101
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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102
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Oliveira G, Egloff AM, Afeyan AB, Wolff JO, Zeng Z, Chernock RD, Zhou L, Messier C, Lizotte P, Pfaff KL, Stromhaug K, Penter L, Haddad RI, Hanna GJ, Schoenfeld JD, Goguen LA, Annino DJ, Jo V, Oppelt P, Pipkorn P, Jackson R, Puram SV, Paniello RC, Rich JT, Webb J, Zevallos JP, Mansour M, Fu J, Dunn GP, Rodig SJ, Ley J, Morris LG, Dunn L, Paweletz CP, Kallogjeri D, Piccirillo JF, Adkins DR, Wu CJ, Uppaluri R. Preexisting tumor-resident T cells with cytotoxic potential associate with response to neoadjuvant anti-PD-1 in head and neck cancer. Sci Immunol 2023; 8:eadf4968. [PMID: 37683037 PMCID: PMC10794154 DOI: 10.1126/sciimmunol.adf4968] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/31/2023] [Indexed: 09/10/2023]
Abstract
About 50% of patients with locally advanced head and neck squamous cell carcinoma (HNSCC) experience recurrences after definitive therapy. The presurgical administration of anti-programmed cell death protein 1 (PD-1) immunotherapy results in substantial pathologic tumor responses (pTR) within the tumor microenvironment (TME). However, the mechanisms underlying the dynamics of antitumor T cells upon neoadjuvant PD-1 blockade remain unresolved, and approaches to increase pathologic responses are lacking. In a phase 2 trial (NCT02296684), we observed that 45% of patients treated with two doses of neoadjuvant pembrolizumab experienced marked pTRs (≥50%). Single-cell analysis of 17,158 CD8+ T cells from 14 tumor biopsies, including 6 matched pre-post neoadjuvant treatment, revealed that responding tumors had clonally expanded putative tumor-specific exhausted CD8+ tumor-infiltrating lymphocytes (TILs) with a tissue-resident memory program, characterized by high cytotoxic potential (CTX+) and ZNF683 expression, within the baseline TME. Pathologic responses after 5 weeks of PD-1 blockade were consistent with activation of preexisting CTX+ZNF683+CD8+ TILs, paralleling loss of viable tumor and associated tumor antigens. Response was associated with high numbers of CD103+PD-1+CD8+ T cells infiltrating pretreatment lesions, whereas revival of nonexhausted persisting clones and clonal replacement were modest. By contrast, nonresponder baseline TME exhibited a relative absence of ZNF683+CTX+ TILs and subsequent accumulation of highly exhausted clones. In HNSCC, revival of preexisting ZNF683+CTX+ TILs is a major mechanism of response in the immediate postneoadjuvant setting.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
| | - Ann Marie Egloff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Alexander B. Afeyan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
| | - Jacquelyn O. Wolff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Zexiang Zeng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca D. Chernock
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Liye Zhou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cameron Messier
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Patrick Lizotte
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Kathleen L Pfaff
- Center for Immuno-Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Kari Stromhaug
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Livius Penter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Hematology, Oncology and Tumor immunology, Campus Virchow Klinikum, Berlin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Robert I. Haddad
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Glenn J. Hanna
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | | | - Laura A. Goguen
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Donald J. Annino
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Vickie Jo
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
| | - Peter Oppelt
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine/Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrik Pipkorn
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Ryan Jackson
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Sidharth V. Puram
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Randal C. Paniello
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jason T. Rich
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jason Webb
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jose P. Zevallos
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mena Mansour
- Department of Pathology and Immunology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jingxin Fu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gavin P. Dunn
- Department of Neurological Surgery, Massachusetts General Hospital; Boston, MA, USA
| | - Scott J. Rodig
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
| | - Jessica Ley
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine/Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Luc G.T. Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lara Dunn
- Department of Medical Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cloud P. Paweletz
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Dorina Kallogjeri
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Jay F. Piccirillo
- Department of Otolaryngology, Washington University School of Medicine; St. Louis, MO, USA
| | - Douglas R. Adkins
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine/Medical Oncology, Washington University School of Medicine, St. Louis, MO, USA
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ravindra Uppaluri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard Medical School; Boston, MA, USA
- Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
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103
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Wu W, Chia T, Lu J, Li X, Guan J, Li Y, Fu F, Zhou S, Feng Y, Deng J, Zou J, Sun J, Yao Y, Ling X, Wu Z, Zhang Y, Xu J, Wang F, Liang X, Wu M, Liu H, Chen B, He K. IL-2Rα-biased agonist enhances antitumor immunity by invigorating tumor-infiltrating CD25 +CD8 + T cells. NATURE CANCER 2023; 4:1309-1325. [PMID: 37550516 DOI: 10.1038/s43018-023-00612-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/06/2023] [Indexed: 08/09/2023]
Abstract
To avoid regulatory T cell promotion and vascular toxicity, the interleukin-2 receptor-β/interleukin-2 receptor-γ (IL-2Rβγ)-biased approach is used by most IL-2 analogs in immuno-oncology. However, recent clinical disappointments in these IL-2 agonists have questioned this strategy. Here we show that both wild-type (IL-2wt) and IL-2Rβγ-attenuated (IL-2α-bias) agonists that preserve IL-2Rα (CD25) activities can effectively expand tumor-specific CD8+ T cells (TSTs) and exhibit better antitumor efficacy and safety than the 'non-α' counterpart (IL-2nα). Mechanistically, TSTs coexpress elevated CD25 and PD-1 and are more susceptible to stimulation by IL-2Rα-proficient agonists. Moreover, the antitumor efficacy of anti-PD-1 depends on activation of PD-1+CD25+ TSTs through autocrine IL-2-CD25 signaling. In individuals with cancer, a low IL-2 signature correlates with non-responsiveness to anti-PD-1 treatment. In mouse models, IL-2α-bias, but not IL-2nα, restores the IL-2 signature and synergizes with anti-PD-1 to eradicate large established tumors. These findings underscore the indispensable function of CD25 in IL-2-based immunotherapy and provide rationales for evaluating IL-2Rα-biased agonists in individuals with cancer.
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Affiliation(s)
- Weiwei Wu
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Tiongsun Chia
- Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China
| | - Jia Lu
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Xue Li
- Department of Immunology, Innovent Guoqing Academy, Suzhou, China
| | - Jian Guan
- Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China
| | - Yaning Li
- Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China
| | - Fenggen Fu
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Shuaixiang Zhou
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Ye Feng
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Junjie Deng
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Jia Zou
- Department of Immunology, Innovent Guoqing Academy, Suzhou, China
| | - Jiya Sun
- Department of Translational Medicine, Innovent Biologics (Suzhou) Co., Ltd., Suzhou, China
| | - Ying Yao
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Xiaomin Ling
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Zhihai Wu
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Ying Zhang
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Jinling Xu
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Feifei Wang
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Xue Liang
- Department of Antibody Discovery and Protein Engineering, Innovent Guoqing Academy, Suzhou, China
| | - Min Wu
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Huisi Liu
- Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China
| | - Bingliang Chen
- Department of Pharmacology and Toxicology, Innovent Guoqing Academy, Suzhou, China
| | - Kaijie He
- Department of Cancer Biology, Innovent Guoqing Academy, Suzhou, China.
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104
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Lan X, Zebley CC, Youngblood B. Cellular and molecular waypoints along the path of T cell exhaustion. Sci Immunol 2023; 8:eadg3868. [PMID: 37656775 PMCID: PMC10618911 DOI: 10.1126/sciimmunol.adg3868] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/09/2023] [Indexed: 09/03/2023]
Abstract
Thirty years of foundational research investigating molecular and cellular mechanisms promoting T cell exhaustion are now enabling rational design of T cell-based therapies for the treatment of chronic infections and cancer. Once described as a static cell fate, it is now well appreciated that the developmental path toward exhaustion is composed of a heterogeneous pool of cells with varying degrees of effector potential that ultimately converge on a terminally differentiated state. Recent description of the developmental stages along the differentiation trajectory of T cell exhaustion has provided insight into past immunotherapeutic success and future opportunities. Here, we discuss the hallmarks of distinct developmental stages occurring along the path to T cell dysfunction and the impact of these discrete CD8+ T cell fates on cancer immunotherapy.
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Affiliation(s)
- Xin Lan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- College of Graduate Health Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Caitlin C. Zebley
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ben Youngblood
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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105
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'IL-2Rα-biased' IL-2 for cancer immunotherapy. NATURE CANCER 2023; 4:1222-1223. [PMID: 37550518 DOI: 10.1038/s43018-023-00613-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
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106
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Lu X, Lofgren SM, Zhao Y, Mazur PK. Multiplexed transcriptomic profiling of the fate of human CAR T cells in vivo via genetic barcoding with shielded small nucleotides. Nat Biomed Eng 2023; 7:1170-1187. [PMID: 37652986 DOI: 10.1038/s41551-023-01085-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 08/01/2023] [Indexed: 09/02/2023]
Abstract
The design of chimeric antigen receptor (CAR) T cells would benefit from knowledge of the fate of the cells in vivo. This requires the permanent labelling of CAR T cell products and their pooling in the same microenvironment. Here, we report a cell-barcoding method for the multiplexed longitudinal profiling of cells in vivo using single-cell RNA sequencing (scRNA-seq). The method, which we named shielded-small-nucleotide-based scRNA-seq (SSN-seq), is compatible with both 3' and 5' single-cell profiling, and enables the recording of cell identity, from cell infusion to isolation, by leveraging the ubiquitous Pol III U6 promoters to robustly express small-RNA barcodes modified with direct-capture sequences. By using SSN-seq to track the dynamics of the states of CAR T cells in a tumour-rechallenge mouse model of leukaemia, we found that a combination of cytokines and small-molecule inhibitors that are used in the ex vivo manufacturing of CAR T cells promotes the in vivo expansion of persistent populations of CD4+ memory T cells. By facilitating the probing of cell-state dynamics in vivo, SSN-seq may aid the development of adoptive cell therapies.
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Affiliation(s)
- Xiaoyin Lu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shane M Lofgren
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yuehui Zhao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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107
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He L, Gao F, Zhu J, Xu Q, Yu Q, Yang M, Huang Y. Homologous recombination deficiency serves as a prognostic biomarker in clear cell renal cell carcinoma. Exp Ther Med 2023; 26:429. [PMID: 37602311 PMCID: PMC10433413 DOI: 10.3892/etm.2023.12128] [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: 10/21/2022] [Accepted: 04/18/2023] [Indexed: 08/22/2023] Open
Abstract
Kidney renal clear cell carcinoma (KIRC) is a frequent malignant tumor characterized by a high degree of heterogeneity and genetic instability. DNA double-strand breaks generated by homologous recombination deficit (HRD) are a well-known contributor to genomic instability, which can encourage tumor development. It is not known, however, whether the molecular characteristics linked with HRD have a predictive role in KIRC. The discovery cohort comprised 501 KIRC patients from The Cancer Genome Atlas database. Genome and transcriptome data of HRD patients were used for comprehensive analysis. Single cell RNA sequencing (scRNA-seq) was used to verify the test results of bulk RNA-seq. In the present study, patients with a high HRD score had a worse prognosis compared with those with a low HRD score. The DNA damage response signaling pathways and immune-related signaling pathways were notably enriched in the HRD-positive subgroup. Further comprehensive analysis of the tumor microenvironment (TME) revealed that the signal of exhausted CD8+ T cells was enriched in the HRD-positive subgroup. Finally, scRNA-seq analyses confirmed that the immune-related signaling pathways were upregulated in HRD-positive patients. In conclusion, the present study not only demonstrated that a high HRD score is a valid prognostic biomarker in KIRC patients, but also revealed the TME in HRD-positive tumors.
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Affiliation(s)
- Liping He
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Feng Gao
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Jingyu Zhu
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Qiaoping Xu
- Department of Clinical Pharmacology, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Cancer Center, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, P.R. China
| | - Qiqi Yu
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Mei Yang
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
| | - Yasheng Huang
- Department of Urology, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang 310007, P.R. China
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108
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Sun L, Kienzler JC, Reynoso JG, Lee A, Shiuan E, Li S, Kim J, Ding L, Monteleone AJ, Owens GC, Phillips JJ, Everson RG, Nathanson D, Cloughesy TF, Li G, Liau LM, Hugo W, Kim W, Prins RM. Immune checkpoint blockade induces distinct alterations in the microenvironments of primary and metastatic brain tumors. J Clin Invest 2023; 133:e169314. [PMID: 37655659 PMCID: PMC10471177 DOI: 10.1172/jci169314] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/12/2023] [Indexed: 09/02/2023] Open
Abstract
In comparison with responses in recurrent glioblastoma (rGBM), the intracranial response of brain metastases (BrM) to immune checkpoint blockade (ICB) is less well studied. Here, we present an integrated single-cell RNA-Seq (scRNA-Seq) study of 19 ICB-naive and 9 ICB-treated BrM samples from our own and published data sets. We compared them with our previously published scRNA-Seq data from rGBM and found that ICB led to more prominent T cell infiltration into BrM than rGBM. These BrM-infiltrating T cells exhibited a tumor-specific phenotype and displayed greater activated/exhausted features. We also used multiplex immunofluorescence and spatial transcriptomics to reveal that ICB reduced a distinct CD206+ macrophage population in the perivascular space, which may modulate T cell entry into BrM. Furthermore, we identified a subset of progenitor exhausted T cells that correlated with longer overall survival in BrM patients. Our study provides a comprehensive immune cellular landscape of ICB's effect on metastatic brain tumors and offers insights into potential strategies for improving ICB efficacy for brain tumor patients.
