1
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Sakamoto T, Furukawa T, Pham HHN, Kuroda K, Tabata K, Kashima Y, Okoshi EN, Morimoto S, Bychkov A, Fukuoka J. A collaborative workflow between pathologists and deep learning for the evaluation of tumour cellularity in lung adenocarcinoma. Histopathology 2022; 81:758-769. [PMID: 35989443 PMCID: PMC9826135 DOI: 10.1111/his.14779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 01/11/2023]
Abstract
AIMS The reporting of tumour cellularity in cancer samples has become a mandatory task for pathologists. However, the estimation of tumour cellularity is often inaccurate. Therefore, we propose a collaborative workflow between pathologists and artificial intelligence (AI) models to evaluate tumour cellularity in lung cancer samples and propose a protocol to apply it to routine practice. METHODS AND RESULTS We developed a quantitative model of lung adenocarcinoma that was validated and tested on 50 cases, and a collaborative workflow where pathologists could access the AI results and adjust their original tumour cellularity scores (adjusted-score) that we tested on 151 cases. The adjusted-score was validated by comparing them with a ground truth established by manual annotation of haematoxylin and eosin slides with reference to immunostains with thyroid transcription factor-1 and napsin A. For training, validation, testing the AI and testing the collaborative workflow, we used 40, 10, 50 and 151 whole slide images of lung adenocarcinoma, respectively. The sensitivity and specificity of tumour segmentation were 97 and 87%, respectively, and the accuracy of nuclei recognition was 99%. One pathologist's visually estimated scores were compared to the adjusted-score, and the pathologist's scores were altered in 87% of cases. Comparison with the ground truth revealed that the adjusted-score was more precise than the pathologists' scores (P < 0.05). CONCLUSION We proposed a collaborative workflow between AI and pathologists as a model to improve daily practice and enhance the prediction of tumour cellularity for genetic tests.
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Affiliation(s)
- Taro Sakamoto
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Tomoi Furukawa
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Hoa H N Pham
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Kishio Kuroda
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan,Department of Pathology, Kameda Medical CenterKamogawaJapan
| | - Kazuhiro Tabata
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Yukio Kashima
- Department of Pathology, Awaji Medical CenterSumotoJapan
| | - Ethan N Okoshi
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan
| | - Shimpei Morimoto
- Innovation Platform and Office for Precision Medicine (iPOP), Graduate School of Biomedical SciencesNagasaki UniversityNagasakiJapan
| | - Andrey Bychkov
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan,Department of Pathology, Kameda Medical CenterKamogawaJapan
| | - Junya Fukuoka
- Department of PathologyNagasaki University Graduate School of Biomedical SciencesNagasakiJapan,Department of Pathology, Kameda Medical CenterKamogawaJapan
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2
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Chen M, Chen R, Jin Y, Li J, Hu X, Zhang J, Fujimoto J, Hubert SM, Gay CM, Zhu B, Tian Y, McGranahan N, Lee WC, George J, Hu X, Chen Y, Wu M, Behrens C, Chow CW, Pham HHN, Fukuoka J, Wu J, Parra ER, Little LD, Gumbs C, Song X, Wu CJ, Diao L, Wang Q, Cardnell R, Zhang J, Wang J, Le X, Gibbons DL, Heymach JV, Jack Lee J, William WN, Cheng C, Glisson B, Wistuba I, Andrew Futreal P, Thomas RK, Reuben A, Byers LA, Zhang J. Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer. Nat Commun 2021; 12:6655. [PMID: 34789716 PMCID: PMC8599854 DOI: 10.1038/s41467-021-26821-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/25/2021] [Indexed: 02/03/2023] Open
Abstract
Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC.
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Affiliation(s)
- Ming Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510060, China. .,The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, 310022, China. .,Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China. .,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang, 310022, China.
