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Yang X, Wu C, Liu W, Fu K, Tian Y, Wei X, Zhang W, Sun P, Luo H, Huang J. A clinical-information-free method for early diagnosis of lung cancer from the patients with pulmonary nodules based on backpropagation neural network model. Comput Struct Biotechnol J 2024; 24:404-411. [PMID: 38813092 PMCID: PMC11134880 DOI: 10.1016/j.csbj.2024.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/15/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Lung cancer is the main cause of cancer-related deaths worldwide. Due to lack of obvious clinical symptoms in the early stage of the lung cancer, it is hard to distinguish between malignancy and pulmonary nodules. Understanding the immune responses in the early stage of malignant lung cancer patients may provide new insights for diagnosis. Here, using high-through-put sequencing, we obtained the TCRβ repertoires in the peripheral blood of 100 patients with Stage I lung cancer and 99 patients with benign pulmonary nodules. Our analysis revealed that the usage frequencies of TRBV, TRBJ genes, and V-J pairs and TCR diversities indicated by D50s, Shannon indexes, Simpson indexes, and the frequencies of the largest TCR clone in the malignant samples were significantly different from those in the benign samples. Furthermore, reduced TCR diversities were correlated with the size of pulmonary nodules. Moreover, we built a backpropagation neural network model with no clinical information to identify lung cancer cases from patients with pulmonary nodules using 15 characteristic TCR clones. Based on the model, we have created a web server named "Lung Cancer Prediction" (LCP), which can be accessed at http://i.uestc.edu.cn/LCP/index.html.
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Affiliation(s)
- Xin Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Changchun Wu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wenwen Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Kaiyu Fu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu 610041, China
| | - Yuke Tian
- Department of medical oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Xing Wei
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Wei Zhang
- Department of medical oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Ping Sun
- Department of Health Management Center & Institute of Health Management, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Jian Huang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
- School of Healthcare Technology, Chengdu Neusoft University, Chengdu, Sichuan 611844, China
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Huang AL, He YZ, Yang Y, Pang M, Zheng GP, Wang HL. Exploring the potential of the TCR repertoire as a tumor biomarker (Review). Oncol Lett 2024; 28:413. [PMID: 38988449 PMCID: PMC11234811 DOI: 10.3892/ol.2024.14546] [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: 02/29/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024] Open
Abstract
T cells play an important role in adaptive immunity. Mature T cells specifically recognize antigens on major histocompatibility complex molecules through T-cell receptors (TCRs). As the TCR repertoire is highly diverse, its analysis is vital in the assessment of T cells. Advances in sequencing technology have provided convenient methods for further investigation of the TCR repertoire. In the present review, the TCR structure and the mechanisms by which TCRs function in tumor recognition are described. In addition, the potential value of the TCR repertoire in tumor diagnosis is reviewed. Furthermore, the role of the TCR repertoire in tumor immunotherapy is introduced, and the relationships between the TCR repertoire and the effects of different tumor immunotherapies are discussed. Based on the reviewed literature, it may be concluded that the TCR repertoire has the potential to serve as a biomarker for tumor prognosis. However, a wider range of cancer types and more diverse subjects require evaluation in future research to establish the TCR repertoire as a biomarker of tumor immunity.
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Affiliation(s)
- An-Li Huang
- Institute of Cancer Biology, Basic Medical Sciences Center, School of Basic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
- The First Clinical Medical College, Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
| | - Yan-Zhao He
- Institute of Cancer Biology, Basic Medical Sciences Center, School of Basic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
| | - Yong Yang
- Institute of Cancer Biology, Basic Medical Sciences Center, School of Basic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
| | - Min Pang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Province Key Laboratory of Respiratory Disease, Department of Pulmonary and Critical Care Medicine, The First Hospital, Shanxi Medical University, Taiyuan, Shanxi 030001, P.R. China
| | - Guo-Ping Zheng
- Centre for Transplantation and Renal Research, Westmead Millennium Institute, University of Sydney, Sydney, New South Wales 2145, Australia
| | - Hai-Long Wang
- Institute of Cancer Biology, Basic Medical Sciences Center, School of Basic Medicine, Shanxi Medical University, Jinzhong, Shanxi 030600, P.R. China
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Cerapio JP, Gravelle P, Quillet-Mary A, Valle C, Martins F, Franchini DM, Syrykh C, Brousset P, Traverse-Glehen A, Ysebaert L, Fournie JJ, Laurent C. Integrated spatial and multimodal single-cell transcriptomics reveal patient-dependent cell heterogeneity in splenic marginal zone lymphoma. J Pathol 2024; 263:442-453. [PMID: 38828498 DOI: 10.1002/path.6296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/22/2023] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Abstract
Biological hallmarks of splenic marginal zone lymphoma (SMZL) remain poorly described. Herein, we performed in-depth SMZL characterization through multimodal single-cell analyses of paired blood/spleen samples. The 3'-single-cell RNA-sequencing, Cellular Indexing of Transcriptomes and Epitopes by sequencing, and 5'-V(D)J single-cell RNA-sequencing datasets were integrated to characterize SMZL transcriptome profiles, including B-cell receptor and T-cell receptor repertoires. Hyperexpanded B-cell clones in the spleen were at a memory-like stage, whereas recirculating tumor B-cells in blood encompassed multiple differentiation stages, indicating an unexpected desynchronization of the B-cell maturation program in SMZL cells. Spatial transcriptomics showed the enrichment of T-effector and T-follicular helper (TFH) signatures in the nodular subtype of SMZL. This latter also exhibited gene-based cell-cell interactions suggestive of dynamic crosstalk between TFH and cancer cells in transcriptomics, further substantiated by using imaging mass cytometry. Our findings provide a comprehensive high-resolution description of SMZL biological hallmarks and characterize, for the first time in situ, inter- and intra-patient heterogeneity at both transcriptomic and protein levels. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Juan Pablo Cerapio
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
| | - Pauline Gravelle
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Anne Quillet-Mary