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Affiliation(s)
- Lu Sun
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
| | - Jenny C. Kienzler
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Inflammation Research Group, Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | | | - Alexander Lee
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
| | | | | | | | - Lizhong Ding
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | | | | | - Joanna J. Phillips
- Helen Diller Family Comprehensive Cancer Center and
- Department of Neurological Surgery, UCSF, San Francisco, California, USA
| | - Richard G. Everson
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - David Nathanson
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Timothy F. Cloughesy
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Neurology/Neuro-Oncology, UCLA, Los Angeles, California, USA
| | | | - Linda M. Liau
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Willy Hugo
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Department of Medicine/Dermatology, UCLA, Los Angeles, California, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
| | - Won Kim
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
| | - Robert M. Prins
- Department of Neurosurgery, UCLA, Los Angeles, California, USA
- Department of Molecular and Medical Pharmacology
- UCLA Jonsson Comprehensive Cancer Center (JCCC), and
- Parker Institute for Cancer Immunotherapy, San Francisco, California, USA
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109
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Li J, Xiao Z, Wang D, Jia L, Nie S, Zeng X, Hu W. The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells. Mol Cancer 2023; 22:141. [PMID: 37649123 PMCID: PMC10466891 DOI: 10.1186/s12943-023-01844-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.
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Affiliation(s)
- Jiangping Li
- Division of Thoracic Tumor Multimodality Treatment, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China.
| | - Zhiwen Xiao
- Department of Otolaryngology Head and Neck Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510655, People's Republic of China
| | - Donghui Wang
- Department of Radiation Oncology, The Third Affiliated Hospital Sun Yat-Sen University, Guangzhou, 510630, People's Republic of China
| | - Lei Jia
- International Health Medicine Innovation Center, Shenzhen University, Shenzhen, 518060, People's Republic of China
| | - Shihong Nie
- Department of Radiation Oncology, West China Hospital, Sichuan University, Cancer Center, Chengdu, 610041, People's Republic of China
| | - Xingda Zeng
- Department of Parasitology of Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
| | - Wei Hu
- Division of Vascular Surgery, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, People's Republic of China
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110
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Tretter C, de Andrade Krätzig N, Pecoraro M, Lange S, Seifert P, von Frankenberg C, Untch J, Zuleger G, Wilhelm M, Zolg DP, Dreyer FS, Bräunlein E, Engleitner T, Uhrig S, Boxberg M, Steiger K, Slotta-Huspenina J, Ochsenreither S, von Bubnoff N, Bauer S, Boerries M, Jost PJ, Schenck K, Dresing I, Bassermann F, Friess H, Reim D, Grützmann K, Pfütze K, Klink B, Schröck E, Haller B, Kuster B, Mann M, Weichert W, Fröhling S, Rad R, Hiltensperger M, Krackhardt AM. Proteogenomic analysis reveals RNA as a source for tumor-agnostic neoantigen identification. Nat Commun 2023; 14:4632. [PMID: 37532709 PMCID: PMC10397250 DOI: 10.1038/s41467-023-39570-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 06/19/2023] [Indexed: 08/04/2023] Open
Abstract
Systemic pan-tumor analyses may reveal the significance of common features implicated in cancer immunogenicity and patient survival. Here, we provide a comprehensive multi-omics data set for 32 patients across 25 tumor types for proteogenomic-based discovery of neoantigens. By using an optimized computational approach, we discover a large number of tumor-specific and tumor-associated antigens. To create a pipeline for the identification of neoantigens in our cohort, we combine DNA and RNA sequencing with MS-based immunopeptidomics of tumor specimens, followed by the assessment of their immunogenicity and an in-depth validation process. We detect a broad variety of non-canonical HLA-binding peptides in the majority of patients demonstrating partially immunogenicity. Our validation process allows for the selection of 32 potential neoantigen candidates. The majority of neoantigen candidates originates from variants identified in the RNA data set, illustrating the relevance of RNA as a still understudied source of cancer antigens. This study underlines the importance of RNA-centered variant detection for the identification of shared biomarkers and potentially relevant neoantigen candidates.
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Affiliation(s)
- Celina Tretter
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Niklas de Andrade Krätzig
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Matteo Pecoraro
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sebastian Lange
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Philipp Seifert
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Clara von Frankenberg
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Johannes Untch
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Gabriela Zuleger
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Mathias Wilhelm
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Computational Mass Spectrometry, Freising, Germany
| | - Daniel P Zolg
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
| | - Florian S Dreyer
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Eva Bräunlein
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Thomas Engleitner
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Sebastian Uhrig
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Precision Oncology Program, NCT Heidelberg, Heidelberg, Germany
| | - Melanie Boxberg
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Julia Slotta-Huspenina
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Sebastian Ochsenreither
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Charité Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Hematology, Oncology and Tumor Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Nikolas von Bubnoff
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Department of Hematology and Oncology, Medical Center, University of Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Sebastian Bauer
- German Cancer Consortium (DKTK), partner site Essen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Medical Oncology and Sarcoma Center, West German Cancer Center, University Hospital Essen, Essen, Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK), partner site Freiburg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Medical Bioinformatics and Systems Medicine (IBSM), Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Philipp J Jost
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Clinical Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- University Comprehensive Cancer Center Graz, Medical University of Graz, Graz, Austria
| | - Kristina Schenck
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Iska Dresing
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Florian Bassermann
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
| | - Helmut Friess
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Daniel Reim
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Department of Surgery, Munich, Germany
| | - Konrad Grützmann
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Core Unit Molecular Tumor Diagnostics (CMTD), NCT Dresden, Dresden, Germany
- Institute for Medical Informatics and Biometry, Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Katrin Pfütze
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Klink
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Evelin Schröck
- German Cancer Consortium (DKTK), partner site Dresden and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
- ERN GENTURIS, Hereditary Cancer Syndrome Center Dresden, Dresden, Germany
- National Center for Tumor Diseases Dresden (NCT/UCC), Dresden, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
- Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Bernhard Haller
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of AI and Informatics in Medicine, Munich, Germany
| | - Bernhard Kuster
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Life Sciences, Chair of Proteomics and Bioanalytics, Freising, Germany
- Technical University of Munich, TUM School of Life Sciences, Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Freising, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Plank Institute of Biochemistry, Munich, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, Institute of Pathology, Munich, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Translational Medical Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IInd Medical Department, Munich, Germany
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany
- Technical University of Munich, TUM School of Medicine, Institute of Molecular Oncology and Functional Genomics, Munich, Germany
| | - Michael Hiltensperger
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany
| | - Angela M Krackhardt
- German Cancer Consortium (DKTK), partner site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Technical University of Munich, TUM School of Medicine, Klinikum rechts der Isar, IIIrd Medical Department, Munich, Germany.
- Technical University of Munich, TUM School of Medicine, Center for Translational Cancer Research (TranslaTUM), Munich, Germany.
- Malteser Krankenhaus St. Franziskus-Hospital, Flensburg, Germany.
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111
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Brightman SE, Becker A, Thota RR, Naradikian MS, Chihab L, Zavala KS, Ramamoorthy Premlal AL, Griswold RQ, Dolina JS, Cohen EEW, Miller AM, Peters B, Schoenberger SP. Neoantigen-specific stem cell memory-like CD4 + T cells mediate CD8 + T cell-dependent immunotherapy of MHC class II-negative solid tumors. Nat Immunol 2023; 24:1345-1357. [PMID: 37400675 PMCID: PMC10382322 DOI: 10.1038/s41590-023-01543-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 05/22/2023] [Indexed: 07/05/2023]
Abstract
CD4+ T cells play key roles in a range of immune responses, either as direct effectors or through accessory cells, including CD8+ T lymphocytes. In cancer, neoantigen (NeoAg)-specific CD8+ T cells capable of direct tumor recognition have been extensively studied, whereas the role of NeoAg-specific CD4+ T cells is less well understood. We have characterized the murine CD4+ T cell response against a validated NeoAg (CLTCH129>Q) expressed by the MHC-II-deficient squamous cell carcinoma tumor model (SCC VII) at the level of single T cell receptor (TCR) clonotypes and in the setting of adoptive immunotherapy. We find that the natural CLTCH129>Q-specific repertoire is diverse and contains TCRs with distinct avidities as measured by tetramer-binding assays and CD4 dependence. Despite these differences, CD4+ T cells expressing high or moderate avidity TCRs undergo comparable in vivo proliferation to cross-presented antigen from growing tumors and drive similar levels of therapeutic immunity that is dependent on CD8+ T cells and CD40L signaling. Adoptive cellular therapy (ACT) with NeoAg-specific CD4+ T cells is most effective when TCR-engineered cells are differentiated ex vivo with IL-7 and IL-15 rather than IL-2 and this was associated with both increased expansion as well as the acquisition and stable maintenance of a T stem cell memory (TSCM)-like phenotype in tumor-draining lymph nodes (tdLNs). ACT with TSCM-like CD4+ T cells results in lower PD-1 expression by CD8+ T cells in the tumor microenvironment and an increased frequency of PD-1+CD8+ T cells in tdLNs. These findings illuminate the role of NeoAg-specific CD4+ T cells in mediating antitumor immunity via providing help to CD8+ T cells and highlight their therapeutic potential in ACT.
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Affiliation(s)
- Spencer E Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Angelica Becker
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Rukman R Thota
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Martin S Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Leila Chihab
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Karla Soria Zavala
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Ryan Q Griswold
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Biomedical Sciences Program, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Joseph S Dolina
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ezra E W Cohen
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Aaron M Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
| | - Bjoern Peters
- Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, UCSD, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stephen P Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, CA, USA.
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112
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Komuro H, Shinohara S, Fukushima Y, Demachi-Okamura A, Muraoka D, Masago K, Matsui T, Sugita Y, Takahashi Y, Nishida R, Takashima C, Ohki T, Shigematsu Y, Watanabe F, Adachi K, Fukuyama T, Hamana H, Kishi H, Miura D, Tanaka Y, Onoue K, Onoguchi K, Yamashita Y, Stratford R, Clancy T, Yamaguchi R, Kuroda H, Doi K, Iwata H, Matsushita H. Single-cell sequencing on CD8 + TILs revealed the nature of exhausted T cells recognizing neoantigen and cancer/testis antigen in non-small cell lung cancer. J Immunother Cancer 2023; 11:e007180. [PMID: 37544663 PMCID: PMC10407349 DOI: 10.1136/jitc-2023-007180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2023] [Indexed: 08/08/2023] Open
Abstract
BACKGROUND CD8+tumor infiltrating lymphocytes (TILs) are often observed in non-small cell lung cancers (NSCLC). However, the characteristics of CD8+ TILs, especially T-cell populations specific for tumor antigens, remain poorly understood. METHODS High throughput single-cell RNA sequencing and single-cell T-cell receptor (TCR) sequencing were performed on CD8+ TILs from three surgically-resected lung cancer specimens. Dimensional reduction for clustering was performed using Uniform Manifold Approximation and Projection. CD8+ TIL TCR specific for the cancer/testis antigen KK-LC-1 and for predicted neoantigens were investigated. Differentially-expressed gene analysis, Gene Set Enrichment Analysis (GSEA) and single sample GSEA was performed to characterize antigen-specific T cells. RESULTS A total of 6998 CD8+ T cells was analyzed, divided into 10 clusters according to their gene expression profile. An exhausted T-cell (exhausted T (Tex)) cluster characterized by the expression of ENTPD1 (CD39), TOX, PDCD1 (PD1), HAVCR2 (TIM3) and other genes, and by T-cell oligoclonality, was identified. The Tex TCR repertoire (Tex-TCRs) contained nine different TCR clonotypes recognizing five tumor antigens including a KK-LC-1 antigen and four neoantigens. By re-clustering the tumor antigen-specific T cells (n=140), it could be seen that the individual T-cell clonotypes were present on cells at different stages of differentiation and functional states even within the same Tex cluster. Stimulating these T cells with predicted cognate peptide indicated that TCR signal strength and subsequent T-cell proliferation and cytokine production was variable but always higher for neoantigens than KK-LC-1. CONCLUSIONS Our approach focusing on T cells with an exhausted phenotype among CD8+ TILs may facilitate the identification of tumor antigens and clarify the nature of the antigen-specific T cells to specify the promising immunotherapeutic targets in patients with NSCLC.
