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Li H, Huang Z, Guo C, Wang Y, Li B, Wang S, Bai N, Chen H, Xue J, Wang D, Zheng Z, Bing Z, Song Y, Xu Y, Huang G, Yu X, Li R, Fung KL, Li J, Song L, Zhu Z, Liu S, Liang N, Li S. Super multiple primary lung cancers harbor high-frequency BRAF and low-frequency EGFR mutations in the MAPK pathway. NPJ Precis Oncol 2024; 8:229. [PMID: 39384982 PMCID: PMC11464572 DOI: 10.1038/s41698-024-00726-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 09/27/2024] [Indexed: 10/11/2024] Open
Abstract
The incidence of multiple primary lung cancer (MPLC) is increasing, with some of our surgical patients exhibiting numerous lesions. We defined lung cancer with five or more primary lesions as super MPLCs. Elucidating the genomic characteristics of this special MPLC subtype can help reduce disease burden and understand tumor evolution. In our cohort of synchronous super early-stage MPLCs (PUMCH-ssesMPLC), whole-exome sequencing on 130 resected malignant specimens from 18 patients provided comprehensive super-MPLC genomic landscapes. Mutations are enriched in PI3k-Akt and MAPK pathways. Their BRAF mutation frequency (31.5%) is significantly higher than MPLC with fewer lesions and early-stage single-lesion cancer, while EGFR mutations are significantly fewer (13.8%). As lesion counts increase, BRAF mutations gradually become dominant. Also, invasive lesions more tend to have classic super-MPLC mutation patterns. High-frequency BRAF mutations, especially Class II, and low-frequency EGFR mutations could be a reason for the limited effectiveness of targeted therapy in super-MPLC patients.
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Affiliation(s)
- Haochen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- School of Medicine, Tsinghua University, Beijing, 100084, China
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Bowen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Sha Wang
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing, 210032, China
| | - Na Bai
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing, 210032, China
| | - Hanlin Chen
- Geneseeq Research Institute, Geneseeq Technology Inc., Nanjing, 210032, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Daoyun Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Zhibo Zheng
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
- Department of International Medical Services, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Yuan Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Guanghua Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Xiaoqing Yu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ruirui Li
- Department of Thoracic Surgery, Aviation General Hospital, Beijing, 100025, China
| | | | - Ji Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lan Song
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Ziwei Zhu
- Zhenyuan (Tianjin) Medical Technology Co. Ltd., Tianjin, 300385, China
| | - Songtao Liu
- Zhenyuan (Tianjin) Medical Technology Co. Ltd., Tianjin, 300385, China
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
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2
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Li C, Nguyen TT, Li JR, Song X, Fujimoto J, Little L, Gumb C, Chow CWB, Wistuba II, Futreal AP, Zhang J, Hubert SM, Heymach JV, Wu J, Amos CI, Zhang J, Cheng C. Multiregional transcriptomic profiling provides improved prognostic insight in localized non-small cell lung cancer. NPJ Precis Oncol 2024; 8:225. [PMID: 39369068 PMCID: PMC11455871 DOI: 10.1038/s41698-024-00680-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/26/2024] [Indexed: 10/07/2024] Open
Abstract
Lung Cancer remains the leading cause of cancer deaths in the USA and worldwide. Non-small cell lung cancer (NSCLC) harbors high transcriptomic intratumor heterogeneity (RNA-ITH) that limits the reproducibility of expression-based prognostic models. In this study, we used multiregional RNA-seq data (880 tumor samples from 350 individuals) from both public (TRACERx) and internal (MDAMPLC) cohorts to investigate the effect of RNA-ITH on prognosis in localized NSCLC at the gene, signature, and tumor microenvironment levels. At the gene level, the maximal expression of hazardous genes (expression negatively associated with survival) but the minimal expression of protective genes (expression positively associated with survival) across different regions within a tumor were more prognostic than the average expression. Following that, we examined whether multiregional expression profiling can improve the performance of prognostic signatures. We investigated 11 gene signatures collected from previous publications and one signature developed in this study. For all of them, the prognostic prediction accuracy can be significantly improved by converting the regional expression of signature genes into sample-specific expression with a simple function-taking the maximal expression of hazardous genes and the minimal expression of protective genes. In the tumor microenvironment, we found a similar rule also seems applicable to immune ITH. We calculated the infiltration levels of major immune cell types in each region of a sample based on expression deconvolution. Prognostic analysis indicated that the region with the lowest infiltration level of protective or highest infiltration level of hazardous immune cells determined the prognosis of NSCLC patients. Our study highlighted the impact of RNA-ITH on the prognostication of NSCLC, which should be taken into consideration to optimize the design and application of expression-based prognostic biomarkers and models. Multiregional assays have the great potential to significantly improve their applications to prognostic stratification.
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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
| | - Thinh T Nguyen
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Latasha Little
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Curtis Gumb
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Chi-Wan B Chow
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andrew P Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Shawna M Hubert
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Christopher I Amos
- 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
| | - 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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3
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Hendriks LEL, Remon J, Faivre-Finn C, Garassino MC, Heymach JV, Kerr KM, Tan DSW, Veronesi G, Reck M. Non-small-cell lung cancer. Nat Rev Dis Primers 2024; 10:71. [PMID: 39327441 DOI: 10.1038/s41572-024-00551-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/19/2024] [Indexed: 09/28/2024]
Abstract
Non-small-cell lung cancer (NSCLC) is one of the most frequent cancer types and is responsible for the majority of cancer-related deaths worldwide. The management of NSCLC has improved considerably, especially in the past 10 years. The systematic screening of populations at risk with low-dose CT, the implementation of novel surgical and radiotherapeutic techniques and a deeper biological understanding of NSCLC that has led to innovative systemic treatment options have improved the prognosis of patients with NSCLC. In non-metastatic NSCLC, the combination of various perioperative strategies and adjuvant immunotherapy in locally advanced disease seem to enhance cure rates. In metastatic NSCLC, the implementation of novel drugs might prolong disease control together with preserving quality of life. The further development of predictive clinical and genetic markers will be essential for the next steps in individualized treatment concepts.
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Affiliation(s)
- Lizza E L Hendriks
- Department of Pulmonary Diseases, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jordi Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Corinne Faivre-Finn
- Radiotherapy Related Research, University of Manchester and The Christie NHS Foundation, Manchester, UK
| | - Marina C Garassino
- Thoracic Oncology Program, Section of Hematology Oncology, Department of Medicine, the University of Chicago, Chicago, IL, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas, M. D. Anderson Cancer Center, Houston, TX, USA
| | - Keith M Kerr
- Department of Pathology, Aberdeen Royal Infirmary and Aberdeen University Medical School, Aberdeen, UK
| | - Daniel S W Tan
- National Cancer Centre Singapore, Duke-NUS Medical School, Singapore, Singapore
| | - Giulia Veronesi
- Department of Thoracic Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Martin Reck
- Airway Research Center North, German Center of Lung Research, Grosshansdorf, Germany.
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4
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Zhao Y, Gao J, Wang J, Fan F, Cheng C, Qian D, Guo R, Zhang Y, Ye T, Augustine M, Lin Y, Shang J, Li H, Pan Y, Huang Q, Chen H, Han H, Gao Z, Wang Q, Zhang S, Zhang M, Fu F, Yan Y, Fernandez Patel S, Vendramin R, Yuan H, Zhang Y, Xiang J, Hu H, Sun Y, Li Y, Litchfield K, Cao Z, Chen H. Genomic and immune heterogeneity of multiple synchronous lung adenocarcinoma at different developmental stages. Nat Commun 2024; 15:7928. [PMID: 39256403 PMCID: PMC11387495 DOI: 10.1038/s41467-024-52139-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 08/28/2024] [Indexed: 09/12/2024] Open
Abstract
Multiple synchronous lung cancers (MSLCs) constitute a unique subtype of lung cancer. To explore the genomic and immune heterogeneity across different pathological stages of MSLCs, we analyse 16 MSLCs from 8 patients using single-cell RNA-seq, single-cell TCR sequencing, and bulk whole-exome sequencing. Our investigation indicates clonally independent tumours with convergent evolution driven by shared driver mutations. However, tumours from the same individual exhibit few shared mutations, indicating independent origins. During the transition from pre-invasive to invasive adenocarcinoma, we observe a shift in T cell phenotypes characterized by increased Treg cells and exhausted CD8+ T cells, accompanied by diminished cytotoxicity. Additionally, invasive adenocarcinomas exhibit greater neoantigen abundance and a more diverse TCR repertoire, indicating heightened heterogeneity. In summary, despite having a common genetic background and environmental exposure, our study emphasizes the individuality of MSLCs at different stages, highlighting their unique genomic and immune characteristics.
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Affiliation(s)
- Yue Zhao
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.
- Institute of Thoracic Oncology, Fudan University, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Jian Gao
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Jun Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Fanfan Fan
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Cheng
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Danwen Qian
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Ran Guo
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhang
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ting Ye
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Marcellus Augustine
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Division of Medicine, University College London, London, UK
| | - Yicong Lin
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Jun Shang
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hang Li
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yunjian Pan
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qingyuan Huang
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haiqing Chen
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Han Han
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhendong Gao
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiming Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Shiyue Zhang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Mou Zhang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Fangqiu Fu
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueren Yan
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanila Fernandez Patel
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Roberto Vendramin
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Hui Yuan
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yawei Zhang
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiaqing Xiang
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong Hu
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yihua Sun
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK.
| | - Zhiwei Cao
- International Human Phenome Institutes (Shanghai), Shanghai, China.
- School of Life Sciences, Fudan University, Shanghai, China.
| | - Haiquan Chen
- Departments of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China.
- Institute of Thoracic Oncology, Fudan University, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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5
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Moghaddam SJ, Savai R, Salehi-Rad R, Sengupta S, Kammer MN, Massion P, Beane JE, Ostrin EJ, Priolo C, Tennis MA, Stabile LP, Bauer AK, Sears CR, Szabo E, Rivera MP, Powell CA, Kadara H, Jenkins BJ, Dubinett SM, Houghton AM, Kim CF, Keith RL. Premalignant Progression in the Lung: Knowledge Gaps and Novel Opportunities for Interception of Non-Small Cell Lung Cancer. An Official American Thoracic Society Research Statement. Am J Respir Crit Care Med 2024; 210:548-571. [PMID: 39115548 PMCID: PMC11389570 DOI: 10.1164/rccm.202406-1168st] [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: 06/13/2024] [Indexed: 08/13/2024] Open
Abstract
Rationale: Despite significant advances in precision treatments and immunotherapy, lung cancer is the most common cause of cancer death worldwide. To reduce incidence and improve survival rates, a deeper understanding of lung premalignancy and the multistep process of tumorigenesis is essential, allowing timely and effective intervention before cancer development. Objectives: To summarize existing information, identify knowledge gaps, formulate research questions, prioritize potential research topics, and propose strategies for future investigations into the premalignant progression in the lung. Methods: An international multidisciplinary team of basic, translational, and clinical scientists reviewed available data to develop and refine research questions pertaining to the transformation of premalignant lung lesions to advanced lung cancer. Results: This research statement identifies significant gaps in knowledge and proposes potential research questions aimed at expanding our understanding of the mechanisms underlying the progression of premalignant lung lesions to lung cancer in an effort to explore potential innovative modalities to intercept lung cancer at its nascent stages. Conclusions: The identified gaps in knowledge about the biological mechanisms of premalignant progression in the lung, together with ongoing challenges in screening, detection, and early intervention, highlight the critical need to prioritize research in this domain. Such focused investigations are essential to devise effective preventive strategies that may ultimately decrease lung cancer incidence and improve patient outcomes.
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6
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Li Y, Chen D, Xu Y, Ding Q, Xu X, Li Y, Mi Y, Chen Y. Prognostic implications, genomic and immune characteristics of lung adenocarcinoma with lepidic growth pattern. J Clin Pathol 2024:jcp-2024-209603. [PMID: 39097406 DOI: 10.1136/jcp-2024-209603] [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: 04/24/2024] [Accepted: 07/17/2024] [Indexed: 08/05/2024]
Abstract
AIMS Conflicting data were provided regarding the prognostic impact and genomic features of lung adenocarcinoma (LUAD) with lepidic growth pattern (LP+A). Delineation of the genomic and immune characteristics of LP+A could provide deeper insights into its prognostic implications and treatment determination. METHODS We conducted a search of articles in PubMed, EMBASE and the Cochrane Library from inception to January 2024. A domestic cohort consisting of 52 LUAD samples was subjected to whole-exome sequencing as internal validation. Data from The Cancer Genomic Atlas and the Gene Expression Omnibus datasets were obtained to characterise the genomic and immune profiles of LP+A. Pooled HRs and rates were calculated. RESULTS The pooled results indicated that lepidic growth pattern was either predominant (0.35, 95% CI 0.22 to 0.56, p<0.01) or minor (HR 0.50, 95% CI 0.36 to 0.70, p<0.01) histological subtype was associated with favourable disease-free survival. Pooled gene mutation rates suggested higher EGFR mutation (0.55, 95% CI 0.46 to 0.64, p<0.01) and lower KRAS mutation (0.14, 95% CI 0.02 to 0.25, p=0.02) in lepidic-predominant LUAD. Lepidic-predominant LUAD had lower tumour mutation burden and pooled positive rate of PD-L1 expression compared with other subtypes. LP+A was characterised by abundance in resting CD4+memory T cells, monocytes and γδ T cells, as well as scarcity of cancer-associated fibroblasts. CONCLUSIONS LP+A was a unique histological subtype with a higher EGFR mutation rate, lower tumour mutation burden and immune checkpoint expression levels. Our findings suggested potential benefits from targeted therapy over immunotherapy in LP+A.