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
| | - Carine Valle
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
| | - Frederic Martins
- Institut Maladies Metaboliques et Cardiovasculaires, INSERM UMR1297, Toulouse, France
| | - Don-Marc Franchini
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Charlotte Syrykh
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Pierre Brousset
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | | | - Loic Ysebaert
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
| | - Jean-Jacques Fournie
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
| | - Camille Laurent
- Université de Toulouse, INSERM UMR1037, CNRS UMR5071, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, Toulouse, France
- Institut Universitaire du Cancer-Oncopole de Toulouse, Toulouse, France
- Laboratoire d'Excellence 'TOUCAN-2', Toulouse, France
- Institut Carnot Lymphome - ADREP CALYM, Paris, France
- Centre Hospitalier Universitaire, Toulouse, France
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Clark EA, Talatala ER, Ye W, Davis RJ, Collins SL, Hillel AT, Ramirez-Solano M, Sheng Q, Wanjalla CN, Mallal SA, Gelbard A. Characterizing the T Cell Repertoire in the Proximal Airway in Health and Disease. Laryngoscope 2024; 134:1757-1764. [PMID: 37787469 PMCID: PMC10947968 DOI: 10.1002/lary.31088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/04/2023]
Abstract
OBJECTIVES Recent translational scientific efforts in subglottic stenosis (SGS) support a disease model where epithelial alterations facilitate microbiome displacement, dysregulated immune activation, and localized fibrosis. Given the observed immune cell infiltrate in SGS, we sought to test the hypothesis that SGS cases possessed a low diversity (highly clonal) adaptive immune response when compared with healthy controls. METHODS Single cell RNA sequencing (scRNA-seq) of subglottic mucosal scar in iSGS (n = 24), iLTS (n = 8), and healthy controls (n = 7) was performed. T cell receptor (TCR) sequences were extracted, analyzed, and used to construct repertoire structure, compare diversity, interrogate overlap, and define antigenic targets using the Immunarch bioinformatics pipeline. RESULTS The proximal airway mucosa in health and disease are equally diverse via Hill framework quantitation (iSGS vs. iLTS vs. Control, p > 0.05). Repertoires do not significantly overlap between individuals (Morisita <0.02). Among iSGS patients, clonality of the TCR repertoire is driven by CD8+ T cells, and iSGS patients possess numerous TCRs targeting viral and intercellular pathogens. High frequency clonotypes do not map to known targets in public datasets. CONCLUSION SGS cases do not possess a lower diversity adaptive immune infiltrate when compared with healthy controls. Interestingly, the TCR repertoire in both health and disease contains a restricted number of high frequency clonotypes that do not significantly overlap between individuals. The target of the high frequency clonotypes in health and disease remain unresolved. LEVEL OF EVIDENCE NA Laryngoscope, 134:1757-1764, 2024.
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Affiliation(s)
- Evan A. Clark
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Edward R.R. Talatala
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Wenda Ye
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Ruth J. Davis
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Samuel L. Collins
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Alexander T. Hillel
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | - Celestine N. Wanjalla
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Simon A. Mallal
- Department of Medicine, Division of Infectious Disease, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Alexander Gelbard
- Department of Otolaryngology-Head & Neck Surgery, Vanderbilt University Medical Center, Nashville, TN
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5
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Zhang J, Wang Y, Huang Y, Tan X, Xu J, Yan Q, Tan J, Zhang Y, Zhang J, Ma Q, Zhu H, Ye J, Zhu Z, Lan W. Characterization of T cell receptor repertoire in penile cancer. Cancer Immunol Immunother 2024; 73:24. [PMID: 38280010 PMCID: PMC10822009 DOI: 10.1007/s00262-023-03615-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/04/2023] [Indexed: 01/29/2024]
Abstract
Tumor-infiltrating lymphocytes (TILs) play a key role in regulating the host immune response and shaping tumor microenvironment. It has been previously shown that T cell infiltration in penile tumors was associated with clinical outcomes. However, few studies have reported the T cell receptor (TCR) repertoire in patients with penile cancer. In the present study, we evaluated the TCR repertoires in tumor and adjacent normal tissues from 22 patients with penile squamous cell carcinoma (PSCC). Analysis of the T cell receptor beta-variable (TRBV) and joining (TRBJ) genes usage and analysis of complementarity determining region 3 (CDR3) length distribution did not show significant differences between tumor and matched normal tissues. Moreover, analysis of the median Jaccard index indicated a limited overlap of TCR repertoire between these groups. Compared with normal tissues, a significantly lower diversity and higher clonality of TCR repertoire was observed in tumor samples, which was associated with clinical characteristics. Further analysis of transcriptional profiles demonstrated that tumor samples with high clonality showed increased expression of genes associated with CD8 + T cells. In addition, we analyzed the TCR repertoire of CD4 + T cells and CD8 + T cells isolated from tumor tissues. We identified that expanded clonotypes were predominantly in the CD8 + T cell compartment, which presented with an exhausted phenotype. Overall, we comprehensively compared TCR repertoire between penile tumor and normal tissues and demonstrated the presence of distinct T cell immune microenvironments in patients with PSCC.
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Affiliation(s)
- Junying Zhang
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Yapeng Wang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Yiqiang Huang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Xintao Tan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jing Xu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Qian Yan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jiao Tan
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China
| | - Yao Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jun Zhang
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Qiang Ma
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Hailin Zhu
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China
| | - Jin Ye
- Urinary Nephropathy Center, The Thirteenth People's Hospital of Chongqing, Chongqing, 400053, People's Republic of China.
| | - Zhaojing Zhu
- Chongqing Key Laboratory of High Active Traditional Chinese Drug Delivery System, Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, 401331, People's Republic of China.
| | - Weihua Lan
- Department of Urology, Daping Hospital, Army Medical University, Chongqing, 400042, People's Republic of China.