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Affiliation(s)
- Hiroyasu Komuro
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of General Thoracic Surgery, Gifu University School of Medicine Graduate School of Medicine, Gifu, Japan
| | - Shuichi Shinohara
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Thoracic Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yasunori Fukushima
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of General Thoracic Surgery, Gifu University School of Medicine Graduate School of Medicine, Gifu, Japan
| | - Ayako Demachi-Okamura
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Daisuke Muraoka
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Katsuhiro Masago
- Pathology and Molecular Diagnostics, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Takuya Matsui
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yusuke Sugita
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Yusuke Takahashi
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Reina Nishida
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Chieko Takashima
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Takashi Ohki
- Department of Respiratory Surgery, Ichinomiya Nishi Hospital, Ichinomiya, Japan
| | - Yoshiki Shigematsu
- Department of Respiratory Surgery, Ichinomiya Nishi Hospital, Ichinomiya, Japan
| | - Fumiaki Watanabe
- Department of Thoracic Surgery, Mie Chuo Medical Center, Tsu, Japan
| | | | - Takashi Fukuyama
- Division of Biomedical Research, Kitasato University Medical Center, Kitamoto, Japan
| | - Hiroshi Hamana
- Department of Immunology, University of Toyama, Toyama, Japan
| | - Hiroyuki Kishi
- Department of Immunology, University of Toyama, Toyama, Japan
| | - Daiki Miura
- Drug Development Division, NEC Corporation, Minato-ku, Japan
| | - Yuki Tanaka
- Drug Development Division, NEC Corporation, Minato-ku, Japan
| | - Kousuke Onoue
- Drug Development Division, NEC Corporation, Minato-ku, Japan
| | | | | | | | - Trevor Clancy
- NEC OncoImmunity AS, Oslo Cancer Cluster, Oslo, Norway
| | - Rui Yamaguchi
- Division of Cancer Systems Biology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Informatics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroaki Kuroda
- Department of Thoracic Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Kiyoshi Doi
- Department of General Thoracic Surgery, Gifu University School of Medicine Graduate School of Medicine, Gifu, Japan
| | - Hisashi Iwata
- Department of General Thoracic Surgery, Gifu University School of Medicine Graduate School of Medicine, Gifu, Japan
| | - Hirokazu Matsushita
- Division of Translational Oncoimmunology, Aichi Cancer Center Research Institute, Nagoya, Japan
- Division of Cancer Immunogenomics, Nagoya University Graduate School of Medicine, Nagoya, Japan
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113
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Martin SD, Bhuiyan I, Soleimani M, Wang G. Biomarkers for Immune Checkpoint Inhibitors in Renal Cell Carcinoma. J Clin Med 2023; 12:4987. [PMID: 37568390 PMCID: PMC10419620 DOI: 10.3390/jcm12154987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Immune checkpoint inhibitor (ICI) therapy has revolutionized renal cell carcinoma treatment. Patients previously thought to be palliative now occasionally achieve complete cures from ICI. However, since immunotherapies stimulate the immune system to induce anti-tumor immunity, they often lead to adverse autoimmunity. Furthermore, some patients receive no benefit from ICI, thereby unnecessarily risking adverse events. In many tumor types, PD-L1 expression levels, immune infiltration, and tumor mutation burden predict the response to ICI and help inform clinical decision making to better target ICI to patients most likely to experience benefits. Unfortunately, renal cell carcinoma is an outlier, as these biomarkers fail to discriminate between positive and negative responses to ICI therapy. Emerging biomarkers such as gene expression profiles and the loss of pro-angiogenic proteins VHL and PBRM-1 show promise for identifying renal cell carcinoma cases likely to respond to ICI. This review provides an overview of the mechanistic underpinnings of different biomarkers and describes the theoretical rationale for their use. We discuss the effectiveness of each biomarker in renal cell carcinoma and other cancer types, and we introduce novel biomarkers that have demonstrated some promise in clinical trials.
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Affiliation(s)
- Spencer D. Martin
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
| | - Ishmam Bhuiyan
- Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
| | - Maryam Soleimani
- Division of Medical Oncology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada;
- British Columbia Cancer Vancouver Centre, Vancouver, BC V5Z 4E6, Canada
| | - Gang Wang
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 1M9, Canada;
- British Columbia Cancer Vancouver Centre, Vancouver, BC V5Z 4E6, Canada
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114
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Li X, Korkut A. Recurrent composite markers of cell types and states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549344. [PMID: 37503180 PMCID: PMC10370072 DOI: 10.1101/2023.07.17.549344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Determining concise sets of genomic markers that identify cell types and states within tissue ecosystems remains challenging. To address this challenge, we developed Recurrent Composite Markers for Biological Identities with Neighborhood Enrichment (RECOMBINE). Validations of RECOMBINE with simulation and transcriptomics data in bulk, single-cell and spatial resolutions demonstrated the method's ability for unbiased selection of composite markers that characterize biological subpopulations. RECOMBINE captured markers of mouse visual cortex from single-cell RNA sequencing data and provided a gene panel for targeted spatial transcriptomics profiling. RECOMBINE identified composite markers of CD8 T cell states including GZMK + HAVCR2 - effector memory cells associated with anti-PD1 therapy response. The method outperformed differential gene expression analysis in characterizing a rare cell subpopulation within mouse intestine. Using RECOMBINE, we uncovered hierarchical gene programs of inter- and intra-tumoral heterogeneity in breast and skin tumors. In conclusion, RECOMBINE offers a data-driven approach for unbiased selection of composite markers, resulting in improved interpretation, discovery, and validation of cell types and states.
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115
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O’Connor RA, Martinez BR, Koppensteiner L, Mathieson L, Akram AR. Cancer-associated fibroblasts drive CXCL13 production in activated T cells via TGF-beta. Front Immunol 2023; 14:1221532. [PMID: 37520560 PMCID: PMC10373066 DOI: 10.3389/fimmu.2023.1221532] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Tumour-reactive T cells producing the B-cell attractant chemokine CXCL13, in solid tumours, promote development of tertiary lymphoid structures (TLS) and are associated with improved prognosis and responsiveness to checkpoint immunotherapy. Cancer associated fibroblasts are the dominant stromal cell type in non-small cell lung cancer (NSCLC) where they co-localise with T cells and can influence T cell activation and exhaustion. We questioned whether CAF directly promote CXCL13-production during T cell activation. Methods We characterised surface markers, cytokine production and transcription factor expression in CXCL13-producing T cells in NSCLC tumours and paired non-cancerous lung samples using flow cytometry. We then assessed the influence of human NSCLC-derived primary CAF lines on T cells from healthy donors and NSCLC patients during activation in vitro measuring CXCL13 production and expression of cell-surface markers and transcription factors by flow cytometry. Results CAFs significantly increased the production of CXCL13 by both CD4+ and CD8+ T cells. CAF-induced CXCL13-producing cells lacked expression of CXCR5 and BCL6 and displayed a T peripheral helper cell phenotype. Furthermore, we demonstrate CXCL13 production by T cells is induced by TGF-β and limited by IL-2. CAF provide TGF-β during T cell activation and reduce availability of IL-2 both directly (by reducing the capacity for IL-2 production) and indirectly, by expanding a population of activated Treg. Inhibition of TGF-β signalling prevented both CAF-driven upregulation of CXCL13 and Treg expansion. Discussion Promoting CXCL13 production represents a newly described immune-regulatory function of CAF with the potential to shape the immune infiltrate of the tumour microenvironment both by altering the effector-function of tumour infiltrating T-cells and their capacity to attract B cells and promote TLS formation.
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Affiliation(s)
- Richard A. O’Connor
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Begoña Roman Martinez
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Lilian Koppensteiner
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Layla Mathieson
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Ahsan R. Akram
- Centre for Inflammation Research, Institute of Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
- Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, United Kingdom
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Zhang Y, Cui K, Yang Y, Liu B, Zhu M, Chen H, Zhao C, Zhou Y, Nie Y. Infiltration of a Unique CD8 +CD274 + Cell Subgroup in Hepatocellular Carcinoma is Associated with Poor Clinical Outcomes. J Hepatocell Carcinoma 2023; 10:1051-1067. [PMID: 37449280 PMCID: PMC10337689 DOI: 10.2147/jhc.s410756] [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: 03/23/2023] [Accepted: 06/10/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction Immune checkpoint (IC) inhibitor-related immunotherapies have attracted considerable attention in hepatocellular carcinoma (HCC). High IC expression and high tumor infiltrating lymphocyte levels are the current indicators of sensitivity to IC inhibitors. Thus, it is imperative to apply precision medicine strategies for patient selection. Methods Six independent HCC cohorts were used for analysis at the single-cell and tissue levels. Multiplex immunofluorescence and immunochemistry staining assays were used to validate our results. A series of methodologies were used for immune-related evaluations. Results Herein, we uncovered a unique CD8+CD274+ cell subpopulation that is associated with tumor progression and poor survival in HCC at the single-cell level. We assessed this subset at the tissue level and found that the prognostic significance of CD274 is dependent on CD8A expression in HCC. Subsequently, we identified a unique high-risk subpopulation that showed high CD8A expression coupled with intense CD274 expression in multiple HCC cohorts. CD8AHighCD274High* subgroup was correlated with malignant indexes and remained an independent prognostic factor when considering the influence of these indexes. Molecular characteristic analyses showed that the CD8AHighCD274High* subgroup harbored more mutations, had higher immune response activity and presented enrichment of cancer-related biological processes. Moreover, this high-risk subpopulation in HCC was characterized by high immune cell infiltration, low tumor purity, and enrichment of cancer-related signatures. Finally, cases with this phenotype demonstrated higher immunomodulator and IC levels and greater sensitivity to IC inhibitors. Conclusion Our findings illustrate that some HCC patients may have a poor prognosis despite high CD8+ T-cell infiltration. These patients would probably benefit from IC inhibitor-based combination treatment.
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Affiliation(s)
- Yong Zhang
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Kaisa Cui
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, 214062, People’s Republic of China
| | - Yaoxiang Yang
- Department of Pathology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Bingxin Liu
- The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, 211166, People’s Republic of China
| | - Minzheng Zhu
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Hanqing Chen
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Chong Zhao
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Youlian Zhou
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
| | - Yuqiang Nie
- Department of Gastroenterology and Hepatology, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, People’s Republic of China
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Peri A, Salomon N, Wolf Y, Kreiter S, Diken M, Samuels Y. The landscape of T cell antigens for cancer immunotherapy. NATURE CANCER 2023:10.1038/s43018-023-00588-x. [PMID: 37415076 DOI: 10.1038/s43018-023-00588-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
The remarkable capacity of immunotherapies to induce durable regression in some patients with metastatic cancer relies heavily on T cell recognition of tumor-presented antigens. As checkpoint-blockade therapy has limited efficacy, tumor antigens have the potential to be exploited for complementary treatments, many of which are already in clinical trials. The surge of interest in this topic has led to the expansion of the tumor antigen landscape with the emergence of new antigen categories. Nonetheless, how different antigens compare in their ability to elicit efficient and safe clinical responses remains largely unknown. Here, we review known cancer peptide antigens, their attributes and the relevant clinical data and discuss future directions.
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Affiliation(s)
- Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Nadja Salomon
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany
| | - Yochai Wolf
- Ella Lemelbaum Institute for Immuno-oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Sebastian Kreiter
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Wang B, Wang K, Jiang P, Ruppin E. Decoupling the correlation between cytotoxic and exhausted T lymphocyte transcriptomic signatures enhances melanoma immunotherapy response prediction from tumor expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524482. [PMID: 36789444 PMCID: PMC9928024 DOI: 10.1101/2023.01.17.524482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background Cytotoxic T lymphocytes (CTL) play a crucial role in anti-cancer immunity. Progression of CTL to terminal exhausted T lymphocytes (ETL) that overexpress inhibitory receptors can substantially decrease effector cytokines production and diminish cytolytic activity and terminal exhausted T cell cannot be reprogrammed by ICIs in tumor microenvironment (TME). However, while the activity levels of CTL and ETL are considered important determinants of immune checkpoint inhibitors (ICIs) response, it has been repeatedly observed that their predictive power of the latter is quite limited. Studying this conundrum on a large scale across the TCGA cohort, we find that ETL and CTL activity (estimated based on conventional gene signatures in the bulk tumor expression) is strongly positively correlated in most cancer types. We hypothesized that the limited predictive power of CTL activity might result from the high concordance of CTL and ETL activities, which mutually cancels out their individual antagonistic effects on ICI response. Methods Consequently, we have set out to identify a set of genes whose expression identifies a subset of patients where the CTL and ETL correlation is diminished, such that the association between these CD8+ T cell states and ICIs response is enhanced. Results Analyzing TCGA melanoma bulk gene expression, we identified a set of genes whose over-expression markedly diminishes the CTL and ETL correlation, termed a decoupling signature (DS). Reassuringly, we first find that the correlation between ETL and CTL activities is indeed markedly lower across high scoring DS patients than that observed across low scoring DS patients in numerous independent melanoma ICIs cohorts. Second, indeed, this successful decoupling increases the power of CTL activity in predicting ICIs response in high DS scoring patients. We show that the resulting prediction accuracy is superior to other state-of-art ICI predictive transcriptomic signatures. Conclusion The new decoupling score boosts the power of CTL activity in predicting ICIs response in melanoma from the tumor bulk expression. Its use enables a two-step stratification approach, where the response of high scoring DS patient can be predicted more accurately that with extant transcriptomic signatures.