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Affiliation(s)
- Yue Li
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Donglai Chen
- Department of Thoracic Surgery, Zhongshan Hospital Fudan University, Shanghai, Shanghai, China
| | - Yi Xu
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qifeng Ding
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xuejun Xu
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yongzhong Li
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yedong Mi
- Department of Thoracic Surgery, Jiangyin People's Hospital, Jiangyin, Jiangsu, China
| | - Yongbing Chen
- Department of Thoracic Surgery, Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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7
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Zhang J, Zhou W, Li N, Li H, Luo H, Jiang B. Multi-omics analysis unveils immunosuppressive microenvironment in the occurrence and development of multiple pulmonary lung cancers. NPJ Precis Oncol 2024; 8:155. [PMID: 39043808 PMCID: PMC11266694 DOI: 10.1038/s41698-024-00651-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 07/10/2024] [Indexed: 07/25/2024] Open
Abstract
Multiple pulmonary lung cancers (MPLCs) are frequently encountered on computed tomography (CT) scanning of chest, yet their intrinsic characteristics associated with genomic features and radiological or pathological textures that may lead to distinct clinical outcomes remain largely unexplored. A total of 27 pulmonary nodules covering different radiological or pathological textures as well as matched adjacent normal tissues and blood samples were collected from patients diagnosed with MPLCs. Whole-exome sequencing (WES) and whole-transcriptome sequencing were performed. The molecular and immune features of MPLCs associated with distinct radiological or pathological textures were comprehensively investigated. Genomics analysis unveiled the distinct branches of pulmonary nodules originating independently within the same individual. EGFR and KRAS mutations were found to be prevalent in MPLCs, exhibiting mutual exclusivity. The group with KRAS mutations exhibited stronger immune signatures compared to the group with EGFR mutations. Additionally, MPLCs exhibited a pronounced immunosuppressive microenvironment, which was particularly distinct when compared with normal tissues. The expression of the FDSCP gene was specifically observed in MPLCs. When categorizing MPLCs based on radiological or pathological characteristics, a progressive increase in mutation accumulation was observed, accompanied by heightened chromatin-level instability as ground-glass opacity component declined or invasive progression occurred. A close association with the immunosuppressive microenvironment was also observed during the progression of pulmonary nodules. Notably, the upregulation of B cell and regulatory T cell marker genes occurred progressively. Immune cell abundance analysis further demonstrated a marked increase in exhausted cells and regulatory T cells during the progression of pulmonary nodules. These results were further validated by independent datasets including nCounter RNA profiling, single-cell RNA sequencing, and spatial transcriptomic datasets. Our study provided a comprehensive representation of the diverse landscape of MPLCs originating within the same individual and emphasized the significant influence of the immunosuppressive microenvironment in the occurrence and development of pulmonary nodules. These findings hold great potential for enhancing the clinical diagnosis and treatment strategies for MPLCs.
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Affiliation(s)
- Jiatao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Wenhao Zhou
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen, China
| | - Na Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen, China
| | - Huaming Li
- Department of Thoracic surgery, The Eighth Affiliated Hospital Sun Yat-sen University, Shenzhen, China
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and Therapy, YuceBio Technology Co., Ltd, Shenzhen, China.
| | - Benyuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China.
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8
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Quek C, Pratapa A, Bai X, Al-Eryani G, Pires da Silva I, Mayer A, Bartonicek N, Harvey K, Maher NG, Conway JW, Kasalo RJ, Ben Cheikh B, Braubach O, Palendira U, Saw RPM, Stretch JR, Shannon KF, Menzies AM, Scolyer RA, Long GV, Swarbrick A, Wilmott JS. Single-cell spatial multiomics reveals tumor microenvironment vulnerabilities in cancer resistance to immunotherapy. Cell Rep 2024; 43:114392. [PMID: 38944836 DOI: 10.1016/j.celrep.2024.114392] [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: 10/13/2023] [Revised: 03/31/2024] [Accepted: 06/07/2024] [Indexed: 07/02/2024] Open
Abstract
Heterogeneous resistance to immunotherapy remains a major challenge in cancer treatment, often leading to disease progression and death. Using CITE-seq and matched 40-plex PhenoCycler tissue imaging, we performed longitudinal multimodal single-cell analysis of tumors from metastatic melanoma patients with innate resistance, acquired resistance, or response to immunotherapy. We established the multimodal integration toolkit to align transcriptomic features, cellular epitopes, and spatial information to provide deeper insights into the tumors. With longitudinal analysis, we identified an "immune-striving" tumor microenvironment marked by peri-tumor lymphoid aggregates and low infiltration of T cells in the tumor and the emergence of MITF+SPARCL1+ and CENPF+ melanoma subclones after therapy. The enrichment of B cell-associated signatures in the molecular composition of lymphoid aggregates was associated with better survival. These findings provide further insights into the establishment of microenvironmental cell interactions and molecular composition of spatial structures that could inform therapeutic intervention.
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Affiliation(s)
- Camelia Quek
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
| | | | - Xinyu Bai
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Ghamdan Al-Eryani
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - Inês Pires da Silva
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, Australia
| | - Aaron Mayer
- Department of Radiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA; Enable Medicine, Stanford, CA, USA
| | - Nenad Bartonicek
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - Kate Harvey
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Nigel G Maher
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Jordan W Conway
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Rebecca J Kasalo
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | | | | | - Umaimainthan Palendira
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Centenary Institute, The University of Sydney, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Kerwin F Shannon
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia; Sydney Head & Neck Cancer Institute, Chris O'Brien Lifehouse Cancer Centre, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital & NSW Health Pathology, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia; Department of Medical Oncology, Royal North Shore and Mater Hospitals, Sydney, NSW, Australia
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; School of Clinical Medicine, St Vincent's Clinical Campus, UNSW Medicine & Health, UNSW Sydney, NSW, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia; Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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9
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Zhang P, Feng J, Rui M, Xie J, Zhang L, Zhang Z. Integrating machine learning and single-cell analysis to uncover lung adenocarcinoma progression and prognostic biomarkers. J Cell Mol Med 2024; 28:e18516. [PMID: 38958577 PMCID: PMC11221317 DOI: 10.1111/jcmm.18516] [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: 03/07/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
The progression of lung adenocarcinoma (LUAD) from atypical adenomatous hyperplasia (AAH) to invasive adenocarcinoma (IAC) involves a complex evolution of tumour cell clusters, the mechanisms of which remain largely unknown. By integrating single-cell datasets and using inferCNV, we identified and analysed tumour cell clusters to explore their heterogeneity and changes in abundance throughout LUAD progression. We applied gene set variation analysis (GSVA), pseudotime analysis, scMetabolism, and Cytotrace scores to study biological functions, metabolic profiles and stemness traits. A predictive model for prognosis, based on key cluster marker genes, was developed using CoxBoost and plsRcox (CPM), and validated across multiple cohorts for its prognostic prediction capabilities, tumour microenvironment characterization, mutation landscape and immunotherapy response. We identified nine distinct tumour cell clusters, with Cluster 6 indicating an early developmental stage, high stemness and proliferative potential. The abundance of Clusters 0 and 6 increased from AAH to IAC, correlating with prognosis. The CPM model effectively distinguished prognosis in immunotherapy cohorts and predicted genomic alterations, chemotherapy drug sensitivity, and immunotherapy responsiveness. Key gene S100A16 in the CPM model was validated as an oncogene, enhancing LUAD cell proliferation, invasion and migration. The CPM model emerges as a novel biomarker for predicting prognosis and immunotherapy response in LUAD patients, with S100A16 identified as a potential therapeutic target.
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Affiliation(s)
- Pengpeng Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Jiaqi Feng
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Min Rui
- Department of PathologyTianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for CancerTianjinChina
| | - Jiping Xie
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Lianmin Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
| | - Zhenfa Zhang
- Department of Lung Cancer, Tianjin Lung Cancer Center, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for CancerTianjin Medical University Cancer Institute and HospitalTianjinChina
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10
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Zhang S, Xiao X, Yi Y, Wang X, Zhu L, Shen Y, Lin D, Wu C. Tumor initiation and early tumorigenesis: molecular mechanisms and interventional targets. Signal Transduct Target Ther 2024; 9:149. [PMID: 38890350 PMCID: PMC11189549 DOI: 10.1038/s41392-024-01848-7] [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: 01/01/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 06/20/2024] Open
Abstract
Tumorigenesis is a multistep process, with oncogenic mutations in a normal cell conferring clonal advantage as the initial event. However, despite pervasive somatic mutations and clonal expansion in normal tissues, their transformation into cancer remains a rare event, indicating the presence of additional driver events for progression to an irreversible, highly heterogeneous, and invasive lesion. Recently, researchers are emphasizing the mechanisms of environmental tumor risk factors and epigenetic alterations that are profoundly influencing early clonal expansion and malignant evolution, independently of inducing mutations. Additionally, clonal evolution in tumorigenesis reflects a multifaceted interplay between cell-intrinsic identities and various cell-extrinsic factors that exert selective pressures to either restrain uncontrolled proliferation or allow specific clones to progress into tumors. However, the mechanisms by which driver events induce both intrinsic cellular competency and remodel environmental stress to facilitate malignant transformation are not fully understood. In this review, we summarize the genetic, epigenetic, and external driver events, and their effects on the co-evolution of the transformed cells and their ecosystem during tumor initiation and early malignant evolution. A deeper understanding of the earliest molecular events holds promise for translational applications, predicting individuals at high-risk of tumor and developing strategies to intercept malignant transformation.
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Affiliation(s)
- Shaosen Zhang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyi Xiao
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Yonglin Yi
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Xinyu Wang
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Lingxuan Zhu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Changping Laboratory, 100021, Beijing, China
| | - Yanrong Shen
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, 510060, China.
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Key Laboratory of Cancer Genomic Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, 100021, Beijing, China.
- Changping Laboratory, 100021, Beijing, China.
- Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.
- CAMS Oxford Institute, Chinese Academy of Medical Sciences, 100006, Beijing, China.
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11
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Seth S, Chen R, Liu Y, Fujimoto J, Hong L, Reuben A, Varghese S, Behrens C, McDowell T, Soto LS, Haymaker C, Weissferdt A, Kalhor N, Wu J, Le X, Vokes NI, Cheng C, Heymach JV, Gibbons DL, Futreal PA, Wistuba II, Kadara H, Zhang J, Moran C, Zhang J. Integrative genomic and transcriptomic profiling of pulmonary sarcomatoid carcinoma identifies molecular subtypes associated with distinct immune features and clinical outcomes. CANCER INNOVATION 2024; 3:e112. [PMID: 38947760 PMCID: PMC11212327 DOI: 10.1002/cai2.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 12/25/2023] [Accepted: 01/05/2024] [Indexed: 07/02/2024]
Abstract
Background Pulmonary sarcomatoid carcinoma (PSC) is a rare and aggressive subtype of non-small cell lung cancer (NSCLC), characterized by the presence of epithelial and sarcoma-like components. The molecular and immune landscape of PSC has not been well defined. Methods Multiomics profiling of 21 pairs of PSCs with matched normal lung tissues was performed through targeted high-depth DNA panel, whole-exome, and RNA sequencing. We describe molecular and immune features that define subgroups of PSC with disparate genomic and immunogenic features as well as distinct clinical outcomes. Results In total, 27 canonical cancer gene mutations were identified, with TP53 the most frequently mutated gene, followed by KRAS. Interestingly, most TP53 and KRAS mutations were earlier genomic events mapped to the trunks of the tumors, suggesting branching evolution in most PSC tumors. We identified two distinct molecular subtypes of PSC, driven primarily by immune infiltration and signaling. The Immune High (IM-H) subtype was associated with superior survival, highlighting the impact of immune infiltration on the biological and clinical features of localized PSCs. Conclusions We provided detailed insight into the mutational landscape of PSC and identified two molecular subtypes associated with prognosis. IM-H tumors were associated with favorable recurrence-free survival and overall survival, highlighting the importance of tumor immune infiltration in the biological and clinical features of PSCs.
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Affiliation(s)
- Sahil Seth
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- TRACTIONThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Graduate School of Biomedical SciencesThe University of Texas MD Anderson and the University of Texas Health Science CenterHoustonTexasUSA
| | - Runzhe Chen
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Yang Liu
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Junya Fujimoto
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Lingzhi Hong
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Susan Varghese
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Tina McDowell
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of EpidemiologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Luisa Solis Soto
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Cara Haymaker
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Annikka Weissferdt
- Department of PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Neda Kalhor
- Department of PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jia Wu
- Department of Imaging PhysicsThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Natalie I Vokes
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Chao Cheng
- Department of MedicineBaylor College of MedicineHoustonTexasUSA
| | - John V. Heymach
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Don L. Gibbons
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - P. Andrew Futreal
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Ignacio I. Wistuba
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Humam Kadara
- Department of Translational Molecular PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jianhua Zhang
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Cesar Moran
- Department of PathologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
| | - Jianjun Zhang
- Department of Genomic MedicineThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
- Department of Thoracic/Head and Neck Medical OncologyThe University of Texas MD Anderson Cancer CenterHoustonTexasUSA
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12
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Chen F, Li J, Li L, Tong L, Wang G, Zou X. Multidimensional biological characteristics of ground glass nodules. Front Oncol 2024; 14:1380527. [PMID: 38841161 PMCID: PMC11150621 DOI: 10.3389/fonc.2024.1380527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
The detection rate of ground glass nodules (GGNs) has increased in recent years because of their malignant potential but relatively indolent biological behavior; thus, correct GGN recognition and management has become a research focus. Many scholars have explored the underlying mechanism of the indolent progression of GGNs from several perspectives, such as pathological type, genomic mutational characteristics, and immune microenvironment. GGNs have different major mutated genes at different stages of development; EGFR mutation is the most common mutation in GGNs, and p53 mutation is the most abundant mutation in the invasive stage of GGNs. Pure GGNs have fewer genomic alterations and a simpler genomic profile and exhibit a gradually evolving genomic mutation profile as the pathology progresses. Compared to advanced lung adenocarcinoma, GGN lung adenocarcinoma has a higher immune cell percentage, is under immune surveillance, and has less immune escape. However, as the pathological progression and solid component increase, negative immune regulation and immune escape increase gradually, and a suppressive immune environment is established gradually. Currently, regular computer tomography monitoring and surgery are the main treatment strategies for persistent GGNs. Stereotactic body radiotherapy and radiofrequency ablation are two local therapeutic alternatives, and systemic therapy has been progressively studied for lung cancer with GGNs. In the present review, we discuss the characterization of the multidimensional molecular evolution of GGNs that could facilitate more precise differentiation of such highly heterogeneous lesions, laying a foundation for the development of more effective individualized treatment plans.