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Abed A, Beasley AB, Reid AL, Law N, Calapre L, Millward M, Lo J, Gray ES. Circulating pre-treatment T-cell receptor repertoire as a predictive biomarker in advanced or metastatic non-small-cell lung cancer patients treated with pembrolizumab alone or in combination with chemotherapy. ESMO Open 2023; 8:102066. [PMID: 37995426 PMCID: PMC10774950 DOI: 10.1016/j.esmoop.2023.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The circulating T-cell receptor (TCR) repertoire is a dynamic representation of overall immune responses in an individual. MATERIALS AND METHODS We prospectively collected baseline blood from patients treated with first-line pembrolizumab monotherapy or in combination with chemotherapy. TCR repertoire metrics were correlated with clinical benefit rate (CBR), progression-free survival (PFS), overall survival (OS) and immune-related adverse events (irAEs). We built a logistic regression classifier by fitting all four TCR-β repertoire metrics to the immune checkpoint inhibitor (ICI) CBR data. In the subsequent receiver operating characteristic (ROC) analysis of the resulting logistic regression model probabilities, the best cut-off value was selected to maximise sensitivity to predict CBR to ICI. RESULTS We observed an association between reduced number of unique clones and CBR among patients treated with pembrolizumab monotherapy (cohort 1) [risk ratio = 2.86, 95% confidence interval (CI) 1.04-8.73, P = 0.039]. For patients treated with pembrolizumab plus chemotherapy (cohort 2), increased number of unique clones [hazard ratio (HR) = 2.96, 95% CI 1.28-6.88, P = 0.012] and Shannon diversity (HR = 2.73, 95% CI 1.08-6.87, P = 0.033), and reduced evenness (HR = 0.43, 95% CI 0.21-0.90, P = 0.025) and convergence (HR = 0.41, 95% CI 0.19-0.90, P = 0.027) were associated with improved PFS, while only an increased number of unique clones (HR = 4.62, 95% CI 1.52-14.02, P = 0.007) were associated with improved OS. Logistic regression models combining the TCR repertoire metrics improved the prediction of CBR (cohorts 1 and 2) and were strongly associated with PFS (cohort 1, HR = 0.38, 95% CI 0.19-0.78, P = 0.009) and OS (cohort 2, HR = 0.20, 95% CI 0.05-0.76, P < 0.0001). Reduced TCR conversion was associated with increased frequency of irAEs needing systemic steroid treatment. CONCLUSION Combined pre-treatment circulating TCR metrics might serve as a predictive biomarker for clinical outcomes among patients with advanced non-small-cell lung cancer treated with pembrolizumab alone or in combination with chemotherapy.
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Affiliation(s)
- A Abed
- Centre for Precision Health, Edith Cowan University, Joondalup; School of Medical and Health Sciences, Edith Cowan University, Joondalup; School of Medicine, University of Western Australia, Crawley.
| | - A B Beasley
- Centre for Precision Health, Edith Cowan University, Joondalup; School of Medical and Health Sciences, Edith Cowan University, Joondalup
| | - A L Reid
- Centre for Precision Health, Edith Cowan University, Joondalup; School of Medical and Health Sciences, Edith Cowan University, Joondalup
| | - N Law
- Department of Medical Oncology, Sir Charles Gairdner Hospital, Nedlands
| | - L Calapre
- Centre for Precision Health, Edith Cowan University, Joondalup; School of Medical and Health Sciences, Edith Cowan University, Joondalup
| | - M Millward
- School of Medicine, University of Western Australia, Crawley
| | - J Lo
- School of Science, Edith Cowan University, Joondalup, Australia
| | - E S Gray
- Centre for Precision Health, Edith Cowan University, Joondalup; School of Medical and Health Sciences, Edith Cowan University, Joondalup.
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Chen H, Xu S, Zhang Y, Chen P. Systematic analysis of lncRNA gene characteristics based on PD-1 immune related pathway for the prediction of non-small cell lung cancer prognosis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9818-9838. [PMID: 37322912 DOI: 10.3934/mbe.2023430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is heterogeneous. Molecular subtyping based on the gene expression profiles is an effective technique for diagnosing and determining the prognosis of NSCLC patients. METHODS Here, we downloaded the NSCLC expression profiles from The Cancer Genome Atlas and the Gene Expression Omnibus databases. ConsensusClusterPlus was used to derive the molecular subtypes based on long-chain noncoding RNA (lncRNA) associated with the PD-1-related pathway. The LIMMA package and least absolute shrinkage and selection operator (LASSO)-Cox analysis were used to construct the prognostic risk model. The nomogram was constructed to predict the clinical outcomes, followed by decision curve analysis (DCA) to validate the reliability of this nomogram. RESULTS We discovered that PD-1 was strongly and positively linked to the T-cell receptor signaling pathway. Furthermore, we identified two NSCLC molecular subtypes yielding a significantly distinctive prognosis. Subsequently, we developed and validated the 13-lncRNA-based prognostic risk model in the four datasets with high AUC values. Patients with low-risk showed a better survival rate and were more sensitive to PD-1 treatment. Nomogram construction combined with DCA revealed that the risk score model could accurately predict the prognosis of NSCLC patients. CONCLUSIONS This study demonstrated that lncRNAs engaged in the T-cell receptor signaling pathway played a significant role in the onset and development of NSCLC, and that they could influence the sensitivity to PD-1 treatment. In addition, the 13 lncRNA model was effective in assisting clinical treatment decision-making and prognosis evaluation.
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Affiliation(s)
- Hejian Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
| | - Shuiyu Xu
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Yuhong Zhang
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Peifeng Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
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8
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Høye E, Dagenborg VJ, Torgunrud A, Lund-Andersen C, Fretland ÅA, Lorenz S, Edwin B, Hovig E, Fromm B, Inderberg EM, Greiff V, Ree AH, Flatmark K. T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases. Gigascience 2022; 12:giad032. [PMID: 37161965 PMCID: PMC10170408 DOI: 10.1093/gigascience/giad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 02/07/2023] [Accepted: 04/25/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite-stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumor-infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T-cell infiltration in CLM using T-cell receptor (TCR) repertoire sequencing. Eighty-five resected CLMs from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T-cell fractions were calculated, repertoire clonality was analyzed based on Hill evenness curves, and TCR sequence convergence was assessed using network analysis. RESULTS Increased T-cell fractions (10.6% vs. 6.3%) were detected in CLMs exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT-exposed tumors independently of the timing of NACT administration and surgery. While private clones made up >90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence. CONCLUSIONS TCR repertoire sequencing can be used to quantify T-cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T-cell clonal expansion in CLM in a clinical context.