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Affiliation(s)
- Binbin Wang
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kun Wang
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Peng Jiang
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Tan J, Fan W, Liu T, Zhu B, Liu Y, Wang S, Wu J, Liu J, Zou F, Wei J, Liu L, Zhang X, Zhuang J, Wang Y, Lin H, Huang X, Chen S, Kuang M, Li J. TREM2 + macrophages suppress CD8 + T-cell infiltration after transarterial chemoembolisation in hepatocellular carcinoma. J Hepatol 2023; 79:126-140. [PMID: 36889359 DOI: 10.1016/j.jhep.2023.02.032] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 01/30/2023] [Accepted: 02/18/2023] [Indexed: 03/10/2023]
Abstract
BACKGROUND & AIMS The immune landscape of hepatocellular carcinoma (HCC) following transarterial chemoembolisation (TACE) remains to be clarified. This study aimed to characterise the immune landscape following TACE and the underlying mechanism of HCC progression. METHODS Tumour samples from five patients with treatment-naive HCC and five patients who received TACE therapy were collected and subjected to single-cell RNA sequencing. Another 22 paired samples were validated using immunofluorescence staining and flow cytometry. To clarify the underlying mechanisms, in vitro co-culture experiments and two types of TREM2-KO/WT mouse models, namely, an HCC cell orthotopic injection model and a spontaneous HCC model, were used. RESULTS A reduced number of CD8+ T cells and an increased number of tumour-associated macrophages (TAMs) were observed in the post-TACE microenvironment. TACE therapy reduced the cluster CD8_C4, which was highly enriched with tumour-specific CD8+ T cells of pre-exhausted phenotype. TREM2 was found to be highly expressed in TAMs following TACE, which was associated with a poor prognosis. TREM2+ TAMs secreted less CXCL9 but more galectin-1 than did TREM2- TAMs. Galectin-1 promoted PD-L1 overexpression in vessel endothelial cells, impeding CD8+ T cell recruitment. TREM2 deficiency also increased CD8+ T cell infiltration, which inhibited tumour growth in both in vivo HCC models. More importantly, TREM2 deficiency enhanced the therapeutic effect of anti-PD-L1 blockade. CONCLUSIONS This study shows that TREM2+ TAMs play an important role in suppressing CD8+ T cells. TREM2 deficiency increased the therapeutic effect of anti-PD-L1 blockade by enhancing antitumour activity of CD8+ T cells. These findings explain the reasons for recurrence and progression after TACE and provide a new target for HCC immunotherapy after TACE. IMPACT AND IMPLICATIONS Studying the immune landscape in post-TACE HCC is important to uncover the mechanisms of HCC progression. By using scRNA sequencing and functional assays, we discovered that both the number and function of CD8+ T cells are compromised, whereas the number of TREM2+ TAMs is increased in post-TACE HCC, correlating with worse prognosis. Moreover, TREM2 deficiency dramatically increases CD8+ T cell infiltration and augments the therapeutic efficacy of anti-PD-L1 blockade. Mechanistically, TREM2+ TAMs display lower CXCL9 and increased Gal-1 secretion than do TREM2- TAMs, with Gal-1 mediating the overexpression of PD-L1 in vessel endothelial cells. These results suggest that TREM2 could be a novel immunotherapeutic target for patients treated with TACE in HCC. This provides an opportunity to break the plateau of limited therapeutic effect. This study has the value of understanding the tumour microenvironment of post-TACE HCC and thinking a new strategy of immunotherapy in the field of HCC. It is therefore of key impact for physicians, scientists and drug developers in the field of liver cancer and gastrointestinal oncology.
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Affiliation(s)
- Jizhou Tan
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China; Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenzhe Fan
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Liu
- Department of Stomatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bowen Zhu
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yafang Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shutong Wang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jian Wu
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jun Liu
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Fan Zou
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jialiang Wei
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lingwei Liu
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaokai Zhang
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jialang Zhuang
- Biobank, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yi Wang
- Department of Stomatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haibiao Lin
- Department of Stomatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianzhang Huang
- Department of Stomatology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Songling Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Ming Kuang
- Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiaping Li
- Department of Interventional Oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China.
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Jiang N, Malone M, Chizari S. Antigen-specific and cross-reactive T cells in protection and disease. Immunol Rev 2023; 316:120-135. [PMID: 37209375 PMCID: PMC10524458 DOI: 10.1111/imr.13217] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/22/2023]
Abstract
Human T cells have a diverse T-cell receptor (TCR) repertoire that endows them with the ability to identify and defend against a broad spectrum of antigens. The universe of possible antigens that T cells may encounter, however, is even larger. To effectively surveil such a vast universe, the T-cell repertoire must adopt a high degree of cross-reactivity. Likewise, antigen-specific and cross-reactive T-cell responses play pivotal roles in both protective and pathological immune responses in numerous diseases. In this review, we explore the implications of these antigen-driven T-cell responses, with a particular focus on CD8+ T cells, using infection, neurodegeneration, and cancer as examples. We also summarize recent technological advances that facilitate high-throughput profiling of antigen-specific and cross-reactive T-cell responses experimentally, as well as computational biology approaches that predict these interactions.
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Affiliation(s)
- Ning Jiang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for Immunology, University of Pennsylvania, Philadelphia, PA, 19104
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104
- Center for Cellular Immunotherapies, University of Pennsylvania, Philadelphia, PA, 19104
- Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Malone
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
| | - Shahab Chizari
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104
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Ding L, Sun L, Bu MT, Zhang Y, Scott LN, Prins RM, Su MA, Lechner MG, Hugo W. Antigen presentation by clonally diverse CXCR5+ B cells to CD4 and CD8 T cells is associated with durable response to immune checkpoint inhibitors. Front Immunol 2023; 14:1176994. [PMID: 37435085 PMCID: PMC10330698 DOI: 10.3389/fimmu.2023.1176994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/22/2023] [Indexed: 07/13/2023] Open
Abstract
Introduction Increased T cell infiltration and interferon gamma (IFNγ) pathway activation are seen in tumors of melanoma patients who respond to ICI (immune checkpoint inhibitor) or MAPK pathway inhibitor (MAPKi) therapies. Yet, the rate of durable tumor control after ICI is almost twice that of MAPKi, suggesting that additional mechanisms may be present in patients responding to ICI therapy that are beneficial for anti-tumor immunity. Methods We used transcriptional analysis and clinical outcomes from patients treated with ICI or MAPKi therapies to delineate immune mechanisms driving tumor response. Results We discovered response to ICI is associated with CXCL13-driven recruitment of CXCR5+ B cells with significantly higher clonal diversity than MAPKi. Our in vitro data indicate that CXCL13 production was increased in human peripheral blood mononuclear cells by anti-PD1, but not MAPKi, treatment. Higher B cell infiltration and B cell receptor (BCR) diversity allows presentation of diverse tumor antigens by B cells, resulting in activation of follicular helper CD4 T cells (Tfh) and tumor reactive CD8 T cells after ICI therapy. Higher BCR diversity and IFNγ pathway score post-ICI are associated with significantly longer patient survival compared to those with either one or none. Conclusions Response to ICI, but not to MAPKi, depends on the recruitment of CXCR5+ B cells into the tumor microenvironment and their productive tumor antigen presentation to follicular helper and cytotoxic, tumor reactive T cells. Our study highlights the potential of CXCL13 and B cell based strategies to enhance the rate of durable response in melanoma patients treated with ICI.
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Affiliation(s)
- Lizhong Ding
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lu Sun
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melissa T. Bu
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Yanjun Zhang
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lauren N. Scott
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California, Los Angeles, Los Angeles, CA, United States
| | - Robert M. Prins
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Neurosurgery, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Maureen A. Su
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Pediatrics, Division of Pediatric Endocrinology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Melissa G. Lechner
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Willy Hugo
- Department of Medicine, Division of Dermatology, University of California, Los Angeles, Los Angeles, CA, United States
- Parker Institute for Cancer Immunotherapy, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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Sun L, Su Y, Jiao A, Wang X, Zhang B. T cells in health and disease. Signal Transduct Target Ther 2023; 8:235. [PMID: 37332039 DOI: 10.1038/s41392-023-01471-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 06/20/2023] Open
Abstract
T cells are crucial for immune functions to maintain health and prevent disease. T cell development occurs in a stepwise process in the thymus and mainly generates CD4+ and CD8+ T cell subsets. Upon antigen stimulation, naïve T cells differentiate into CD4+ helper and CD8+ cytotoxic effector and memory cells, mediating direct killing, diverse immune regulatory function, and long-term protection. In response to acute and chronic infections and tumors, T cells adopt distinct differentiation trajectories and develop into a range of heterogeneous populations with various phenotype, differentiation potential, and functionality under precise and elaborate regulations of transcriptional and epigenetic programs. Abnormal T-cell immunity can initiate and promote the pathogenesis of autoimmune diseases. In this review, we summarize the current understanding of T cell development, CD4+ and CD8+ T cell classification, and differentiation in physiological settings. We further elaborate the heterogeneity, differentiation, functionality, and regulation network of CD4+ and CD8+ T cells in infectious disease, chronic infection and tumor, and autoimmune disease, highlighting the exhausted CD8+ T cell differentiation trajectory, CD4+ T cell helper function, T cell contributions to immunotherapy and autoimmune pathogenesis. We also discuss the development and function of γδ T cells in tissue surveillance, infection, and tumor immunity. Finally, we summarized current T-cell-based immunotherapies in both cancer and autoimmune diseases, with an emphasis on their clinical applications. A better understanding of T cell immunity provides insight into developing novel prophylactic and therapeutic strategies in human diseases.
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Affiliation(s)
- Lina Sun
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Yanhong Su
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Anjun Jiao
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Xin Wang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China
| | - Baojun Zhang
- Department of Pathogenic Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Institute of Infection and Immunity, Translational Medicine Institute, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, 710061, China.
- Xi'an Key Laboratory of Immune Related Diseases, Xi'an, Shannxi, 710061, China.
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Ng JWK, Tan KW, Guo DY, Lai JJH, Fan X, Poon Z, Lim TH, Lim AST, Lim TKH, Hwang WYK, Li S, Eaves CJ, Goh YT, Cheung AMS. Cord blood-derived V δ2 + and V δ2 - T cells acquire differential cell state compositions upon in vitro expansion. SCIENCE ADVANCES 2023; 9:eadf3120. [PMID: 37327346 PMCID: PMC10275585 DOI: 10.1126/sciadv.adf3120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 05/10/2023] [Indexed: 06/18/2023]
Abstract
Human cord blood-derived γδ T cells (CBγδ) display a highly diverse TCRγδ repertoire and have a unique subtype composition different from fetal or adult peripheral blood counterparts. We expanded CBγδ in vitro using an irradiated Epstein-Barr virus-transformed feeder cell-based modified rapid expansion protocol (REP). Single-cell RNA sequencing tracked progressive differentiation of naïve CBγδ into cells expressing neoantigen-reactive tumor-infiltrating lymphocyte as well as tissue-resident memory precursor-like and antigen-presenting cell-like gene signatures. TCRγδ clonal tracing revealed a bias toward cytotoxic effector differentiation in a much larger proportion of Vδ2- clones compared to Vδ2+ clones, resulting in the former being more cytotoxic at the population level. These clonotype-specific differentiation dynamics were not restricted to REP and were recapitulated upon secondary nonviral antigen stimulations. Thus, our data showed intrinsic cellular differences between major subtypes of human γδ T cells already in operation at early postnatal stage and highlighted key areas of consideration in optimizing cell manufacturing processes.
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Affiliation(s)
- Jeremy Wee Kiat Ng
- Department of Molecular Pathology, Translational Pathology Centre, Singapore General Hospital, Singapore, Singapore
| | - Kar Wai Tan
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
- Tessa Therapeutics Ltd, Singapore, Singapore
| | - Dian Yan Guo
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Joey Jia Hui Lai
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Xiubo Fan
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
| | - Zhiyong Poon
- Department of Clinical Translational Research, Singapore General Hospital, Singapore, Singapore
- Critical Analytics for Manufacturing Personalized-Medicine, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Tse Hui Lim
- Department of Molecular Pathology, Cytogenetics Laboratory, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Department of Molecular Pathology, Cytogenetics Laboratory, Singapore General Hospital, Singapore, Singapore
| | - Tony Kiat Hon Lim
- Department of Molecular Pathology, Translational Pathology Centre, Singapore General Hospital, Singapore, Singapore
| | - William Ying Khee Hwang
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
- National Cancer Centre Singapore, Singapore, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | | | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Alice Man Sze Cheung
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
- Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
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Piper M, Kluger H, Ruppin E, Hu-Lieskovan S. Immune Resistance Mechanisms and the Road to Personalized Immunotherapy. Am Soc Clin Oncol Educ Book 2023; 43:e390290. [PMID: 37459578 DOI: 10.1200/edbk_390290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
What does the future of cancer immunotherapy look like and how do we get there? Find out where we've been and where we're headed in A Report on Resistance: The Road to personalized immunotherapy.
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Affiliation(s)
- Miles Piper
- School of Medicine, University of Utah, Salt Lake City, UT
| | | | - Eytan Ruppin
- Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Siwen Hu-Lieskovan
- School of Medicine, University of Utah, Salt Lake City, UT
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
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125
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Lybaert L, Thielemans K, Feldman SA, van der Burg SH, Bogaert C, Ott PA. Neoantigen-directed therapeutics in the clinic: where are we? Trends Cancer 2023; 9:503-519. [PMID: 37055237 PMCID: PMC10414146 DOI: 10.1016/j.trecan.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 04/15/2023]
Abstract
In the past decade, immune checkpoint inhibitors (ICIs) and chimeric antigen receptor (CAR) T cell therapy have brought immunotherapy to the forefront of cancer treatment; however, only subsets of patients benefit from current approaches. Neoantigen-driven therapeutics specifically redirect the immune system of the patient to enable or reinduce its ability to recognize and eliminate cancer cells. The tumor specificity of this strategy spares healthy and normal cells from being attacked. Consistent with this concept, initial clinical trials have demonstrated the feasibility, safety, and immunogenicity of neoantigen-directed personalized vaccines. We review neoantigen-driven therapy strategies as well as their promise and clinical successes to date.