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Affiliation(s)
- Furong Chen
- Department of Oncology, The First People’s Hospital of Shuangliu District/West China (Airport) Hospital, Sichuan University, Chengdu, China
| | - Jiangtao Li
- Department of Oncology, The First People’s Hospital of Shuangliu District/West China (Airport) Hospital, Sichuan University, Chengdu, China
| | - Lei Li
- Department of Respiratory and Critical Care Medicine, Clinical Research Center for Respiratory Disease, West China Hospital, Sichuan University, Chengdu, China
- Department of State Key Laboratory of Respiratory Health and Multimobidity, West China Hospital, Sichuan University, Chengdu, China
| | - Lunbing Tong
- Department of Respiratory Medicine, Chengdu Seventh People’s Hospital/Affiliated Cancer Hospital of Chengdu Medical College, Chengdu, China
| | - Gang Wang
- Department of Respiratory and Critical Care Medicine, Clinical Research Center for Respiratory Disease, West China Hospital, Sichuan University, Chengdu, China
- Department of State Key Laboratory of Respiratory Health and Multimobidity, West China Hospital, Sichuan University, Chengdu, China
| | - Xuelin Zou
- Department of Respiratory Medicine, Chengdu Seventh People’s Hospital/Affiliated Cancer Hospital of Chengdu Medical College, Chengdu, China
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13
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Hu X, Zhu B, Vokes N, Fujimoto J, Rojas Alvarez FR, Heeke S, Moreira AL, Solis LM, Haymaker C, Velcheti V, Sterman DH, Pass HI, Cheng C, Lee JJ, Zhang J, Wei Z, Wu J, Le X, Ostrin E, Toumazis I, Gibbons D, Su D, Fukuoka J, Antonoff MB, Gerber DE, Li C, Kadara H, Wang L, Davis M, Heymach JV, Hannash S, Wistuba I, Dubinett S, Alexandrov L, Lippman S, Spira A, Futreal AP, Reuben A, Zhang J. The evolution of lung adenocarcinoma precursors is associated with chromosomal instability and transition from innate to adaptive immune response/evasion. RESEARCH SQUARE 2024:rs.3.rs-4396272. [PMID: 38798564 PMCID: PMC11118701 DOI: 10.21203/rs.3.rs-4396272/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Studying lung adenocarcinoma (LUAD) early carcinogenesis is challenging, primarily due to the lack of LUAD precursors specimens. We amassed multi-omics data from 213 LUAD and LUAD precursors to identify molecular features underlying LUAD precancer evolution. We observed progressively increasing mutations, chromosomal aberrations, whole genome doubling and genomic instability from precancer to invasive LUAD, indicating aggravating chromosomal instability (CIN). Telomere shortening, a crucial genomic alteration linked to CIN, emerged at precancer stage. Moreover, later-stage lesions demonstrated increasing cancer stemness and decreasing alveolar identity, suggesting epithelial de-differentiation during early LUAD carcinogenesis. The innate immune cells progressively diminished from precancer to invasive LUAD, concomitant with a gradual recruitment of adaptive immune cells (except CD8+ and gamma-delta T cells that decreased in later stages) and upregulation of numerous immune checkpoints, suggesting LUAD precancer evolution is associated with a shift from innate to adaptive immune response and immune evasion mediated by various mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bo Zhu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Natalie Vokes
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | | | - Frank R. Rojas Alvarez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Simon Heeke
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Andre L. Moreira
- Department of Pathology, New York University Langone Medical Center, New York, 10012, USA
| | - Luisa M. Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vamsidhar Velcheti
- Department of Medical oncology, New York University, New York, 10012, USA
| | | | - Harvey I. Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, 10016, USA
| | - Chao Cheng
- Department of Medicine, Epidemiology and Population Science, Baylor College of Medicine. Houston, TX, 77030, USA
| | - Jack J. Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Zhubo Wei
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiuning Le
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Edwin Ostrin
- Department of General Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Iakovos Toumazis
- Department of Health Services Research, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Don Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, 310022, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Mara B. Antonoff
- Department of Thoracic & Cardiovasc Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - David E. Gerber
- Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chenyang Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, 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
| | - Mark Davis
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - John V. Heymach
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir Hannash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Steven Dubinett
- Departments of Medicine and Pathology, University of California Los Angeles and Greater Los Angeles Healthcare System, Los Angeles, CA, 90095, USA
| | - Ludmil Alexandrov
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Scott Lippman
- Moores Cancer Center, UC San Diego School of Medicine, San Diego, CA, 92037, USA
| | - Avrum Spira
- Pathology & Laboratory Medicine, and Bioinformatics, Boston University, Boston, MA, 02215, USA
| | - Andrew P. Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Lead contact
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14
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Khosravi G, Mostafavi S, Bastan S, Ebrahimi N, Gharibvand RS, Eskandari N. Immunologic tumor microenvironment modulators for turning cold tumors hot. Cancer Commun (Lond) 2024; 44:521-553. [PMID: 38551889 PMCID: PMC11110955 DOI: 10.1002/cac2.12539] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/03/2024] [Accepted: 03/12/2024] [Indexed: 05/23/2024] Open
Abstract
Tumors can be classified into distinct immunophenotypes based on the presence and arrangement of cytotoxic immune cells within the tumor microenvironment (TME). Hot tumors, characterized by heightened immune activity and responsiveness to immune checkpoint inhibitors (ICIs), stand in stark contrast to cold tumors, which lack immune infiltration and remain resistant to therapy. To overcome immune evasion mechanisms employed by tumor cells, novel immunologic modulators have emerged, particularly ICIs targeting cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and programmed cell death protein 1/programmed death-ligand 1(PD-1/PD-L1). These agents disrupt inhibitory signals and reactivate the immune system, transforming cold tumors into hot ones and promoting effective antitumor responses. However, challenges persist, including primary resistance to immunotherapy, autoimmune side effects, and tumor response heterogeneity. Addressing these challenges requires innovative strategies, deeper mechanistic insights, and a combination of immune interventions to enhance the effectiveness of immunotherapies. In the landscape of cancer medicine, where immune cold tumors represent a formidable hurdle, understanding the TME and harnessing its potential to reprogram the immune response is paramount. This review sheds light on current advancements and future directions in the quest for more effective and safer cancer treatment strategies, offering hope for patients with immune-resistant tumors.
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Affiliation(s)
- Gholam‐Reza Khosravi
- Department of Medical ImmunologySchool of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Samaneh Mostafavi
- Department of ImmunologyFaculty of Medical SciencesTarbiat Modares UniversityTehranIran
| | - Sanaz Bastan
- Department of Medical ImmunologySchool of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Narges Ebrahimi
- Department of Medical ImmunologySchool of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Roya Safari Gharibvand
- Department of ImmunologySchool of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Nahid Eskandari
- Department of Medical ImmunologySchool of MedicineIsfahan University of Medical SciencesIsfahanIran
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15
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Wang Y, Huang Z, Li B, Xue J, Guo C, Bing Z, Zheng Z, Song Y, Xu Y, Huang G, Li H, Yu X, Xia Y, Li R, Si X, Zhang L, Li J, Song L, Xiong Y, Gu D, Song M, Zhou Z, Chen R, Feng Z, Bie Z, Li X, Yang H, Li S, Liang N. Clonal expansion of shared T cell receptors reveals the existence of immune commonality among different lesions of synchronous multiple primary lung cancer. Cancer Immunol Immunother 2024; 73:111. [PMID: 38668781 PMCID: PMC11052747 DOI: 10.1007/s00262-024-03703-8] [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: 12/20/2023] [Accepted: 04/14/2024] [Indexed: 04/29/2024]
Abstract
The increase in the detection rate of synchronous multiple primary lung cancer (MPLC) has posed remarkable clinical challenges due to the limited understanding of its pathogenesis and molecular features. Here, comprehensive comparisons of genomic and immunologic features between MPLC and solitary lung cancer nodule (SN), as well as different lesions of the same patient, were performed. Compared with SN, MPLC displayed a lower rate of EGFR mutation but higher rates of BRAF, MAP2K1, and MTOR mutation, which function exactly in the upstream and downstream of the same signaling pathway. Considerable heterogeneity in T cell receptor (TCR) repertoire exists among not only different patients but also among different lesions of the same patient. Invasive lesions of MPLC exhibited significantly higher TCR diversity and lower TCR expansion than those of SN. Intriguingly, different lesions of the same patient always shared a certain proportion of TCR clonotypes. Significant clonal expansion could be observed in shared TCR clonotypes, particularly in those existing in all lesions of the same patient. In conclusion, this study provided evidences of the distinctive mutational landscape, activation of oncogenic signaling pathways, and TCR repertoire in MPLC as compared with SN. The significant clonal expansion of shared TCR clonotypes demonstrated the existence of immune commonality among different lesions of the same patient and shed new light on the individually tailored precision therapy for MPLC.
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Affiliation(s)
- Yadong Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhicheng Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bowen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchao Xue
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Guo
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhongxing Bing
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhibo Zheng
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Song
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Xu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guanghua Huang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Haochen Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoqing Yu
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yankai Xia
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ruirui Li
- Department of Cardiothoracic Surgery, Civil Aviation General Hospital, Beijing, China
| | - Xiaoyan Si
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Pulmonary and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ji Li
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lan Song
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | | | | | - Zhe Feng
- Department of Cardiothoracic Surgery, The Sixth Hospital of Beijing, Beijing, China
| | - Zhixin Bie
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoguang Li
- Minimally Invasive Tumor Therapies Center, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Huaxia Yang
- State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Rheumatology and Clinical Immunology, National Clinical Research Center for Dermatologic and Immunologic Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, The Ministry of Education Key Laboratory, Beijing, China.
| | - Shanqing Li
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Naixin Liang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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16
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Parra ER, Zhang J, Duose DY, Gonzalez-Kozlova E, Redman MW, Chen H, Manyam GC, Kumar G, Zhang J, Song X, Lazcano R, Marques-Piubelli ML, Laberiano-Fernandez C, Rojas F, Zhang B, Taing L, Jhaveri A, Geisberg J, Altreuter J, Michor F, Provencher J, Yu J, Cerami E, Moravec R, Kannan K, Luthra R, Alatrash G, Huang HH, Xie H, Patel M, Nie K, Harris J, Argueta K, Lindsay J, Biswas R, Van Nostrand S, Kim-Schulze S, Gray JE, Herbst RS, Wistuba II, Gettinger S, Kelly K, Bazhenova L, Gnjatic S, Lee JJ, Zhang J, Haymaker C. Multi-omics Analysis Reveals Immune Features Associated with Immunotherapy Benefit in Patients with Squamous Cell Lung Cancer from Phase III Lung-MAP S1400I Trial. Clin Cancer Res 2024; 30:1655-1668. [PMID: 38277235 PMCID: PMC11016892 DOI: 10.1158/1078-0432.ccr-23-0251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/06/2023] [Accepted: 01/24/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE Identifying molecular and immune features to guide immune checkpoint inhibitor (ICI)-based regimens remains an unmet clinical need. EXPERIMENTAL DESIGN Tissue and longitudinal blood specimens from phase III trial S1400I in patients with metastatic squamous non-small cell carcinoma (SqNSCLC) treated with nivolumab monotherapy (nivo) or nivolumab plus ipilimumab (nivo+ipi) were subjected to multi-omics analyses including multiplex immunofluorescence (mIF), nCounter PanCancer Immune Profiling Panel, whole-exome sequencing, and Olink. RESULTS Higher immune scores from immune gene expression profiling or immune cell infiltration by mIF were associated with response to ICIs and improved survival, except regulatory T cells, which were associated with worse overall survival (OS) for patients receiving nivo+ipi. Immune cell density and closer proximity of CD8+GZB+ T cells to malignant cells were associated with superior progression-free survival and OS. The cold immune landscape of NSCLC was associated with a higher level of chromosomal copy-number variation (CNV) burden. Patients with LRP1B-mutant tumors had a shorter survival than patients with LRP1B-wild-type tumors. Olink assays revealed soluble proteins such as LAMP3 increased in responders while IL6 and CXCL13 increased in nonresponders. Upregulation of serum CXCL13, MMP12, CSF-1, and IL8 were associated with worse survival before radiologic progression. CONCLUSIONS The frequency, distribution, and clustering of immune cells relative to malignant ones can impact ICI efficacy in patients with SqNSCLC. High CNV burden may contribute to the cold immune microenvironment. Soluble inflammation/immune-related proteins in the blood have the potential to monitor therapeutic benefit from ICI treatment in patients with SqNSCLC.
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Affiliation(s)
- Edwin Roger Parra
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jiexin Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Yawa Duose
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - Mary W. Redman
- SWOG Statistical Center, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Hong Chen
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ganiraju C. Manyam
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gayatri Kumar
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rossana Lazcano
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mario L. Marques-Piubelli
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Caddie Laberiano-Fernandez
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Frank Rojas
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Baili Zhang
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Len Taing
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Aashna Jhaveri
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jacob Geisberg
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jennifer Altreuter
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Franziska Michor
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - James Provencher
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Joyce Yu
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Ethan Cerami
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Radim Moravec
- Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, NCI, Bethesda, Maryland
| | - Kasthuri Kannan
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Alatrash
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer, Houston, Texas
| | - Hsin-Hui Huang
- Precision Immunology Institute, Mount Sinai, New York, New York
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hui Xie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - Kai Nie
- Precision Immunology Institute, Mount Sinai, New York, New York
| | - Jocelyn Harris
- Precision Immunology Institute, Mount Sinai, New York, New York
| | | | - James Lindsay
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Roshni Biswas
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen Van Nostrand
- CIMAC-CIDC Network, Pipeline Development and Portal Integration, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Seunghee Kim-Schulze
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Roy S. Herbst
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut
| | - Ignacio I. Wistuba
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Karen Kelly
- International Association for the Study of Lung Cancer, Denver, Colorado
| | - Lyudmila Bazhenova
- University of California San Diego Moores Cancer Center, La Jolla, California
| | - Sacha Gnjatic
- Department of Oncological Sciences, Mount Sinai, New York, New York
- Tisch Cancer Institute, Mount Sinai, New York, New York
- Precision Immunology Institute, Mount Sinai, New York, New York
- Icahn School of Medicine at Mount Sinai, New York, New York
| | - J. Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic-Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cara Haymaker
- Departments of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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17
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Wang X, Shi J, Liu Z. Advancements in the diagnosis and treatment of sub‑centimeter lung cancer in the era of precision medicine (Review). Mol Clin Oncol 2024; 20:28. [PMID: 38414512 PMCID: PMC10895471 DOI: 10.3892/mco.2024.2726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024] Open
Abstract
Lung cancer is the malignancy with the highest global mortality rate and imposes a substantial burden on society. The increasing popularity of lung cancer screening has led to increasing number of patients being diagnosed with pulmonary nodules due to their potential for malignancy, causing considerable distress in the affected population. However, the diagnosis and treatment of sub-centimeter grade pulmonary nodules remain controversial. The evolution of genetic detection technology and the development of targeted drugs have positioned the diagnosis and treatment of lung cancer in the precision medicine era, leading to a marked improvement in the survival rate of patients with lung cancer. It has been established that lung cancer driver genes serve a key role in the development and progression of sub-centimeter lung cancer. The present review aimed to consolidate the findings on genes associated with sub-centimeter lung cancer, with the intent of serving as a reference for future studies and the personalized management of sub-centimeter lung cancer through genetic testing.