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Affiliation(s)
- Eirik Høye
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
| | - Vegar J Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Department of Gastroenterological Surgery, The Norwegian Radium Hospital, 0379 Oslo, Norway
| | - Annette Torgunrud
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Christin Lund-Andersen
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
| | - Åsmund A Fretland
- The Intervention Centre, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
- Department of Hepato-Pancreato-Biliary Surgery, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
| | - Susanne Lorenz
- Department of Core Facilities, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
| | - Bjørn Edwin
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- The Intervention Centre, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
- Department of Hepato-Pancreato-Biliary Surgery, Rikshospitalet, Oslo University Hospital, 0372 Oslo, Norway
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
| | - Bastian Fromm
- The Arctic University Museum of Norway, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Else M Inderberg
- Translational Research Unit, Department of Cellular Therapy, Oslo University Hospital, 0379 Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Anne H Ree
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- Department of Oncology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0379 Oslo, Norway
- Institute of Clinical Medicine, Medical Faculty, University of Oslo, 0318 Oslo, Norway
- Department of Gastroenterological Surgery, The Norwegian Radium Hospital, 0379 Oslo, Norway
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9
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Wang M, Gao P, Ren L, Duan J, Yang S, Wang H, Wang H, Sun J, Gao X, Li B, Li S, Su W. Profiling the peripheral blood T cell receptor repertoires of gastric cancer patients. Front Immunol 2022; 13:848113. [PMID: 35967453 PMCID: PMC9367216 DOI: 10.3389/fimmu.2022.848113] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/04/2022] [Indexed: 12/24/2022] Open
Abstract
Cancer driven by somatic mutations may express neoantigens that can trigger T-cell immune responses. Since T-cell receptor (TCR) repertoires play critical roles in anti-tumor immune responses for oncology, next-generation sequencing (NGS) was used to profile the hypervariable complementarity-determining region 3 (CDR3) of the TCR-beta chain in peripheral blood samples from 68 gastric cancer patients and 49 healthy controls. We found that most hyper-expanded CDR3 are individual-specific, and the gene usage of TRBV3-1 is more frequent in the tumor group regardless of tumor stage than in the healthy control group. We identified 374 hyper-expanded tumor-specific CDR3, which may play a vital role in anti-tumor immune responses. The patients with stage IV gastric cancer have higher EBV-specific CDR3 abundance than the control. In conclusion, analysis of the peripheral blood TCR repertoires may provide the biomarker for gastric cancer prognosis and guide future immunotherapy.
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Affiliation(s)
- Mengyao Wang
- Department of Computer Science, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | | | - Laifeng Ren
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jingjing Duan
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Silu Yang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Haina Wang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Hongxia Wang
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Junning Sun
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | | | - Bo Li
- BGI-Shenzhen, Shenzhen, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
- *Correspondence: Wen Su, ; Shuaicheng Li,
| | - Wen Su
- Department of Immunology, Shanxi Province Cancer Hospital/ Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
- *Correspondence: Wen Su, ; Shuaicheng Li,
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10
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Wang X, Muzaffar J, Kirtane K, Song F, Johnson M, Schell MJ, Li J, Yoder SJ, Conejo-Garcia JR, Guevara-Patino JA, Bonomi M, Bhateja P, Rocco JW, Steuer CE, Saba NF, Chung CH. T cell repertoire in peripheral blood as a potential biomarker for predicting response to concurrent cetuximab and nivolumab in head and neck squamous cell carcinoma. J Immunother Cancer 2022; 10:e004512. [PMID: 35676062 PMCID: PMC9185557 DOI: 10.1136/jitc-2022-004512] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND T cell receptor (TCR) signaling profile is a fundamental property that underpins both adaptive and innate immunity in the host. Despite its potential clinical relevance, the TCR repertoire in peripheral blood has not been thoroughly explored for its value as an immunotherapy efficacy biomarker in head and neck squamous cell carcinoma (HNSCC). The purpose of the present study is to characterize and compare the TCR repertoire in peripheral blood mononuclear cells (PBMC) from patients with HNSCC treated with the combination of cetuximab and nivolumab. METHODS We used the immunoSEQ assay to sequence the TCR beta (TCR-B) chain repertoire from serially obtained PBMC at baseline and during the treatments from a total of 41 patients who received the combination (NCT03370276). Key TCR repertoire metrics, including diversity and clonality, were calculated and compared between patients with different therapy responses and clinical characteristics (eg, human papillomavirus (HPV) status and smoking history). Patient survival outcomes were compared according to patient groups stratified by the TCR-B clonotyping. To confirm the observed patterns in TCR spectrum, samples from patients who achieved complete response (CR) and partial response (PR) were further profiled with the immunoSEQ deep resolution assay. RESULTS Our data indicated that the patients who achieved CR and PR had an increased TCR sequence diversity in their baseline samples, this tendency being more pronounced in HPV-negative patients or those with a smoking history. Notably, the CR/PR group had the lowest proportion of patients with oligoclonal TCR clones (2 out of 8 patients), followed by the stable disease group (9 out of 20 patients) and lastly the progressive disease group (7 out of 10 patients). An overall trend toward favorable patient survival was also observed in the polyclonal group. Finally, we reported the shared TCR clones across patients within the same response group, as well as the shared clones by aligning immunoSEQ reads with TCR data retrieved from The Cancer Genome Atlas- head and neck squamous cell carcinoma (TCGA-HNSC) cohort. CONCLUSIONS Our data suggest that, despite the great clinical heterogeneity of HNSCC and the limited responders in the present cohort, the peripheral TCR repertoires from pretreatment PBMC may be developed as biomarkers for the benefit of immunotherapy in HNSCC.
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Affiliation(s)
- Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Jameel Muzaffar
- Department of Head and Neck-Endocrine Oncology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Kedar Kirtane
- Department of Head and Neck-Endocrine Oncology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Feifei Song
- Department of Head and Neck-Endocrine Oncology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Matthew Johnson
- Department of Head and Neck-Endocrine Oncology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Jiannong Li
- Department of Biostatistics and Bioinformatics, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Sean J Yoder
- Department of Molecular Genomics Core, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Jose R Conejo-Garcia
- Department of Immunology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Jose A Guevara-Patino
- Department of Immunology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
| | - Marcelo Bonomi
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Priyanka Bhateja
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - James W Rocco
- Department of Otolaryngology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Conor E Steuer
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H Lee Moffitt Cancer Center and Research Center Inc, Tampa, Florida, USA
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11
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He T, Baik JM, Kato C, Yang H, Fan Z, Cham J, Zhang L. Novel Ensemble Feature Selection Approach and Application in Repertoire Sequencing Data. Front Genet 2022; 13:821832. [PMID: 35559031 PMCID: PMC9086194 DOI: 10.3389/fgene.2022.821832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/25/2022] [Indexed: 01/18/2023] Open
Abstract
The T and B cell repertoire make up the adaptive immune system and is mainly generated through somatic V(D)J gene recombination. Thus, the VJ gene usage may be a potential prognostic or predictive biomarker. However, analysis of the adaptive immune system is challenging due to the heterogeneity of the clonotypes that make up the repertoire. To address the heterogeneity of the T and B cell repertoire, we proposed a novel ensemble feature selection approach and customized statistical learning algorithm focusing on the VJ gene usage. We applied the proposed approach to T cell receptor sequences from recovered COVID-19 patients and healthy donors, as well as a group of lung cancer patients who received immunotherapy. Our approach identified distinct VJ genes used in the COVID-19 recovered patients comparing to the healthy donors and the VJ genes associated with the clinical response in the lung cancer patients. Simulation studies show that the ensemble feature selection approach outperformed other state-of-the-art feature selection methods based on both efficiency and accuracy. It consistently yielded higher stability and sensitivity with lower false discovery rates. When integrated with different classification methods, the ensemble feature selection approach had the best prediction accuracy. In conclusion, the proposed novel approach and the integration procedure is an effective feature selection technique to aid in correctly classifying different subtypes to better understand the signatures in the adaptive immune response associated with disease or the treatment in order to improve treatment strategies.