| | - Runzhe Chen
- grid.12981.330000 0001 2360 039XDepartment of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510060 China ,grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ying Jin
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Jun Li
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xin Hu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jiexin Zhang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Junya Fujimoto
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Shawna M. Hubert
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Carl M. Gay
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Bo Zhu
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Yanhua Tian
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA ,grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Nicholas McGranahan
- grid.11485.390000 0004 0422 0975Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, WC1E6BT UK
| | - Won-Chul Lee
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Julie George
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Otorhinolaryngology, Head and Neck Surgery, University Hospital Cologne, 50937 Cologne, Germany
| | - Xiao Hu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Yamei Chen
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Meijuan Wu
- grid.410726.60000 0004 1797 8419The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang 310022 China ,grid.9227.e0000000119573309Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022 China ,Zhejiang Key Laboratory of Radiation Oncology, Hangzhou, Zhejiang 310022 China
| | - Carmen Behrens
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chi-Wan Chow
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Hoa H. N. Pham
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Junya Fukuoka
- grid.174567.60000 0000 8902 2273Department of Pathology, Nagasaki University Graduate school of Biomedical Sciences, Nagasaki, Japan
| | - Jia Wu
- grid.240145.60000 0001 2291 4776Department of Image Physics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Edwin Roger Parra
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Latasha D. Little
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Curtis Gumbs
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xingzhi Song
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chang-Jiun Wu
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Lixia Diao
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Qi Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Robert Cardnell
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianhua Zhang
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jing Wang
- grid.240145.60000 0001 2291 4776Department of Bioinformatics and Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Xiuning Le
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Don L. Gibbons
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - John V. Heymach
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - J. Jack Lee
- grid.240145.60000 0001 2291 4776Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - William N. William
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Chao Cheng
- grid.39382.330000 0001 2160 926XInstitute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas 77030 USA
| | - Bonnie Glisson
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Ignacio Wistuba
- grid.240145.60000 0001 2291 4776Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - P. Andrew Futreal
- grid.240145.60000 0001 2291 4776Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Roman K. Thomas
- grid.6190.e0000 0000 8580 3777Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, 50931 Germany ,grid.411097.a0000 0000 8852 305XDepartment of Pathology, Medical Faculty, University Hospital Cologne, Cologne, 50931 Germany ,grid.7497.d0000 0004 0492 0584DKFZ, German Cancer Research Center and German Cancer Consortium (DKTK), Heidelberg, 69115 Germany
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
| | - Lauren A. Byers
- grid.240145.60000 0001 2291 4776Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas 77030 USA
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA. .,Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas, 77030, USA.
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3
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Dejima H, Hu X, Chen R, Zhang J, Fujimoto J, Parra ER, Haymaker C, Hubert SM, Duose D, Solis LM, Su D, Fukuoka J, Tabata K, Pham HHN, Mcgranahan N, Zhang B, Ye J, Ying L, Little L, Gumbs C, Chow CW, Estecio MR, Godoy MCB, Antonoff MB, Sepesi B, Pass HI, Behrens C, Zhang J, Vaporciyan AA, Heymach JV, Scheet P, Lee JJ, Wu J, Futreal PA, Reuben A, Kadara H, Wistuba II, Zhang J. Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features. Nat Commun 2021; 12:2722. [PMID: 33976164 PMCID: PMC8113327 DOI: 10.1038/s41467-021-22890-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 03/31/2021] [Indexed: 12/13/2022] Open
Abstract
The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.
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Affiliation(s)
- Hitoshi Dejima
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Hu
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Runzhe Chen
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiexin Zhang
- Department of Bioinformatics & Computational Biology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Edwin R Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Cara Haymaker
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shawna M Hubert
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dzifa Duose
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luisa M Solis
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Su
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Nicholas Mcgranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, UK
| | - Baili Zhang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jie Ye
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Latasha Little
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Curtis Gumbs
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chi-Wan Chow
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marcos Roberto Estecio
- Department of Epigenetics and Molecular Carcinogenesis, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center of Cancer Epigenetics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Myrna C B Godoy
- Department of Thoracic Imaging, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Boris Sepesi
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, USA
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Scheet
- Department of Epidemiology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Wu
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Humam Kadara
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Jianjun Zhang
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Thoracic/Head and Neck Medical Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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4
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Hu X, Estecio MR, Chen R, Reuben A, Wang L, Fujimoto J, Carrot-Zhang J, McGranahan N, Ying L, Fukuoka J, Chow CW, Pham HHN, Godoy MCB, Carter BW, Behrens C, Zhang J, Antonoff MB, Sepesi B, Lu Y, Pass HI, Kadara H, Scheet P, Vaporciyan AA, Heymach JV, Wistuba II, Lee JJ, Futreal PA, Su D, Issa JPJ, Zhang J. Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. Nat Commun 2021; 12:687. [PMID: 33514726 PMCID: PMC7846738 DOI: 10.1038/s41467-021-20907-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/17/2020] [Indexed: 12/17/2022] Open
Abstract
The evolution of DNA methylome and methylation intra-tumor heterogeneity (ITH) during early carcinogenesis of lung adenocarcinoma has not been systematically studied. We perform reduced representation bisulfite sequencing of invasive lung adenocarcinoma and its precursors, atypical adenomatous hyperplasia, adenocarcinoma in situ and minimally invasive adenocarcinoma. We observe gradual increase of methylation aberrations and significantly higher level of methylation ITH in later-stage lesions. The phylogenetic patterns inferred from methylation aberrations resemble those based on somatic mutations suggesting parallel methylation and genetic evolution. De-convolution reveal higher ratio of T regulatory cells (Tregs) versus CD8 + T cells in later-stage diseases, implying progressive immunosuppression with neoplastic progression. Furthermore, increased global hypomethylation is associated with higher mutation burden, copy number variation burden and AI burden as well as higher Treg/CD8 ratio, highlighting the potential impact of methylation on chromosomal instability, mutagenesis and tumor immune microenvironment during early carcinogenesis of lung adenocarcinomas.