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Affiliation(s)
- Xiao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Jingwei Shi
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu 210008, P.R. China
| | - Zhengcheng Liu
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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18
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Liu XD, Zhang Y, He HY. Targeted next-generation sequencing of 491 lung cancers in clinical practice: Implications for future detection strategy and targeted therapy. Heliyon 2024; 10:e27591. [PMID: 38496837 PMCID: PMC10944278 DOI: 10.1016/j.heliyon.2024.e27591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/03/2024] [Accepted: 03/04/2024] [Indexed: 03/19/2024] Open
Abstract
Although lung cancer remains the most common cause of global cancer-related mortality, the identification of oncogenic driver alterations and the development of targeted drugs has dramatically altered the therapeutic landscape. In this retrospective study, we found that 97.7% samples carried at least one mutation in the 25 genes tested in our cohort. 53.6% samples were positive for EGFR mutations, followed by TP53 (41.1%), KRAS (11.8%), ERBB2 (4.3%). EGFR mutations were mainly found in female adenocarcinomas, while TP53 was mainly found in male non-adenocarcinomas. Significant differences can be found in the mutation rate of EGFR (60.9% vs 11.9%), KRAS (12.2% vs 25.0%), STK11 (1.5% vs 11.9%), FGFR3 (2.4% vs 0.0%) and ERBB4 (1.2% vs 6.1%) between adenocarcinoma in our cohort and TCGA-LUAD data (all p < 0.001). What's more, we found that the mutation of EGFR increased significantly from adenocarcinomas in situ (AIS, 21.4%) to microinvasive adenocarcinomas (MIA, 52.4%) and invasive adenocarcinomas (IA, 61.1%), while the mutation of ERBB2 dropped markedly from AIS (21.4%) to MIA (9.5%) and IA (4.1%). At last, comparations between targeted NGS and ARMS-based single gene test in the detection of EGFR showed a 94.6% consistence. In conclusion, targeted NGS can provide a comprehensive mutational profile of lung cancer. Considering the high mutation rate of EGFR in NSCLC of Asian populations, a specialized detection strategy should be conducted.
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Affiliation(s)
- Xiao-dan Liu
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Zhang
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
| | - Hui-ying He
- Department of Pathology, School of Basic Medical Sciences, Peking University Third Hospital, Peking University Health Science Center, Beijing, 100191, China
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19
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Reeves MQ, Balmain A. Mutations, Bottlenecks, and Clonal Sweeps: How Environmental Carcinogens and Genomic Changes Shape Clonal Evolution during Tumor Progression. Cold Spring Harb Perspect Med 2024; 14:a041388. [PMID: 38052482 PMCID: PMC10910358 DOI: 10.1101/cshperspect.a041388] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The transition from a single, initiated cell to a full-blown malignant tumor involves significant genomic evolution. Exposure to carcinogens-whether directly mutagenic or not-can drive progression toward malignancy, as can stochastic acquisition of cancer-promoting genetic events. Mouse models using both carcinogens and germline genetic manipulations have enabled precise inquiry into the evolutionary dynamics that take place as a tumor progresses from benign to malignant to metastatic stages. Tumor progression is characterized by changes in somatic point mutations and copy-number alterations, even though any single tumor can itself have a high or low burden of genomic alterations. Further, lineage-tracing, single-cell analyses and CRISPR barcoding have revealed the distinct clonal dynamics within benign and malignant tumors. Application of these tools in a range of mouse models can shed unique light on the patterns of clonal evolution that take place in both mouse and human tumors.
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Affiliation(s)
- Melissa Q Reeves
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA
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20
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Xiong Y, Ma Y, Liu K, Lei J, Zhao J, Zhu J, Wang W, Wen M, Wang X, Sun Y, Zhao Y, Han Y, Jiang T, Liu Y. A gene-based score for the risk stratification of stage IA lung adenocarcinoma. Respir Res 2024; 25:18. [PMID: 38178073 PMCID: PMC10765678 DOI: 10.1186/s12931-023-02647-4] [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: 09/25/2022] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
OBJECTIVE We aim to molecularly stratify stage IA lung adenocarcinoma (LUAD) for precision medicine. METHODS Twelve multi-institution datasets (837 cases of IA) were used to classify the high- and low-risk types (based on survival status within 5 years), and the biological differences were compared. Then, a gene-based classifying score (IA score) was trained, tested and validated by several machine learning methods. Furthermore, we estimated the significance of the IA score in the prognostic assessment, chemotherapy prediction and risk stratification of stage IA LUAD. We also developed an R package for the clinical application. The SEER database (15708 IA samples) and TCGA Pan-Cancer (1881 stage I samples) database were used to verify clinical significance. RESULTS Compared with the low-risk group, the high-risk group of stage IA LUAD has obvious enrichment of the malignant pathway and more driver mutations and copy number variations. The effect of the IA score on the classification of high- and low-risk stage IA LUAD was much better than that of classical clinicopathological factors (training set: AUC = 0.9, validation set: AUC = 0.7). The IA score can significantly predict the prognosis of stage IA LUAD and has a prognostic effect for stage I pancancer. The IA score can effectively predict chemotherapy sensitivity and occult metastasis or invasion in stage IA LUAD. The R package IAExpSuv has a good risk probability prediction effect for both groups and single stages of IA LUAD. CONCLUSIONS The IA score can effectively stratify the risk of stage IA LUAD, offering good assistance in precision medicine.
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Affiliation(s)
- Yanlu Xiong
- Department of Thoracic Surgery, First Medical Center, Chinese PLA General Hospital and PLA Medical School, Beijing, China
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
- Innovation Center for Advanced Medicine, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yongfu Ma
- Department of Thoracic Surgery, First Medical Center, Chinese PLA General Hospital and PLA Medical School, Beijing, China
| | - Kun Liu
- Department of Epidemiology, Ministry of Education Key Laboratory of Hazard Assessment and Control in Special Operational Environment, School of Public Health, Air Force Medical University, Xi'an, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jinbo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jianfei Zhu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
- Department of Thoracic Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Wenchen Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Miaomiao Wen
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Xuejiao Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Ying Sun
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yabo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yong Han
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
- Department of Thoracic Surgery, Air Force Medical Center, Fourth Military Medical University, Beijing, China.
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China.
| | - Yang Liu
- Department of Thoracic Surgery, First Medical Center, Chinese PLA General Hospital and PLA Medical School, Beijing, China.
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21
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Haga Y, Sakamoto Y, Kajiya K, Kawai H, Oka M, Motoi N, Shirasawa M, Yotsukura M, Watanabe SI, Arai M, Zenkoh J, Shiraishi K, Seki M, Kanai A, Shiraishi Y, Yatabe Y, Matsubara D, Suzuki Y, Noguchi M, Kohno T, Suzuki A. Whole-genome sequencing reveals the molecular implications of the stepwise progression of lung adenocarcinoma. Nat Commun 2023; 14:8375. [PMID: 38102134 PMCID: PMC10724178 DOI: 10.1038/s41467-023-43732-y] [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: 01/31/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
The mechanism underlying the development of tumors, particularly at early stages, still remains mostly elusive. Here, we report whole-genome long and short read sequencing analysis of 76 lung cancers, focusing on very early-stage lung adenocarcinomas such as adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma. The obtained data is further integrated with bulk and spatial transcriptomic data and epigenomic data. These analyses reveal key events in lung carcinogenesis. Minimal somatic mutations in pivotal driver mutations and essential proliferative factors are the only detectable somatic mutations in the very early-stage of AIS. These initial events are followed by copy number changes and global DNA hypomethylation. Particularly, drastic changes are initiated at the later AIS stage, i.e., in Noguchi type B tumors, wherein cancer cells are exposed to the surrounding microenvironment. This study sheds light on the pathogenesis of lung adenocarcinoma from integrated pathological and molecular viewpoints.
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Affiliation(s)
- Yasuhiko Haga
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yoshitaka Sakamoto
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Keiko Kajiya
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Hitomi Kawai
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Miho Oka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
- Ono Pharmaceutical Co., Ltd., Ibaraki, Japan
| | - Noriko Motoi
- Department of Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Pathology, Saitama Cancer Center, 780 Komuro, Ina, Kita-Adachi-gun, Saitama, 362-0806, Japan
| | - Masayuki Shirasawa
- Department of Thoracic Oncology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masaya Yotsukura
- Department of Thoracic Surgery, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Shun-Ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Miyuki Arai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Junko Zenkoh
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Kouya Shiraishi
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Department of Clinical Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan
| | - Yuichi Shiraishi
- Division of Genome Analysis Platform Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daisuke Matsubara
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
| | - Masayuki Noguchi
- Department of Diagnostic Pathology, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan
- Clinical Cancer Research Division, Shonan Research Institute of Innovative Medicine, Shonan Kamakura General Hospital, 1370-1 Okamoto, Kamakura, Kanagawa, 247-8533, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan.
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22
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Lu M, Zhang X, Chu Q, Chen Y, Zhang P. Susceptibility Genes Associated with Multiple Primary Cancers. Cancers (Basel) 2023; 15:5788. [PMID: 38136334 PMCID: PMC10741435 DOI: 10.3390/cancers15245788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
With advancements in treatment and screening techniques, we have been witnessing an era where more cancer survivors harbor multiple primary cancers (MPCs), affecting approximately one in six patients. Identifying MPCs is crucial for tumor staging and subsequent treatment choices. However, the current clinicopathological criteria for clinical application are limited and insufficient, making it challenging to differentiate them from recurrences or metastases. The emergence of next-generation sequencing (NGS) technology has provided a genetic perspective for defining multiple primary cancers. Researchers have found that, when considering multiple tumor pairs, it is crucial not only to examine well-known essential mutations like MLH1/MSH2, EGFR, PTEN, BRCA1/2, CHEK2, and TP53 mutations but also to explore certain pleiotropic loci. Moreover, specific deleterious mutations may serve as regulatory factors in second cancer development following treatment. This review aims to discuss these susceptibility genes and provide an explanation of their functions based on the signaling pathway background. Additionally, the association network between genetic signatures and different tumor pairs will be summarized.
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Affiliation(s)
| | | | | | | | - Peng Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; (M.L.)
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23
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Chen P, Rojas FR, Hu X, Serrano A, Zhu B, Chen H, Hong L, Bandyoyadhyay R, Aminu M, Kalhor N, Lee JJ, El Hussein S, Khoury JD, Pass HI, Moreira AL, Velcheti V, Sterman DH, Fukuoka J, Tabata K, Su D, Ying L, Gibbons DL, Heymach JV, Wistuba II, Fujimoto J, Solis Soto LM, Zhang J, Wu J. Pathomic Features Reveal Immune and Molecular Evolution From Lung Preneoplasia to Invasive Adenocarcinoma. Mod Pathol 2023; 36:100326. [PMID: 37678674 PMCID: PMC10841057 DOI: 10.1016/j.modpat.2023.100326] [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: 03/26/2023] [Revised: 08/12/2023] [Accepted: 08/29/2023] [Indexed: 09/09/2023]
Abstract
Recent statistics on lung cancer, including the steady decline of advanced diseases and the dramatically increasing detection of early-stage diseases and indeterminate pulmonary nodules, mark the significance of a comprehensive understanding of early lung carcinogenesis. Lung adenocarcinoma (ADC) is the most common histologic subtype of lung cancer, and atypical adenomatous hyperplasia is the only recognized preneoplasia to ADC, which may progress to adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) and eventually to invasive ADC. Although molecular evolution during early lung carcinogenesis has been explored in recent years, the progress has been significantly hindered, largely due to insufficient materials from ADC precursors. Here, we employed state-of-the-art deep learning and artificial intelligence techniques to robustly segment and recognize cells on routinely used hematoxylin and eosin histopathology images and extracted 9 biology-relevant pathomic features to decode lung preneoplasia evolution. We analyzed 3 distinct cohorts (Japan, China, and United States) covering 98 patients, 162 slides, and 669 regions of interest, including 143 normal, 129 atypical adenomatous hyperplasia, 94 AIS, 98 MIA, and 205 ADC. Extracted pathomic features revealed progressive increase of atypical epithelial cells and progressive decrease of lymphocytic cells from normal to AAH, AIS, MIA, and ADC, consistent with the results from tissue-consuming and expensive molecular/immune profiling. Furthermore, pathomics analysis manifested progressively increasing cellular intratumor heterogeneity along with the evolution from normal lung to invasive ADC. These findings demonstrated the feasibility and substantial potential of pathomics in studying lung cancer carcinogenesis directly from the low-cost routine hematoxylin and eosin staining.
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Affiliation(s)
- Pingjun Chen
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Frank R Rojas
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bo Zhu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hong Chen
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingzhi Hong
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rukhmini Bandyoyadhyay
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muhammad Aminu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Neda Kalhor
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siba El Hussein
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, New York
| | - Joseph D Khoury
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Harvey I Pass
- Department of Surgery, NYU Langone Health, New York, New York
| | - Andre L Moreira
- Department of Pathology, NYU Langone Health, New York, New York
| | - Vamsidhar Velcheti
- Department of Medicine, NYU Grossman School of Medicine, New York, New York
| | - Daniel H Sterman
- Department of Medicine, NYU Grossman School of Medicine, New York, New York; Department of Cardiothoracic Surgery, NYU Grossman School of Medicine, New York, New York
| | - Junya Fukuoka
- Department of Pathology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Dan Su
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Lisha Ying
- Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luisa M Solis Soto
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jia Wu
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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24
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Wang Z, Yang L, Wang W, Zhou H, Chen J, Ma Z, Wang X, Zhang Q, Liu H, Zhou C, Guo Z, Zhang X. Comparative immunological landscape between pre- and early-stage LUAD manifested as ground-glass nodules revealed by scRNA and scTCR integrated analysis. Cell Commun Signal 2023; 21:325. [PMID: 37957625 PMCID: PMC10644515 DOI: 10.1186/s12964-023-01322-x] [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: 06/18/2023] [Accepted: 09/16/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Mechanism underlying the malignant progression of precancer to early-stage lung adenocarcinoma (LUAD) as well as their indolence nature remains elusive. METHODS Single-cell RNA sequencing (scRNA) with simultaneous T cell receptor (TCR) sequencing on 5 normal lung tissues, 3 precancerous and 4 early-stage LUAD manifested as pulmonary ground-glass nodules (GGNs) were performed. RESULTS Through this integrated analysis, we have delineated five key modules that drive the malignant progression of early-stage LUAD in a disease stage-dependent manner. These modules are related to cell proliferation and metabolism, immune response, mitochondria, cilia, and cell adhesion. We also find that the tumor micro-environment (TME) of early-stage LUAD manifested as GGN are featured with regulatory T (Tregs) cells accumulation with three possible origins, and loss-functional state (decreased clonal expansion and cytotoxicity) of CD8 + T cells. Instead of exhaustion, the CD8 + T cells are featured with a shift to memory phenotype, which is significantly different from the late stage LUAD. Furthermore, we have identified monocyte-derived macrophages that undergo a lipid-phenotype transition and may contribute to the suppressive TME. Intense interaction between stromal cells, myeloid cells including lipid associated macrophages and LAMP3 + DCs, and lymphocytes were also characterized. CONCLUSIONS Our work provides new insight into the molecular and cellular mechanism underlying malignant progression of LUAD manifested as GGN, and pave way for novel immunotherapies for GGN. Video Abstract.
