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Kuah CY, Monfries R, Quartagno M, Seckl MJ, Ghorani E. What is the optimal duration, dose and frequency for anti-PD1 therapy of non-small cell lung cancer? Ther Adv Med Oncol 2023; 15:17588359231210271. [PMID: 37954230 PMCID: PMC10638879 DOI: 10.1177/17588359231210271] [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: 03/02/2023] [Accepted: 10/09/2023] [Indexed: 11/14/2023] Open
Abstract
Over the past decade, immune checkpoint inhibitors (ICIs) have transformed the management of multiple malignancies including lung cancer. However, the optimal use of these agents in terms of duration, dose and administration frequency remains unknown. Focusing on anti-PD1 agents nivolumab and pembrolizumab in the context of non-small cell lung cancer, we argue that several lines of evidence suggest current administration regimens of these drugs may result in overtreatment with potentially important implications for cost, quality of life and toxicity. This review summarizes evidence for the scope to optimize anti-PD1 regimens, the limitations of existing data and potential approaches to solve these problems including with a novel multi-arm clinical trial design implemented in the recently opened REFINE-Lung study.
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Affiliation(s)
- Chii Yang Kuah
- Department of Medical Oncology, Charing Cross Hospital Campus of Imperial College London, UK
| | - Robert Monfries
- Department of Medical Oncology, Charing Cross Hospital Campus of Imperial College London, UK
| | - Matteo Quartagno
- Institute for Clinical Trials and Methodology, University College London, London, UK
| | - Michael J. Seckl
- Department of Medical Oncology, Charing Cross Hospital Campus of Imperial College London W6 8RF, UK
| | - Ehsan Ghorani
- Department of Medical Oncology, Charing Cross Hospital Campus of Imperial College London W6 8RF, UK
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Abstract
T cells can acquire a broad spectrum of differentiation states following activation. At the extreme ends of this continuum are short-lived cells equipped with effector machinery and more quiescent, long-lived cells with heightened proliferative potential and stem cell-like developmental plasticity. The latter encompass stem-like exhausted T cells and memory T cells, both of which have recently emerged as key determinants of cancer immunity and response to immunotherapy. Here, we discuss key similarities and differences in the regulation and function of stem-like exhausted CD8+ T cells and memory CD8+ T cells, and consider their context-specific contributions to protective immunity in diverse outcomes of cancer, including tumour escape, long-term control and eradication. Finally, we emphasize how recent advances in the understanding of the molecular regulation of stem-like exhausted T cells and memory T cells are being explored for clinical benefit in cancer immunotherapies such as checkpoint inhibition, adoptive cell therapy and vaccination.
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Affiliation(s)
- Thomas Gebhardt
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia.
| | - Simone L Park
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ian A Parish
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia.
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
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Ghorani E, Swanton C, Quezada SA. Cancer cell-intrinsic mechanisms driving acquired immune tolerance. Immunity 2023; 56:2270-2295. [PMID: 37820584 DOI: 10.1016/j.immuni.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Immune evasion is a hallmark of cancer, enabling tumors to survive contact with the host immune system and evade the cycle of immune recognition and destruction. Here, we review the current understanding of the cancer cell-intrinsic factors driving immune evasion. We focus on T cells as key effectors of anti-cancer immunity and argue that cancer cells evade immune destruction by gaining control over pathways that usually serve to maintain physiological tolerance to self. Using this framework, we place recent mechanistic advances in the understanding of cancer immune evasion into broad categories of control over T cell localization, antigen recognition, and acquisition of optimal effector function. We discuss the redundancy in the pathways involved and identify knowledge gaps that must be overcome to better target immune evasion, including the need for better, routinely available tools that incorporate the growing understanding of evasion mechanisms to stratify patients for therapy and trials.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology and Immunotherapy Unit, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Medical Oncology, Imperial College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London, UK.
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4
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Guo W, Zhou B, Bie F, Huai Q, Xue X, Guo L, Tan F, Xue Q, Zhao L, Gao S. Single-cell RNA sequencing analysis reveals transcriptional heterogeneity of multiple primary lung cancer. Clin Transl Med 2023; 13:e1453. [PMID: 37846760 PMCID: PMC10580343 DOI: 10.1002/ctm2.1453] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023] Open
Abstract
INTRODUCTION With the advancements in early diagnosis, more and more patients with multiple primary lung cancer (MPLC) have been identified. However, the progression of MPLC involves complex changes in cell composition and metabolic function, which remains largely controversial. OBJECTIVE Our study aims to comprehensively reveal the cellular characteristics and inter-cellular connections of MPLC. METHODS We performed scRNA-seq from 23 samples of six MPLC patients, combined with bulk whole-exome sequencing. We performed trajectory analysis to investigate the transition of different cell types during the development of MPLC. RESULTS A total of 1 67 397 cells were sequenced derived from tumour and adjacent tissues of MPLC patients, and tumour, normal, immune and stromal cells were identified. Two states of epithelial cells were identified, which were associated with immune response and cell death, respectively. Furthermore, both CD8+ naïve and memory T cells participated in the differentiation of CD8+ T cells. The terminal states of CD8+ T cells were exhausted T cells and cytotoxic T cells, which positively regulated cell death and were implicated in the regulation of cytokine production, respectively. Two main subpopulations of B cells with distinct functions were identified, which participate in the regulation of the immune response and antigen presentation, respectively. In addition, we found a specific type of endothelial cells that were abundant in tumour samples, with an increasing trend from normal to tumour samples. CONCLUSIONS Our study showed the comprehensive landscape of different cells of MPLC, which might reveal the key cellular mechanisms and, therefore, may provide new insights into the early diagnosis and treatment of MPLC.
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Affiliation(s)
- Wei Guo
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
- Key Laboratory of Minimally Invasive Therapy Research for Lung CancerChinese Academy of Medical SciencesBeijingP. R. China
| | - Bolun Zhou
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Fenglong Bie
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
- Department of Thoracic SurgeryShandong Provincial Hospital Affiliated to Shandong First Medical UniversityJinanShandongP. R. China
| | - Qilin Huai
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Xuemin Xue
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Lei Guo
- Department of PathologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Fengwei Tan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
- Key Laboratory of Minimally Invasive Therapy Research for Lung CancerChinese Academy of Medical SciencesBeijingP. R. China
| | - Qi Xue
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
- Key Laboratory of Minimally Invasive Therapy Research for Lung CancerChinese Academy of Medical SciencesBeijingP. R. China
| | - Liang Zhao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
| | - Shugeng Gao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingP. R. China
- Key Laboratory of Minimally Invasive Therapy Research for Lung CancerChinese Academy of Medical SciencesBeijingP. R. China
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5
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Deng C, Wang Y, Fu F, Li D, Zheng Q, Jin Y, Li Y, Chen H, Zhang Y. Tumor-derived Vimentin as a novel biomarker for distinct subtypes predicting adjuvant chemotherapy resistance and T-cell-inflamed phenotype in small cell lung cancer. MedComm (Beijing) 2023; 4:e370. [PMID: 37789961 PMCID: PMC10542987 DOI: 10.1002/mco2.370] [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: 02/20/2023] [Revised: 08/07/2023] [Accepted: 08/10/2023] [Indexed: 10/05/2023] Open
Abstract
Despite recent progress in subtype classification for small cell lung carcinoma (SCLC), little is known about the biomarker for triple-negative (ASCL1, NEUROD1, and POU2F3 negative) tumors. The long-term survival, adjuvant chemotherapy (ACT) response, and immune milieu in different SCLC subtypes have also not been well established. Here, we retrospectively collected a large cohort of 192 primary SCLC tumors and reported that ASCL1-, NEUROD1- and POU2F3-dominant subtypes counted for 61.38%, 19.31%, and 6.21%, respectively. Subtype intra-tumoral heterogeneity and co-expression at the single-cell level existed substantially. The expression of tumor-derived Vimentin (VIM) was nearly restricted to triple-negative SCLC tumors (15/19, 78.9%) while YAP1 expression was distributed widely in other subtypes. The SCLC subtyping model was independently prognostic of OS and RFS (p < 0.001 and p = 0.043). In particular, patients with ASCL1-positive SCLC tumors can benefit more from ACT, and VIM-positive tumors did the opposite. Compared with other subtypes, the VIM-dominant SCLC subtype was associated with abundant but functionally impaired CD4+ and CD8+ T-cells, which highly expressed inhibitory checkpoints and potentially benefit from PD-L1 blockade therapy. Our study showed that tumor-derived SCLC-V subtype could independently predict ACT response. The distinct immune landscape between subtypes may help inform personalized immune therapeutic approaches.
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Affiliation(s)
- Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yue Wang
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Di Li
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qiang Zheng
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yan Jin
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Yuan Li
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
- Department of PathologyFudan University Shanghai Cancer CenterShanghaiChina
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic EngineeringFudan University Shanghai Cancer CenterShanghaiChina
- Institute of Thoracic OncologyFudan UniversityShanghaiChina
- Department of OncologyShanghai Medical CollegeFudan UniversityShanghaiChina
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6
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Davis L, Miller RE, Wong YNS. The Landscape of Adoptive Cellular Therapies in Ovarian Cancer. Cancers (Basel) 2023; 15:4814. [PMID: 37835509 PMCID: PMC10571827 DOI: 10.3390/cancers15194814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Ovarian cancers are typically poorly immunogenic and have demonstrated disappointing responses to immune checkpoint inhibitor (ICI) therapy. Adoptive cellular therapy (ACT) offers an alternative method of harnessing the immune system that has shown promise, especially with the success of chimeric antigen receptor T-cell (CAR-T) therapy in haematologic malignancies. So far, ACT has led to modest results in the treatment of solid organ malignancies. This review explores the possibility of ACT as an effective alternative or additional treatment to current standards of care in ovarian cancer. We will highlight the potential of ACTs, such as CAR-T, T-cell receptor therapy (TCR-T), tumour-infiltrating lymphocytes (TILs) and cell-based vaccines, whilst also discussing their challenges. We will present clinical studies for these approaches in the treatment of immunologically 'cold' ovarian cancer and consider the rationale for future research.
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Affiliation(s)
- Lucy Davis
- Royal Free Hospital, London NW3 2QG, UK;
| | - Rowan E Miller
- Department of Medical Oncology, University College London Hospital, London NW1 3PG, UK;
- Department of Medical Oncology, St Bartholomew’s Hospital, London EC1A 7BE, UK
| | - Yien Ning Sophia Wong
- Royal Free Hospital, London NW3 2QG, UK;
- Department of Medical Oncology, University College London Hospital, London NW1 3PG, UK;
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7
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Guo M, Abd-Rabbo D, Bertol BC, Carew M, Lukhele S, Snell LM, Xu W, Boukhaled GM, Elsaesser H, Halaby MJ, Hirano N, McGaha TL, Brooks DG. Molecular, metabolic, and functional CD4 T cell paralysis in the lymph node impedes tumor control. Cell Rep 2023; 42:113047. [PMID: 37651234 PMCID: PMC10578141 DOI: 10.1016/j.celrep.2023.113047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 07/14/2023] [Accepted: 08/11/2023] [Indexed: 09/02/2023] Open
Abstract
CD4 T cells are central effectors of anti-cancer immunity and immunotherapy, yet the regulation of CD4 tumor-specific T (TTS) cells is unclear. We demonstrate that CD4 TTS cells are quickly primed and begin to divide following tumor initiation. However, unlike CD8 TTS cells or exhaustion programming, CD4 TTS cell proliferation is rapidly frozen in place by a functional interplay of regulatory T cells and CTLA4. Together these mechanisms paralyze CD4 TTS cell differentiation, redirecting metabolic circuits, and reducing their accumulation in the tumor. The paralyzed state is actively maintained throughout cancer progression and CD4 TTS cells rapidly resume proliferation and functional differentiation when the suppressive constraints are alleviated. Overcoming their paralysis established long-term tumor control, demonstrating the importance of rapidly crippling CD4 TTS cells for tumor progression and their potential restoration as therapeutic targets.