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Affiliation(s)
- Xin Hu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Runzhe Chen
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Alexandre Reuben
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Junya Fujimoto
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jian Carrot-Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Nicholas McGranahan
- Cancer Research United Kingdom-University College London Lung Cancer Centre of Excellence, London, SW73RP, UK
| | - Lisha Ying
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, 310022, Hangzhou, China
- Zhejiang Cancer Research Institute, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Chi-Wan Chow
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 8528523, Japan
| | - Myrna C B Godoy
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Brett W Carter
- Department of Thoracic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Carmen Behrens
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, 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
| | - Mara B Antonoff
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Boris Sepesi
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Center of Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Harvey I Pass
- Department of Cardiothoracic Surgery, New York University Langone Medical Center, New York, NY, 10016, USA
| | - Humam Kadara
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Paul Scheet
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ara A Vaporciyan
- Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - John V Heymach
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ignacio I Wistuba
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - P Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Dan Su
- Department of Pathology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), 310022, Hangzhou, China.
| | | | - Jianjun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
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5
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Montero MA, Aricak O, Kis L, Yoshikawa A, De Petris L, Grundberg O, Pham HHN, Roden AC, Fukuoka J, Attanoos R, Guijarro R, Alarcón F, Lindström K, Ortiz-Villalón C. Clinicopathological significance of the expression of PD-L1 in non-small cell lung cancer. Ann Diagn Pathol 2021; 51:151701. [PMID: 33485052 DOI: 10.1016/j.anndiagpath.2021.151701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 10/22/2022]
Abstract
INTRODUCTION PD1/PD-L1 pathway targeting therapies are nowadays an established treatment option for patients with NSCLC. We assessed whether PD-L1 expression in NSCLC tumor cells was associated with specific clinical features or overall survival using four different clones. METHODS AND RESULTS A retrospective study included formalin-fixed paraffin embedded (FFPE) surgical tumors from 482 patients. PD-L1 status was assessed with immunohistochemistry in tumor cells on tissue microarrays using clones 28-8, 22C3, SP263 and SP142. Associations with OS were assessed by Kaplan-Meier and multivariate Cox's regression analysis. Patients' median age: 68 years (39-86); histology: adenocarcinoma (AdCa) 61%, squamous-cell carcinoma (SqCC) 33%, and large cell carcinoma (LCC) 6%; p-stage: IA (46%), IB (30%), IIA (10%), IIB (11,4%), IIIA (1,2%), IIIB - IV (0,4%). PD-L1 positivity (≥1%) in NSCLC for clones 28-8, 22C3, SP263, SP142 was 41.5%, 34.2%, 42.7%, 10.4%, respectively (Pearson Chi-square p < 0.0001). PD-L1 expression was correlated with histology, tumor size and grading. Statistically significant association between PD-L1 expression and OS in NSCLC and Non-AdCa was observed with clone SP142 (log-rank p = 0.045 and p = 0.05, respectively). Statistically significant association between PD-L1 expression and OS in LCC was observed with clones 22C3 (log-rank p = 0.009) and SP263 (log-rank p = 0.050). CONCLUSIONS Overexpression of the PD-L1 clone SP142 was associated with poor overall survival in NSCLC and Non-AdCa. Clones 22C3 and SP263 were associated with poor prognosis in LCC. PD-L1 status might serve as a prognostic marker in NSCLC.
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Affiliation(s)
- M Angeles Montero
- Department of Histopathology, Manchester University NHS Foundation Trust, UK
| | - Ozan Aricak
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden
| | - Lorand Kis
- Department of Oncology-Pathology (Onkpat), Karolinska Institute, Sweden
| | - Akira Yoshikawa
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Pathology, Kameda Medical Center, Kamogawa, Japan
| | - Luigi De Petris
- Department of Oncology-Pathology (Onkpat), Karolinska Institute, Sweden; Thoracic Oncology Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Oscar Grundberg
- Thoracic Oncology Center, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Hoa H N Pham
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Anja C Roden
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Pathology, Kameda Medical Center, Kamogawa, Japan
| | | | | | - Felix Alarcón
- Department of Oncology-Pathology (Onkpat), Karolinska Institute, Sweden
| | - Kati Lindström
- Division of History of Science, Technology and Environment, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Cristian Ortiz-Villalón
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden; Department of Oncology-Pathology (Onkpat), Karolinska Institute, Sweden.
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