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Affiliation(s)
- Tao He
- Department of Mathematics, San Francisco State University, San Francisco, CA, United States
| | - Jason Min Baik
- Department of Mathematics, San Francisco State University, San Francisco, CA, United States
| | - Chiemi Kato
- Department of Mathematics, San Francisco State University, San Francisco, CA, United States
| | - Hai Yang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
| | - Zenghua Fan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jason Cham
- Department of Medicine, Scripps Green Hospital, La Jolla, CA, United States
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, United States
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12
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Wang Z, Zhong Y, Zhang Z, Zhou K, Huang Z, Yu H, Liu L, Liu S, Yang H, Zhou J, Fan J, Wu L, Sun Y. Characteristics and Clinical Significance of T-Cell Receptor Repertoire in Hepatocellular Carcinoma. Front Immunol 2022; 13:847263. [PMID: 35371059 PMCID: PMC8965762 DOI: 10.3389/fimmu.2022.847263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Several studies have demonstrated that the T-cell receptor (TCR) repertoire is associated with prognosis and immune therapy response in several types of cancer. However, the comprehensive features of TCR repertoire in tumor-infiltrating and circulating T cells, as well as its clinical significance of diagnosis in hepatocellular carcinoma (HCC) patients, are still unknown. In this study, we perform paired tumor/peritumoral tissues and peripheral blood samples from 58 patients with HCC and sequenced them with high-throughput TCR to comprehensively analyze the characteristics of TCR and the clinical significance of peripheral TCR sequence. By exploring the abundance and diversity of TCR repertoires, we observe that there was a significantly higher TCR diversity in peripheral blood than in tumoral and peritumoral tissues, while tumoral and peritumoral tissues showed similar TCR diversity. A substantial difference in the usage frequencies of several Vβ, Jβ genes, and TCRβ VJ pairings was found among three types of tissues. Moreover, we reveal that HCC patients have a unique profile of TCR repertoire in peripheral blood in contrast to healthy individuals. We further establish an HCC diagnostic model based on TCRβ VJ pairing usage in peripheral blood, which yields a best-fit area under the curve (AUC) of 0.9746 ± 0.0481 (sensitivity = 0.9675 ± 0.0603, specificity = 0.9998 ± 0.0007, average of 100 repeats) in the test set. Our study describes the characteristics of tissue infiltration and circulating T-cell bank in patients with HCC and shows the potential of using circulating TCR sequence as a biomarker for the non-invasive diagnosis of patients with HCC.
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Affiliation(s)
- Zifei Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
| | - Yu Zhong
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
| | - Zefan Zhang
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Kaiqian Zhou
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Zhihao Huang
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Hao Yu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
| | - Longqi Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, China
| | - Shiping Liu
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhou
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Jia Fan
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
| | - Liang Wu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute at Shenzhen, Shenzhen, China
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, Shenzhen, China
| | - Yunfan Sun
- Zhong-Hua Precision Medical Center, Zhongshan Hospital, Fudan University-BGI, Shanghai, China
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai, China
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13
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Cai G, Guan Z, Jin Y, Su Z, Chen X, Liu Q, Wang C, Yin X, Zhang L, Ye G, Luo W. Circulating T-Cell Repertoires Correlate With the Tumor Response in Patients With Breast Cancer Receiving Neoadjuvant Chemotherapy. JCO Precis Oncol 2022; 6:e2100120. [PMID: 35025620 PMCID: PMC8769146 DOI: 10.1200/po.21.00120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 10/11/2021] [Accepted: 12/10/2021] [Indexed: 12/28/2022] Open
Abstract
PURPOSE Neoadjuvant chemotherapy (NAC) has been widely used in patients with breast cancer to minish tumor burden and increase resection rate of cancer. T-cell repertoire has been believed to be able to monitor antitumor immune responses. This study aimed to explore the dynamic change of T-cell repertoire and its clinical value in evaluating the tumor response in patients with breast cancer receiving NAC. MATERIALS AND METHODS Ninety-four patients who underwent NAC before surgery were recruited, and peripheral blood samples were collected at multiple time points during NAC. High-throughput T-cell receptor (TCR)-β sequencing was used to characterize the T-cell repertoire of every sample and analyzed the changes in circulating T-cell repertoire during NAC. RESULTS We found that the diversity of TCR repertoires was associated with age and clinical stage of the patients with breast cancer. The distribution of Vβ and Jβ genes in TCR repertoires was skewed in patients with human epidermal growth factor receptor 2-positive (HER2+) breast cancer. Vβ20.1 and Vβ30 expression levels before NAC correlate with tumor response after all cycles of NAC in HER2- and HER2+ patients, respectively. Some CDR3 motifs that correlated with clinical response in either HER2+ or HER2- patients were identified. Besides, TCR repertoire evolved during NAC and the diversity of TCR repertoire decreased more after two cycles of NAC in patients with good tumor response after all cycles of NAC (P = .0061). CONCLUSION Our results demonstrated that TCR repertoire correlated with the characteristics of the tumor, such as the expression status of HER2. Moreover, some characteristics of TCR repertoires that correlated with clinical response were identified and they might provide useful information to tailor therapeutic regimens at the early cycle of NAC.