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Affiliation(s)
- Mengdi Guo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Diala Abd-Rabbo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bruna C Bertol
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Madeleine Carew
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sabelo Lukhele
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Laura M Snell
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Microbiology and Immunology and Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Wenxi Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Giselle M Boukhaled
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Heidi Elsaesser
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marie Jo Halaby
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Naoto Hirano
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Tracy L McGaha
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - David G Brooks
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Immunology, University of Toronto, Toronto, ON, Canada.
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8
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SUN LU, TAN HUAICHENG, YU TING, LIANG RUICHAO. Identification of lncRNAs associated with T cells as potential biomarkers and therapeutic targets in lung adenocarcinoma. Oncol Res 2023; 31:967-988. [PMID: 37744265 PMCID: PMC10513944 DOI: 10.32604/or.2023.042309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the most common and deadliest subtype of lung cancer. To select more targeted and effective treatments for individuals, further advances in classifying LUAD are urgently needed. The number, type, and function of T cells in the tumor microenvironment (TME) determine the progression and treatment response of LUAD. Long noncoding RNAs (lncRNAs), may regulate T cell differentiation, development, and activation. Thus, our aim was to identify T cell-related lncRNAs (T cell-Lncs) in LUAD and to investigate whether T cell-Lncs could serve as potential stratifiers and therapeutic targets. Seven T cell-Lncs were identified to further establish the T cell-related lncRNA risk score (TRS) in LUAD. Low TRS individuals were characterized by robust immune status, fewer genomic alterations, and remarkably longer survival than high TRS individuals. The excellent accuracy of TRS in predicting overall survival (OS) was validated in the TCGA-LUAD training cohort and the GEO-LUAD validation cohort. Our data demonstrated the favorable predictive power of the TRS-based nomogram, which had important clinical significance in estimating the survival probability for individuals. In addition, individuals with low TRS could respond better to chemotherapy and immunotherapy than those with high TRS. LINC00525 was identified as a valuable study target, and the ability of LUAD to proliferate or invade was significantly attenuated by downregulation of LINC00525. In conclusion, the TRS established by T cell-Lncs could unambiguously classify LUAD patients, predict their prognosis and guide their management. Moreover, our identified T cell-Lncs could provide potential therapeutic targets for LUAD.
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Affiliation(s)
- LU SUN
- Department of Targeting Therapy & Immunology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - HUAICHENG TAN
- Department of Targeting Therapy & Immunology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - TING YU
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - RUICHAO LIANG
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
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9
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Li C, Zhang B, Schaafsma E, Reuben A, Wang L, Turk MJ, Zhang J, Cheng C. TimiGP: Inferring cell-cell interactions and prognostic associations in the tumor immune microenvironment through gene pairs. Cell Rep Med 2023; 4:101121. [PMID: 37467716 PMCID: PMC10394258 DOI: 10.1016/j.xcrm.2023.101121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 04/11/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023]
Abstract
Determining the prognostic association of different immune cell types in the tumor microenvironment is critical for understanding cancer biology and developing new therapeutic strategies. However, this is challenging in certain cancer types, where the abundance of different immune subsets is highly correlated. In this study, we develop a computational method named TimiGP to overcome this challenge. Based on bulk gene expression and survival data, TimiGP infers cell-cell interactions that reveal the association between immune cell relative abundance and prognosis. As demonstrated in metastatic melanoma, TimiGP prioritizes immune cells critical in prognosis based on the identified cell-cell interactions. Highly consistent results are obtained by TimiGP when applied to seven independent melanoma datasets and when different cell-type marker sets are used as inputs. Additionally, TimiGP can leverage single-cell RNA sequencing data to delineate the tumor immune microenvironment at high resolutions across a wide range of cancer types.
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Affiliation(s)
- Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA
| | - Baoyi Zhang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77030, USA
| | - Evelien Schaafsma
- Department of Microbiology and Immunology, Dartmouth College, Hanover, NH 03755, USA
| | - Alexandre Reuben
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA
| | - Mary Jo Turk
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA; Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth Houston, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Lung Cancer Genomics Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Lung Cancer Interception Program, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX 77030, USA.
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10
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Chu Y, Dai E, Li Y, Han G, Pei G, Ingram DR, Thakkar K, Qin JJ, Dang M, Le X, Hu C, Deng Q, Sinjab A, Gupta P, Wang R, Hao D, Peng F, Yan X, Liu Y, Song S, Zhang S, Heymach JV, Reuben A, Elamin YY, Pizzi MP, Lu Y, Lazcano R, Hu J, Li M, Curran M, Futreal A, Maitra A, Jazaeri AA, Ajani JA, Swanton C, Cheng XD, Abbas HA, Gillison M, Bhat K, Lazar AJ, Green M, Litchfield K, Kadara H, Yee C, Wang L. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Nat Med 2023; 29:1550-1562. [PMID: 37248301 DOI: 10.1038/s41591-023-02371-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Tumor-infiltrating T cells offer a promising avenue for cancer treatment, yet their states remain to be fully characterized. Here we present a single-cell atlas of T cells from 308,048 transcriptomes across 16 cancer types, uncovering previously undescribed T cell states and heterogeneous subpopulations of follicular helper, regulatory and proliferative T cells. We identified a unique stress response state, TSTR, characterized by heat shock gene expression. TSTR cells are detectable in situ in the tumor microenvironment across various cancer types, mostly within lymphocyte aggregates or potential tertiary lymphoid structures in tumor beds or surrounding tumor edges. T cell states/compositions correlated with genomic, pathological and clinical features in 375 patients from 23 cohorts, including 171 patients who received immune checkpoint blockade therapy. We also found significantly upregulated heat shock gene expression in intratumoral CD4/CD8+ cells following immune checkpoint blockade treatment, particularly in nonresponsive tumors, suggesting a potential role of TSTR cells in immunotherapy resistance. Our well-annotated T cell reference maps, web portal and automatic alignment/annotation tool could provide valuable resources for T cell therapy optimization and biomarker discovery.
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Affiliation(s)
- Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yating Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krupa Thakkar
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Jiang-Jiang Qin
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Can Hu
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pravesh Gupta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa P Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Hu
- Department of Human Genetics, Emory School of Medicine, Atlanta, GA, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Curran
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Xiang-Dong Cheng
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maura Gillison
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Michael Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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11
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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: 17] [Impact Index Per Article: 17.0] [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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12
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Maniar R, Wang PH, Washburn RS, Kratchmarov R, Coley SM, Saqi A, Pan SS, Hu J, Shu CA, Rizvi NA, Henick BS, Reiner SL. Self-Renewing CD8+ T-cell Abundance in Blood Associates with Response to Immunotherapy. Cancer Immunol Res 2023; 11:164-170. [PMID: 36512052 PMCID: PMC9898128 DOI: 10.1158/2326-6066.cir-22-0524] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Treatment with immune checkpoint blockade (ICB) often fails to elicit durable antitumor immunity. Recent studies suggest that ICB does not restore potency to terminally dysfunctional T cells, but instead drives proliferation and differentiation of self-renewing progenitor T cells into fresh, effector-like T cells. Antitumor immunity catalyzed by ICB is characterized by mobilization of antitumor T cells in systemic circulation and tumor. To address whether abundance of self-renewing T cells in blood is associated with immunotherapy response, we used flow cytometry of peripheral blood from a cohort of patients with metastatic non-small cell lung cancer (NSCLC) treated with ICB. At baseline, expression of T-cell factor 1 (TCF1), a marker of self-renewing T cells, was detected at higher frequency in effector-memory (CCR7-) CD8+ T cells from patients who experienced durable clinical benefit compared to those with primary resistance to ICB. On-treatment blood samples from patients benefiting from ICB also exhibited a greater frequency of TCF1+CCR7-CD8+ T cells and higher proportions of TCF1 expression in treatment-expanded PD-1+CCR7-CD8+ T cells. The observed correlation of TCF1 frequency in CCR7-CD8+ T cells and response to ICB suggests that broader examination of self-renewing T-cell abundance in blood will determine its potential as a noninvasive, predictive biomarker of response and resistance to immunotherapy.
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Affiliation(s)
- Rohan Maniar
- Division of Hematology & Oncology, Columbia University Irving Medical Center; New York, NY, USA
| | - Peter H. Wang
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, NY, USA
| | - Robert S. Washburn
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, NY, USA
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, NY, USA
| | - Shana M. Coley
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center; New York, NY; USA
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center; New York, NY; USA
| | - Samuel S. Pan
- Department of Biostatistics, Mailman School of Public Health, Columbia University; New York, NY; USA
| | - Jianhua Hu
- Department of Biostatistics, Mailman School of Public Health, Columbia University; New York, NY; USA
| | - Catherine A. Shu
- Division of Hematology & Oncology, Columbia University Irving Medical Center; New York, NY, USA
| | - Naiyer A. Rizvi
- Division of Hematology & Oncology, Columbia University Irving Medical Center; New York, NY, USA
| | - Brian S. Henick
- Division of Hematology & Oncology, Columbia University Irving Medical Center; New York, NY, USA
- Corresponding Authors: Brian S. Henick, 161 Fort Washington Avenue, Herbert Irving Pavilion 3 Floor, New York, NY 10032, Ph: 212-305-3997, ; Steven L. Reiner, 701 West 168 Street, HHSC Room 912, New York, NY 10032, Ph: 212-305-5177,
| | - Steven L. Reiner
- Department of Microbiology and Immunology, Columbia University Irving Medical Center; New York, NY, USA
- Department of Pediatrics, Vagelos College of Physicians and Surgeons; Columbia University Irving Medical Center New York, NY, USA
- Corresponding Authors: Brian S. Henick, 161 Fort Washington Avenue, Herbert Irving Pavilion 3 Floor, New York, NY 10032, Ph: 212-305-3997, ; Steven L. Reiner, 701 West 168 Street, HHSC Room 912, New York, NY 10032, Ph: 212-305-5177,
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13
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Huynh M, Crane MJ, Jamieson AM. The lung, the niche, and the microbe: Exploring the lung microbiome in cancer and immunity. Front Immunol 2023; 13:1094110. [PMID: 36733391 PMCID: PMC9888758 DOI: 10.3389/fimmu.2022.1094110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/29/2022] [Indexed: 01/18/2023] Open
Abstract
The lung is a complex and unique organ system whose biology is strongly influenced by environmental exposure, oxygen abundance, connection to extrapulmonary systems via a dense capillary network, and an array of immune cells that reside in the tissue at steady state. The lung also harbors a low biomass community of commensal microorganisms that are dynamic during both health and disease with the capacity to modulate regulatory immune responses during diseases such as cancer. Lung cancer is the third most common cancer worldwide with the highest mortality rate amongst cancers due to the difficulty of an early diagnosis. This review discusses the current body of work addressing the interactions between the lung microbiota and the immune system, and how these two components of the pulmonary system are linked to lung cancer development and outcomes. Bringing in lessons from broader studies examining the effects of the gut microbiota on cancer outcomes, we highlight many challenges and gaps in this nascent field.