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Affiliation(s)
| | | | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Sjoerd H van der Burg
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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126
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Wischnewski V, Maas RR, Aruffo PG, Soukup K, Galletti G, Kornete M, Galland S, Fournier N, Lilja J, Wirapati P, Lourenco J, Scarpa A, Daniel RT, Hottinger AF, Brouland JP, Losurdo A, Voulaz E, Alloisio M, Hegi ME, Lugli E, Joyce JA. Phenotypic diversity of T cells in human primary and metastatic brain tumors revealed by multiomic interrogation. NATURE CANCER 2023; 4:908-924. [PMID: 37217652 PMCID: PMC10293012 DOI: 10.1038/s43018-023-00566-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 04/19/2023] [Indexed: 05/24/2023]
Abstract
The immune-specialized environment of the healthy brain is tightly regulated to prevent excessive neuroinflammation. However, after cancer development, a tissue-specific conflict between brain-preserving immune suppression and tumor-directed immune activation may ensue. To interrogate potential roles of T cells in this process, we profiled these cells from individuals with primary or metastatic brain cancers via integrated analyses on the single-cell and bulk population levels. Our analysis revealed similarities and differences in T cell biology between individuals, with the most pronounced differences observed in a subgroup of individuals with brain metastasis, characterized by accumulation of CXCL13-expressing CD39+ potentially tumor-reactive T (pTRT) cells. In this subgroup, high pTRT cell abundance was comparable to that in primary lung cancer, whereas all other brain tumors had low levels, similar to primary breast cancer. These findings indicate that T cell-mediated tumor reactivity can occur in certain brain metastases and may inform stratification for treatment with immunotherapy.
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Grants
- Breast Cancer Research Foundation, Carigest Foundation, Fondation ISREC, Ludwig Institute for Cancer Research, and the University of Lausanne
- Erwin-Schrödinger Fellowship from the Austrian Science Fund (FWF, J4343-B28)
- Fondazione Italiana per la Ricerca sul Cancro-Associazione Italiana per la Ricerca sul Cancro (FIRC-AIRC)
- Fondation ISREC, CHUV Lausanne
- Swiss Institute of Bioinformatics, Ludwig Institute for Cancer Research, and the University of Lausanne
- Associazione Italiana per la Ricerca sul Cancro (AIRC IG 20676 and AIRC 5x1000 UniCanVax 22757)
- Humanitas Clinical and Research Center
- CRI Lloyd J. Old STAR (CRI Award 3914), Associazione Italiana per la Ricerca sul Cancro (AIRC IG 20676 and AIRC 5x1000 UniCanVax 22757), Italian Ministry of Health (Agreement 82/2015).
- CHUV Lausanne
- Ludwig Institute for Cancer Research, and the University of Lausanne
- Fondation ISREC
- Breast Cancer Research Foundation
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Affiliation(s)
- Vladimir Wischnewski
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Roeltje R Maas
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Paola Guerrero Aruffo
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Klara Soukup
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Giovanni Galletti
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Mara Kornete
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sabine Galland
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Nadine Fournier
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Johanna Lilja
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
| | - Pratyaksha Wirapati
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Joao Lourenco
- Translational Data Science, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Alice Scarpa
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Roy T Daniel
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Andreas F Hottinger
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Oncology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Jean-Philippe Brouland
- Department of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Agnese Losurdo
- Oncology Department, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Emanuele Voulaz
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Marco Alloisio
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
- Division of Thoracic Surgery, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Monika E Hegi
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Neuroscience Research Center, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
- Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Enrico Lugli
- Laboratory of Translational Immunology, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Johanna A Joyce
- Department of Oncology, University of Lausanne, Lausanne, Switzerland.
- Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.
- Agora Cancer Research Centre Lausanne, Lausanne, Switzerland.
- Lundin Family Brain Tumor Research Center, Departments of Oncology and Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland.
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127
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Liu S, Bradley P, Sun W. Neural Network Models for Sequence-Based TCR and HLA Association Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.25.542327. [PMID: 37293077 PMCID: PMC10245990 DOI: 10.1101/2023.05.25.542327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
T cells rely on their T cell receptors (TCRs) to recognize foreign antigens presented by human leukocyte antigen (HLA) proteins. TCRs contain a record of an individual's past immune activities, and some TCRs are observed only in individuals with certain HLA alleles. As a result, characterising TCRs requires a thorough understanding of TCR-HLA associations. To this end, we propose a neural network method named Deep learning Prediction of TCR-HLA association (DePTH) to predict TCR-HLA associations based on their amino acid sequences. We show that the DePTH can be used to quantify the functional similarities of HLA alleles, and that these HLA similarities are associated with the survival outcomes of cancer patients who received immune checkpoint blockade treatment.
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Affiliation(s)
- Si Liu
- Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Philip Bradley
- Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA
- Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
| | - Wei Sun
- Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA
- Department of Biostatistics, University of Washington, Seattle, USA
- Department of Biostatistics, University of North Carolina, Chapel Hill, USA
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128
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Bawden E, Gebhardt T. The multifaceted roles of CD4 + T cells and MHC class II in cancer surveillance. Curr Opin Immunol 2023; 83:102345. [PMID: 37245413 DOI: 10.1016/j.coi.2023.102345] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/29/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
CD4+ T cells exhibit diverse functions in cancer surveillance. Concordantly, single-cell transcriptional analyses have revealed several distinct CD4+ T-cell differentiation states in tumours, including cytotoxic and regulatory subsets associated with favourable or unfavourable outcomes, respectively. These transcriptional states are determined and further shaped by dynamic interactions of CD4+ T cells with different types of immune cells, stromal cells and cancer cells. Therefore, we discuss the cellular networks in the tumour microenvironment (TME) that either promote or impede CD4+ T-cell cancer surveillance. We consider antigen/Major histocompatibility complexclass-II (MHC-II)-dependent interactions of CD4+ T cells with both professional antigen-presenting cells and cancer cells, the latter of which can directly express MHC-II, at least in some tumours. Additionally, we examine recent single-cell RNA sequencing studies that have shed light on the phenotype and functions of cancer-specific CD4+ T cells in human tumours.
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Affiliation(s)
- Emma Bawden
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Thomas Gebhardt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
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129
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Jani S, Church CD, Nghiem P. Insights into anti-tumor immunity via the polyomavirus shared across human Merkel cell carcinomas. Front Immunol 2023; 14:1172913. [PMID: 37287968 PMCID: PMC10242112 DOI: 10.3389/fimmu.2023.1172913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Understanding and augmenting cancer-specific immunity is impeded by the fact that most tumors are driven by patient-specific mutations that encode unique antigenic epitopes. The shared antigens in virus-driven tumors can help overcome this limitation. Merkel cell carcinoma (MCC) is a particularly interesting tumor immunity model because (1) 80% of cases are driven by Merkel cell polyomavirus (MCPyV) oncoproteins that must be continually expressed for tumor survival; (2) MCPyV oncoproteins are only ~400 amino acids in length and are essentially invariant between tumors; (3) MCPyV-specific T cell responses are robust and strongly linked to patient outcomes; (4) anti-MCPyV antibodies reliably increase with MCC recurrence, forming the basis of a standard clinical surveillance test; and (5) MCC has one of the highest response rates to PD-1 pathway blockade among all solid cancers. Leveraging these well-defined viral oncoproteins, a set of tools that includes over 20 peptide-MHC class I tetramers has been developed to facilitate the study of anti-tumor immunity across MCC patients. Additionally, the highly immunogenic nature of MCPyV oncoproteins forces MCC tumors to develop robust immune evasion mechanisms to survive. Indeed, several immune evasion mechanisms are active in MCC, including transcriptional downregulation of MHC expression by tumor cells and upregulation of inhibitory molecules including PD-L1 and immunosuppressive cytokines. About half of patients with advanced MCC do not persistently benefit from PD-1 pathway blockade. Herein, we (1) summarize the lessons learned from studying the anti-tumor T cell response to virus-positive MCC; (2) review immune evasion mechanisms in MCC; (3) review mechanisms of resistance to immune-based therapies in MCC and other cancers; and (4) discuss how recently developed tools can be used to address open questions in cancer immunotherapy. We believe detailed investigation of this model cancer will provide insight into tumor immunity that will likely also be applicable to more common cancers without shared tumor antigens.
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Affiliation(s)
- Saumya Jani
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Candice D. Church
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Paul Nghiem
- Department of Medicine, University of Washington, Seattle, WA, United States
- Fred Hutchinson Cancer Center, Seattle, WA, United States
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130
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Ai Q, Li F, Zou S, Zhang Z, Jin Y, Jiang L, Chen H, Deng X, Peng C, Mou N, Wen C, Shen B, Zhan Q. Targeting KRAS G12V mutations with HLA class II-restricted TCR for the immunotherapy in solid tumors. Front Immunol 2023; 14:1161538. [PMID: 37287989 PMCID: PMC10243368 DOI: 10.3389/fimmu.2023.1161538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/08/2023] [Indexed: 06/09/2023] Open
Abstract
KRAS mutation is a significant driving factor of tumor, and KRASG12V mutation has the highest incidence in solid tumors such as pancreatic cancer and colorectal cancer. Thus, KRASG12V neoantigen-specific TCR-engineered T cells could be a promising cancer treatment approach for pancreatic cancer. Previous studies had reported that KRASG12V-reactive TCRs originated from patients' TILs could recognized KRASG12V neoantigen presented by specific HLA subtypes and remove tumor persistently in vitro and in vivo. However, TCR drugs are different from antibody drugs in that they are HLA-restricted. The different ethnic distribution of HLA greatly limits the applicability of TCR drugs in Chinese population. In this study, we have identified a KRASG12V-specific TCR which recognized classII MHC from a colorectal cancer patient. Interestingly, we observed that KRASG12V-specific TCR-engineered CD4+ T cells, not CD8+ T cells, demonstrated significant efficacy in vitro and in xenograft mouse model, exhibiting stable expression and targeting specificity of TCR when co-cultured with APCs presenting KRASG12V peptides. TCR-engineered CD4+ T cells were co-cultured with APCs loaded with neoantigen, and then HLA subtypes were identified by the secretion of IFN-γ. Collectively, our data suggest that TCR-engineered CD4+ T cells can be used to target KRASG12V mutation presented by HLA-DPB1*03:01 and DPB1*14:01, which provide a high population coverage and are more suitable for the clinical transformation for Chinese, and mediate tumor killing effect like CD8+ T cells. This TCR hold promise for precision therapy in immunotherapy of solid tumors as an attractive candidate.
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Affiliation(s)
- Qi Ai
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fanlu Li
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siyi Zou
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zehui Zhang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yangbing Jin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chenghong Peng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nan Mou
- Department of Cell Therapy, Shanghai Genbase Biotechnology Co., Ltd, Shanghai, China
| | - Chenlei Wen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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131
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Lechner MG, Zhou Z, Hoang AT, Huang N, Ortega J, Scott LN, Chen HC, Patel AY, Yakhshi-Tafti R, Kim K, Hugo W, Famini P, Drakaki A, Ribas A, Angell TE, Su MA. Clonally expanded, thyrotoxic effector CD8 + T cells driven by IL-21 contribute to checkpoint inhibitor thyroiditis. Sci Transl Med 2023; 15:eadg0675. [PMID: 37196065 PMCID: PMC10227862 DOI: 10.1126/scitranslmed.adg0675] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/19/2023] [Indexed: 05/19/2023]
Abstract
Autoimmune toxicity occurs in up to 60% of patients treated with immune checkpoint inhibitor (ICI) therapy for cancer and represents an increasing clinical challenge for expanding the use of these treatments. To date, human immunopathogenic studies of immune-related adverse events (IRAEs) have relied on sampling of circulating peripheral blood cells rather than affected tissues. Here, we directly obtained thyroid specimens from individuals with ICI-thyroiditis, one of the most common IRAEs, and compared immune infiltrates with those from individuals with spontaneous autoimmune Hashimoto's thyroiditis (HT) or no thyroid disease. Single-cell RNA sequencing revealed a dominant, clonally expanded population of thyroid-infiltrating cytotoxic CXCR6+ CD8+ T cells (effector CD8+ T cells) present in ICI-thyroiditis but not HT or healthy controls. Furthermore, we identified a crucial role for interleukin-21 (IL-21), a cytokine secreted by intrathyroidal T follicular (TFH) and T peripheral helper (TPH) cells, as a driver of these thyrotoxic effector CD8+ T cells. In the presence of IL-21, human CD8+ T cells acquired the activated effector phenotype with up-regulation of the cytotoxic molecules interferon-γ (IFN-γ) and granzyme B, increased expression of the chemokine receptor CXCR6, and thyrotoxic capacity. We validated these findings in vivo using a mouse model of IRAEs and further demonstrated that genetic deletion of IL-21 signaling protected ICI-treated mice from thyroid immune infiltration. Together, these studies reveal mechanisms and candidate therapeutic targets for individuals who develop IRAEs.
