results. The consequence is overtreatment, with its associated risks and complications, in screened populations and an increased risk of cancer in under-screened populations. Methods to improve cervical cancer risk assessment, particularly assays to predict regression of precursor lesions or clearance of hrHPV infection, would benefit both populations. Here we show that women who have lower risk results on follow-up testing relative to index testing have evidence of enhanced T cell clonal expansion in the index cervical cytology sample compared to women who persist with higher risk results from index to follow-up. We further show that a machine learning classifier based on the index sample T cells predicts this transition to lower risk with 95% accuracy (19/20) by leave-one-out cross-validation. Using T cell receptor deep sequencing and machine learning, we identified a biophysicochemical motif in the complementarity-determining region 3 of T cell receptor β chains whose presence predicts this transition. While these results must still be tested on an independent cohort in a prospective study, they suggest that this approach could improve cervical cancer screening by helping distinguish women likely to spontaneously regress from those at elevated risk of progression to cancer. The advancement of such a strategy could reduce surveillance frequency and overtreatment in screened populations and improve the delivery of screening to under-screened populations.
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Affiliation(s)
- Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Jared Ostmeyer
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Lisa Quirk
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Wei Zhang
- Department of Neurology and Neurotherapeutics, Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Bradley Sirak
- Center for Immunization and Infection Research, Moffitt Cancer Center, Tampa, FL, United States
| | - Anna R Giuliano
- Center for Immunization and Infection Research, Moffitt Cancer Center, Tampa, FL, United States
| | - Song Zhang
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Nancy Monson
- Department of Neurology and Neurotherapeutics, Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
| | - Jasmin Tiro
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States
| | - Elena Lucas
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, United States.,Department of Pathology, Parkland Health and Hospital System, Dallas, TX, United States
| | - Lindsay G Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX, United States.,Department of Neurology and Neurotherapeutics, Department of Immunology, UT Southwestern Medical Center, Dallas, TX, United States
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22
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Wu M, Zhao M, Wu H, Lu Q. Immune repertoire: Revealing the "real-time" adaptive immune response in autoimmune diseases. Autoimmunity 2021; 54:61-75. [PMID: 33650440 DOI: 10.1080/08916934.2021.1887149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The diversity of the immune repertoire (IR) enables the human immune system to distinguish multifarious antigens (Ags) that humans may encounter throughout life. At the same time, bias or abnormalities in the IR also pay a contribution to the pathogenesis of autoimmune diseases. Rapid advancements in high-throughput sequencing (HTS) technology have ushered in a new era of immune studies, revealing novel molecules and pathways that might result in autoimmunity. In the field of IR, HTS can monitor the immune response status and identify disease-specific immune repertoires. In this review, we summarize updated progress on the mechanisms of the IR and current related studies on four autoimmune diseases, particularly focusing on systemic lupus erythematosus (SLE). These autoimmune diseases can exhibit slightly or significantly skewed IRs and provide novel insights that inform our comprehending of disease pathogenesis and provide potential targets for diagnosis and treatment.
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Affiliation(s)
- Meiyu Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Ming Zhao
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China.,Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, Jiangsu, China
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23
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Wang Y, Liu Y, Chen L, Chen Z, Wang X, Jiang R, Zhao K, He X. T Cell Receptor Beta-Chain Profiling of Tumor Tissue, Peripheral Blood and Regional Lymph Nodes From Patients With Papillary Thyroid Carcinoma. Front Immunol 2021; 12:595355. [PMID: 33679738 PMCID: PMC7930746 DOI: 10.3389/fimmu.2021.595355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/25/2021] [Indexed: 11/29/2022] Open
Abstract
Objective: To study the characteristics of the T cell receptor (TCR) repertoire in cancer tissue, peripheral blood and regional lymph nodes (LNs) from patients with papillary thyroid carcinoma (PTC). Methods: PTC tissue, peripheral blood mononuclear cells (PBMCs) and regional LNs of six patients with papillary thyroid carcinoma were harvested. T cell receptor beta-chain (TCRβ) profiling was performed though high-throughput sequencing (HTS), and IMonitor, MiXCR and VDJtools were used to analyze the characteristics of the TCR repertoire. Results: The results of IMonitor and those of MiXCR and VDJtools were very similar. The unique CDR3 of TCRβ from LNs was higher than that of PBMCs, and the CDR3 of TCRβ from LNs was higher than that of PTC tissue. Shannon's diversity index, D50, inverse Simpson index_mean and normalized Shannon's diversity index_mean of CDR3 from LNs were higher than those of PTCs and PBMCs. The HEC (high expansion clones) rate of CDR3 sequences at the amino acid level in PTC tissue was higher than that of PBMCs, which was higher than that of LNs. The V-J HEC rate of CDR3 was highest in PTC tissue, followed by PBMCs and LNs. Conclusion: TCR CDR3 profiling showed differences among and within the PBMCs, PTC tissues and regional LNs of PTC, including unique CDR3, CDR3 HEC at the amino acid level, CDR3 V-J HEC at the amino acid level, Shannon's diversity index and D50. The TCRβ repertoire of PTC tissue, peripheral blood and regional LNs of PTC provide a reference for further study of immunity mechanisms against PTC.
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Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yuanchao Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Li Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Zuoyu Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
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24
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Greiff V, Yaari G, Cowell LG. Mining adaptive immune receptor repertoires for biological and clinical information using machine learning. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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