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Affiliation(s)
| | | | - Amanda M. Jamieson
- Department of Molecular Microbiology & Immunology, Brown University, Providence, RI, United States
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14
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Tietscher S, Wagner J, Anzeneder T, Langwieder C, Rees M, Sobottka B, de Souza N, Bodenmiller B. A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer. Nat Commun 2023; 14:98. [PMID: 36609566 PMCID: PMC9822999 DOI: 10.1038/s41467-022-35238-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 11/24/2022] [Indexed: 01/09/2023] Open
Abstract
Immune checkpoint therapy in breast cancer remains restricted to triple negative patients, and long-term clinical benefit is rare. The primary aim of immune checkpoint blockade is to prevent or reverse exhausted T cell states, but T cell exhaustion in breast tumors is not well understood. Here, we use single-cell transcriptomics combined with imaging mass cytometry to systematically study immune environments of human breast tumors that either do or do not contain exhausted T cells, with a focus on luminal subtypes. We find that the presence of a PD-1high exhaustion-like T cell phenotype is associated with an inflammatory immune environment with a characteristic cytotoxic profile, increased myeloid cell activation, evidence for elevated immunomodulatory, chemotactic, and cytokine signaling, and accumulation of natural killer T cells. Tumors harboring exhausted-like T cells show increased expression of MHC-I on tumor cells and of CXCL13 on T cells, as well as altered spatial organization with more immature rather than mature tertiary lymphoid structures. Our data reveal fundamental differences between immune environments with and without exhausted T cells within luminal breast cancer, and show that expression of PD-1 and CXCL13 on T cells, and MHC-I - but not PD-L1 - on tumor cells are strong distinguishing features between these environments.
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Affiliation(s)
- Sandra Tietscher
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.,Life Science Zurich Graduate School, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Johanna Wagner
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Division of Translational Medical Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | | | | | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Natalie de Souza
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.,Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Bernd Bodenmiller
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland. .,Institute for Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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15
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Cheng Q, Wang W, Liu J, Lv Z, Ji W, Yu J, Zhang W, Yang Y. Elevated MPP6 expression correlates with an unfavorable prognosis, angiogenesis and immune evasion in hepatocellular carcinoma. Front Immunol 2023; 14:1173848. [PMID: 37207207 PMCID: PMC10189050 DOI: 10.3389/fimmu.2023.1173848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/11/2023] [Indexed: 05/21/2023] Open
Abstract
Background Membrane palmitoylated proteins (MPPs) are engaged in various biological processes, such as cell adhesion and cell polarity. Dysregulated MPP members have different effects on hepatocellular carcinoma (HCC) development. However, the role of MPP6 in HCC has been unknown. Method HCC transcriptome and clinical data from different public databases were downloaded and analyzed, and the results were further validated by qRT-PCR, Western blotting and immunohistochemistry (IHC) using HCC cell lines and tissues. The association between MPP6 and prognosis, potential pathogenic mechanisms, angiogenesis, immune evasion, tumor mutation burden (TMB) and treatment response in HCC patients was analyzed by bioinformatics and IHC staining. Results MPP6 was significantly overexpressed in HCC, and its expression was related to T stage, pathologic stage, histologic grade and adverse prognosis in HCC patients. Gene set enrichment analysis revealed that differentially expressed genes were mainly enriched in the synthesis of genetic materials and the WNT signaling pathway. GEPIA database analysis and IHC staining suggested that MPP6 expression had a positive correlation with angiogenesis. Single-cell dataset analysis indicated that MPP6 was associated with features of the tumor microenvironment. Additional analyses discovered that MPP6 expression was inversely related to immune cell infiltration and was involved in tumor immune evasion. MPP6 expression was positively associated with TMB, and patients with high TMB had an adverse prognosis. Immunotherapy was more effective in HCC patients with low MPP6 expression, whereas those with high MPP6 expression responded better to sorafenib, gemcitabine, 5-FU, and doxorubicin. Conclusions Elevated MPP6 expression is associated with an unfavorable prognosis, angiogenesis and immune evasion in HCC. Moreover, MPP6 has the potential to be used to assess TMB and treatment response. Therefore, MPP6 might serve as a novel prognostic biomarker and therapeutic target for HCC.
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16
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Yang B, Li X, Zhang W, Fan J, Zhou Y, Li W, Yin J, Yang X, Guo E, Li X, Fu Y, Liu S, Hu D, Qin X, Dou Y, Xiao R, Lu F, Wang Z, Qin T, Wang W, Zhang Q, Li S, Ma D, Mills GB, Chen G, Sun C. Spatial heterogeneity of infiltrating T cells in high-grade serous ovarian cancer revealed by multi-omics analysis. Cell Rep Med 2022; 3:100856. [PMID: 36543113 PMCID: PMC9798026 DOI: 10.1016/j.xcrm.2022.100856] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/03/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Tumor-infiltrating lymphocytes (TILs), especially CD8+ TILs, represent a favorable prognostic factor in high-grade serous ovarian cancer (HGSOC) and other tumor lineages. Here, we analyze the spatial heterogeneity of different TIL subtypes in HGSOC. We integrated RNA sequencing, whole-genome sequencing, bulk T cell receptor (TCR) sequencing, as well as single-cell RNA/TCR sequencing to investigate the characteristics and differential composition of TILs across different HGSOC sites. Two immune "cold" patterns in ovarian cancer are identified: (1) ovarian lesions with low infiltration of mainly dysfunctional T cells and immunosuppressive Treg cells and (2) omental lesions infiltrated with non-tumor-specific bystander cells. Exhausted CD8 T cells that are preferentially enriched in ovarian tumors exhibit evidence for expansion and cytotoxic activity. Inherent tumor immune microenvironment characteristics appear to be the main contributor to the spatial differences in TIL status. The landscape of spatial heterogeneity of TILs may inform potential strategies for therapeutic manipulation in HGSOC.
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Affiliation(s)
- Bin Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiong Li
- Department of Gynecology & Obstetrics, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Zhang
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Junpeng Fan
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yong Zhou
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Wenting Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingjing Yin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaohang Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ensong Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Fu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Si Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dianxing Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yingyu Dou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rourou Xiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Funian Lu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zizhuo Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Tianyu Qin
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Qinghua Zhang
- Department of Gynecology & Obstetrics, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuaicheng Li
- City University of Hong Kong, Shenzhen Research Institute, Shenzhen 518083, China
| | - Ding Ma
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gordon B Mills
- Department of Cell, Development and Cancer Biology, Oregon Health and Sciences University, Portland, OR 97201, USA; Knight Cancer Institute, Portland, OR 97201, USA; Department of Systems Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gang Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Chaoyang Sun
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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17
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Abstract
Significance: Immune cell therapy involves the administration of immune cells into patients, and it has emerged as one of the most common type of immunotherapy for cancer treatment. Knowledge on the biology and metabolism of the adoptively transferred immune cells and the metabolic requirements of different cell types in the tumor is fundamental for the development of immune cell therapy with higher efficacy. Recent Advances: Adoptive T cell therapy has been shown to be effective in limited types of cancer. Different types and generations of adoptive T cell therapies have evolved in the recent decade. This review covers the basic principles and development of these therapies in cancer treatment. Critical Issues: Our review provides an overview on the basic concepts on T cell metabolism and highlights the metabolic requirements of T and adoptively transferred T cells. Future Directions: Integrating the knowledge just cited will facilitate the development of strategies to maximize the expansion of adoptively transferred T cells ex vivo and in vivo and to promote their durability and antitumor effects. Antioxid. Redox Signal. 37, 1303-1324.
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Affiliation(s)
- Ge Hui Tan
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Department of Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, United Kingdom
| | - Carmen Chak-Lui Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Center for Oncology and Immunology, Hong Kong Science Park, Hong Kong, SAR, China
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18
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Zhou Z, Tao C, Li J, Tang JCO, Chan ASC, Zhou Y. Chimeric antigen receptor T cells applied to solid tumors. Front Immunol 2022; 13:984864. [PMID: 36389701 PMCID: PMC9659902 DOI: 10.3389/fimmu.2022.984864] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
Chimeric antigen receptor T cell (CAR-T) therapy is novel tumor immunotherapy that enables autologous T to express synthetic receptors to specifically recognize the surface tumor-associated antigens for exerting subsequent antitumor effects, and eliminating the resistance, metastases and recurrence of cancer. Although CAR T cells have exhibited success in eradicating hematologic malignancies, their applications to solid tumors has not yet been achieved due to obstacles such as the immune-suppressor tumor microenvironment and lack of tumor specific target antigens. In this review, we presented advancements in the development of CAR T cell therapy in solid tumors, and offered a brief summary of the challenges, as well as novel engineering and pharmaceutical interventions to overcome these barriers. Looking forward, we discussed the latest studies which are expected to reach the clinicals in the next few years, including CRISPR screens-based CAR modification and CAR T cells driven from progenitor-like T cells. Collectively, this review may inspire researchers and clinicians to develop clinical available strategies of CAR T cell therapies in solid tumor.
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Affiliation(s)
- Zhongguo Zhou
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Can Tao
- School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Jianting Li
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Johnny Cheuk-on Tang
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong, Hong Kong SAR, China
- Kamford Genetics Company Limited, Hong Kong, Hong Kong SAR, China
| | - Albert Sun-chi Chan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yuanyuan Zhou
- School of Biomedical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, China
- *Correspondence: Yuanyuan Zhou,
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19
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Bu X, Liu S, Wen D, Kan A, Xu Y, Lin X, Shi M. Comprehensive characterization of enhancer RNA in hepatocellular carcinoma reveals three immune subtypes with implications for immunotherapy. Mol Ther Oncolytics 2022; 26:226-244. [PMID: 35919459 PMCID: PMC9310078 DOI: 10.1016/j.omto.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 07/03/2022] [Indexed: 12/21/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is highly heterogeneous. Molecular subtyping for guiding immunotherapy is warranted. Previous studies have indicated that enhancer RNAs (eRNAs) are involved in tumor heterogeneity and immune infiltration. However, the eRNA landscape and its correlation with immune infiltration in HCC remain unknown. Here we first revealed the genome-wide eRNA landscape in two HCC cohorts. Then we divided individuals with HCC into three immune-related clusters (C1, C2, and C3) based on eRNA expression profiles. The prognosis, biological properties, immune infiltration, clinical features, genomic features, and drug response were analyzed. C1 was enriched in immune infiltration and potentially sensitive to immune checkpoint inhibitors (ICIs). C2 displayed features of immune depletion, high proliferation activity, malignant clinical features, and the worst prognosis. C2 may benefit from targeted therapy. C3 presented moderate immune infiltration, metabolism-related signatures, and the best prognosis. Transarterial chemoembolization (TACE) may be effective for C3. Finally, we constructed a 51-eRNA classifier for subtype prediction and validated its efficacy in The Cancer Genome Atlas (TCGA) cohort and Sun Yat-sen University Cancer Center (SYSUCC) cohort. Our results provide a novel method for immune classification of HCC, shed new light on tumor heterogeneity, and may aid in HCC immunotherapy.