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Affiliation(s)
- Melissa G. Lechner
- Division of Endocrinology, Diabetes, and Metabolism, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Zikang Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Aline T. Hoang
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
- Drexel Medical School; Philadelphia, PA 19129
| | - Nicole Huang
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Jessica Ortega
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Lauren N. Scott
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Ho-Chung Chen
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Anushi Y. Patel
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Rana Yakhshi-Tafti
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
- Rosalind Franklin Medical School; Chicago, IL 60064
| | - Kristy Kim
- UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Willy Hugo
- Division of Dermatology, Department of Medicine, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Pouyan Famini
- Division of Endocrinology, Diabetes, and Metabolism, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Alexandra Drakaki
- Division of Hematology and Oncology, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Antoni Ribas
- Division of Hematology and Oncology, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
| | - Trevor E. Angell
- Division of Endocrinology and Diabetes, USC Keck School of Medicine; Los Angeles, CA 90033
| | - Maureen A. Su
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
- Division of Pediatric Endocrinology, UCLA David Geffen School of Medicine; Los Angeles, CA 90095
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132
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Sievers C, Craveiro M, Friedman J, Robbins Y, Yang X, Bai K, Nguyen A, Redman JM, Chari R, Soon-Shiong P, Schlom J, Gulley J, Allen CT. Phenotypic plasticity and reduced tissue retention of exhausted tumor-infiltrating T cells following neoadjuvant immunotherapy in head and neck cancer. Cancer Cell 2023; 41:887-902.e5. [PMID: 37059104 PMCID: PMC10175181 DOI: 10.1016/j.ccell.2023.03.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 01/24/2023] [Accepted: 03/21/2023] [Indexed: 04/16/2023]
Abstract
Neoadjuvant immunotherapies (NITs) have led to clinical benefits in several cancers. Characterization of the molecular mechanisms underlying responses to NIT may lead to improved treatment strategies. Here we show that exhausted, tumor-infiltrating CD8+ T (Tex) cells display local and systemic responses to concurrent neoadjuvant TGF-β and PD-L1 blockade. NIT induces a significant and selective increase in circulating Tex cells associated with reduced intratumoral expression of the tissue-retention marker CD103. TGF-β-driven CD103 expression on CD8+ T cells is reversed following TGF-β neutralization in vitro, implicating TGF-β in T cell tissue retention and impaired systemic immunity. Transcriptional changes implicate T cell receptor signaling and glutamine metabolism as important determinants of enhanced or reduced Tex treatment response, respectively. Our analysis illustrates physiological and metabolic changes underlying T cell responses to NIT, highlighting the interplay between immunosuppression, tissue retention, and systemic anti-tumor immunity and suggest antagonism of T cell tissue retention as a promising neoadjuvant treatment strategy.
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Affiliation(s)
- Cem Sievers
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Marco Craveiro
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jay Friedman
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yvette Robbins
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xinping Yang
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ke Bai
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Jason M Redman
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Raj Chari
- Genome Modification Core, Laboratory Animal Sciences Program, Frederick National Lab for Cancer Research, Frederick, MD, USA
| | | | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - James Gulley
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clint T Allen
- Head and Neck Section, Surgical Oncology Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Vensko SP, Olsen K, Bortone D, Smith CC, Chai S, Beckabir W, Fini M, Jadi O, Rubinsteyn A, Vincent BG. LENS: Landscape of Effective Neoantigens Software. Bioinformatics 2023; 39:btad322. [PMID: 37184881 PMCID: PMC10246587 DOI: 10.1093/bioinformatics/btad322] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 04/04/2023] [Accepted: 05/12/2023] [Indexed: 05/16/2023] Open
Abstract
MOTIVATION Elimination of cancer cells by T cells is a critical mechanism of anti-tumor immunity and cancer immunotherapy response. T cells recognize cancer cells by engagement of T cell receptors with peptide epitopes presented by major histocompatibility complex molecules on the cancer cell surface. Peptide epitopes can be derived from antigen proteins coded for by multiple genomic sources. Bioinformatics tools used to identify tumor-specific epitopes via analysis of DNA and RNA-sequencing data have largely focused on epitopes derived from somatic variants, though a smaller number have evaluated potential antigens from other genomic sources. RESULTS We report here an open-source workflow utilizing the Nextflow DSL2 workflow manager, Landscape of Effective Neoantigens Software (LENS), which predicts tumor-specific and tumor-associated antigens from single nucleotide variants, insertions and deletions, fusion events, splice variants, cancer-testis antigens, overexpressed self-antigens, viruses, and endogenous retroviruses. The primary advantage of LENS is that it expands the breadth of genomic sources of discoverable tumor antigens using genomics data. Other advantages include modularity, extensibility, ease of use, and harmonization of relative expression level and immunogenicity prediction across multiple genomic sources. We present an analysis of 115 acute myeloid leukemia samples to demonstrate the utility of LENS. We expect LENS will be a valuable platform and resource for T cell epitope discovery bioinformatics, especially in cancers with few somatic variants where tumor-specific epitopes from alternative genomic sources are an elevated priority. AVAILABILITY AND IMPLEMENTATION More information about LENS, including code, workflow documentation, and instructions, can be found at (https://gitlab.com/landscape-of-effective-neoantigens-software).
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Affiliation(s)
- Steven P Vensko
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Kelly Olsen
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Dante Bortone
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Christof C Smith
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Shengjie Chai
- Uber Technologies, Inc., San Francisco, CA, United States
| | - Wolfgang Beckabir
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Misha Fini
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Othmane Jadi
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Alex Rubinsteyn
- Department of Genetics, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin G Vincent
- Lineberger Comprehensive Cancer Center, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Department of Microbiology and Immunology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Computational Medicine Program, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
- Division of Hematology, Department of Medicine, University of North Carolina—Chapel Hill, Chapel Hill, NC, United States
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134
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Chatani PD, Lowery FJ, Parikh NB, Hitscherich KJ, Yossef R, Hill V, Gartner JJ, Paria B, Florentin M, Ray S, Bera A, Parkhust M, Robbins P, Krishna S, Rosenberg SA. Cell surface marker-based capture of neoantigen-reactive CD8 + T-cell receptors from metastatic tumor digests. J Immunother Cancer 2023; 11:jitc-2022-006264. [PMID: 37258038 DOI: 10.1136/jitc-2022-006264] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/23/2023] [Indexed: 06/02/2023] Open
Abstract
BACKGROUND Cellular immunotherapies using autologous tumor-infiltrating lymphocytes (TIL) can induce durable regression of epithelial cancers in selected patients with treatment-refractory metastatic disease. As the genetic engineering of T cells with tumor-reactive T-cell receptors (TCRs) comes to the forefront of clinical investigation, the rapid, scalable, and cost-effective detection of patient-specific neoantigen-reactive TIL remains a top priority. METHODS We analyzed the single-cell transcriptomic states of 31 neoantigen-specific T-cell clonotypes to identify cell surface dysfunction markers that best identified the metastatic transcriptional states enriched with antitumor TIL. We developed an efficient method to capture neoantigen-reactive TCRs directly from resected human tumors based on cell surface co-expression of CD39, programmed cell death protein-1, and TIGIT dysfunction markers (CD8+ TILTP). RESULTS TILTP TCR isolation achieved a high degree of correlation with single-cell transcriptomic signatures that identify neoantigen-reactive TCRs, making it a cost-effective strategy using widely available resources. Reconstruction of additional TILTP TCRs from tumors identified known and novel antitumor TCRs, showing that at least 39.5% of TILTP TCRs are neoantigen-reactive or tumor-reactive. Despite their substantial enrichment for neoantigen-reactive TCR clonotypes, clonal dynamics of 24 unique antitumor TILTP clonotypes from four patients indicated that most in vitro expanded TILTP populations failed to demonstrate neoantigen reactivity, either by loss of neoantigen-reactive clones during TIL expansion, or through functional impairment during cognate neoantigen recognition. CONCLUSIONS While direct usage of in vitro-expanded CD8+ TILTP as a source for cellular therapy might be precluded by profound TIL dysfunction, isolating TILTP represents a streamlined effective approach to rapidly identify neoantigen-reactive TCRs to design engineered cellular immunotherapies against cancer.
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Affiliation(s)
- Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Biman Paria
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Florentin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alakesh Bera
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Maria Parkhust
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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135
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Abstract
Recent advances in cancer immunotherapy - ranging from immune-checkpoint blockade therapy to adoptive cellular therapy and vaccines - have revolutionized cancer treatment paradigms, yet the variability in clinical responses to these agents has motivated intense interest in understanding how the T cell landscape evolves with respect to response to immune intervention. Over the past decade, the advent of multidimensional single-cell technologies has provided the unprecedented ability to dissect the constellation of cell states of lymphocytes within a tumour microenvironment. In particular, the rapidly expanding capacity to definitively link intratumoural phenotypes with the antigen specificity of T cells provided by T cell receptors (TCRs) has now made it possible to focus on investigating the properties of T cells with tumour-specific reactivity. Moreover, the assessment of TCR clonality has enabled a molecular approach to track the trajectories, clonal dynamics and phenotypic changes of antitumour T cells over the course of immunotherapeutic intervention. Here, we review the current knowledge on the cellular states and antigen specificities of antitumour T cells and examine how fine characterization of T cell dynamics in patients has provided meaningful insights into the mechanisms underlying effective cancer immunotherapy. We highlight those T cell subsets associated with productive T cell responses and discuss how diverse immunotherapies might leverage the pre-existing tumour-reactive T cell pool or instruct de novo generation of antitumour specificities. Future studies aimed at elucidating the factors associated with the elicitation of productive antitumour T cell immunity are anticipated to instruct the design of more efficacious treatment strategies.
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Affiliation(s)
- Giacomo Oliveira
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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136
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Huang R, Zhao B, Hu S, Zhang Q, Su X, Zhang W. Adoptive neoantigen-reactive T cell therapy: improvement strategies and current clinical researches. Biomark Res 2023; 11:41. [PMID: 37062844 PMCID: PMC10108522 DOI: 10.1186/s40364-023-00478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/21/2023] [Indexed: 04/18/2023] Open
Abstract
Neoantigens generated by non-synonymous mutations of tumor genes can induce activation of neoantigen-reactive T (NRT) cells which have the ability to resist the growth of tumors expressing specific neoantigens. Immunotherapy based on NRT cells has made preeminent achievements in melanoma and other solid tumors. The process of manufacturing NRT cells includes identification of neoantigens, preparation of neoantigen expression vectors or peptides, induction and activation of NRT cells, and analysis of functions and phenotypes. Numerous improvement strategies have been proposed to enhance the potency of NRT cells by engineering TCR, promoting infiltration of T cells and overcoming immunosuppressive factors in the tumor microenvironment. In this review, we outline the improvement of the preparation and the function assessment of NRT cells, and discuss the current status of clinical trials related to NRT cell immunotherapy.
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Affiliation(s)
- Ruichen Huang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Bi Zhao
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China
| | - Shi Hu
- Department of Biophysics, College of Basic Medical Sciences, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Qian Zhang
- National Key Laboratory of Medical Immunology, Institute of Immunology, Second Military Medical University, 800 Xiangyin Road, Shanghai, 200433, People's Republic of China
| | - Xiaoping Su
- School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325000, People's Republic of China.
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Second Military Medical University, Shanghai, 200433, People's Republic of China.
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137
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Zhao J, Fong A, Seow SV, Toh HC. Organoids as an Enabler of Precision Immuno-Oncology. Cells 2023; 12:cells12081165. [PMID: 37190074 DOI: 10.3390/cells12081165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/27/2023] [Accepted: 04/13/2023] [Indexed: 05/17/2023] Open
Abstract
Since the dawn of the past century, landmark discoveries in cell-mediated immunity have led to a greater understanding of the innate and adaptive immune systems and revolutionised the treatment of countless diseases, including cancer. Today, precision immuno-oncology (I/O) involves not only targeting immune checkpoints that inhibit T-cell immunity but also harnessing immune cell therapies. The limited efficacy in some cancers results mainly from a complex tumour microenvironment (TME) that, in addition to adaptive immune cells, comprises innate myeloid and lymphoid cells, cancer-associated fibroblasts, and the tumour vasculature that contribute towards immune evasion. As the complexity of TME has called for more sophisticated human-based tumour models, organoids have allowed the dynamic study of spatiotemporal interactions between tumour cells and individual TME cell types. Here, we discuss how organoids can study the TME across cancers and how these features may improve precision I/O. We outline the approaches to preserve or recapitulate the TME in tumour organoids and discuss their potential, advantages, and limitations. We will discuss future directions of organoid research in understanding cancer immunology in-depth and identifying novel I/O targets and treatment strategies.
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Affiliation(s)
- Junzhe Zhao
- Cancer and Stem Cell Biology Programme, Duke-NUS Medical School, Singapore 169857, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
- Doctor of Medicine Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Antoinette Fong
- Doctor of Medicine Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - See Voon Seow
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 168583, Singapore
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138
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Tippalagama R, Chihab LY, Kearns K, Lewis S, Panda S, Willemsen L, Burel JG, Lindestam Arlehamn CS. Antigen-specificity measurements are the key to understanding T cell responses. Front Immunol 2023; 14:1127470. [PMID: 37122719 PMCID: PMC10140422 DOI: 10.3389/fimmu.2023.1127470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.