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Affiliation(s)
- Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Wenqiang Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Huanhuan Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Juan Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Zeheng Ma
- Department of Thoracic Surgery Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Xiaoyan Wang
- Department of Pathological Department, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Quncheng Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Haiyang Liu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Chao Zhou
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China
| | - Zhiping Guo
- Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
- Henan Provincial Key Laboratory of Chronic Diseases and Health Management, Zhengzhou, 450003, Henan, China.
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Weiwu Road No.7, Zhengzhou, 450003, Henan, China.
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25
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Zhang JT, Zhang J, Wang SR, Yan LX, Qin J, Yin K, Chu XP, Wang MM, Hong HZ, Lv ZY, Dong S, Jiang BY, Zhang XC, Liu X, Zhou Q, Wu YL, Zhong WZ. Spatial downregulation of CD74 signatures may drive invasive component development in part-solid lung adenocarcinoma. iScience 2023; 26:107699. [PMID: 37810252 PMCID: PMC10550719 DOI: 10.1016/j.isci.2023.107699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 05/23/2023] [Accepted: 08/18/2023] [Indexed: 10/10/2023] Open
Abstract
Pulmonary nodules with part-solid imaging features manifest during the progression from preinvasive to invasive lung adenocarcinoma. To define the spatial composition and evolutionary trajectories of early-stage lung adenocarcinoma, we combined spatial transcriptomics (ST) and pathological annotations from 20 part-solid nodules (PSNs), four of which were matched with single-cell RNA sequencing. Two malignant cell populations (MC1 and MC2) were identified, and a linear evolutionary relationship was observed. Compared to MC2, the pre-existing malignant MC1 exhibited a lower metastatic signature, corresponding to the preinvasive component (lepidic) on pathology and the ground glass component on PSN imaging. Higher immune infiltration was observed among MC1 regions in ST profiles, and further analysis revealed that macrophages may be involved in this process through the CD74 axis. This work provides deeper insights into the evolutionary process and spatial immune cell composition behind PSNs and highlights the mechanisms of immune escape behind this adenocarcinoma trajectory.
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Affiliation(s)
- Jia-Tao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | | | - Song-Rong Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Li-Xu Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jing Qin
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Kai Yin
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiang-Peng Chu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Meng-Min Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Hui-Zhao Hong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Zhi-Yi Lv
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Song Dong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Xiang Liu
- Echo Biotech Co, Ltd, Beijing, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital, (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
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26
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Hu Q, Frank ML, Gao Y, Ji L, Peng M, Chen C, Wang B, Hu Y, Wu Z, Li J, Shu L, He Q, Zhang Y, Xia X, Zhang J, Yi X, Reuben A, Yu F. Spatial heterogeneity of T cell repertoire across NSCLC tumors, tumor edges, adjacent and distant lung tissues. Oncoimmunology 2023; 12:2233399. [PMID: 37876834 PMCID: PMC10591778 DOI: 10.1080/2162402x.2023.2233399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 07/02/2023] [Indexed: 10/26/2023] Open
Abstract
Background A better understanding of T cells in lung cancer and their distribution across tumor-adjacent lungs and peripheral blood is needed to improve efficacy and minimize toxicity from immunotherapy to lung cancer patients. Methods Here, we performed CDR3β TCR sequencing of 136 samples from 20 patients with early-stage NSCLC including peripheral blood mononuclear cells, tumors, tumor edges (<1 cm from tumor), as well as adjacent lungs 1 cm, 2 cm, 5 cm, and 10 cm away from the tumor to gain insight into the spatial heterogeneity of T cells across the lungs in patients with NSCLC. PD-L1, CD4, and CD8 expression was assessed using immunohistochemical staining, and genomic features were derived by targeted sequencing of 1,021 cancer-related genes. Multiplex immunohistochemistry against PD-1, CTLA4, LAG3, and TIM3 was performed on four patients to assess T cell exhaustion. Results Our study reveals a decreasing gradient in TIL Tumor Infiltrating Lymphocytes homology with tumor edge, adjacent lungs, and peripheral blood but no discernible distance-associated patterns of T cell trafficking within the adjacent lung itself. Furthermore, we show a decrease in pathogen-specific TCRs in regions with high T cell clonality and PD-L1 expression. Conclusions Exclusion in T exhaustion cells at play across the lungs of patients with NSCLC may potentially be the mechanism for lung cancer occurrence.
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Affiliation(s)
- Qikang Hu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Meredith L. Frank
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Yang Gao
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, P. R. China
- Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha, China
- Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Changsha, China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing, China
| | - Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Bin Wang
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Yan Hu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zeyu Wu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Jina Li
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lu Shu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
| | | | | | | | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, USA
- Lung Cancer Genomics Program, University of Texas MD Anderson Cancer Center, Houston, USA
- Lung Cancer Interception Program, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing, China
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, P. R. China
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung Cancer, The Second Xiangya Hospital of Central South University, Changsha, China
- Early-Stage Lung Cancer Center, The Second Xiangya Hospital of Central South University, Changsha, China
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27
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Ying L, Zhang C, Reuben A, Tian Y, Jin J, Wang C, Bai J, Liu X, Fang J, Feng T, Xu C, Zhu R, Huang M, Lyu Y, Lu T, Pan X, Zhang J, Su D. Immune-active tumor-adjacent tissues are associated with favorable prognosis in stage I lung squamous cell carcinoma. iScience 2023; 26:107732. [PMID: 37694148 PMCID: PMC10483046 DOI: 10.1016/j.isci.2023.107732] [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: 03/05/2023] [Revised: 07/07/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
The immunogenomic features of tumor-adjacent lungs (TALs) in stage I lung squamous cell carcinoma (LUSC) are not clear. Multiomics analyses of tumor tissues and paired TALs from 59 stage I LUSC patients were performed. Compared to tumors, TALs exhibited a better-preserved immune contexture indicated by upregulation of immune pathways, increased immune infiltration, and higher expression of immune effector molecules. Notably, TALs had no mutations in PTEN and KEAP1, a lower incidence of human leukocyte antigen (HLA) loss and higher expression of HLA class I genes, major histocompatibility complex (MHC) I chaperones, and interferon (IFN)-γ-associated genes. Digital spatial profiling validated the generally higher immune infiltration in TALs and revealed a higher level of immune heterogeneity in LUSC tumors. Importantly, patients with higher immune infiltration in TALs had significantly longer survival, while high immune heterogeneity was associated with inferior patient survival. Our work can be considered in the selection of patients for adjuvant therapy, especially immunotherapy.
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Affiliation(s)
- Lisha Ying
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | | | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yiping Tian
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jiaoyue Jin
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Canming Wang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jing Bai
- Geneplus-Beijing Institute, Beijing, China
| | - Xinyuan Liu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- The Second Clinical Medical College, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang 310053, China
| | - Jianfei Fang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Tingting Feng
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Chenyang Xu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Rui Zhu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Minran Huang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yingqi Lyu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Tingting Lu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Department of Oncology, The First Clinical Medical College of Wenzhou Medical University, Wenzhou, Zhejiang 325015, China
| | - Xiaodan Pan
- Human Tissue Bank, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jianjun Zhang
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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28
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Xiang C, Zhang M, Shang Z, Chen S, Zhao J, Ding B, Jiang D, Zhu Q, Teng H, Zhu L, Shao J, Zhao R, Ye M, Yu Y, Han Y. Single-cell profiling reveals the trajectory of FOLR2-expressing tumor-associated macrophages to regulatory T cells in the progression of lung adenocarcinoma. Cell Death Dis 2023; 14:493. [PMID: 37532692 PMCID: PMC10397223 DOI: 10.1038/s41419-023-06021-6] [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: 12/30/2022] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/04/2023]
Abstract
An immunosuppressive microenvironment enriched with regulatory CD4+ T lymphocytes (Tregs) facilitates the progression of lung adenocarcinoma (LUAD). This study aims to investigate the cellular mechanism underlying the formation of the immunosuppressive microenvironment in LUAD. LUAD samples (n = 12) and normal lung samples (n = 3) were obtained from patients with different pathological stages of LUAD. Single-cell RNA sequencing was performed to classify cellular components and analyze the transcriptomes, including transcription factors/targets and chemokine ligands/receptors, followed by bioinformatics study such as pseudotime analysis. Myeloid cells and T cells were the most abundant cell types in tumors and normal lung tissues, while tumor-associated macrophage-folate receptor 2 (TAM-FOLR2) and CD4+ nuclear receptor subfamily 4 group A member 3 (NR4A3) exhibited sharp increases in invasive adenocarcinoma (IA). The enrichment of TAM-FOLR2 in IA might result from alveolar resident macrophage-resistin (ARM-RETN) transformation and recruitment of dendritic cells (DCs) and other TAMs, as evidenced by temporal trajectories and differential expression profiles of chemokine ligands/receptors versus those in the early stages of tumors. High expression of CCL17/19/22 was observed in IA as well as in DCs, along with the strong interaction of TAM-FOLR2 with DCs. The results of pseudotime analysis suggested that CD4+NR4A3 might potentially convert to CD4+FOXP3, further supported by the high expression of NR4A3 target genes in CD4+FOXP3 cells. This study provides a single-cell transcriptome atlas from preinvasive to invasive LUAD and reveals a potential ARM-RETN/TAM-FOLR2/DCs/CD4+NR4A3/CD4+FOXP3 trajectory in shaping the immune suppressive microenvironment along the pathogenesis of LUAD.
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Affiliation(s)
- Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Min Zhang
- Novogene Co., Ltd., Beijing, 100015, China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Bowen Ding
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Dong Jiang
- Novogene Co., Ltd., Beijing, 100015, China
| | - Qian Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Min Ye
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China
| | - Yang Yu
- Novogene Co., Ltd., Beijing, 100015, China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China.
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29
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Chen Z, Lau KS. Advances in Mapping Tumor Progression from Precancer Atlases. Cancer Prev Res (Phila) 2023; 16:439-447. [PMID: 37167978 PMCID: PMC10523872 DOI: 10.1158/1940-6207.capr-22-0473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/22/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
Tissue profiling technologies present opportunities for understanding transition from precancerous lesions to malignancy, which may impact risk stratification, prevention, and even cancer treatment. A human precancer atlas building effort is ongoing to tackle the significant challenge of decoding the heterogeneity among cells, specimens, and patients. Here, we discuss the findings resulting from atlases built across precancer types, including those found in colon, breast, lung, stomach, cervix, and skin, using bulk, single-cell, and spatial profiling strategies. We highlight two main themes that emerge across precancer types: the ordering of molecular events that occur during tumor progression and the fluctuation of microenvironmental response during precancer progression. We further highlight the key challenges of data integration across large cohorts of patients, and the need for computational tools to reliably annotate and quality control high-volume, high-dimensional data.
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Affiliation(s)
- Zhengyi Chen
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ken S. Lau
- Epithelial Biology Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Program in Chemical and Physical Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
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30
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Shang J, Jiang H, Zhao Y, Lai J, Shi L, Yang J, Chen H, Zheng Y. Differences of molecular events driving pathological and radiological progression of lung adenocarcinoma. EBioMedicine 2023; 94:104728. [PMID: 37506543 PMCID: PMC10406962 DOI: 10.1016/j.ebiom.2023.104728] [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: 02/10/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Ground-glass opacity (GGO)-like lung adenocarcinoma (LUAD) has been detected increasingly in the clinic and its inert property and superior survival indicate unique biological characteristics. However, we do not know much about them, which hampers identification of key reasons for the inert property of GGO-like LUAD. METHODS Using whole-exome sequencing and RNA sequencing, taking into account both radiological and pathological classifications of the same 197 patients concomitantly, we systematically interrogate genes driving the progression from GGO to solid nodule and potential reasons for the inertia of GGO. Using flow cytometry and IHC, we validated the abundance of immune cells and activity of cell proliferation. FINDINGS Identifying the differences between GGO and solid nodule, we found adenocarcinoma in situ/minimally invasive adenocarcinoma (AIS/MIA) and GGO-like LUAD exhibited lower TP53 mutation frequency and less active cell proliferation-related pathways than solid nodule in LUAD. Identifying the differences in GGO between AIS/MIA and LUAD, we noticed that EGFR mutation frequency and CNV load were significantly higher in LUAD than in AIS/MIA. Regulatory T cell was also higher in LUAD, while CD8+ T cell decreased from AIS/MIA to LUAD. Finally, we constructed a transcriptomic signature to quantify the development from GGO to solid nodule, which was an independent predictor of patients' prognosis in 11 external LUAD datasets. INTERPRETATION Our results provide deeper insights into the indolent nature of GGO and provide a molecular basis for the treatment of GGO-like LUAD. FUNDING This study was supported in part by the National Natural Science Foundation of China (32170657), the National Natural Science Foundation of China (82203037), and Shanghai Sailing Program (22YF1408900).
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Affiliation(s)
- Jun Shang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - He Jiang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Yue Zhao
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Jinglei Lai
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China
| | - Jingcheng Yang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China; Greater Bay Area Institute of Precision Medicine, 115 Jiaoxi Road, Guangzhou, China.
| | - Haiquan Chen
- Department of Thoracic Surgery, Shanghai Cancer Center, Fudan University, Shanghai, China; Institute of Thoracic Oncology, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China.