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Affiliation(s)
- Xiaoyun Bu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shuang Liu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dongsheng Wen
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Anna Kan
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yujie Xu
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Xuanjia Lin
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ming Shi
- Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
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20
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Wang PH, Washburn R, Maniar R, Mu M, Ringham O, Kratchmarov R, Henick BS, Reiner SL. Cutting Edge: Promoting T Cell Factor 1 + T Cell Self-Renewal to Improve Programmed Cell Death Protein 1 Blockade. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:660-664. [PMID: 35905999 PMCID: PMC9387677 DOI: 10.4049/jimmunol.2200317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/25/2022] [Indexed: 01/04/2023]
Abstract
Immune checkpoint blockade is limited by resistance to treatment, with many patients not achieving durable antitumor responses. Self-renewing (T cell factor 1+ [TCF1+]) CD8+ T cells have recently been implicated in efficacy of anti-programmed cell death protein 1 (anti-PD-1). Mice challenged with syngeneic tumors were treated with anti-PD-1 and/or a reversible inhibitor of PI3K δ, designed to promote T cell self-renewal. Growth of tumors in untreated mice was characterized by waning proportions of TCF1+ T cells, suggesting self-renewing T cells become limiting for successful immunotherapy. Higher proportions of TCF1+ T cells in tumor and blood correlated with better control of tumor growth. Combining anti-PD-1 and inhibitor of PI3K δ conferred superior protection compared with either monotherapy and was associated with higher frequency of TCF1+ T cells in tumor and blood compared with anti-PD-1 alone. These findings reveal predictive importance of self-renewing T cells in anti-tumor immunity and suggest that resistance-directed strategies to enhance T cell self-renewal could potentiate the efficacy of PD-1 blockade.
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Affiliation(s)
- Peter H Wang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Robert Washburn
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Rohan Maniar
- Division of Hematology-Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY; and
| | - Michael Mu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Olivia Ringham
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Radomir Kratchmarov
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
| | - Brian S Henick
- Division of Hematology-Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY; and
| | - Steven L Reiner
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY;
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY
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21
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Wolf Y, Samuels Y. Intratumor Heterogeneity and Antitumor Immunity Shape One Another Bidirectionally. Clin Cancer Res 2022; 28:2994-3001. [PMID: 35380639 PMCID: PMC9306293 DOI: 10.1158/1078-0432.ccr-21-1355] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/10/2022] [Accepted: 03/28/2022] [Indexed: 01/07/2023]
Abstract
Over the last decade, it has become clear that the genomic landscapes of tumors profoundly impact their immunogenicity and how tumor cells interact with immune cells. Whereas past discoveries mainly focused on the interplay between tumor immunogenicity and tumor mutational burden (TMB), under the assumption that a higher mutation load would give rise to a better patient response to immune checkpoint blockade therapies, we and others have underlined intratumor heterogeneity (ITH) as an important determinant of the magnitude of the antitumor response and the nature of the tumor microenvironment. In this review, we define TMB versus ITH and how the two factors are being inferred from data, examine key findings in the cancer immunogenomics literature deciphering the complex cross-talk between TMB, ITH, and antitumor immunity in human cancers and in vivo models, and discuss the mutual influence of ITH and immunity-how the antitumor response can give rise to tumors with higher ITH, and how higher ITH can put shackles on the antitumor response.
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Affiliation(s)
- Yochai Wolf
- Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.,Corresponding Authors: Yochai Wolf, Ella Lemelbaum Institute for Immuno-Oncology and Skin Cancer, Sheba Medical Center, Tel Hashomer, Ramat Gan 5265601, Israel. E-mail: ; and Yardena Samuels, Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 761000, Israel. E-mail:
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22
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Jaeger AM, Stopfer LE, Ahn R, Sanders EA, Sandel DA, Freed-Pastor WA, Rideout WM, Naranjo S, Fessenden T, Nguyen KB, Winter PS, Kohn RE, Westcott PMK, Schenkel JM, Shanahan SL, Shalek AK, Spranger S, White FM, Jacks T. Deciphering the immunopeptidome in vivo reveals new tumour antigens. Nature 2022; 607:149-155. [PMID: 35705813 PMCID: PMC9945857 DOI: 10.1038/s41586-022-04839-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 05/06/2022] [Indexed: 11/09/2022]
Abstract
Immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex class I (MHC-I) molecules1-5. Current approaches to profiling of MHC-I-associated peptides, collectively known as the immunopeptidome, are limited to in vitro investigation or bulk tumour lysates, which limits our understanding of cancer-specific patterns of antigen presentation in vivo6. To overcome these limitations, we engineered an inducible affinity tag into the mouse MHC-I gene (H2-K1) and targeted this allele to the KrasLSL-G12D/+Trp53fl/fl mouse model (KP/KbStrep)7. This approach enabled us to precisely isolate MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma and from lung adenocarcinoma (LUAD) in vivo. In addition, we profiled the LUAD immunopeptidome from the alveolar type 2 cell of origin up to late-stage disease. Differential peptide presentation in LUAD was not predictable by mRNA expression or translation efficiency and is probably driven by post-translational mechanisms. Vaccination with peptides presented by LUAD in vivo induced CD8+ T cell responses in naive mice and tumour-bearing mice. Many peptides specific to LUAD, including immunogenic peptides, exhibited minimal expression of the cognate mRNA, which prompts the reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance8. Beyond cancer, the KbStrep allele is compatible with other Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease and autoimmunity.
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Affiliation(s)
- Alex M Jaeger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Lauren E Stopfer
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryuhjin Ahn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emma A Sanders
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Demi A Sandel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - William A Freed-Pastor
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - William M Rideout
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Santiago Naranjo
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Tim Fessenden
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Kim B Nguyen
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Peter S Winter
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ryan E Kohn
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Peter M K Westcott
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Jason M Schenkel
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sean-Luc Shanahan
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Alex K Shalek
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of MGH, Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Stefani Spranger
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Forest M White
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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23
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Halima A, Vuong W, Chan TA. Next-generation sequencing: unraveling genetic mechanisms that shape cancer immunotherapy efficacy. J Clin Invest 2022; 132:154945. [PMID: 35703181 PMCID: PMC9197511 DOI: 10.1172/jci154945] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Immunity is governed by fundamental genetic processes. These processes shape the nature of immune cells and set the rules that dictate the myriad complex cellular interactions that power immune systems. Everything from the generation of T cell receptors and antibodies, control of epitope presentation, and recognition of pathogens by the immunoediting of cancer cells is, in large part, made possible by core genetic mechanisms and the cellular machinery that they encode. In the last decade, next-generation sequencing has been used to dissect the complexities of cancer immunity with potent effect. Sequencing of exomes and genomes has begun to reveal how the immune system recognizes “foreign” entities and distinguishes self from non-self, especially in the setting of cancer. High-throughput analyses of transcriptomes have revealed deep insights into how the tumor microenvironment affects immunotherapy efficacy. In this Review, we discuss how high-throughput sequencing has added to our understanding of how immune systems interact with cancer cells and how cancer immunotherapies work.
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Affiliation(s)
- Ahmed Halima
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Winston Vuong
- Department of Radiation Oncology, Taussig Cancer Institute, and
| | - Timothy A Chan
- Department of Radiation Oncology, Taussig Cancer Institute, and.,Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio, USA.,National Center for Regenerative Medicine, Cleveland, Ohio, USA
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24
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Vesely C, Wong YNS, Childs A, Akarca AU, Dhami P, Vaikkinen H, Conde L, Herrero J, Ogunbiyi O, Gander A, Luong TV, Thirlwell C, Caplin M, Toumpanakis C, Peggs K, Quezada SA, Marafioti T, Meyer T. Systematic Evaluation of the Immune Environment of Small Intestinal Neuroendocrine Tumors. Clin Cancer Res 2022; 28:2657-2668. [PMID: 35320356 PMCID: PMC9359734 DOI: 10.1158/1078-0432.ccr-21-4203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/01/2022] [Accepted: 03/21/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE The immune tumor microenvironment and the potential therapeutic opportunities for immunotherapy in small intestinal neuroendocrine tumors (siNET) have not been fully defined. EXPERIMENTAL DESIGN Herein, we studied 40 patients with primary and synchronous metastatic siNETs, and matched blood and normal tissue obtained during surgery. We interrogated the immune checkpoint landscape using multi-parametric flow cytometry. In addition, matched FFPE tissue was obtained for multi-parametric IHC to determine the relative abundance and distribution of T-cell infiltrate. Tumor mutational burden (TMB) was also assessed and correlated with immune infiltration. RESULTS Effector tumor-infiltrating lymphocytes (TIL) had a higher expression of PD-1 in the tumor microenvironment compared with the periphery. In addition, CD8+ TILs had a significantly higher co-expression of PD-1/ICOS and PD-1/CTLA-4 (cytotoxic T lymphocyte antigen-4) and higher levels of PD-1 expression compared with normal tissue. IHC revealed that the majority of cases have ≤10% intra-tumoral T cells but a higher number of peri-tumoral T cells, demonstrating an "exclusion" phenotype. Finally, we confirmed that siNETs have a low TMB compared with other tumor types in the TCGA database but did not find a correlation between TMB and CD8/Treg ratio. CONCLUSIONS Taken together, these results suggest that a combination therapy approach will be required to enhance the immune response, using PD-1 as a checkpoint immunomodulator backbone in combination with other checkpoint targeting molecules (CTLA-4 or ICOS), or with drugs targeting other pathways to recruit "excluded" T cells into the tumor microenvironment to treat patients with siNETs.
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Affiliation(s)
- Clare Vesely
- UCL Cancer Institute, UCL, London, United Kingdom
| | - Yien Ning Sophia Wong
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | - Alexa Childs
- UCL Cancer Institute, UCL, London, United Kingdom.,Royal Free Hospital, Pond Street, London, United Kingdom
| | | | - Pawan Dhami
- UCL Cancer Institute, UCL, London, United Kingdom
| | | | - Lucia Conde
- UCL Cancer Institute, UCL, London, United Kingdom
| | | | | | - Amir Gander
- Royal Free Hospital, Pond Street, London, United Kingdom
| | - Tu Vinh Luong
- Royal Free Hospital, Pond Street, London, United Kingdom
| | - Chrissie Thirlwell
- UCL Cancer Institute, UCL, London, United Kingdom.,The University of Exeter Medical School, Exeter, United Kingdom
| | - Martyn Caplin
- Royal Free Hospital, Pond Street, London, United Kingdom
| | | | - Karl Peggs
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | - Sergio A. Quezada
- UCL Cancer Institute, UCL, London, United Kingdom.,Cancer Immunology Unit, Research Department of Hematology, UCL Cancer Institute, UCL, London, United Kingdom
| | | | - Tim Meyer
- UCL Cancer Institute, UCL, London, United Kingdom.,Royal Free Hospital, Pond Street, London, United Kingdom.,Corresponding Author: Tim Meyer, UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD. Phone: 44-207-679-6731; E-mail;
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25
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Abstract
Two papers published in this edition of Cancer Cell (Zheng et al., 2022 and Veatch et al., 2022) provide an elegant illustration of how single-cell sequencing can be used to define a molecular phenotype which identifies tumor-specific T cells.
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Affiliation(s)
- James Reading
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kane Foster
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Kroopa Joshi
- Department of Medical Oncology, The Royal Marsden NHS Foundation Trust, London, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, UK.