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Affiliation(s)
- Gengxi Cai
- The First People's Hospital of Foshan, Foshan, China
| | - Zhanwen Guan
- The First People's Hospital of Foshan, Foshan, China
| | - Yabin Jin
- The First People's Hospital of Foshan, Foshan, China
| | - Zuhui Su
- The First People's Hospital of Foshan, Foshan, China
| | | | - Qing Liu
- The First People's Hospital of Foshan, Foshan, China
| | | | - Xiaoxia Yin
- Cyberspace Institute of Advanced Technology, Guangzhou University, Guangzhou, China
| | - Lifang Zhang
- The First People's Hospital of Foshan, Foshan, China
| | - Guolin Ye
- The First People's Hospital of Foshan, Foshan, China
| | - Wei Luo
- The First People's Hospital of Foshan, Foshan, China
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14
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Leem G, Jeon M, Kim KW, Jeong S, Choi SJ, Lee YJ, Kim ES, Lee JI, Ha SY, Park SH, Shim HS, Lee JG, Kang SM, Shin EC. Tumour-infiltrating bystander CD8 + T cells activated by IL-15 contribute to tumour control in non-small cell lung cancer. Thorax 2021; 77:769-780. [PMID: 34853159 DOI: 10.1136/thoraxjnl-2021-217001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 11/08/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Tumour-unrelated, virus-specific bystander CD8+ T cells were recently shown to be abundant among tumour-infiltrating lymphocytes (TILs). However, their roles in tumour immunity have not been elucidated yet. METHODS We studied the characteristics of bystander CD8+ TILs from non-small cell lung cancer (NSCLC) tissues (N=66) and their activation by interleukin (IL)-15 to repurpose them for tumour immunotherapy. RESULTS We show that bystander CD8+ TILs specific to various viruses are present in human NSCLC tissues. We stimulated CD8+ TILs ex vivo using IL-15 without cognate antigens and found that IL-15 treatment upregulated NKG2D expression on CD8+ TILs, resulting in NKG2D-dependent production of interferon (IFN)-γ (p=0.0006). Finally, we tested whether IL-15 treatment can control tumour growth in a murine NSCLC model with or without a history of murine cytomegalovirus (MCMV) infection. IL-15 treatment reduced the number of tumour nodules in the lung only in mice with MCMV infection (p=0.0037). We confirmed that MCMV-specific bystander CD8+ TILs produced interferon (IFN)-γ after IL-15 treatment, and that IL-15 treatment in MCMV-infected mice upregulated tumour necrosis factor-α and IFN-γ responsive genes in tumour microenvironment. CONCLUSION Thus, the study demonstrates that bystander CD8+ TILs can be repurposed by IL-15 for tumour immunotherapy.
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Affiliation(s)
- Galam Leem
- Division of Gastroenterology, Department of Internal Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea (the Republic of)
| | - Minwoo Jeon
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Kun Woo Kim
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Incheon, Korea (the Republic of)
| | - Seongju Jeong
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Seong Jin Choi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Yong Joon Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Eui-Soon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Jae-Ik Lee
- Department of Thoracic and Cardiovascular Surgery, Gachon University Gil Medical Center, Incheon, Korea (the Republic of)
| | - Seung Yeon Ha
- Department of Pathology, Gachon University Gil Medical Center, Incheon, Korea (the Republic of)
| | - Su-Hyung Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
| | - Hyo Sup Shim
- Department of Thoracic and Cardiovascular Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea (the Republic of)
| | - Jin Gu Lee
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea (the Republic of)
| | - Shin Myung Kang
- Division of Pulmonology and Allergy, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea (the Republic of)
| | - Eui-Cheol Shin
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Korea (the Republic of)
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15
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Dong N, Moreno-Manuel A, Calabuig-Fariñas S, Gallach S, Zhang F, Blasco A, Aparisi F, Meri-Abad M, Guijarro R, Sirera R, Camps C, Jantus-Lewintre E. Characterization of Circulating T Cell Receptor Repertoire Provides Information about Clinical Outcome after PD-1 Blockade in Advanced Non-Small Cell Lung Cancer Patients. Cancers (Basel) 2021; 13:cancers13122950. [PMID: 34204662 PMCID: PMC8231221 DOI: 10.3390/cancers13122950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Immune checkpoint blockers (ICBs) have demonstrated durable anti-tumor responses in advanced non-small cell lung cancer (NSCLC). Despite progress in development of new predictive biomarkers, such as PD-L1 expression, TMB, or MSI, there is still an urge for a better selection of patients that will benefit from the blockade of PD-1/PD-L1 axis. In this study, peripheral blood T cell receptor beta chain (TCR-β) repertoire, at baseline (PRE) and first response (FR) assessment, was analyzed with high-throughput sequencing in a cohort of advanced NSCLC patients receiving first-line pembrolizumab. Our results suggest that measuring TCR-β features in peripheral blood may be a potential tool to assess patients’ immune response. Furthermore, the usage of the TRBV20-1 segment highly predicts host response and survival in anti-PD-1 treated NSCLC patients. Abstract Despite the success of immunotherapies in lung cancer, development of new biomarkers for patient selection is urgently needed. This study aims to explore minimally invasive approaches to characterize circulating T cell receptor beta chain (TCR-β) repertoire in a cohort of advanced non-small cell lung cancer (NSCLC) patients treated with first-line pembrolizumab. Peripheral blood samples were obtained at two time points: i) pretreatment (PRE) and ii) first response assessment (FR). Next-generation sequencing (NGS) was used to analyze the hypervariable complementary determining region 3 (CDR3) of TCR-β chain. Richness, evenness, convergence, and Jaccard similarity indexes plus variable (V) and joining (J)-gene usage were studied. Our results revealed that increased richness during treatment was associated with durable clinical benefit (DCB; p = 0.046), longer progression-free survival (PFS; p = 0.007) and overall survival (OS; p = 0.05). Patients with Jaccard similarity index ≥0.0605 between PRE and FR samples showed improved PFS (p = 0.021). Higher TRBV20-1 PRE usage was associated with DCB (p = 0.027). TRBV20-1 levels ≥9.14% in PRE and ≥9.02% in FR significantly increased PFS (p = 0.025 and p = 0.016) and OS (p = 0.035 and p = 0.018). Overall, analysis of circulating TCR-β repertoire may provide information about the immune response in anti-PD-1 treated NSCLC patients; in this scenario, it can also offer important information about the clinical outcome.
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Affiliation(s)
- Ning Dong
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
| | - Andrea Moreno-Manuel
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
| | - Silvia Calabuig-Fariñas
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Sandra Gallach
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
| | - Feiyu Zhang
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
| | - Ana Blasco
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Medical Oncology, Hospital General Universitario de Valencia, 46014 Valencia, Spain;
| | - Francisco Aparisi
- Department of Medical Oncology, Hospital General de Requena, 46340 Valencia, Spain;
| | - Marina Meri-Abad
- Department of Medical Oncology, Hospital General Universitario de Valencia, 46014 Valencia, Spain;
| | - Ricardo Guijarro
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Surgery, Universitat de València, 46010 Valencia, Spain
- Department of Thoracic Surgery, Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Rafael Sirera
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Medical Oncology, Hospital General Universitario de Valencia, 46014 Valencia, Spain;
- Department of Medicine, Universitat de València, 46010 Valencia, Spain
- Correspondence: (C.C.); (E.J.-L.)
| | - Eloísa Jantus-Lewintre
- Molecular Oncology Laboratory, Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (N.D.); (A.M.-M.); (S.C.-F.); (S.G.); (F.Z.)