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139
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Naulaerts S, Datsi A, Borras DM, Antoranz Martinez A, Messiaen J, Vanmeerbeek I, Sprooten J, Laureano RS, Govaerts J, Panovska D, Derweduwe M, Sabel MC, Rapp M, Ni W, Mackay S, Van Herck Y, Gelens L, Venken T, More S, Bechter O, Bergers G, Liston A, De Vleeschouwer S, Van Den Eynde BJ, Lambrechts D, Verfaillie M, Bosisio F, Tejpar S, Borst J, Sorg RV, De Smet F, Garg AD. Multiomics and spatial mapping characterizes human CD8 + T cell states in cancer. Sci Transl Med 2023; 15:eadd1016. [PMID: 37043555 DOI: 10.1126/scitranslmed.add1016] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Clinically relevant immunological biomarkers that discriminate between diverse hypofunctional states of tumor-associated CD8+ T cells remain disputed. Using multiomics analysis of CD8+ T cell features across multiple patient cohorts and tumor types, we identified tumor niche-dependent exhausted and other types of hypofunctional CD8+ T cell states. CD8+ T cells in "supportive" niches, like melanoma or lung cancer, exhibited features of tumor reactivity-driven exhaustion (CD8+ TEX). These included a proficient effector memory phenotype, an expanded T cell receptor (TCR) repertoire linked to effector exhaustion signaling, and a cancer-relevant T cell-activating immunopeptidome composed of largely shared cancer antigens or neoantigens. In contrast, "nonsupportive" niches, like glioblastoma, were enriched for features of hypofunctionality distinct from canonical exhaustion. This included immature or insufficiently activated T cell states, high wound healing signatures, nonexpanded TCR repertoires linked to anti-inflammatory signaling, high T cell-recognizable self-epitopes, and an antiproliferative state linked to stress or prodeath responses. In situ spatial mapping of glioblastoma highlighted the prevalence of dysfunctional CD4+:CD8+ T cell interactions, whereas ex vivo single-cell secretome mapping of glioblastoma CD8+ T cells confirmed negligible effector functionality and a promyeloid, wound healing-like chemokine profile. Within immuno-oncology clinical trials, anti-programmed cell death protein 1 (PD-1) immunotherapy facilitated glioblastoma's tolerogenic disparities, whereas dendritic cell (DC) vaccines partly corrected them. Accordingly, recipients of a DC vaccine for glioblastoma had high effector memory CD8+ T cells and evidence of antigen-specific immunity. Collectively, we provide an atlas for assessing different CD8+ T cell hypofunctional states in immunogenic versus nonimmunogenic cancers.
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Affiliation(s)
- Stefan Naulaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
- Ludwig Institute for Cancer Research, Brussels 1200, Belgium
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
- De Duve Institute, UCLouvain, Brussels 1200, Belgium
| | - Angeliki Datsi
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Daniel M Borras
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Asier Antoranz Martinez
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Julie Messiaen
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Isaure Vanmeerbeek
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Jenny Sprooten
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Raquel S Laureano
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Jannes Govaerts
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Dena Panovska
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Marleen Derweduwe
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Michael C Sabel
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Marion Rapp
- Department of Neurosurgery, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Weiming Ni
- IsoPlexis Corporation, Branford, CT 06405-2801, USA
| | - Sean Mackay
- IsoPlexis Corporation, Branford, CT 06405-2801, USA
| | - Yannick Van Herck
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven and Department of General Medical Oncology, UZ Leuven, Leuven 3000, Belgium
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Tom Venken
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
- VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Sanket More
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
| | - Oliver Bechter
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven and Department of General Medical Oncology, UZ Leuven, Leuven 3000, Belgium
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB Center for Cancer Biology, KU Leuven, Leuven 3000, Belgium
- Department of Neurological Surgery, UCSF Comprehensive Cancer Center, UCSF, San Francisco, CA 94143-0350, USA
| | - Adrian Liston
- VIB Center for Brain and Disease Research, Leuven 3000, Belgium
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Steven De Vleeschouwer
- Department of Neurosurgery, University Hospitals Leuven, Leuven 3000, Belgium
- Laboratory of Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, KU Leuven, Leuven 3000, Belgium
- Leuven Brain Institute (LBI), Leuven 3000, Belgium
| | - Benoit J Van Den Eynde
- Ludwig Institute for Cancer Research, Brussels 1200, Belgium
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 4BH, UK
- De Duve Institute, UCLouvain, Brussels 1200, Belgium
| | - Diether Lambrechts
- Laboratory of Translational Genetics, Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
- VIB Center for Cancer Biology, VIB, Leuven 3000, Belgium
| | - Michiel Verfaillie
- Neurosurgery Department, Europaziekenhuizen - Cliniques de l'Europe, Sint-Elisabeth, Brussels 1180, Belgium
| | - Francesca Bosisio
- Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Sabine Tejpar
- Laboratory for Molecular Digestive Oncology, Department of Oncology, KU Leuven, Leuven 3000, Belgium
| | - Jannie Borst
- Department of Immunology and Oncode Institute, Leiden University Medical Center, Leiden 2333 ZA, Netherlands
| | - Rüdiger V Sorg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty, Heinrich Heine University Hospital, Düsseldorf 40225, Germany
| | - Frederik De Smet
- Laboratory for Precision Cancer Medicine, Translational Cell and Tissue Research, Department of Imaging and Pathology, KU Leuven, Leuven 3000, Belgium
| | - Abhishek D Garg
- Laboratory of Cell Stress & Immunity, Department of Cellular and Molecular Medicine, KU Leuven, Leuven 3000, Belgium
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140
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Pai JA, Hellmann MD, Sauter JL, Mattar M, Rizvi H, Woo HJ, Shah N, Nguyen EM, Uddin FZ, Quintanal-Villalonga A, Chan JM, Manoj P, Allaj V, Baine MK, Bhanot UK, Jain M, Linkov I, Meng F, Brown D, Chaft JE, Plodkowski AJ, Gigoux M, Won HH, Sen T, Wells DK, Donoghue MTA, de Stanchina E, Wolchok JD, Loomis B, Merghoub T, Rudin CM, Chow A, Satpathy AT. Lineage tracing reveals clonal progenitors and long-term persistence of tumor-specific T cells during immune checkpoint blockade. Cancer Cell 2023; 41:776-790.e7. [PMID: 37001526 PMCID: PMC10563767 DOI: 10.1016/j.ccell.2023.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/21/2022] [Accepted: 03/07/2023] [Indexed: 04/12/2023]
Abstract
Paired single-cell RNA and T cell receptor sequencing (scRNA/TCR-seq) has allowed for enhanced resolution of clonal T cell dynamics in cancer. Here, we report a scRNA/TCR-seq analysis of 187,650 T cells from 31 tissue regions, including tumor, adjacent normal tissues, and lymph nodes (LN), from three patients with non-small cell lung cancer after immune checkpoint blockade (ICB). Regions with viable cancer cells are enriched for exhausted CD8+ T cells, regulatory CD4+ T cells (Treg), and follicular helper CD4+ T cells (TFH). Tracking T cell clonotypes across tissues, combined with neoantigen specificity assays, reveals that TFH and tumor-specific exhausted CD8+ T cells are clonally linked to TCF7+SELL+ progenitors in tumor draining LNs, and progressive exhaustion trajectories of CD8+ T, Treg, and TFH cells with proximity to the tumor microenvironment. Finally, longitudinal tracking of tumor-specific CD8+ and CD4+ T cell clones reveals persistence in the peripheral blood for years after ICB therapy.
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Affiliation(s)
- Joy A Pai
- Department of Pathology, Stanford University, Stanford, CA, USA; Immunology Program, Stanford University, Stanford, CA, USA
| | - Matthew D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer L Sauter
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira Rizvi
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hyung Jun Woo
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nisargbhai Shah
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Evelyn M Nguyen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Cancer Biology Program, Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fathema Z Uddin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Joseph M Chan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viola Allaj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina K Baine
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Umesh K Bhanot
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mala Jain
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Linkov
- Precision Pathology Center, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fanli Meng
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David Brown
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jamie E Chaft
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Andrew J Plodkowski
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mathieu Gigoux
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen H Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triparna Sen
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA
| | - Daniel K Wells
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA; Santa Ana Bio, Alameda, CA, USA
| | - Mark T A Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Brian Loomis
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew Chow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Cornell Medical College, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA; Immunology Program, Stanford University, Stanford, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA; Parker Institute for Cancer Immunotherapy, Stanford University, Stanford, CA, USA.
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141
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Rosenberg SA, Parkhurst MR, Robbins PF. Adoptive cell transfer immunotherapy for patients with solid epithelial cancers. Cancer Cell 2023; 41:646-648. [PMID: 37037613 PMCID: PMC10184665 DOI: 10.1016/j.ccell.2023.03.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Efforts to apply adoptive cell transfer (ACT) immunotherapy to patients with common epithelial cancers have been stimulated by the demonstration that the majority of these patients contain lymphocytes reactive against the expressed products of their cancer mutations. Early efforts to specifically target these antigens have been promising.
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Affiliation(s)
- Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
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142
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Ali LR, Garrido-Castro AC, Lenehan PJ, Bollenrucher N, Stump CT, Dougan M, Goel S, Shapiro GI, Tolaney SM, Dougan SK. PD-1 blockade and CDK4/6 inhibition augment nonoverlapping features of T cell activation in cancer. J Exp Med 2023; 220:e20220729. [PMID: 36688919 PMCID: PMC9884581 DOI: 10.1084/jem.20220729] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/08/2022] [Accepted: 01/03/2023] [Indexed: 02/02/2023] Open
Abstract
We performed single-cell RNA-sequencing and T cell receptor clonotype tracking of breast and ovarian cancer patients treated with the CDK4/6 inhibitor ribociclib and PD-1 blockade. We highlight evidence of two orthogonal treatment-associated phenomena: expansion of T cell effector populations and promotion of T cell memory formation. Augmentation of the antitumor memory pool by ribociclib boosts the efficacy of subsequent PD-1 blockade in mouse models of melanoma and breast cancer, pointing toward sequential therapy as a potentially safe and synergistic strategy in patients.
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Affiliation(s)
- Lestat R. Ali
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Ana C. Garrido-Castro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Patrick J. Lenehan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
| | - Naima Bollenrucher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Courtney T. Stump
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Dougan
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Shom Goel
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | - Geoffrey I. Shapiro
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Sara M. Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephanie K. Dougan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Immunology, Harvard Medical School, Boston, MA, USA
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143
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Inozume T. Adoptive cell transfer therapy for melanoma. Exp Dermatol 2023; 32:250-255. [PMID: 36382355 DOI: 10.1111/exd.14707] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/17/2022]
Abstract
Adoptive cell transfer (ACT) of tumor-infiltrating lymphocytes (TILs) for melanoma is an example of the most successful cancer immune therapy. It achieves a durable complete response about ~20% of patients, and they might be cured. However, the ratio of patients with durable benefits is not high, and its complicated procedure prevents its diffusion. Therefore, many efforts to enhance the effect and simplify the protocol of TIL therapy have been made so far, resulting in the establishment of a simple and effective current TIL therapy that has been propagated to other institutes and countries. Moreover, TIL therapy and translational research using clinical samples derived from durable responders elucidate the important element for developing more effective cancer immune therapies in the future. This review introduced the brief history, attempts for the improvement and important findings elucidated by translational research of ACT for melanoma.
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Affiliation(s)
- Takashi Inozume
- Department of Dermatology, Graduate School of Medicine, Chiba University, Chiba, Japan
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144
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Fenton GA, Mitchell DA. Cellular Cancer Immunotherapy Development and Manufacturing in the Clinic. Clin Cancer Res 2023; 29:843-857. [PMID: 36383184 PMCID: PMC9975672 DOI: 10.1158/1078-0432.ccr-22-2257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/22/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022]
Abstract
The transfusion of naturally derived or modified cellular therapies, referred to as adoptive cell therapy (ACT), has demonstrated clinical efficacy in the treatment of hematologic malignancies and metastatic melanoma. In addition, cellular vaccination, such as dendritic cell-based cancer vaccines, continues to be actively explored. The manufacturing of these therapies presents a considerable challenge to expanding the use of ACT as a viable treatment modality, particularly at academic production facilities. Furthermore, the expanding commercial interest in ACT presents new opportunities as well as strategic challenges for the future vision of cellular manufacturing in academic centers. Current trends in the production of ACT at tertiary care centers and prospects for improved manufacturing practices that will foster further clinical benefit are reviewed herein.
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Affiliation(s)
- Graeme A Fenton
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, Florida.,Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
| | - Duane A Mitchell
- Lillian S. Wells Department of Neurosurgery, University of Florida, Gainesville, Florida.,Preston A. Wells Jr. Center for Brain Tumor Therapy, University of Florida, Gainesville, Florida
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145
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Foy SP, Jacoby K, Bota DA, Hunter T, Pan Z, Stawiski E, Ma Y, Lu W, Peng S, Wang CL, Yuen B, Dalmas O, Heeringa K, Sennino B, Conroy A, Bethune MT, Mende I, White W, Kukreja M, Gunturu S, Humphrey E, Hussaini A, An D, Litterman AJ, Quach BB, Ng AHC, Lu Y, Smith C, Campbell KM, Anaya D, Skrdlant L, Huang EYH, Mendoza V, Mathur J, Dengler L, Purandare B, Moot R, Yi MC, Funke R, Sibley A, Stallings-Schmitt T, Oh DY, Chmielowski B, Abedi M, Yuan Y, Sosman JA, Lee SM, Schoenfeld AJ, Baltimore D, Heath JR, Franzusoff A, Ribas A, Rao AV, Mandl SJ. Non-viral precision T cell receptor replacement for personalized cell therapy. Nature 2023; 615:687-696. [PMID: 36356599 PMCID: PMC9768791 DOI: 10.1038/s41586-022-05531-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 11/04/2022] [Indexed: 11/12/2022]
Abstract
T cell receptors (TCRs) enable T cells to specifically recognize mutations in cancer cells1-3. Here we developed a clinical-grade approach based on CRISPR-Cas9 non-viral precision genome-editing to simultaneously knockout the two endogenous TCR genes TRAC (which encodes TCRα) and TRBC (which encodes TCRβ). We also inserted into the TRAC locus two chains of a neoantigen-specific TCR (neoTCR) isolated from circulating T cells of patients. The neoTCRs were isolated using a personalized library of soluble predicted neoantigen-HLA capture reagents. Sixteen patients with different refractory solid cancers received up to three distinct neoTCR transgenic cell products. Each product expressed a patient-specific neoTCR and was administered in a cell-dose-escalation, first-in-human phase I clinical trial ( NCT03970382 ). One patient had grade 1 cytokine release syndrome and one patient had grade 3 encephalitis. All participants had the expected side effects from the lymphodepleting chemotherapy. Five patients had stable disease and the other eleven had disease progression as the best response on the therapy. neoTCR transgenic T cells were detected in tumour biopsy samples after infusion at frequencies higher than the native TCRs before infusion. This study demonstrates the feasibility of isolating and cloning multiple TCRs that recognize mutational neoantigens. Moreover, simultaneous knockout of the endogenous TCR and knock-in of neoTCRs using single-step, non-viral precision genome-editing are achieved. The manufacture of neoTCR engineered T cells at clinical grade, the safety of infusing up to three gene-edited neoTCR T cell products and the ability of the transgenic T cells to traffic to the tumours of patients are also demonstrated.