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26
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Neoantigen-specific CD8 T cell responses in the peripheral blood following PD-L1 blockade might predict therapy outcome in metastatic urothelial carcinoma. Nat Commun 2022; 13:1935. [PMID: 35410325 PMCID: PMC9001725 DOI: 10.1038/s41467-022-29342-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/07/2022] [Indexed: 12/14/2022] Open
Abstract
CD8+ T cell reactivity towards tumor mutation-derived neoantigens is widely believed to facilitate the antitumor immunity induced by immune checkpoint blockade (ICB). Here we show that broadening in the number of neoantigen-reactive CD8+ T cell (NART) populations between pre-treatment to 3-weeks post-treatment distinguishes patients with controlled disease compared to patients with progressive disease in metastatic urothelial carcinoma (mUC) treated with PD-L1-blockade. The longitudinal analysis of peripheral CD8+ T cell recognition of patient-specific neopeptide libraries consisting of DNA barcode-labelled pMHC multimers in a cohort of 24 patients from the clinical trial NCT02108652 also shows that peripheral NARTs derived from patients with disease control are characterised by a PD1+ Ki67+ effector phenotype and increased CD39 levels compared to bystander bulk- and virus-antigen reactive CD8+ T cells. The study provides insights into NART characteristics following ICB and suggests that early-stage NART expansion and activation are associated with response to ICB in patients with mUC. Immune checkpoint blockade therapy is successful in a high proportion of cancer patients, but others remain unresponsive. Authors here show that therapeutic success might be predictable in metastatic bladder cancer by longitudinal analysis of the early neoantigen-specific CD8 T cell response in peripheral blood.
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27
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Xia T, Guo J, Zhang B, Xue W, Deng S, Liu Y, Cui B. A Novel Quantification System Combining iTRAQ Technology and Multi-Omics Assessment to Predict Prognosis and Immunotherapy Efficacy in Colon Cancer. Front Bioeng Biotechnol 2022; 10:862619. [PMID: 35445008 PMCID: PMC9014007 DOI: 10.3389/fbioe.2022.862619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Colon cancer is one of the most common cancer types, although it has certain unique genetic features. This study aimed to develop a unique score for assessing prognosis and immunotherapy efficacy using integrated multi-omics analysis.Methods: Isobaric tagging for relative and absolute quantification (iTRAQ) based proteomic analysis was used to screen differentially expressed proteins (DEP) between tumor and normal samples. DEP mRNA obtained from TCGA were clustered into different categories to show landscape-related prognosis and function. Following that, DEG was extracted from DEP mRNA, and the DEP-related score (DEPRS) was constructed to investigate the difference in immunotherapy prognosis and sensitivity. Finally, WCGNA, random forest, and artificial neural networks were used to screen for key genes. The prognostic value and protein level of these genes were validated.Results: A total of 243 DEPs were identified through iTRAQ analysis, and the corresponding DEP mRNA was clustered into three. Following a series of tests, 1,577 DEGs were identified from overlapped DEP mRNA clusters and were classified into three gene clusters. The two types of clusters described above shared comparable characteristics in terms of prognosis and function. Then, it was established that a high DEPRS indicated a poor prognosis and DEPRS had significant associations with TMB, MSI status, and immunotherapeutic response. Finally, the key genes HART3 and FBLN2 were identified and were found to be implicated in immunotherapy and prognosis.Conclusion: The development of a DEPRS based on multi-omics analysis will aid in improving our understanding of colon cancer and guiding a more effective immunotherapy strategy. DEPRS and key genes are used as biomarkers in the clinical evaluation of patients.
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Affiliation(s)
- Tianyi Xia
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
| | - Junnan Guo
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
| | - Bomiao Zhang
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
| | - Weinan Xue
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
| | - Shenhui Deng
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanlong Liu
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
- *Correspondence: Binbin Cui, ; Yanlong Liu,
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin Medial University, Harbin, China
- *Correspondence: Binbin Cui, ; Yanlong Liu,
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28
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Li P, Zhu X, Cao G, Wu R, Li K, Yuan W, Chen B, Sun G, Xia X, Zhang H, Wang X, Yin Z, Lu L, Gao Y. 1α,25(OH) 2D 3 reverses exhaustion and enhances antitumor immunity of human cytotoxic T cells. J Immunother Cancer 2022; 10:jitc-2021-003477. [PMID: 35318258 PMCID: PMC8943781 DOI: 10.1136/jitc-2021-003477] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Epidemiological surveys have revealed that low serum vitamin D level was correlated with increased risk of tumors. Dysfunctional T cells in patients with tumor are characterized as exhausted with high levels of immune checkpoint receptors (ICRs). However, whether the reduced level of vitamin D in patients with cancer correlates with cytotoxic T-cell exhaustion is unknown. METHODS Periphery blood samples from 172 patients with non-small cell lung cancer (NSCLC) were prospectively collected. Patients with NSCLC received one course of intravenous docetaxel (75 mg/m2) followed by treatment with or without rocaltrol at a dose of 0.5-2.0 µg/day for total of 3 weeks. We performed phenotypical and functional analysis of T-cell through flow cytometry. Vitamin D receptor (VDR) knockout and overexpression CD8+ and Vδ2+ T cells were constructed using Cas9-gRNA targeted and overexpressing approaches to identify 1α,25(OH)2D3/VDR-mediated transcription regulation for ICRs or antitumor activity in T cells. RESULTS We show that serum level of vitamin D is negatively correlated with expression of programmed cell death-1 (PD-1), T-cell immunoreceptor with Ig and ITIM domains (TIGIT), and T-cell immunoglobulin and mucin-domain containing-3 (Tim-3), but positively correlated with CD28 expression on CD8+ and Vγ9Vδ2+ T cells in patients with NSCLC. 1α,25(OH)2D3, the active form of vitamin D, promotes the nuclear translocation of VDR, which binds to the promoter region of Pdcd1, Tim3, and Tigit genes and inhibits their expression. Besides, 1α,25(OH)2D3 pretreatment also promotes the methylation of CpG island in the promoter region of the Pdcd1 gene and increases H3K27 acetylation at the promoter region of the Cd28 gene, which leads to surface PD-1 downregulation and CD28 upregulation, respectively. We further reveal that VDR-mediated Ca2+ influx enhanced expression of Th1 cytokines via T-cell receptor activation. Functionally, 1α,25(OH)2D3 pretreated CD8+ T cells or Vγ9Vδ2+ T cells showed increased Th1 cytokine production and enhanced antitumor immunity. Finally, oral 1α,25(OH)2D3 could also decrease expression of PD-1, Tim-3, TIGIT and increase expression of CD28, resulting in cytokine production (associated with antitumor immunity) by cytotoxic T cells of patients with NSCLC. CONCLUSIONS Our findings uncover the pleiotropic effects of 1α,25(OH)2D3 in rescuing the exhausted phenotype of human cytotoxic T cells in patients with tumor and in promoting their antitumor immunity. TRIAL REGISTRATION NUMBER ChiCTR2100051135.
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Affiliation(s)
- Peng Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Xinhai Zhu
- Department of Oncology, First Affiliated Hospital, Jinan University, Jinan University, Guangzhou, Guangdong, China
| | - Guangchao Cao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Ruan Wu
- Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui, China
| | - Ke Li
- Department of Infectious Disease, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Wenhui Yuan
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Biyun Chen
- Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Guodong Sun
- Department of Orthopedics, First Affiliated Hospital, Jinan University, Guangzhou, Guangdong, China
| | - Xichun Xia
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Hua Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Xiao Wang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Zhinan Yin
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China.,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China
| | - Yunfei Gao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai Institute of Translational Medicine, Zhuhai People's Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, China .,The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
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29
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Lowery FJ, Krishna S, Yossef R, Parikh NB, Chatani PD, Zacharakis N, Parkhurst MR, Levin N, Sindiri S, Sachs A, Hitscherich KJ, Yu Z, Vale NR, Lu YC, Zheng Z, Jia L, Gartner JJ, Hill VK, Copeland AR, Nah SK, Masi RV, Gasmi B, Kivitz S, Paria BC, Florentin M, Kim SP, Hanada KI, Li YF, Ngo LT, Ray S, Shindorf ML, Levi ST, Shepherd R, Toy C, Parikh AY, Prickett TD, Kelly MC, Beyer R, Goff SL, Yang JC, Robbins PF, Rosenberg SA. Molecular signatures of antitumor neoantigen-reactive T cells from metastatic human cancers. Science 2022; 375:877-884. [PMID: 35113651 DOI: 10.1126/science.abl5447] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The accurate identification of antitumor T cell receptors (TCRs) represents a major challenge for the engineering of cell-based cancer immunotherapies. By mapping 55 neoantigen-specific TCR clonotypes (NeoTCRs) from 10 metastatic human tumors to their single-cell transcriptomes, we identified signatures of CD8+ and CD4+ neoantigen-reactive tumor-infiltrating lymphocytes (TILs). Neoantigen-specific TILs exhibited tumor-specific expansion with dysfunctional phenotypes, distinct from blood-emigrant bystanders and regulatory TILs. Prospective prediction and testing of 73 NeoTCR signature-derived clonotypes demonstrated that half of the tested TCRs recognized tumor antigens or autologous tumors. NeoTCR signatures identified TCRs that target driver neoantigens and nonmutated viral or tumor-associated antigens, suggesting a common metastatic TIL exhaustion program. NeoTCR signatures delineate the landscape of TILs across metastatic tumors, enabling successful TCR prediction based purely on TIL transcriptomic states for use in cancer immunotherapy.
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Affiliation(s)
- Frank J Lowery
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sri Krishna
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rami Yossef
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Neilesh B Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Praveen D Chatani
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nikolaos Zacharakis
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria R Parkhurst
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Noam Levin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sivasish Sindiri
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abraham Sachs
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kyle J Hitscherich
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhiya Yu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nolan R Vale
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong-Chen Lu
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhili Zheng
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Jia
- National Institutes of Health Library, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jared J Gartner
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Victoria K Hill
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy R Copeland
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shirley K Nah
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert V Masi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Billel Gasmi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Scott Kivitz
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Biman C Paria
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maria Florentin
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanghyun P Kim
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ken-Ichi Hanada
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yong F Li
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lien T Ngo
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Satyajit Ray
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mackenzie L Shindorf
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shoshana T Levi
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan Shepherd
- Vector Production Facility, Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Bethesda, MD 20892, USA
| | - Chris Toy
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anup Y Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Todd D Prickett
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael C Kelly
- Single Cell Analysis Facility, Cancer Research Technology Program, Frederick National Laboratory, Bethesda, MD 20892, USA
| | - Rachel Beyer
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie L Goff
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul F Robbins
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven A Rosenberg
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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30
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Zhang J, Song C, Tian Y, Yang X. Single-Cell RNA Sequencing in Lung Cancer: Revealing Phenotype Shaping of Stromal Cells in the Microenvironment. Front Immunol 2022; 12:802080. [PMID: 35126365 PMCID: PMC8807562 DOI: 10.3389/fimmu.2021.802080] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
The lung tumor microenvironment, which is composed of heterogeneous cell populations, plays an important role in the progression of lung cancer and is closely related to therapeutic efficacy. Increasing evidence has shown that stromal components play a key role in regulating tumor invasion, metastasis and drug resistance. Therefore, a better understanding of stromal components in the tumor microenvironment is helpful for the diagnosis and treatment of lung cancer. Rapid advances in technology have brought our understanding of disease into the genetic era, and single-cell RNA sequencing has enabled us to describe gene expression profiles with unprecedented resolution, enabling quantitative analysis of gene expression at the single-cell level to reveal the correlations among heterogeneity, signaling pathways, drug resistance and microenvironment molding in lung cancer, which is important for the treatment of this disease. In this paper, several common single-cell RNA sequencing methods and their advantages and disadvantages are briefly introduced to provide a reference for selection of suitable methods. Furthermore, we review the latest progress of single-cell RNA sequencing in the study of stromal cells in the lung tumor microenvironment.