- Unidad Mixta TRIAL, Centro Investigación Príncipe Felipe—Fundación Investigación, Hospital General Universitario de Valencia, 46014 Valencia, Spain; (A.B.); (R.G.); (R.S.)
- Centro de Investigación Biomédica en Red Cáncer, CIBERONC, 28029 Madrid, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
- Correspondence: (C.C.); (E.J.-L.)
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16
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Blair TC, Alice AF, Zebertavage L, Crittenden MR, Gough MJ. The Dynamic Entropy of Tumor Immune Infiltrates: The Impact of Recirculation, Antigen-Specific Interactions, and Retention on T Cells in Tumors. Front Oncol 2021; 11:653625. [PMID: 33968757 PMCID: PMC8101411 DOI: 10.3389/fonc.2021.653625] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/06/2021] [Indexed: 12/13/2022] Open
Abstract
Analysis of tumor infiltration using conventional methods reveals a snapshot view of lymphocyte interactions with the tumor environment. However, lymphocytes have the unique capacity for continued recirculation, exploring varied tissues for the presence of cognate antigens according to inflammatory triggers and chemokine gradients. We discuss the role of the inflammatory and cellular makeup of the tumor environment, as well as antigen expressed by cancer cells or cross-presented by stromal antigen presenting cells, on recirculation kinetics of T cells. We aim to discuss how current cancer therapies may manipulate lymphocyte recirculation versus retention to impact lymphocyte exclusion in the tumor.
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Affiliation(s)
- Tiffany C Blair
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Alejandro F Alice
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Lauren Zebertavage
- Molecular Microbiology and Immunology, Oregon Health and Sciences University (OHSU), Portland, OR, United States.,Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
| | - Marka R Crittenden
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States.,The Oregon Clinic, Portland, OR, United States
| | - Michael J Gough
- Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, United States
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17
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Yang H, Wang Y, Jia Z, Wang Y, Yang X, Wu P, Song Y, Xu H, Gu D, Chen R, Xia X, Bing Z, Gao C, Cao L, Li S, Cao Z, Liang N. Characteristics of T-Cell Receptor Repertoire and Correlation With EGFR Mutations in All Stages of Lung Cancer. Front Oncol 2021; 11:537735. [PMID: 33777727 PMCID: PMC7991722 DOI: 10.3389/fonc.2021.537735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 01/26/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide, and its occurrence is related to the accumulation of gene mutations and immune escape of the tumor. Sequencing of the T-cell receptor (TCR) repertoire can reveal the immunosurveillance status of the tumor microenvironment, which is related to tumor escape and immunotherapy. This study aimed to determine the characteristics and clinical significance of the TCR repertoire in lung cancer. To comprehensively profile the TCR repertoire, results from high-throughput sequencing of samples from 93 Chinese patients with lung cancer were analyzed. We found that the TCR clonality of tissues was related to smoking, with higher clonality in patients who had quit smoking for less than 1 year. As expected, TCR clonality was correlated with stages: patients with stage IV disease showed higher clonality than others. The correlation between TCR repertoire and epidermal growth factor receptor (EGFR) status was also investigated. Patients with EGFR non-L858R mutations showed higher clonality and a lower Shannon index than other groups, including patients with EGFR L858R mutation and wild-type EGFR. Furthermore, we analyzed the TCR similarity metrics—that is, the TCR shared between postoperative peripheral blood and tissue of patients with non-distant metastasis of lung cancer. A similar trend was found, in which patients with EGFR L858R mutations had lower overlap index (OLI) and Morisita index (MOI) scores. Moreover, the OLI showed a positive correlation with several clinical characteristics, including the tumor mutational burden of tissues and the maximum somatic allele frequency of blood; OLI showed a negative correlation with the ratio of CD4+CD28+ in CD4+ cells and the ratio of CD8+CD28+ in CD8+ cells. In conclusion, TCR clonality and TCR similarity metrics correlated with clinical characteristics of patients with lung cancer. Differences in TCR clonality, Shannon index, and OLI across EGFR subtypes provide information to improve understanding about varied responses to immunotherapy in patients with different EGFR mutations.
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Affiliation(s)
- Huaxia Yang
- Department of Rheumatology and Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ziqi Jia
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanyu Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoying Yang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Pancheng Wu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Huihui Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Dejian Gu
- Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Rongrong Chen
- Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Xuefeng Xia
- Medical Center, Geneplus-Beijing Institute, Beijing, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Chao Gao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhili Cao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
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18
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Wang Y, Liu Y, Chen L, Chen Z, Wang X, Jiang R, Zhao K, He X. T Cell Receptor Beta-Chain Profiling of Tumor Tissue, Peripheral Blood and Regional Lymph Nodes From Patients With Papillary Thyroid Carcinoma. Front Immunol 2021; 12:595355. [PMID: 33679738 PMCID: PMC7930746 DOI: 10.3389/fimmu.2021.595355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/25/2021] [Indexed: 11/29/2022] Open
Abstract
Objective: To study the characteristics of the T cell receptor (TCR) repertoire in cancer tissue, peripheral blood and regional lymph nodes (LNs) from patients with papillary thyroid carcinoma (PTC). Methods: PTC tissue, peripheral blood mononuclear cells (PBMCs) and regional LNs of six patients with papillary thyroid carcinoma were harvested. T cell receptor beta-chain (TCRβ) profiling was performed though high-throughput sequencing (HTS), and IMonitor, MiXCR and VDJtools were used to analyze the characteristics of the TCR repertoire. Results: The results of IMonitor and those of MiXCR and VDJtools were very similar. The unique CDR3 of TCRβ from LNs was higher than that of PBMCs, and the CDR3 of TCRβ from LNs was higher than that of PTC tissue. Shannon's diversity index, D50, inverse Simpson index_mean and normalized Shannon's diversity index_mean of CDR3 from LNs were higher than those of PTCs and PBMCs. The HEC (high expansion clones) rate of CDR3 sequences at the amino acid level in PTC tissue was higher than that of PBMCs, which was higher than that of LNs. The V-J HEC rate of CDR3 was highest in PTC tissue, followed by PBMCs and LNs. Conclusion: TCR CDR3 profiling showed differences among and within the PBMCs, PTC tissues and regional LNs of PTC, including unique CDR3, CDR3 HEC at the amino acid level, CDR3 V-J HEC at the amino acid level, Shannon's diversity index and D50. The TCRβ repertoire of PTC tissue, peripheral blood and regional LNs of PTC provide a reference for further study of immunity mechanisms against PTC.