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MESH Headings
- Humans
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Biopsy
- Cell- and Tissue-Based Therapy/adverse effects
- Cell- and Tissue-Based Therapy/methods
- Cytokine Release Syndrome/complications
- Disease Progression
- Encephalitis/complications
- Gene Editing
- Gene Knock-In Techniques
- Gene Knockout Techniques
- Genes, T-Cell Receptor alpha
- Genes, T-Cell Receptor beta
- Mutation
- Neoplasms/complications
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- Patient Safety
- Precision Medicine/adverse effects
- Precision Medicine/methods
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Transgenes/genetics
- HLA Antigens/immunology
- CRISPR-Cas Systems
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Affiliation(s)
| | | | - Daniela A Bota
- Department of Neurology and Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, USA
| | | | - Zheng Pan
- PACT Pharma, South San Francisco, CA, USA
| | | | - Yan Ma
- PACT Pharma, South San Francisco, CA, USA
| | - William Lu
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Ines Mende
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | | | | | - Duo An
- PACT Pharma, South San Francisco, CA, USA
| | | | | | | | - Yue Lu
- Institute for Systems Biology, Seattle, WA, USA
| | - Chad Smith
- PACT Pharma, South San Francisco, CA, USA
| | - Katie M Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | - Roel Funke
- PACT Pharma, South San Francisco, CA, USA
| | | | | | - David Y Oh
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bartosz Chmielowski
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles, CA, USA
| | - Mehrdad Abedi
- Division of Hematology/Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Yuan Yuan
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Jeffrey A Sosman
- Department of Medicine and Robert H. Lurie Cancer Center, Northwestern University, Evanston, IL, USA
| | - Sylvia M Lee
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adam J Schoenfeld
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY, USA
| | - David Baltimore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | | | - Antoni Ribas
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center at the University of California, Los Angeles, CA, USA.
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146
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Puig-Saus C, Sennino B, Peng S, Wang CL, Pan Z, Yuen B, Purandare B, An D, Quach BB, Nguyen D, Xia H, Jilani S, Shao K, McHugh C, Greer J, Peabody P, Nayak S, Hoover J, Said S, Jacoby K, Dalmas O, Foy SP, Conroy A, Yi MC, Shieh C, Lu W, Heeringa K, Ma Y, Chizari S, Pilling MJ, Ting M, Tunuguntla R, Sandoval S, Moot R, Hunter T, Zhao S, Saco JD, Perez-Garcilazo I, Medina E, Vega-Crespo A, Baselga-Carretero I, Abril-Rodriguez G, Cherry G, Wong DJ, Hundal J, Chmielowski B, Speiser DE, Bethune MT, Bao XR, Gros A, Griffith OL, Griffith M, Heath JR, Franzusoff A, Mandl SJ, Ribas A. Neoantigen-targeted CD8 + T cell responses with PD-1 blockade therapy. Nature 2023; 615:697-704. [PMID: 36890230 PMCID: PMC10441586 DOI: 10.1038/s41586-023-05787-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells1-14. The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8+ T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.
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Affiliation(s)
- Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
| | | | | | | | | | | | | | - Duo An
- PACT Pharma, San Francisco, CA, USA
| | | | | | - Huiming Xia
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Sameeha Jilani
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yan Ma
- PACT Pharma, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Sidi Zhao
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Justin D Saco
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivan Perez-Garcilazo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Egmidio Medina
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Agustin Vega-Crespo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ignacio Baselga-Carretero
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Gabriel Abril-Rodriguez
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Grace Cherry
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Deborah J Wong
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Bartosz Chmielowski
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Daniel E Speiser
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Alena Gros
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Antoni Ribas
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
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147
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Sanromán ÁF, Joshi K, Au L, Chain B, Turajlic S. TCR sequencing: applications in immuno-oncology research. IMMUNO-ONCOLOGY TECHNOLOGY 2023; 17:100373. [PMID: 36908996 PMCID: PMC9996383 DOI: 10.1016/j.iotech.2023.100373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
•T-cell receptor (TCR) interaction with major histocompatibility complex-antigen complexes leads to antitumour responses.•TCR sequencing analysis allows characterisation of T cells that recognise tumour neoantigens.•T-cell clonal revival and clonal replacement potentially underpin immunotherapy responses.
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Affiliation(s)
- Á F Sanromán
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - K Joshi
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK.,Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - L Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK.,Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Australia
| | - B Chain
- Division of Infection and Immunity, University College London, London, UK.,Department of Computer Science, University College London, London, UK
| | - S Turajlic
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK.,Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
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148
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van den Bulk J, van der Ploeg M, Ijsselsteijn ME, Ruano D, van der Breggen R, Duhen R, Peeters KCMJ, Fariña-Sarasqueta A, Verdegaal EME, van der Burg SH, Duhen T, de Miranda NFCC. CD103 and CD39 coexpression identifies neoantigen-specific cytotoxic T cells in colorectal cancers with low mutation burden. J Immunother Cancer 2023; 11:jitc-2022-005887. [PMID: 36792124 PMCID: PMC9933759 DOI: 10.1136/jitc-2022-005887] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Expression of CD103 and CD39 has been found to pinpoint tumor-reactive CD8+ T cells in a variety of solid cancers. We aimed to investigate whether these markers specifically identify neoantigen-specific T cells in colorectal cancers (CRCs) with low mutation burden. EXPERIMENTAL DESIGN Whole-exome and RNA sequencing of 11 mismatch repair-proficient (MMR-proficient) CRCs and corresponding healthy tissues were performed to determine the presence of putative neoantigens. In parallel, tumor-infiltrating lymphocytes (TILs) were cultured from the tumor fragments and, in parallel, CD8+ T cells were flow-sorted from their respective tumor digests based on single or combined expression of CD103 and CD39. Each subset was expanded and subsequently interrogated for neoantigen-directed reactivity with synthetic peptides. Neoantigen-directed reactivity was determined by flow cytometric analyses of T cell activation markers and ELISA-based detection of IFN-γ and granzyme B release. Additionally, imaging mass cytometry was applied to investigate the localization of CD103+CD39+ cytotoxic T cells in tumors. RESULTS Neoantigen-directed reactivity was only encountered in bulk TIL populations and CD103+CD39+ (double positive, DP) CD8+ T cell subsets but never in double-negative or single-positive subsets. Neoantigen-reactivity detected in bulk TIL but not in DP CD8+ T cells could be attributed to CD4+ T cells. CD8+ T cells that were located in direct contact with cancer cells in tumor tissues were enriched for CD103 and CD39 expression. CONCLUSION Coexpression of CD103 and CD39 is characteristic of neoantigen-specific CD8+ T cells in MMR-proficient CRCs with low mutation burden. The exploitation of these subsets in the context of adoptive T cell transfer or engineered T cell receptor therapies is a promising avenue to extend the benefits of immunotherapy to an increasing number of CRC patients.
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Affiliation(s)
- Jitske van den Bulk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manon van der Ploeg
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruud van der Breggen
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rebekka Duhen
- Basic Immunology Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
| | - Koen C M J Peeters
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Els M E Verdegaal
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | - Thomas Duhen
- Anti-Cancer Immune Response Lab, Earle A Chiles Research Institute, Portland, Oregon, USA
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149
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Brightman SE, Naradikian MS, Thota RR, Becker A, Montero L, Bahmanof M, Premlal ALR, Greenbaum JA, Peters B, Cohen EE, Miller AM, Schoenberger SP. Tumor cells fail to present MHC-II-restricted epitopes derived from oncogenes to CD4+ T cells. JCI Insight 2023; 8:165570. [PMID: 36512410 PMCID: PMC9977289 DOI: 10.1172/jci.insight.165570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
CD4+ T cells play a critical role in antitumor immunity via recognition of peptide antigens presented on MHC class II (MHC-II). Although some solid cancers can be induced to express MHC-II, the extent to which this enables direct recognition by tumor-specific CD4+ T cells is unclear. We isolated and characterized T cell antigen receptors (TCRs) from naturally primed CD4+ T cells specific for 2 oncoproteins, HPV-16 E6 and the activating KRASG12V mutation, from patients with head and neck squamous cell carcinoma and pancreatic ductal adenocarcinoma, respectively, and determined their ability to recognize autologous or human leukocyte antigen-matched antigen-expressing tumor cells. We found in both cases that the TCRs were capable of recognizing peptide-loaded target cells expressing the relevant MHC-II or B cell antigen-presenting cells (APCs) when the antigens were endogenously expressed and directed to the endosomal pathway but failed to recognize tumor cells expressing the source protein even after induction of surface MHC-II expression by IFN-γ or transduction with CIITA. These results suggest that priming and functional recognition of both a nuclear (E6) and a membrane-associated (KRAS) oncoprotein are predominantly confined to crosspresenting APCs rather than via direct recognition of tumor cells induced to express MHC-II.
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Affiliation(s)
- Spencer E. Brightman
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Biomedical Sciences Program, School of Medicine, UCSD, La Jolla, California, USA
| | - Martin S. Naradikian
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA.,Novartis, San Diego, California, USA
| | - Rukman R. Thota
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Angelica Becker
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,IconOVir Bio, San Diego, California, USA
| | - Leslie Montero
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Milad Bahmanof
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
| | | | | | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California, USA.,Department of Medicine, UCSD, La Jolla, California, USA
| | - Ezra E.W. Cohen
- Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA
| | - Aaron M. Miller
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA.,Division of Hematology and Oncology, UCSD Moores Cancer Center, La Jolla, California, USA
| | - Stephen P. Schoenberger
- Division of Developmental Immunology, La Jolla Institute for Immunology, La Jolla, California, USA
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150
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Chow A, Uddin FZ, Liu M, Dobrin A, Nabet BY, Mangarin L, Lavin Y, Rizvi H, Tischfield SE, Quintanal-Villalonga A, Chan JM, Shah N, Allaj V, Manoj P, Mattar M, Meneses M, Landau R, Ward M, Kulick A, Kwong C, Wierzbicki M, Yavner J, Egger J, Chavan SS, Farillas A, Holland A, Sridhar H, Ciampricotti M, Hirschhorn D, Guan X, Richards AL, Heller G, Mansilla-Soto J, Sadelain M, Klebanoff CA, Hellmann MD, Sen T, de Stanchina E, Wolchok JD, Merghoub T, Rudin CM. The ectonucleotidase CD39 identifies tumor-reactive CD8 + T cells predictive of immune checkpoint blockade efficacy in human lung cancer. Immunity 2023; 56:93-106.e6. [PMID: 36574773 PMCID: PMC9887636 DOI: 10.1016/j.immuni.2022.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 12/27/2022]
Abstract
Improved identification of anti-tumor T cells is needed to advance cancer immunotherapies. CD39 expression is a promising surrogate of tumor-reactive CD8+ T cells. Here, we comprehensively profiled CD39 expression in human lung cancer. CD39 expression enriched for CD8+ T cells with features of exhaustion, tumor reactivity, and clonal expansion. Flow cytometry of 440 lung cancer biospecimens revealed weak association between CD39+ CD8+ T cells and tumoral features, such as programmed death-ligand 1 (PD-L1), tumor mutation burden, and driver mutations. Immune checkpoint blockade (ICB), but not cytotoxic chemotherapy, increased intratumoral CD39+ CD8+ T cells. Higher baseline frequency of CD39+ CD8+ T cells conferred improved clinical outcomes from ICB therapy. Furthermore, a gene signature of CD39+ CD8+ T cells predicted benefit from ICB, but not chemotherapy, in a phase III clinical trial of non-small cell lung cancer. These findings highlight CD39 as a proxy of tumor-reactive CD8+ T cells in human lung cancer.
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Affiliation(s)
- Andrew Chow
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Fathema Z Uddin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Liu
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anton Dobrin
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barzin Y Nabet
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Levi Mangarin
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yonit Lavin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hira Rizvi
- Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sam E Tischfield
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alvaro Quintanal-Villalonga
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joseph M Chan
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nisargbhai Shah
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viola Allaj
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parvathy Manoj
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maximiliano Meneses
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca Landau
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mariana Ward
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Amanda Kulick
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charlene Kwong
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew Wierzbicki
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica Yavner
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jacklynn Egger
- Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Abigail Farillas
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliya Holland
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Harsha Sridhar
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Metamia Ciampricotti
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Hirschhorn
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Xiangnan Guan
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Glenn Heller
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge Mansilla-Soto
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michel Sadelain
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Christopher A Klebanoff
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Breast Medicine Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Matthew D Hellmann
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Triparna Sen
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jedd D Wolchok
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Taha Merghoub
- Ludwig Collaborative and Swim Across America Laboratory, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Charles M Rudin
- Thoracic Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA; Druckenmiler Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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