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31
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Tanaka M, Lum L, Hu K, Ledezma-Soto C, Samad B, Superville D, Ng K, Adams Z, Kersten K, Fong L, Combes AJ, Krummel M, Reeves M. Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538140. [PMID: 37162860 PMCID: PMC10168251 DOI: 10.1101/2023.04.25.538140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Intratumoral heterogeneity (ITH)-defined as genetic and cellular diversity within a tumor-is linked to failure of immunotherapy and an inferior anti-tumor immune response. The underlying mechanism of this association is unknown. To address this question, we modeled heterogeneous tumors comprised of a pro-inflammatory ("hot") and an immunosuppressive ("cold") tumor population, labeled with YFP and RFP tags respectively to enable precise spatial tracking. The resulting mixed-population tumors exhibited distinct regions comprised of YFP+ (hot) cells, RFP+ (cold) cells, or a mixture. We found that tumor regions occupied by hot tumor cells (YFP+) harbored more total T cells and a higher frequency of Th1 cells and IFNγ+ CD8 T cells compared to regions occupied by cold tumor cells (RFP+), whereas immunosuppressive macrophages showed the opposite spatial pattern. We identified the chemokine CX3CL1, produced at higher levels by our cold tumors, as a mediator of intratumoral macrophage accumulation, particularly immunosuppressive CD206Hi macrophages. Furthermore, we examined the response of heterogeneous tumors to a therapeutic combination of PD-1 blockade and CD40 agonist on a region-by-region basis. While the combination successfully increases Th1 abundance in "cold" tumor regions, it fails to bring overall T cell activity to the same level as seen in "hot" regions. The presence of the "cold" cells thus ultimately leads to a failure of the therapy to induce tumor rejection. Collectively, our results demonstrate that the organization of heterogeneous tumor cells has a profound impact on directing the spatial organization and function of tumor-infiltrating immune cells as well as on responses to immunotherapy.
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Affiliation(s)
- Miho Tanaka
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Lotus Lum
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Hu
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Cecilia Ledezma-Soto
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Bushra Samad
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Daphne Superville
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Kenneth Ng
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Zoe Adams
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Kelly Kersten
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Alexis J Combes
- UCSF CoLabs, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
- Division of Gastroenterology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Matthew Krummel
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- ImmunoX Initiative, University of California San Francisco, San Francisco, CA, USA
| | - Melissa Reeves
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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32
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Cui Y, Li J, Zhang P, Yin D, Wang Z, Dai J, Wang W, Zhang E, Guo R. B4GALT1 promotes immune escape by regulating the expression of PD-L1 at multiple levels in lung adenocarcinoma. J Exp Clin Cancer Res 2023; 42:146. [PMID: 37303063 DOI: 10.1186/s13046-023-02711-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
BACKGROUND Invasive adenocarcinoma (IAC), which is typically preceded by minimally invasive adenocarcinoma (MIA), is the dominant pathological subtype of early-stage lung adenocarcinoma (LUAD). Identifying the molecular events underlying the progression from MIA to IAC may provide a crucial perspective and boost the exploration of novel strategies for early-stage LUAD diagnosis and treatment. METHODS Transcriptome sequencing of four pairs of MIA and IAC tumours obtained from four multiple primary lung cancer patients was performed to screen out beta-1,4-galactosyltransferase1 (B4GALT1). Function and mechanism experiments in vitro and in vivo were performed to explore the regulatory mechanism of B4GALT1-mediated immune evasion by regulating programmed cell death ligand 1 (PD-L1). RESULTS B4GALT1, a key gene involved in N-glycan biosynthesis, was highly expressed in IAC samples. Further experiments revealed that B4GALT1 regulated LUAD cell proliferation and invasion both in vitro and in vivo and was related to the impaired antitumour capacity of CD8 + T cells. Mechanistically, B4GALT1 directly mediates the N-linked glycosylation of PD-L1 protein, thus preventing PD-L1 degradation at the posttranscriptional level. In addition, B4GALT1 stabilized the TAZ protein via glycosylation, which activated CD274 at the transcriptional level. These factors lead to lung cancer immune escape. Importantly, inhibition of B4GALT1 increased CD8 + T-cell abundance and activity and enhanced the antitumour immunity of anti-PD-1 therapy in vivo. CONCLUSION B4GALT1 is a critical molecule in the development of early-stage LUAD and may be a novel target for LUAD intervention and immunotherapy.
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Affiliation(s)
- Yanan Cui
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Jun Li
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Pengpeng Zhang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Dandan Yin
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Zhong Fu Road, Gulou District, Nanjing, Jiangsu, 210003, P. R. China
| | - Ziyu Wang
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Jiali Dai
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China
| | - Wei Wang
- Department of Thoracic Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
| | - Erbao Zhang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, 211166, China.
| | - Renhua Guo
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, P. R. China.
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33
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Huzar J, Shenoy M, Sanderford MD, Kumar S, Miura S. Bootstrap confidence for molecular evolutionary estimates from tumor bulk sequencing data. FRONTIERS IN BIOINFORMATICS 2023; 3:1090730. [PMID: 37261293 PMCID: PMC10228696 DOI: 10.3389/fbinf.2023.1090730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 03/28/2023] [Indexed: 06/02/2023] Open
Abstract
Bulk sequencing is commonly used to characterize the genetic diversity of cancer cell populations in tumors and the evolutionary relationships of cancer clones. However, bulk sequencing produces aggregate information on nucleotide variants and their sample frequencies, necessitating computational methods to predict distinct clone sequences and their frequencies within a sample. Interestingly, no methods are available to measure the statistical confidence in the variants assigned to inferred clones. We introduce a bootstrap resampling approach that combines clone prediction and statistical confidence calculation for every variant assignment. Analysis of computer-simulated datasets showed the bootstrap approach to work well in assessing the reliability of predicted clones as well downstream inferences using the predicted clones (e.g., mapping metastatic migration paths). We found that only a fraction of inferences have good bootstrap support, which means that many inferences are tentative for real data. Using the bootstrap approach, we analyzed empirical datasets from metastatic cancers and placed bootstrap confidence on the estimated number of mutations involved in cell migration events. We found that the numbers of driver mutations involved in metastatic cell migration events sourced from primary tumors are similar to those where metastatic tumors are the source of new metastases. So, mutations with driver potential seem to keep arising during metastasis. The bootstrap approach developed in this study is implemented in software available at https://github.com/SayakaMiura/CloneFinderPlus.
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Affiliation(s)
- Jared Huzar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Madelyn Shenoy
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Maxwell D Sanderford
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
- Center for Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayaka Miura
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, United States
- Department of Biology, Temple University, Philadelphia, PA, United States
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34
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Ji XY, Li H, Chen HH, Lin J. Diagnostic performance of RASSF1A and SHOX2 methylation combined with EGFR mutations for differentiation between small pulmonary nodules. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04745-8. [PMID: 37097393 DOI: 10.1007/s00432-023-04745-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 04/03/2023] [Indexed: 04/26/2023]
Abstract
BACKGROUND AND AIM Aberrant methylation of Ras association domain family 1, isoform A (RASSF1A), and short-stature homeobox gene 2 (SHOX2) promoters has been validated as a pair of valuable biomarkers for diagnosing early lung adenocarcinomas (LUADs). Epidermal growth factor receptor (EGFR) is the key driver mutation in lung carcinogenesis. This study aimed to investigate the aberrant promoter methylation of RASSF1A and SHOX2, and the genetic mutation of EGFR in 258 specimens of early LUADs. METHODS We retrospectively selected 258 paraffin-embedded samples of pulmonary nodules measuring 2 cm or less in diameter and evaluated the diagnostic performance of individual biomarker assays and multiple panels between noninvasive (group 1) and invasive lesions (groups 2A and 2B). Then, we investigated the interaction between genetic and epigenetic alterations. RESULTS The degree of RASSF1A and SHOX2 promoter methylation and EGFR mutation was significantly higher in invasive lesions than in noninvasive lesions. The three biomarkers distinguished between noninvasive and invasive lesions with reliable sensitivity and specificity: 60.9% sensitivity [95% confidence interval (CI) 52.41-68.78] and 80.0% specificity (95% CI 72.14-86.07). The novel panel biomarkers could further discriminate among three invasive pathological subtypes (area under the curve value > 0.6). The distribution of RASSF1A methylation and EGFR mutation was considerably exclusive in early LUAD (P = 0.002). CONCLUSION DNA methylation of RASSF1A and SHOX2 is a pair of promising biomarkers, which may be used in combination with other driver alterations, such as EGFR mutation, to support the differential diagnosis of LUADs, especially for stage I.
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Affiliation(s)
- Xiang-Yu Ji
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China
| | - Hong Li
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Hui-Hui Chen
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Jie Lin
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, People's Republic of China.
- National Virtual and Reality Experimental Education Center for Medical Morphology, Southern Medical University, Guangzhou, People's Republic of China.
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35
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Zhu J, Wang W, Xiong Y, Xu S, Chen J, Wen M, Zhao Y, Lei J, Jiang T. Evolution of lung adenocarcinoma from preneoplasia to invasive adenocarcinoma. Cancer Med 2023; 12:5545-5557. [PMID: 36325966 PMCID: PMC10028051 DOI: 10.1002/cam4.5393] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/16/2022] [Accepted: 10/21/2022] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE Mutations in driver genes contribute to the development and progression of lung adenocarcinoma (LUAD). However, in the dynamic evolutionary process from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and eventually to invasive adenocarcinoma (IAC), the role of driver genes is currently unclear. This study aimed to analyse the role of driver gene status in the progression of LUAD from preneoplasia to IAC. METHODS Patients with LUAD who underwent surgery in our centre from March 2015 to December 2019 were retrospectively analysed, and LUAD patients with tumour sizes ≤3.0 cm and pN0 were included in the final analysis. The mutation status of common driver genes, including EGFR, ALK and ROS1, was detected. According to the pathological characteristics, the patients were divided into three stages: AIS, MIA and IAC. We analysed the distribution of driver gene mutation frequencies across three stages of LUAD. In addition, we performed univariate and multivariate analyses of IAC patients to screen for relevant variables (driver genes and clinicopathological features) affecting their prognosis. RESULTS Ultimately, 759 patients with LUAD were enrolled, including 135, 130, and 494 cases of AIS, MIA, and IAC, respectively. EGFR mutations were identified in 359 (61.8%) patients, and with the transition from AIS to MIA, the frequency of EGFR mutations increased from 33.3% to 50.8%, p = 0.004, whereas the frequency of EGFR mutations was comparable for MIA and IAC (50.8% vs. 50.2%, p = 0.922). Moreover, ALK and ROS1 gene fusions were identified in 17 cases (2.2%) and 2 cases (3.0‰) respectively. For AIS, neither ALK gene nor ROS1 gene fusions were observed. When the tumour progressed to MIA, the ALK fusion frequency was 2.3% (3/130), which was basically consistent with the ALK fusion frequency of 2.8% in IAC, p = 0.143. For IAC, fusions of ROS1 fell into this category. In addition, we found that 40 patients (5.3%) developed metastasis/recurrence, and 14 patients (1.8%) died of cancer-specific related diseases. Notably, for AIS, there were no recurrences and no deaths, and for MIA, only 1 patient died with LUAD. Finally, survival analysis was performed in patients with stage IA invasive adenocarcinoma, and EGFR-mutant patients showed better DFS than EGFR-wild-type patients (p = 0.036). Conversely, patients with ALK fusions showed worse DFS than those with ALK wild-type (p = 0.004), and the same results were found in OS analysis. CONCLUSIONS The accumulation of EGFR driver gene mutation frequencies mediates the progression of LUAD from AIS to MIA. When the tumour progresses to stage IA invasive adenocarcinoma, multivariate analysis based on driver gene status can be used as a pivotal prognostic factor.
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Affiliation(s)
- Jianfei Zhu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
- Department of Thoracic Surgery, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Wenchen Wang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yanlu Xiong
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Shuonan Xu
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jiankuan Chen
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Miaomiao Wen
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yabo Zhao
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Jie Lei
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
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Kong W, Chen T, Li Y. Diagnosis, Monitoring, and Prognosis of Liquid Biopsy in Cancer Immunotherapy. Methods Mol Biol 2023; 2695:127-143. [PMID: 37450116 DOI: 10.1007/978-1-0716-3346-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy (LB), as a minimally invasive method of gleaning insight into the dynamics of diseases through a patient fluid sample, represents an interesting tool that can advise in disease monitoring, treatment selection, early diagnosis, evaluation of the response, and prognosis. Cancer immunotherapy is a breakthrough in cancer treatment, which is now recognized as the "fourth pillar" of cancer treatment, after surgery, chemotherapy, and radiotherapy. Liquid biopsy offers a different befalling for beneath invasive diagnosis, real-time accommodating monitoring, and analysis options, involving the isolation of circulating biomarkers, such as cell-free DNA (cfDNA), circulating tumor cells (CTCs), exosomes, and microRNAs (miRNAs). The biomarkers herein have great potential to allow the realization of liquid biopsy for predicting the immunotherapy response and precision medicine. Liquid biopsy offers an alternative, less invasive approach to select cancer patients who would benefit from immunotherapy and to monitor patients during their disease course. This review focuses on the use of liquid biopsy in the immunotherapy treatment of patients with cancer. In this review, we addressed the different promising liquid biopsy-based biomarkers in cancer patients that enable the selection of patients who benefit from immunotherapy and the monitoring of patients during this therapy.