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Affiliation(s)
- Yizeng Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Yuanchao Liu
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Li Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Zuoyu Chen
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xiaoning Wang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoyu Jiang
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Ke Zhao
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
| | - Xianghui He
- Department of General Surgery, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
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19
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Li N, Yuan J, Tian W, Meng L, Liu Y. T-cell receptor repertoire analysis for the diagnosis and treatment of solid tumor: A methodology and clinical applications. Cancer Commun (Lond) 2020; 40:473-483. [PMID: 32677768 PMCID: PMC7571402 DOI: 10.1002/cac2.12074] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022] Open
Abstract
T cells, which are involved in adaptive immunity, are essential in the elimination of tumor cells. Mature T cells can specifically recognize the antigen on the major histocompatibility complex (MHC) molecule through T‐cell receptors (TCR). The unique rearrangement mechanisms during T‐cell maturation provide great diversity to TCR, ensuring specific recognition between T cells and antigens. Thus, TCR repertoire analysis occupied an important position in T‐cell regarding research. Nowadays, next‐generation sequencing technology allows the simultaneous detection of TCR sequences with high throughput, and several evaluation indexes facilitate the measure of TCR repertoire. Based on this new methodology, discoveries are made across a range of tumor types. Results have shed light on the TCR repertoire differences between cancer patients and healthy control as well as between individual's lesions, paracancer, and peripheral blood samples. The potential of TCR repertoire as a biomarker for immunotherapy efficacy is also widely studied as TCR repertoire represents different baseline within individuals and shows dynamic change during treatment. Accurate delineation of the T‐cell repertoire can further the understanding of the immune system response to tumorigenesis. Still, existing researches are insufficient to clarify the specific clinical implications of TCR dynamic change and the definite role of TCR repertoire diversity during the treatment process. The results of some studies are even contrary. In this article, we reviewed TCR rearrangement mechanisms and analysis methods. Recent progress of TCR sequencing technology in tumor research is also discussed. In conclusion, intensive studies over an extended range of cancer types and a broadened group of subjects should be carried to solidify the TCR repertoire's position as an immunotherapy biomarker.
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Affiliation(s)
- Na Li
- Department of Central Laboratory, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, 110044, P. R. China
| | - Jiani Yuan
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Wenjia Tian
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Lin Meng
- Novogene Corporation Limited, Beijing, 100083, P. R. China
| | - Yongyu Liu
- Department of Thoracic Surgery, Shenyang Tenth People's Hospital, Shenyang Chest Hospital, Shenyang, Liaoning, 110044, P. R. China
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20
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Song Z, Chen X, Shi Y, Huang R, Wang W, Zhu K, Lin S, Wang M, Tian G, Yang J, Chen G. Evaluating the Potential of T Cell Receptor Repertoires in Predicting the Prognosis of Resectable Non-Small Cell Lung Cancers. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 18:73-83. [PMID: 32995352 PMCID: PMC7488751 DOI: 10.1016/j.omtm.2020.05.020] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 01/07/2023]
Abstract
For resectable cancer patients, a method that could precisely predict the risk of postoperative recurrence would be crucial for guiding adjuvant treatment. Since T cell receptor (TCR) repertoires had been shown to be closely related to the dynamics of cancers, here we enrolled a cohort of patients to evaluate the potential of TCR repertoires in predicting the prognosis of resectable non-small cell lung cancers. Specifically, TCRβ repertoires were analyzed in surgical tumor tissues and matched adjacent non-tumor tissues from 39 patients enrolled with resectable non-small cell lung cancer, through target enrichment and high-throughput sequencing. As a result, there are significant differences between the TCR repertories of tumor samples and those of matched adjacent non-tumor samples as evaluated by criteria like the number of clonotypes. In addition, TCR repertoires were significantly associated with a few clinical features, as well as somatic mutations. Finally, certain TCRβ variable-joining (V-J) pairings were featured to build a logistic regression model in predicting postoperative recurrence of resectable non-small cell lung cancers with a testing area under the receiver operating characteristic curve (AUC) of around 0.9. Thus, we hypothesize that TCR repertoires could be potentially used to predict prognosis after curative surgery for non-small cell lung cancer patients.
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Affiliation(s)
- Zhengbo Song
- Department of Medical Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310022, China
| | | | - Yi Shi
- Department of Molecular Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China
| | - Rongfang Huang
- Department of Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China
| | - Wenxian Wang
- Department of Medical Oncology, Cancer Hospital of University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou 310022, China
| | - Kunshou Zhu
- Department of Thoracic Surgery, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China
| | - Shaofeng Lin
- Department of Thoracic Surgery, Fujian Cancer Hospital & Fujian Medical University Cancer Hospital, Fuzhou 350014, China
| | - Minxian Wang
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA
| | - Geng Tian
- Geneis Beijing, Beijing 100102, China
| | | | - Gang Chen
- Department of Pathology, Fujian Medical University Cancer Hospital & Fujian Cancer Hospital, Fuzhou 350014, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou 350014, China
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21
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Aversa I, Malanga D, Fiume G, Palmieri C. Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy. Int J Mol Sci 2020; 21:ijms21072378. [PMID: 32235561 PMCID: PMC7177412 DOI: 10.3390/ijms21072378] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 02/08/2023] Open
Abstract
The T cells are key players of the response to checkpoint blockade immunotherapy (CBI) and monitoring the strength and specificity of antitumor T-cell reactivity remains a crucial but elusive component of precision immunotherapy. The entire assembly of T-cell receptor (TCR) sequences accounts for antigen specificity and strength of the T-cell immune response. The TCR repertoire hence represents a “footprint” of the conditions faced by T cells that dynamically evolves according to the challenges that arise for the immune system, such as tumor neo-antigenic load. Hence, TCR repertoire analysis is becoming increasingly important to comprehensively understand the nature of a successful antitumor T-cell response, and to improve the success and safety of current CBI.
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Affiliation(s)
- Ilenia Aversa
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Donatella Malanga
- Interdepartmental Center of Services (CIS), Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
- Correspondence:
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