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31
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Feng S, Huang C, Guo L, Wang H, Liu H. A novel epithelial-mesenchymal transition-related gene signature for prognosis prediction in patients with lung adenocarcinoma. Heliyon 2022; 8:e08713. [PMID: 35036605 PMCID: PMC8753132 DOI: 10.1016/j.heliyon.2022.e08713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/16/2021] [Accepted: 12/31/2021] [Indexed: 11/16/2022] Open
Abstract
Traditional pathological diagnoses and clinical methods are insufficient to accurately predict the prognosis of lung adenocarcinoma (LUAD). Epithelial-mesenchymal transition (EMT) process is closely related to tumor cell migration. However, the prognostic value of EMT-related genes in LUAD is still unclear. In this study, we collected bulk RNA-sequencing (RNA-seq) and microarray data of LUAD patients from public databases and identified different expressed EMT-related genes in tumor and normal tissues. Then, we used the least absolute shrinkage and selection operator Cox regression model to develop a multigene signature in the cancer genome atlas (TCGA) cohort and validated the model in the OncoSG (Singapore Oncology Data Portal) cohort as well as other datasets. Finally, we constructed a 12-gene signature to divide LUAD patients into high-risk and low-risk groups of overall survival (OS), which has a better stability and accuracy in predicating the OS of patients compared with some other published signatures of LUAD. In addition, evaluation of the risk model using the time-related receiver operating characteristic (ROC) curve confirmed the predictive ability of the model. Functional analysis showed that these genes are related to immunity. CD8 T cell and CD4 T cell types were significantly negatively correlated with the risk score in the analysis of immune infiltration. In general, our model provides useful information that may help clinicians better predict the prognosis of LUAD patients and provides potential targets for immunotherapy of LUAD.
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Affiliation(s)
- Shengyu Feng
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Ce Huang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Liuling Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Hao Wang
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China
| | - Hailiang Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China.,Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, College of Life Sciences, Shihezi University, Shihezi, 832003, China
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32
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Multi-Omics Profiling of the Tumor Microenvironment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:283-326. [DOI: 10.1007/978-3-030-91836-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Federico L, McGrail DJ, Bentebibel SE, Haymaker C, Ravelli A, Forget MA, Karpinets T, Jiang P, Reuben A, Negrao MV, Li J, Khairullah R, Zhang J, Weissferdt A, Vaporciyan AA, Antonoff MB, Walsh G, Lin SY, Futreal A, Wistuba I, Roth J, Byers LA, Gaudreau PO, Uraoka N, Cruz AF, Dejima H, Lazcano RN, Solis LM, Parra ER, Lee JJ, Swisher S, Cascone T, Heymach JV, Zhang J, Sepesi B, Gibbons DL, Bernatchez C. Distinct tumor-infiltrating lymphocyte landscapes are associated with clinical outcomes in localized non-small-cell lung cancer. Ann Oncol 2022; 33:42-56. [PMID: 34653632 PMCID: PMC10019222 DOI: 10.1016/j.annonc.2021.09.021] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/11/2021] [Accepted: 09/30/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Despite the importance of tumor-infiltrating T lymphocytes (TILs) in cancer biology, the relationship between TIL phenotypes and their prognostic relevance for localized non-small-cell lung cancer (NSCLC) has not been well established. PATIENTS AND METHODS Fresh tumor and normal adjacent tissue was prospectively collected from 150 patients with localized NSCLC. Tissue was comprehensively characterized by high-dimensional flow cytometry of TILs integrated with immunogenomic data from multiplex immunofluorescence, T-cell receptor sequencing, exome sequencing, RNA sequencing, targeted proteomics, and clinicopathologic features. RESULTS While neither the magnitude of TIL infiltration nor specific TIL subsets were significantly prognostic alone, the integration of high-dimensional flow cytometry data identified two major immunotypes (IM1 and IM2) that were predictive of recurrence-free survival independent of clinical characteristics. IM2 was associated with poor prognosis and characterized by the presence of proliferating TILs expressing cluster of differentiation 103, programmed cell death protein 1, T-cell immunoglobulin and mucin-domain containing protein 3, and inducible T-cell costimulator. Conversely, IM1 was associated with good prognosis and differentiated by an abundance of CD8+ T cells expressing cytolytic enzymes, CD4+ T cells lacking the expression of inhibitory receptors, and increased levels of B-cell infiltrates and tertiary lymphoid structures. While increased B-cell infiltration was associated with good prognosis, the best prognosis was observed in patients with tumors exhibiting high levels of both B cells and T cells. These findings were validated in patient tumors from The Cancer Genome Atlas. CONCLUSIONS Our study suggests that although the number of infiltrating T cells is not associated with patient survival, the nature of the infiltrating T cells, resolved in distinct TIL immunotypes, is prognostically relevant in NSCLC and may inform therapeutic approaches to clinical care.
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Affiliation(s)
- L Federico
- Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-E Bentebibel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Ravelli
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M-A Forget
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P Jiang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Khairullah
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Weissferdt
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M B Antonoff
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Walsh
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S-Y Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L A Byers
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P-O Gaudreau
- Department of Oncology, Queens' University and the Canadian Cancer Trials Group, Kingston, Canada
| | - N Uraoka
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Cruz
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Dejima
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - L M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E R Parra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J J Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Swisher
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Cascone
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - B Sepesi
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - D L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - C Bernatchez
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
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34
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Testa U, Pelosi E, Castelli G. Molecular charcterization of lung adenocarcinoma combining whole exome sequencing, copy number analysis and gene expression profiling. Expert Rev Mol Diagn 2021; 22:77-100. [PMID: 34894979 DOI: 10.1080/14737159.2022.2017774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Lung cancer is the leading cause of cancer mortality worldwide; lung adenocarcinoma (LUAD) corresponds to about 40% of lung cancers. LUAD is a genetically heterogeneous disease and the definition of this heterogeneity is of fundamental importance for prognosis and treatment. AREAS COVERED Based on primary literature, this review provides an updated analysis of multiomics studies based on the study of mutation profiling, copy number alterations and gene expression allowing for definition of molecular subgroups, prognostic factors based on molecular biomarkers, and identification of therapeutic targets. The authors sum up by providing the reader with their expert opinion on the potentialities of multiomics analysis of LUADs. EXPERT OPINION A detailed and comprehensive study of the co-occurring genetic abnormalities characterizing different LUAD subsets represents a fundamental tool for a better understanding of the disease heterogeneity and for the identification of subgroups of patients responding or resistant to targeted treatments and for the discovery of new therapeutic targets. It is expected that a comprehensive characterization of LUADs may provide a fundamental contribution to improve the survival of LUAD patients.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, Rome, Italy
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35
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Zhang H, Liu C, Li L, Feng X, Wang Q, Li J, Xu S, Wang S, Yang Q, Shen Z, Su J, Su X, Sun R, Zhou X, Wang J, Zhou Y, Jiao B, Ding W, Cao X, Wang Y, Huang Y, Ye L. Genomic evidence of lung carcinogenesis associated with coal smoke in Xuanwei area, China. Natl Sci Rev 2021; 8:nwab152. [PMID: 34987843 PMCID: PMC8692936 DOI: 10.1093/nsr/nwab152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/05/2021] [Accepted: 08/13/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Honglei Zhang
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Chao Liu
- Department of Nuclear Medicine, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Li Li
- Biotherapy Center, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Xu Feng
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Qing Wang
- Department of Oncology, Qujing First People's Hospital, China
| | - Jihua Li
- Qujing Center for Disease Control and Prevention, China
| | - Shaobin Xu
- Supercomputing Platform of Kunming Institute of Zoology, Kunming Biological Diversity Center of Instruments, Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Shuting Wang
- Department of Thoracic Surgery II, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Qianlu Yang
- Department of Thoracic Surgery I, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Zhenghai Shen
- Department of Thoracic Surgery I, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Jinhua Su
- Department of Thoracic Surgery, Xuanwei People's Hospital, China
| | - Xiaosan Su
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Ruifen Sun
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Xuhong Zhou
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Junliang Wang
- Center for Scientific Research, Yunnan University of Chinese Medicine, China
| | - Yongchun Zhou
- Department of Thoracic Surgery I, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Baowei Jiao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, China
| | - Wanbao Ding
- Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, China
| | - Xianbao Cao
- Department of Otolaryngology, First People's Hospital of Yunnan Province, the Affiliated Hospital of Kunming University of Science and Technology, China
| | - Yue Wang
- The Affiliated Hospital of Guizhou Medical University, China
| | - Yunchao Huang
- Department of Thoracic Surgery I, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
| | - Lianhua Ye
- Department of Thoracic Surgery I, Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Hospital, China
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36
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Au L, Hatipoglu E, Robert de Massy M, Litchfield K, Beattie G, Rowan A, Schnidrig D, Thompson R, Byrne F, Horswell S, Fotiadis N, Hazell S, Nicol D, Shepherd STC, Fendler A, Mason R, Del Rosario L, Edmonds K, Lingard K, Sarker S, Mangwende M, Carlyle E, Attig J, Joshi K, Uddin I, Becker PD, Sunderland MW, Akarca A, Puccio I, Yang WW, Lund T, Dhillon K, Vasquez MD, Ghorani E, Xu H, Spencer C, López JI, Green A, Mahadeva U, Borg E, Mitchison M, Moore DA, Proctor I, Falzon M, Pickering L, Furness AJS, Reading JL, Salgado R, Marafioti T, Jamal-Hanjani M, Kassiotis G, Chain B, Larkin J, Swanton C, Quezada SA, Turajlic S. Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma. Cancer Cell 2021; 39:1497-1518.e11. [PMID: 34715028 PMCID: PMC8599450 DOI: 10.1016/j.ccell.2021.10.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 10/06/2021] [Indexed: 02/08/2023]
Abstract
ADAPTeR is a prospective, phase II study of nivolumab (anti-PD-1) in 15 treatment-naive patients (115 multiregion tumor samples) with metastatic clear cell renal cell carcinoma (ccRCC) aiming to understand the mechanism underpinning therapeutic response. Genomic analyses show no correlation between tumor molecular features and response, whereas ccRCC-specific human endogenous retrovirus expression indirectly correlates with clinical response. T cell receptor (TCR) analysis reveals a significantly higher number of expanded TCR clones pre-treatment in responders suggesting pre-existing immunity. Maintenance of highly similar clusters of TCRs post-treatment predict response, suggesting ongoing antigen engagement and survival of families of T cells likely recognizing the same antigens. In responders, nivolumab-bound CD8+ T cells are expanded and express GZMK/B. Our data suggest nivolumab drives both maintenance and replacement of previously expanded T cell clones, but only maintenance correlates with response. We hypothesize that maintenance and boosting of a pre-existing response is a key element of anti-PD-1 mode of action.
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Affiliation(s)
- Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emine Hatipoglu
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Marc Robert de Massy
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Gordon Beattie
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Rachael Thompson
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Nicos Fotiadis
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London SW3 6JJ, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Robert Mason
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sarah Sarker
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Eleanor Carlyle
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Kroopa Joshi
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Imran Uddin
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Pablo D Becker
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Mariana Werner Sunderland
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ayse Akarca
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ignazio Puccio
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - William W Yang
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Tom Lund
- Translational Immune Oncology Lab, Centre for Molecular Pathology, The Royal Marsden Hospital, Sutton SM2 5PT, UK
| | - Kim Dhillon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Marcos Duran Vasquez
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ehsan Ghorani
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - José I López
- Department of Pathology, Cruces University Hospital, Biocruces-Bizkaia Institute, 48903 Barakaldo, Bizkaia, Spain
| | - Anna Green
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Ula Mahadeva
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, St Thomas' Hospital, London SE1 7EH, UK
| | - Elaine Borg
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Miriam Mitchison
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Ian Proctor
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Lisa Pickering
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - James L Reading
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK
| | - Roberto Salgado
- Division of Research, Peter MacCallum Cancer Centre, Melbourne VIC 300, Australia; Department of Pathology, GZA-ZNA Hospitals, Wilrijk, Antwerp, Belgium
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospital, London NW1 2BU, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London NW1 1AT, UK
| | - Benny Chain
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - James Larkin
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London WC1E 6DD, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London WC1E 6DD, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK.