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Affiliation(s)
- Weiying Kong
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Tengxiang Chen
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China.
| | - Yixin Li
- The Department of Histology and Embryology, Guizhou Medical University, Guiyang, Guizhou, China
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Yu F, Peng M, Bai J, Zhu X, Zhang B, Tang J, Liu W, Chen C, Wang X, Chen M, Tan S, Sun Y, Liang Q, Li J, Hu Y, Liao A, Hu H, He Y, Xiao X, Wang B, Xing G, Xu Y, Chen R, Xia X, Chen X. Comprehensive characterization of genomic and radiologic features reveals distinct driver patterns of RTK/RAS pathway in ground-glass opacity pulmonary nodules. Int J Cancer 2022; 151:2020-2030. [PMID: 36029220 PMCID: PMC9805018 DOI: 10.1002/ijc.34238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 01/09/2023]
Abstract
Ground-glass opacity (GGO)-associated pulmonary nodules have been known as a radiologic feature of early-stage lung cancers and exhibit an indolent biological behavior. However, the correlation between driver genes and radiologic features as well as the immune microenvironment remains poorly understood. We performed a custom 1021-gene panel sequencing of 334 resected pulmonary nodules presenting as GGO from 262 Chinese patients. A total of 130 multiple pulmonary nodules were sampled from 58 patients. Clinical-pathologic and radiologic parameters of these pulmonary nodules were collected. Immunohistochemistry (IHC) and multiplex immunofluorescent staining (mIF) were applied to analyze proliferation and immune cell markers of GGO-associated pulmonary nodules. Compared with pure GGO nodules, mixed GGO nodules were enriched for invasive adenocarcinoma (IAC) (182/216 vs 73/118, P < .001). Eighty-eight percent (294/334) of GGO-associated nodules carried at least one mutation in EGFR/ERBB2/BRAF/KRAS/MAP2K1 of the RTK/RAS signaling pathway, and the alterations in these driver genes were mutually exclusive. The analysis of multifocal pulmonary nodules from the same patient revealed evidence of functional convergence on RTK/RAS pathways. Nodules with ERBB2/BRAF/MAP2K1 mutations tended to be more indolent than those with EGFR and KRAS mutations. IHC and mIF staining showed that KRAS-mutant GGO nodules displayed higher infiltration of CD4+ T cell and CD8+ T cell as well as stronger proliferation and immune inhibitory signals. Our study demonstrates a driver landscape of radiologically detectable GGO-associated pulmonary nodules in Chinese patients and supports that different driver patterns in RTK/RAS pathway are corresponding to different radiologic features.
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Affiliation(s)
- Fenglei Yu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Muyun Peng
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jing Bai
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xiuli Zhu
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Bingyu Zhang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jingqun Tang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Wenliang Liu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Chen Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xiang Wang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Mingjiu Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Sichuang Tan
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yi Sun
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of PathologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Qingchun Liang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of PathologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jina Li
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Yan Hu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Aihui Liao
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgeryHunan Geological and Mineral HospitalChangshaChina
| | - Huali Hu
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of General SurgeryHunan Geological and Mineral HospitalChangshaChina
| | - Yu He
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xiao Xiao
- Geneplus‐ShenzhenShenzhenGuangdong ProvinceChina
| | - Bin Wang
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of Thoracic SurgeryThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Guanlan Xing
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Yaping Xu
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Rongrong Chen
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xuefeng Xia
- Geneplus‐Beijing InstitutePeking University Medical Industrial ParkBeijingChina
| | - Xiaofeng Chen
- Hunan Key Laboratory of Early Diagnosis and Precise Treatment of Lung CancerThe Second Xiangya Hospital of Central South UniversityChangshaChina,Early‐Stage Lung Cancer CenterThe Second Xiangya Hospital of Central South UniversityChangshaChina,Department of AnesthesiaThe Second Xiangya Hospital of Central South UniversityChangshaChina
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Delineating the dynamic evolution from preneoplasia to invasive lung adenocarcinoma by integrating single-cell RNA sequencing and spatial transcriptomics. Exp Mol Med 2022; 54:2060-2076. [PMID: 36434043 PMCID: PMC9722784 DOI: 10.1038/s12276-022-00896-9] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/18/2022] [Accepted: 10/05/2022] [Indexed: 11/27/2022] Open
Abstract
The cell ecology and spatial niche implicated in the dynamic and sequential process of lung adenocarcinoma (LUAD) from adenocarcinoma in situ (AIS) to minimally invasive adenocarcinoma (MIA) and subsequent invasive adenocarcinoma (IAC) have not yet been elucidated. Here, we performed an integrative analysis of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) to characterize the cell atlas of the invasion trajectory of LUAD. We found that the UBE2C + cancer cell subpopulation constantly increased during the invasive process of LUAD with remarkable elevation in IAC, and its spatial distribution was in the peripheral cancer region of the IAC, representing a more malignant phenotype. Furthermore, analysis of the TME cell type subpopulation showed a constant decrease in mast cells, monocytes, and lymphatic endothelial cells, which were implicated in the whole process of invasive LUAD, accompanied by an increase in NK cells and MALT B cells from AIS to MIA and an increase in Tregs and secretory B cells from MIA to IAC. Notably, for AIS, cancer cells, NK cells, and mast cells were colocalized in the cancer region; however, for IAC, Tregs colocalized with cancer cells. Finally, communication and interaction between cancer cells and TME cell-induced constitutive activation of TGF-β signaling were involved in the invasion of IAC. Therefore, our results reveal the specific cellular information and spatial architecture of cancer cells and TME subpopulations, as well as the cellular interaction between them, which will facilitate the identification and development of precision medicine in the invasive process of LUAD from AIS to IAC.
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Cheng H, Guo Z, Zhang X, Wang XJ, Li Z, Huo WW, Zhong HC, Li XJ, Wu XW, Li WH, Chen ZW, Wu TC, Gan XF, Zhong BL, Lyubetsky VA, Rusin LY, Yang J, Zhao Q, Cao QD, Yang JR. Lack of evolutionary convergence in multiple primary lung cancer suggests insufficient specificity of personalized therapy. J Genet Genomics 2022; 50:330-340. [PMID: 36414223 DOI: 10.1016/j.jgg.2022.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 11/20/2022]
Abstract
Multiple primary lung cancer (MPLC) is an increasingly prevalent subtype of lung cancer. According to recent genomic studies, the different lesions of a single MPLC patient exhibit functional similarities that may reflect evolutionary convergence. We performed whole-exome sequencing for a unique cohort of MPLC patients with multiple samples from each lesion found. Using our own and other relevant public data, evolutionary tree reconstruction revealed that cancer driver gene mutations occurred at the early trunk, indicating evolutionary contingency rather than adaptive convergence. Additionally, tumors from the same MPLC patient are as genetically diverse as those from different patients, while within-tumor genetic heterogeneity is significantly lower. Furthermore, the aberrant molecular functions enriched in mutated genes for a sample show a strong overlap with other samples from the same tumor, but not with samples from other tumors or other patients. Overall, there is no evidence of adaptive convergence during the evolution of MPLC. Most importantly, the similar between-tumor diversity and between-patient diversity suggest that personalized therapies may not adequately account for the genetic diversity among different tumors in an MPLC patient. To fully exploit the strategic value of precision medicine, targeted therapies should be designed and delivered on a per-lesion basis.
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Affiliation(s)
- Hua Cheng
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Ziyan Guo
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiaoyu Zhang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiao-Jin Wang
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zizhang Li
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wen-Wen Huo
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Hong-Cheng Zhong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiao-Jian Li
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiang-Wen Wu
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Wen-Hao Li
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Zhuo-Wen Chen
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Tian-Chi Wu
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Xiang-Feng Gan
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Bei-Long Zhong
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China
| | - Vassily A Lyubetsky
- Kharkevich Institute for Information Transmission Problems Russian Academy Sciences, Moscow 127051, Russia; Department of Mathematical Logic and Theory of Algorithms, Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Leonid Yu Rusin
- Kharkevich Institute for Information Transmission Problems Russian Academy Sciences, Moscow 127051, Russia
| | - Junnan Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Qiyi Zhao
- Department of Infectious Diseases, Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510630, China; Guangdong Provincial Key Laboratory of Liver Disease Research the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510630, China
| | - Qing-Dong Cao
- Department of Thoracic Surgery, The Fifth Affiliated Hospital, Sun Yat-Sen University, Zhuhai, Guangdong 519000, China.
| | - Jian-Rong Yang
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Program in Cancer Research, Zhongshan School of Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.
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40
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Rahal Z, Sinjab A, Wistuba II, Kadara H. Game of clones: Battles in the field of carcinogenesis. Pharmacol Ther 2022; 237:108251. [PMID: 35850404 PMCID: PMC10249058 DOI: 10.1016/j.pharmthera.2022.108251] [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: 03/01/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 11/22/2022]
Abstract
Recent advances in bulk sequencing approaches as well as genomic decoding at the single-cell level have revealed surprisingly high somatic mutational burdens in normal tissues, as well as increased our understanding of the landscape of "field cancerization", that is, molecular and immune alterations in mutagen-exposed normal-appearing tissues that recapitulated those present in tumors. Charting the somatic mutational landscapes in normal tissues can have strong implications on our understanding of how tumors arise from mutagenized epithelium. Making sense of those mutations to understand the progression along the pathologic continuum of normal epithelia, preneoplasias, up to malignant tissues will help pave way for identification of ideal targets that can guide new strategies for preventing or eliminating cancers at their earliest stages of development. In this review, we will provide a brief history of field cancerization and its implications on understanding early stages of cancer pathogenesis and deviation from the pathologically "normal" state. The review will provide an overview of how mutations accumulating in normal tissues can lead to a patchwork of mutated cell clones that compete while maintaining an overall state of functional homeostasis. The review also explores the role of clonal competition in directing the fate of normal tissues and summarizes multiple mechanisms elicited in this phenomenon and which have been linked to cancer development. Finally, we highlight the importance of understanding mutations in normal tissues, as well as clonal competition dynamics (in both the epithelium and the microenvironment) and their significance in exploring new approaches to combatting cancer.
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Affiliation(s)
- Zahraa Rahal
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, USA.
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Xiang C, Ji C, Cai Y, Teng H, Wang Y, Zhao R, Shang Z, Guo L, Chen S, Lizaso A, Lin J, Wang H, Li B, Zhang Z, Zhao J, Wei J, Liu J, Zhu L, Fang W, Han Y. Distinct mutational features across preinvasive and invasive subtypes identified through comprehensive profiling of surgically resected lung adenocarcinoma. Mod Pathol 2022; 35:1181-1192. [PMID: 35641658 PMCID: PMC9424111 DOI: 10.1038/s41379-022-01076-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 01/11/2023]
Abstract
Lung adenocarcinoma (LUAD) is a heterogeneous disease. Our study aimed to understand the unique molecular features of preinvasive to invasive LUAD subtypes. We retrospectively analyzed the clinical, histopathological, and molecular data of 3,254 Chinese patients with preinvasive lesions (n = 252), minimally invasive adenocarcinomas (n = 479), and invasive LUAD (n = 2,523). Molecular data were elucidated using a targeted 68-gene next-generation sequencing panel. Our findings revealed four preinvasive lesion-predominant gene mutations, including MAP2K1 insertion-deletions (indels), BRAF non-V600E kinase mutations, and exon 20 insertions (20ins) in both EGFR and ERBB2, which we referred to as mutations enriched in AIS (MEA). The detection rate of MEA in invasive tumors was relatively lower. MAP2K1 missense mutations, which were likely passenger mutations, co-occurred with oncogenic driver mutations, while small indels were mutually exclusive from other genes regardless of the invasion level. BRAF non-V600E kinase-mutant invasive adenocarcinomas (IAC) had significantly higher mutation rates in tumor suppressor genes but lower frequency of co-occurring oncogenic driver mutations than non-kinase-mutant IAC, suggesting the potential oncogenic activity of BRAF non-V600E kinase mutations albeit weaker than BRAF V600E. Moreover, similar to the extremely low frequency of MAP2K1 indels in IAC, BRAF non-V600E kinase domain mutations co-occurring with TSC1 mutations were exclusively found in preinvasive lesions. Compared with EGFR L858R and exon 19 deletion, patients with preinvasive lesions harboring 20ins in either EGFR or ERBB2 were significantly younger, while those with IAC had similar age. Furthermore, our study demonstrated distinct mutational features for subtypes of oncogene mutations favored by different invasion patterns in adenocarcinomas. In conclusion, our data demonstrate distinct mutational features between preinvasive lesions and invasive tumors with MEA, suggesting the involvement of MEA in the early stages of tumorigenesis. Further pre-clinical studies are required to establish the role of these genes in the malignant transformation of LUAD.
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Affiliation(s)
- Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Chunyu Ji
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yiran Cai
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Yulu Wang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Zhanxian Shang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | | | - Jing Lin
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Haozhe Wang
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Bing Li
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Zhou Zhang
- Burning Rock Biotech, Guangzhou, 510300, China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinzhi Wei
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jiaxin Liu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Wentao Fang
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, China.
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Distinct cellular immune profiles in lung adenocarcinoma manifesting as pure ground glass opacity versus solid nodules. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04289-3. [DOI: 10.1007/s00432-022-04289-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/14/2022] [Indexed: 10/15/2022]
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43
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Zhang G, Yan B, Guo Y, Yang H, Li J. "Sandwich" Strategy to Intensify EGFR Blockade by Concurrent Tyrosine Kinase Inhibitor and Monoclonal Antibody Treatment in Highly Selected Patients. Front Oncol 2022; 12:952939. [PMID: 35903676 PMCID: PMC9321780 DOI: 10.3389/fonc.2022.952939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/16/2022] [Indexed: 02/03/2023] Open
Abstract
EGFR TKIs are not curative, and targeted resistance inevitably results in therapeutic failure. Additionally, there are numerous uncommon EGFR mutations that are insensitive to EGFR TKIs, and there is a lack of clinical strategies to overcome these limitations. EGFR TKI and mAbs target EGFR at different sites, and a combination regimen for delaying/preventing resistance to targeted therapy or obtaining more intensive inhibition for uncommon mutations at cellular, animal and human levels has been explored. This review critically focuses on a combination strategy for uncommon EGFR mutation-positive NSCLC, and discuss the preclinical data, clinical implications, limitations and future prospects of the combination strategy.
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Affiliation(s)
- Guoqing Zhang
- Department of Thoracic Surgery and Lung Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Beibei Yan
- Department of Thoracic Surgery and Lung Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanan Guo
- Department of Thoracic Surgery and Lung Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hang Yang
- Department of Thoracic Surgery and Lung Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jindong Li
- Department of Thoracic Surgery and Lung Transplantation, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Parker AL, Toulabi L, Oike T, Kanke Y, Patel D, Tada T, Taylor S, Beck JA, Bowman E, Reyzer ML, Butcher D, Kuhn S, Pauly GT, Krausz KW, Gonzalez FJ, Hussain SP, Ambs S, Ryan BM, Wang XW, Harris CC. Creatine riboside is a cancer cell-derived metabolite associated with arginine auxotrophy. J Clin Invest 2022; 132:157410. [PMID: 35838048 PMCID: PMC9282934 DOI: 10.1172/jci157410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/25/2022] [Indexed: 12/17/2022] Open
Abstract
The metabolic dependencies of cancer cells have substantial potential to be exploited to improve the diagnosis and treatment of cancer. Creatine riboside (CR) is identified as a urinary metabolite associated with risk and prognosis in lung and liver cancer. However, the source of high CR levels in patients with cancer as well as their implications for the treatment of these aggressive cancers remain unclear. By integrating multiomics data on lung and liver cancer, we have shown that CR is a cancer cell–derived metabolite. Global metabolomics and gene expression analysis of human tumors and matched liquid biopsies, together with functional studies, revealed that dysregulation of the mitochondrial urea cycle and a nucleotide imbalance were associated with high CR levels and indicators of a poor prognosis. This metabolic phenotype was associated with reduced immune infiltration and supported rapid cancer cell proliferation that drove aggressive tumor growth. CRhi cancer cells were auxotrophic for arginine, revealing a metabolic vulnerability that may be exploited therapeutically. This highlights the potential of CR not only as a poor-prognosis biomarker but also as a companion biomarker to inform the administration of arginine-targeted therapies in precision medicine strategies to improve survival for patients with cancer.