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37
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van der Leun AM, Hoekstra ME, Reinalda L, Scheele CLGJ, Toebes M, van de Graaff MJ, Chen LYY, Li H, Bercovich A, Lubling Y, David E, Thommen DS, Tanay A, van Rheenen J, Amit I, van Kasteren SI, Schumacher TN. Single-cell analysis of regions of interest (SCARI) using a photosensitive tag. Nat Chem Biol 2021; 17:1139-1147. [PMID: 34504322 PMCID: PMC7611907 DOI: 10.1038/s41589-021-00839-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/24/2021] [Indexed: 11/25/2022]
Abstract
The functional activity and differentiation potential of cells are determined by their interactions with surrounding cells. Approaches that allow unbiased characterization of cell states while at the same time providing spatial information are of major value to assess this environmental influence. However, most current techniques are hampered by a tradeoff between spatial resolution and cell profiling depth. Here, we develop a photocage-based technology that allows isolation and in-depth analysis of live cells from regions of interest in complex ex vivo systems, including primary human tissues. The use of a highly sensitive 4-nitrophenyl(benzofuran) cage coupled to a set of nanobodies allows high-resolution photo-uncaging of different cell types in areas of interest. Single-cell RNA-sequencing of spatially defined CD8+ T cells is used to exemplify the feasibility of identifying location-dependent cell states. The technology described here provides a valuable tool for the analysis of spatially defined cells in diverse biological systems, including clinical samples.
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Affiliation(s)
- Anne M van der Leun
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mirjam E Hoekstra
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Luuk Reinalda
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Colinda L G J Scheele
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
- VIB-KULeuven Center for Cancer Biology, Leuven, Belgium
| | - Mireille Toebes
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Michel J van de Graaff
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
- SeraNovo, Leiden, Netherlands
| | - Linda Y Y Chen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Hanjie Li
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Shenzhen Institute of Synthetic Biology, Shenzhen, China
| | - Akhiad Bercovich
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Yaniv Lubling
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daniela S Thommen
- Division of Molecular Oncology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute, Rehovot, Israel
| | - Jacco van Rheenen
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sander I van Kasteren
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands.
| | - Ton N Schumacher
- Division of Molecular Oncology & Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands.
- Department of Hematology, Leiden University Medical Center, Leiden, Netherlands.
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38
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Chow A, Hellmann MD. Insights from prospective multi-omic profiling of lymphocytes in resected lung cancer. Ann Oncol 2021; 33:4-5. [PMID: 34715315 DOI: 10.1016/j.annonc.2021.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 11/01/2022] Open
Affiliation(s)
- A Chow
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Weill Cornell Medical College, New York, USA.
| | - M D Hellmann
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA; Weill Cornell Medical College, New York, USA; Parker Institute for Cancer Immunotherapy, Memorial Sloan Kettering Cancer Center, New York, USA
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39
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Capitani N, Patrussi L, Baldari CT. Nature vs. Nurture: The Two Opposing Behaviors of Cytotoxic T Lymphocytes in the Tumor Microenvironment. Int J Mol Sci 2021; 22:ijms222011221. [PMID: 34681881 PMCID: PMC8540886 DOI: 10.3390/ijms222011221] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 11/16/2022] Open
Abstract
Similar to Janus, the two-faced god of Roman mythology, the tumor microenvironment operates two opposing and often conflicting activities, on the one hand fighting against tumor cells, while on the other hand, favoring their proliferation, survival and migration to other sites to establish metastases. In the tumor microenvironment, cytotoxic T cells-the specialized tumor-cell killers-also show this dual nature, operating their tumor-cell directed killing activities until they become exhausted and dysfunctional, a process promoted by cancer cells themselves. Here, we discuss the opposing activities of immune cells populating the tumor microenvironment in both cancer progression and anti-cancer responses, with a focus on cytotoxic T cells and on the molecular mechanisms responsible for the efficient suppression of their killing activities as a paradigm of the power of cancer cells to shape the microenvironment for their own survival and expansion.
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40
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Dall'Olio FG, Marabelle A, Caramella C, Garcia C, Aldea M, Chaput N, Robert C, Besse B. Tumour burden and efficacy of immune-checkpoint inhibitors. Nat Rev Clin Oncol 2021; 19:75-90. [PMID: 34642484 DOI: 10.1038/s41571-021-00564-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 01/07/2023]
Abstract
Accumulating evidence suggests that a high tumour burden has a negative effect on anticancer immunity. The concept of tumour burden, simply defined as the total amount of cancer in the body, in contrast to molecular tumour burden, is often poorly understood by the wider medical community; nonetheless, a possible role exists in defining the optimal treatment strategy for many patients. Historically, tumour burden has been assessed using imaging. In particular, CT scans have been used to evaluate both the number and size of metastases as well as the number of organs involved. These methods are now often complemented by metabolic tumour burden, measured using the more recently developed 2-deoxy-2-[18F]-fluoro-D-glucose (FDG)-PET/CT. Serum-based biomarkers, such as lactate dehydrogenase, can also reflect tumour burden and are often also correlated with a poor response to immune-checkpoint inhibitors. Other circulating markers (such as circulating free tumour DNA and/or circulating tumour cells) are also attracting research interest as surrogate markers of tumour burden. In this Review, we summarize evidence supporting the utility of tumour burden as a biomarker to guide the use of immune-checkpoint inhibitors. We also describe data and provide perspective on the various tools used for tumour burden assessment, with a particular emphasis on future therapeutic strategies that might address the issue of inferior outcomes among patients with cancer with a high tumour burden.
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Affiliation(s)
- Filippo G Dall'Olio
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France.,Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.,Department of Specialized, Experimental and Diagnostic Medicine, University of Bologna, Bologna, Italy
| | - Aurélien Marabelle
- Drug Development Department, Gustave Roussy, Villejuif, France.,Faculty of Medicine, University Paris-Saclay, Kremlin Bicêtre, France.,Institut national de la santé et de la recherche médicale (INSERM), Gustave Roussy, Villejuif, France
| | - Caroline Caramella
- Department of Radiology, Hôpital Marie Lannelongue, Le Plessis-Robinson, France
| | - Camilo Garcia
- Department of Nuclear Medicine and Endocrine Oncology, Institut Gustave Roussy and University Paris-Saclay, Villejuif, France
| | - Mihaela Aldea
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Nathalie Chaput
- Laboratory of Immunomonitoring in Oncology, Gustave Roussy, Villejuif, France.,Faculty of Pharmacy, University Paris-Saclay, Chatenay-Malabry, France
| | - Caroline Robert
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France.,Faculty of Medicine, University Paris-Saclay, Kremlin Bicêtre, France.,Institut national de la santé et de la recherche médicale (INSERM), Gustave Roussy, Villejuif, France
| | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France. .,Faculty of Medicine, University Paris-Saclay, Kremlin Bicêtre, France.
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41
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Kim N, Eum HH, Lee HO. Clinical Perspectives of Single-Cell RNA Sequencing. Biomolecules 2021; 11:biom11081161. [PMID: 34439827 PMCID: PMC8394304 DOI: 10.3390/biom11081161] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 12/16/2022] Open
Abstract
The ability of single-cell genomics to resolve cellular heterogeneity is highly appreciated in cancer and is being exploited for precision medicine. In the recent decade, we have witnessed the incorporation of cancer genomics into the clinical decision-making process for molecular-targeted therapies. Compared with conventional genomics, which primarily focuses on the specific and sensitive detection of the molecular targets, single-cell genomics addresses intratumoral heterogeneity and the microenvironmental components impacting the treatment response and resistance. As an exploratory tool, single-cell genomics provides an unprecedented opportunity to improve the diagnosis, monitoring, and treatment of cancer. The results obtained upon employing bulk cancer genomics indicate that single-cell genomics is at an early stage with respect to exploration of clinical relevance and requires further innovations to become a widely utilized technology in the clinic.
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Affiliation(s)
- Nayoung Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hye Hyeon Eum
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (N.K.); (H.H.E.)
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
- Correspondence: ; Tel.: +82-2-2258-8155
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42
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Turati VA, Guerra-Assunção JA, Potter NE, Gupta R, Ecker S, Daneviciute A, Tarabichi M, Webster AP, Ding C, May G, James C, Brown J, Conde L, Russell LJ, Ancliff P, Inglott S, Cazzaniga G, Biondi A, Hall GW, Lynch M, Hubank M, Macaulay I, Beck S, Van Loo P, Jacobsen SE, Greaves M, Herrero J, Enver T. Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia. NATURE CANCER 2021; 2:835-852. [PMID: 34734190 PMCID: PMC7611923 DOI: 10.1038/s43018-021-00219-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 05/11/2021] [Indexed: 05/01/2023]
Abstract
Comparison of intratumor genetic heterogeneity in cancer at diagnosis and relapse suggests that chemotherapy induces bottleneck selection of subclonal genotypes. However, evolutionary events subsequent to chemotherapy could also explain changes in clonal dominance seen at relapse. We, therefore, investigated the mechanisms of selection in childhood B-cell precursor acute lymphoblastic leukemia (BCP-ALL) during induction chemotherapy where maximal cytoreduction occurs. To distinguish stochastic versus deterministic events, individual leukemias were transplanted into multiple xenografts and chemotherapy administered. Analyses of the immediate post-treatment leukemic residuum at single-cell resolution revealed that chemotherapy has little impact on genetic heterogeneity. Rather, it acts on extensive, previously unappreciated, transcriptional and epigenetic heterogeneity in BCP-ALL, dramatically reducing the spectrum of cell states represented, leaving a genetically polyclonal but phenotypically uniform population with hallmark signatures relating to developmental stage, cell cycle and metabolism. Hence, canalization of cell state accounts for a significant component of bottleneck selection during induction chemotherapy.