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Affiliation(s)
- Amelia L Parker
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Leila Toulabi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Takahiro Oike
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Yasuyuki Kanke
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Daxeshkumar Patel
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Takeshi Tada
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Sheryse Taylor
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Jessica A Beck
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Elise Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Michelle L Reyzer
- National Research Resource for Imaging Mass Spectrometry, Vanderbilt University, Nashville, Tennessee, USA
| | - Donna Butcher
- Pathology and Histotechnology Laboratory, Frederick National Laboratory, Frederick, Maryland, USA
| | - Skyler Kuhn
- Center for Cancer Research Collaborative Bioinformatics Resource
| | | | | | | | - S Perwez Hussain
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA.,Liver Cancer Program, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, Maryland, USA
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45
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Chen K, Yang A, Carbone DP, Kanu N, Liu K, Wang R, Nie Y, Shen H, Bai J, Wu L, Li H, Shi Y, Mok T, Yu J, Yang F, Wu S, Jamal-Hanjani M, Wang J. Spatiotemporal genomic analysis reveals distinct molecular features in recurrent stage I non-small cell lung cancers. Cell Rep 2022; 40:111047. [PMID: 35830809 DOI: 10.1016/j.celrep.2022.111047] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
Stage I non-small cell lung cancer (NSCLC) presents diverse outcomes. To identify molecular features leading to tumor recurrence in early-stage NSCLC, we perform multiregional whole-exome sequencing (WES), RNA sequencing, and plasma-targeted circulating tumor DNA (ctDNA) detection analysis between recurrent and recurrent-free stage I NSCLC patients (CHN-P cohort) who had undergone R0 resection with a median 5-year follow-up time. Integrated analysis indicates that the multidimensional clinical and genomic model can stratify the prognosis of stage I NSCLC in both CHN-P and EUR-T cohorts and correlates with positive pre-surgical deep next generation sequencing (NGS) ctDNA detection. Increased genomic instability related to DNA interstrand crosslinks and double-strand break repair processes is significantly associated with early tumor relapse. This study reveals important molecular insights into stage I NSCLC and may inform clinical postoperative treatment and follow-up strategies.
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Affiliation(s)
- Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Airong Yang
- Berry Oncology Corporation, Beijing 100102, China
| | | | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ke Liu
- Berry Oncology Corporation, Beijing 100102, China
| | - Ruiru Wang
- Berry Oncology Corporation, Beijing 100102, China
| | - Yuntao Nie
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Haifeng Shen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China
| | - Jian Bai
- Berry Oncology Corporation, Beijing 100102, China
| | - Lin Wu
- Berry Oncology Corporation, Beijing 100102, China
| | - Hui Li
- Berry Oncology Corporation, Beijing 100102, China
| | - Yanbin Shi
- Berry Oncology Corporation, Beijing 100102, China
| | - Tony Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- University of Chinese Academy of Sciences, Beijing 100101, China
| | - Fan Yang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
| | - Shuangxiu Wu
- Berry Oncology Corporation, Beijing 100102, China.
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Jun Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing 100044, China.
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46
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Zhao Y, Shang J, Gao J, Han H, Gao Z, Yan Y, Zheng Q, Ye T, Fu F, Deng C, Ma Z, Zhang Y, Zheng D, Zheng S, Li Y, Cao Z, Shi L, Chen H. Increased Tumor Intrinsic Growth Potential and Decreased Immune Function Orchestrate the Progression of Lung Adenocarcinoma. Front Immunol 2022; 13:921761. [PMID: 35844495 PMCID: PMC9283781 DOI: 10.3389/fimmu.2022.921761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background The overall 5-year survival of lung cancer was reported to be only ~15%, with lung adenocarcinoma (LUAD) as the main pathological subtype. Before developing into invasive stages, LUAD undergoes pre-invasive stages of adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA), where surgical resection gives an excellent 5-year survival rate. Given the dramatic decline of prognosis from pre-invasive to invasive stages, a deeper understanding of key molecular changes driving the progression of LUAD is highly needed. Methods In this study, we performed whole-exome sequencing and RNA sequencing on surgically resected 24 AIS, 74 MIA, 99 LUAD specimens, and their adjacent paired normal tissues. Survival data were obtained by follow-up after surgery. Key molecular events were found by comparing the gene expression profiles of tumors with different stages. Finally, to measure the level of imbalance between tumor intrinsic growth potential and immune microenvironment, a tumor progressive (TP) index was developed to predict tumor progression and patients’ survival outcome and validated by external datasets. Results As tumors progressed to more invasive stages, they acquired higher growth potential, mutational frequency of tumor suppressor genes, somatic copy number alterations, and tumor mutation burden, along with suppressed immune function. To better predict tumor progression and patients’ outcome, TP index were built to measure the imbalance between tumor intrinsic growth potential and immune microenvironment. Patients with a higher TP index had significantly worse recurrence-free survival [Hazard ratio (HR), 10.47; 95% CI, 3.21–34.14; p < 0.0001] and overall survival (OS) [Hazard ratio (HR), 4.83e8; 95% CI, 0–Inf; p = 0.0013]. We used The Cancer Genome Atlas (TCGA)-LUAD dataset for validation and found that patients with a higher TP index had significantly worse OS (HR, 1.10; 95% CI, 0.83–1.45; p = 0.048), demonstrating the prognostic value of the TP index for patients with LUAD. Conclusions The imbalance of tumor intrinsic growth potential and immune function orchestrate the progression of LUAD, which can be measured by TP index. Our study provided new insights into predicting survival of patients with LUAD and new target discovery for LUAD through assessing the imbalance between tumor intrinsic growth potential and immune function.
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Affiliation(s)
- Yue Zhao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jun Shang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jian Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- International Human Phenome Institutes (Shanghai), Shanghai, China
| | - Han Han
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhendong Gao
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yueren Yan
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qiang Zheng
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ting Ye
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Fangqiu Fu
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chaoqiang Deng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zelin Ma
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhang
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Difan Zheng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shanbo Zheng
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Zhiwei Cao
- School of Life Sciences, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
| | - Leming Shi
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, School of Life Sciences and Shanghai Cancer Center, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
| | - Haiquan Chen
- Department of Thoracic Surgery and State Key Laboratory of Genetic Engineering, Fudan University Shanghai Cancer Center, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- *Correspondence: Haiquan Chen, ; Leming Shi, ; Zhiwei Cao,
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47
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Fu B, Lu L, Huang H. Constructing a Prognostic Gene Signature for Lung Adenocarcinoma Based on Weighted Gene Co-Expression Network Analysis and Single-Cell Analysis. Int J Gen Med 2022; 15:5441-5454. [PMID: 35685695 PMCID: PMC9173729 DOI: 10.2147/ijgm.s353848] [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: 12/17/2021] [Accepted: 05/27/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Lung adenocarcinoma (LUAD) has a high degree of intratumor heterogeneity. Advanced single-cell RNA sequencing (scRNA-seq) technologies have offered tools to analyze intratumor heterogeneity, which improves the accuracy of identifying biomarkers based on single-cell expression data, and thus helps in predicting prognosis of cancer patients and assisting decision-makings for cancer treatment. Patients and Methods ScRNA-seq data containing two LUAD and two para-cancerous tissue samples were included to identify different cell clusters in tumor tissues. To identify the most relevant modules and important cell subpopulations (clusters) in LUAD tissues, weighted gene co-expression network analysis (WGCNA) was performed. Subsequently, LUAD molecular subtypes were constructed by unsupervised consensus clustering based on genes in key modules. Using differential analysis, univariate Cox regression analysis, and least absolute shrinkage and selection operator (LASSO) regression analysis, a prognostic model of LUAD was established. Results A total of 14 cell clusters belonging to 10 cell types in LUAD were identified. The turquoise module was the most relevant to LUAD among all the modules; cluster 10 (C10, lung epithelial cells) was found to be the most strongly associated with the turquoise module. LUAD samples were divided into two groups of distinct molecular subtypes. Based on the 165 shared genes between the turquoise module and C10, 511 DEGs between the two molecular subtypes were obtained, and five of them were selected to construct the gene signature, which was validated to be an independent prognostic marker of LUAD. Conclusion Fourteen cell clusters co-existed in LUAD, which contributed to its intratumor heterogeneity. Two molecular subtypes of LUAD were identified and a five-gene signature was developed and validated to be significantly associated with prognostic and clinical characteristics of LUAD patients.
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Affiliation(s)
- Biqian Fu
- Internal Medicine-Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, People’s Republic of China
| | - Lin Lu
- Internal Medicine-Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, People’s Republic of China
| | - Haifu Huang
- Internal Medicine-Oncology, Shenzhen Hospital of Guangzhou University of Traditional Chinese Medicine, Shenzhen, People’s Republic of China
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48
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Li X, Chen K, Yang F, Wang J. Perspectives on early-stage lung cancer identification and challenges to thoracic surgery. Chronic Dis Transl Med 2022; 8:79-82. [PMID: 35774430 DOI: 10.1002/cdt3.28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/12/2022] [Accepted: 04/20/2022] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xiao Li
- Department of Thoracic Surgery Peking University People's Hospital Beijing 100044 China
| | - Kezhong Chen
- Department of Thoracic Surgery Peking University People's Hospital Beijing 100044 China
| | - Fan Yang
- Department of Thoracic Surgery Peking University People's Hospital Beijing 100044 China
| | - Jun Wang
- Department of Thoracic Surgery Peking University People's Hospital Beijing 100044 China
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49
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Xu H, Clemenceau JR, Park S, Choi J, Lee SH, Hwang TH. Spatial heterogeneity and organization of tumor mutation burden with immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer. J Pathol Inform 2022; 13:100105. [PMID: 36268064 PMCID: PMC9577053 DOI: 10.1016/j.jpi.2022.100105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 02/07/2023] Open
Abstract
Background High tumor mutation burden (TMB-H) could result in an increased number of neoepitopes from somatic mutations expressed by a patient's own tumor cell which can be recognized and targeted by neighboring tumor-infiltrating lymphocytes (TILs). Deeper understanding of spatial heterogeneity and organization of tumor cells and their neighboring immune infiltrates within tumors could provide new insights into tumor progression and treatment response. Methods Here we first developed computational approaches using whole slide images (WSIs) to predict bladder cancer patients' TMB status and TILs across tumor regions, and then investigate spatial heterogeneity and organization of regions harboring TMB-H tumor cells and TILs within tumors, as well as their prognostic utility. Results: In experiments using WSIs from The Cancer Genome Atlas (TCGA) bladder cancer (BLCA), our findings show that computational pathology can reliably predict patient-level TMB status and delineate spatial TMB heterogeneity and co-organization with TILs. TMB-H patients with low spatial heterogeneity enriched with high TILs show improved overall survival. Conclusions Computational approaches using WSIs have the potential to provide rapid and cost-effective TMB testing and TILs detection. Survival analysis illuminates potential clinical utility of spatial heterogeneity and co-organization of TMB and TILs as a prognostic biomarker in BLCA which warrants further validation in future studies.
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Affiliation(s)
- Hongming Xu
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian 116024, China
- Liaoning Key Laboratory of Integrated Circuit and Biomedical Electronic System, Dalian University of Technology, Dalian 116024, China
| | - Jean René Clemenceau
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sunho Park
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Jinhwan Choi
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
| | - Sung Hak Lee
- Department of Hospital Pathology, Seoul St.Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, South Korea
| | - Tae Hyun Hwang
- Department of Artificial Intelligence and Informatics, Mayo Clinic, Jacksonville, FL 32224, USA
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50
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Yin W, Jin J, Bao H, Chen H, Wang C, Cheng G, Wu C, Wu M, Yan J, Wu X, Shao Y, Ni X, Su D. Tumor infiltrating lymphocytes-based subtypes and genomic characteristics of EBV- associated lymphoepithelioma-like carcinoma. J Pathol 2022; 257:650-662. [PMID: 35451500 DOI: 10.1002/path.5916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/19/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022]
Abstract
Tumor infiltrating lymphocytes (TILs) offer a key for morphological diagnosis of lymphoepithelioma-like carcinoma (LELC) and are the foundation of onco-immunology. To date, no reports have found a specific risk stratification value of TILs and related it to genomic variation in LELC. Based on the stromal TILs (str-TILs) ratio, we classified 105 EBV-associated LELC cases into two subtypes: patients with ≥ 60% str-TILs area ratio in tumor were classified as subtype I, and otherwise as subtype II. Subtype I patients had significantly better progression-free survival (PFS) and overall survival (OS). We also explored genomic characteristics of EBV-associated LELC within different involved organs. We performed whole-exome sequencing for 51 patients with enough tissue and analyzed genomic characteristics of EBV-associated LELC. Overall, EBV-associated LELCs were characterized by low somatic mutation rate and copy number variations; the enriched genetic lesions affected RTK-RAS, PI3K and cell cycle pathways. Moreover, EBV-associated LELCs from different organs were more similar to each other genetically as compared with other traditional carcinomas of the same sites -as evidenced by unsupervised clustering based on the quantitative data from both mutation signature and chromosomal aneuploidies. Notably, EBV-associated LELC patients with oncogenic driver alterations showed a worse prognosis compared with patients without such alterations. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- WenJuan Yin
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - JiaoYue Jin
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, PR China
| | - HanLin Chen
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, PR China
| | - CanMing Wang
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - GuoPing Cheng
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - ChaoQi Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - Meijuan Wu
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - Junrong Yan
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, PR China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, PR China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc., Nanjing, Jiangsu, PR China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, PR China
| | - Xinghao Ni
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - Dan Su
- Department of Pathology, The Cancer Hospital of the University of Chinese Academy of Sciences(Zhejiang Cancer Hospital, Hangzhou, Zhejiang, PR China.,Institute of Basic Medicine and Cancer (IBMC)s, Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
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