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Affiliation(s)
| | | | | | - Rajeev Gupta
- UCL Cancer Institute, University College London, United Kingdom
| | - Simone Ecker
- UCL Cancer Institute, University College London, United Kingdom
| | | | | | - Amy P. Webster
- UCL Cancer Institute, University College London, United Kingdom
| | - Chuling Ding
- UCL Cancer Institute, University College London, United Kingdom
| | - Gillian May
- UCL Cancer Institute, University College London, United Kingdom
| | - Chela James
- UCL Cancer Institute, University College London, United Kingdom
| | - John Brown
- UCL Cancer Institute, University College London, United Kingdom
| | - Lucia Conde
- UCL Cancer Institute, University College London, United Kingdom
| | - Lisa J. Russell
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, UK
| | - Phil Ancliff
- Great Ormond Street Hospital, London, United Kingdom
| | - Sarah Inglott
- Great Ormond Street Hospital, London, United Kingdom
| | - Giovanni Cazzaniga
- Centro Ricerca M. Tettamanti, University of Milano Bicocca, Monza, Italy
| | - Andrea Biondi
- University of Milano-Bicocca, Department of Pediatrics, Fondazione MBBM/Ospedale San Gerardo, Monza, Italy
| | | | - Mark Lynch
- Fluidigm Corporation, San Francisco, CA, USA
| | - Mike Hubank
- Institute of Cancer Research, Sutton, United Kingdom
- Royal Marsden Hospital, Sutton, United Kingdom
| | | | - Stephan Beck
- UCL Cancer Institute, University College London, United Kingdom
| | | | - Sten E. Jacobsen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
- Center for Hematology and Regenerative Medicine, Department of Medicine and Department of Cell and Molecular Biology, Karolinska Institutet and Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mel Greaves
- Institute of Cancer Research, Sutton, United Kingdom
| | - Javier Herrero
- UCL Cancer Institute, University College London, United Kingdom
| | - Tariq Enver
- UCL Cancer Institute, University College London, United Kingdom
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43
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Quintelier K, Couckuyt A, Emmaneel A, Aerts J, Saeys Y, Van Gassen S. Analyzing high-dimensional cytometry data using FlowSOM. Nat Protoc 2021; 16:3775-3801. [PMID: 34172973 DOI: 10.1038/s41596-021-00550-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/31/2021] [Indexed: 02/06/2023]
Abstract
The dimensionality of cytometry data has strongly increased in the last decade, and in many situations the traditional manual downstream analysis becomes insufficient. The field is therefore slowly moving toward more automated approaches, and in this paper we describe the protocol for analyzing high-dimensional cytometry data using FlowSOM, a clustering and visualization algorithm based on a self-organizing map. FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and can help to gain deeper insights in fields such as immunology and oncology. Since the original FlowSOM publication (2015), we have validated the tool on a wide variety of datasets, and to write this protocol, we made use of this experience to improve the user-friendliness of the package (e.g., comprehensive functions replacing commonly required scripts). Where the original paper focused mainly on the algorithm description, this protocol offers user guidelines on how to implement the procedure, detailed parameter descriptions and troubleshooting recommendations. The protocol provides clearly annotated R code, and is therefore relevant for all scientists interested in computational high-dimensional analyses without requiring a strong bioinformatics background. We demonstrate the complete workflow, starting from data preparation (such as compensation, transformation and quality control), including detailed discussion of the different FlowSOM parameters and visualization options, and concluding with how the results can be further used to answer biological questions, such as statistical comparison between groups of interest. An average FlowSOM analysis takes 1-3 h to complete, though quality issues can increase this time considerably.
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Affiliation(s)
- Katrien Quintelier
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium.,Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Artuur Couckuyt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Annelies Emmaneel
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Joachim Aerts
- Department of Pulmonary Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium.,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium
| | - Sofie Van Gassen
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium. .,Data Mining and Modeling for Biomedicine Group, VIB Center for Inflammation Research, Ghent, Belgium.
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44
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Veatch JR, Simon S, Riddell SR. Tumor-infiltrating lymphocytes make inroads in non-small-cell lung cancer. Nat Med 2021; 27:1339-1341. [PMID: 34385706 DOI: 10.1038/s41591-021-01445-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua R Veatch
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- University of Washington, Seattle, WA, USA
| | - Sylvain Simon
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Stanley R Riddell
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- University of Washington, Seattle, WA, USA.
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45
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Abstract
Next-generation sequencing technologies have revolutionized our ability to catalog the landscape of somatic mutations in tumor genomes. These mutations can sometimes create so-called neoantigens, which allow the immune system to detect and eliminate tumor cells. However, efforts that stimulate the immune system to eliminate tumors based on their molecular differences have had less success than has been hoped for, and there are conflicting reports about the role of neoantigens in the success of this approach. Here we review some of the conflicting evidence in the literature and highlight key aspects of the tumor-immune interface that are emerging as major determinants of whether mutation-derived neoantigens will contribute to an immunotherapy response. Accounting for these factors is expected to improve success rates of future immunotherapy approaches.
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Affiliation(s)
- Andrea Castro
- Biomedical Informatics Program, University of California San Diego, La Jolla, California 92093, USA
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
| | - Maurizio Zanetti
- Department of Medicine, University of California San Diego, La Jolla, California 92093, USA
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, California 92093, USA;
- The Laboratory of Immunology, Moores Cancer Center, University of California San Diego, La Jolla, California 92093, USA
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46
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Wiecek AJ, Jacobson DH, Lason W, Secrier M. Pan-Cancer Survey of Tumor Mass Dormancy and Underlying Mutational Processes. Front Cell Dev Biol 2021; 9:698659. [PMID: 34307377 PMCID: PMC8299471 DOI: 10.3389/fcell.2021.698659] [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: 04/21/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Tumor mass dormancy is the key intermediate step between immune surveillance and cancer progression, yet due to its transitory nature it has been difficult to capture and characterize. Little is understood of its prevalence across cancer types and of the mutational background that may favor such a state. While this balance is finely tuned internally by the equilibrium between cell proliferation and cell death, the main external factors contributing to tumor mass dormancy are immunological and angiogenic. To understand the genomic and cellular context in which tumor mass dormancy may develop, we comprehensively profiled signals of immune and angiogenic dormancy in 9,631 cancers from the Cancer Genome Atlas and linked them to tumor mutagenesis. We find evidence for immunological and angiogenic dormancy-like signals in 16.5% of bulk sequenced tumors, with a frequency of up to 33% in certain tissues. Mutations in the CASP8 and HRAS oncogenes were positively selected in dormant tumors, suggesting an evolutionary pressure for controlling cell growth/apoptosis signals. By surveying the mutational damage patterns left in the genome by known cancer risk factors, we found that aging-induced mutations were relatively depleted in these tumors, while patterns of smoking and defective base excision repair were linked with increased tumor mass dormancy. Furthermore, we identified a link between APOBEC mutagenesis and dormancy, which comes in conjunction with immune exhaustion and may partly depend on the expression of the angiogenesis regulator PLG as well as interferon and chemokine signals. Tumor mass dormancy also appeared to be impaired in hypoxic conditions in the majority of cancers. The microenvironment of dormant cancers was enriched in cytotoxic and regulatory T cells, as expected, but also in macrophages and showed a reduction in inflammatory Th17 signals. Finally, tumor mass dormancy was linked with improved patient survival outcomes. Our analysis sheds light onto the complex interplay between dormancy, exhaustion, APOBEC activity and hypoxia, and sets directions for future mechanistic explorations.
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Affiliation(s)
- Anna Julia Wiecek
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Daniel Hadar Jacobson
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom.,UCL Cancer Institute, Paul O'Gorman Building, University College London, London, United Kingdom
| | - Wojciech Lason
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
| | - Maria Secrier
- Department of Genetics, Evolution and Environment, UCL Genetics Institute, University College London, London, United Kingdom
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47
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Abstract
Oligometastatic non-small cell lung cancer (NSCLC) has been recognized as a unique, yet common, clinical entity over the past 2-3 decades. Numerous retrospective series and early phase single arm trials have demonstrated the efficacy and safety of aggressive approaches in select patients. In addition, results from recent randomized trials have demonstrated potential benefits of radiation therapy and surgery as a form of local ablative therapy (LAT) in prolonging disease-free survival and overall survival. However, more questions remain given the limitation of existing clinical evidence and the lack of well validated biomarkers. Advances in late stage randomized trials with biological correlatives may further clarify the role of LAT to assist with clinical decision making in treating patients with oligometastatic NSCLC. In this review, we discuss the clinical and biologic data surrounding patient selection for LAT in oligometastatic NSCLC, as well as future directions in prospective and translational studies.
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Affiliation(s)
- Xingzhe Li
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Puneeth Iyengar
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX.
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48
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Lee HW. Multidiscipline Immunotherapy-Based Rational Combinations for Robust and Durable Efficacy in Brain Metastases from Renal Cell Carcinoma. Int J Mol Sci 2021; 22:ijms22126290. [PMID: 34208157 PMCID: PMC8230742 DOI: 10.3390/ijms22126290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Advanced imaging techniques for diagnosis have increased awareness on the benefits of brain screening, facilitated effective control of extracranial disease, and prolonged life expectancy of metastatic renal cell carcinoma (mRCC) patients. Brain metastasis (BM) in patients with mRCC (RCC-BM) is associated with grave prognoses, a high degree of morbidity, dedicated assessment, and unresponsiveness to conventional systemic therapeutics. The therapeutic landscape of RCC-BM is rapidly changing; however, survival outcomes remain poor despite standard surgery and radiation, highlighting the unmet medical needs and the requisite for advancement in systemic therapies. Immune checkpoint inhibitors (ICIs) are one of the most promising strategies to treat RCC-BM. Understanding the role of brain-specific tumor immune microenvironment (TIME) is important for developing rationale-driven ICI-based combination strategies that circumvent tumor intrinsic and extrinsic factors and complex positive feedback loops associated with resistance to ICIs in RCC-BM via combination with ICIs involving other immunological pathways, anti-antiangiogenic multiple tyrosine kinase inhibitors, and radiotherapy; therefore, novel combination approaches are being developed for synergistic potential against RCC-BM; however, further prospective investigations with longer follow-up periods are required to improve the efficacy and safety of combination treatments and to elucidate dynamic predictive biomarkers depending on the interactions in the brain TIME.
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Affiliation(s)
- Hye-Won Lee
- Center for Urologic Cancer, National Cancer Center, Department of Urology, Goyang 10408, Korea
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49
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Pasetto A, Lu YC. Single-Cell TCR and Transcriptome Analysis: An Indispensable Tool for Studying T-Cell Biology and Cancer Immunotherapy. Front Immunol 2021; 12:689091. [PMID: 34163487 PMCID: PMC8215674 DOI: 10.3389/fimmu.2021.689091] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/10/2021] [Indexed: 12/18/2022] Open
Abstract
T cells have been known to be the driving force for immune response and cancer immunotherapy. Recent advances on single-cell sequencing techniques have empowered scientists to discover new biology at the single-cell level. Here, we review the single-cell techniques used for T-cell studies, including T-cell receptor (TCR) and transcriptome analysis. In addition, we summarize the approaches used for the identification of T-cell neoantigens, an important aspect for T-cell mediated cancer immunotherapy. More importantly, we discuss the applications of single-cell techniques for T-cell studies, including T-cell development and differentiation, as well as the role of T cells in autoimmunity, infectious disease and cancer immunotherapy. Taken together, this powerful tool not only can validate previous observation by conventional approaches, but also can pave the way for new discovery, such as previous unidentified T-cell subpopulations that potentially responsible for clinical outcomes in patients with autoimmunity or cancer.
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Affiliation(s)
- Anna Pasetto
- Department of Laboratory Medicine, Division of Clinical Microbiology, ANA FUTURA, Karolinska Institutet, Stockholm, Sweden
| | - Yong-Chen Lu
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States.,Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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50
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Abstract
The observation and analysis of intra-tumour heterogeneity (ITH), particularly in genomic studies, has advanced our understanding of the evolutionary forces that shape cancer growth and development. However, only a subset of the variation observed in a single tumour will have an impact on cancer evolution, highlighting the need to distinguish between functional and non-functional ITH. Emerging studies highlight a role for the cancer epigenome, transcriptome and immune microenvironment in functional ITH. Here, we consider the importance of both genetic and non-genetic ITH and their role in tumour evolution, and present the rationale for a broad research focus beyond the cancer genome. Systems-biology analytical approaches will be necessary to outline the scale and importance of functional ITH. By allowing a deeper understanding of tumour evolution this will, in time, encourage development of novel therapies and improve outcomes for patients.
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Affiliation(s)
- James R M Black
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK.
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