Whole-exome Sequencing of Epstein-Barr Virus-associated Pulmonary Carcinoma With Low Lymphocytic Infiltration Shows Molecular Features Similar to Those of Classic Pulmonary Lymphoepithelioma-like Carcinoma: Evidence to Support Grouping Together as One Disease Entity.

Szczegóły
Abstrakt

Tytuł:: Whole-exome Sequencing of Epstein-Barr Virus-associated Pulmonary Carcinoma With Low Lymphocytic Infiltration Shows Molecular Features Similar to Those of Classic Pulmonary Lymphoepithelioma-like Carcinoma: Evidence to Support Grouping Together as One Disease Entity.
Autorzy:: Yeh YC; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital.; School of Medicine.; Institute of Biomedical Informatics.
Ho HL; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital.; Department of Biotechnology and Laboratory Science in Medicine.
Lin CI; Department of Pathology, Taipei Hospital, Ministry of Health and Welfare, Taipei, Taiwan.
Chou TY; Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital.; Institute of Clinical Medicine, National Yang Ming Chiao Tung University.
Wang YC; Institute of Biomedical Informatics.
Źródło:: The American journal of surgical pathology [Am J Surg Pathol] 2021 Nov 01; Vol. 45 (11), pp. 1476-1486.
Typ publikacji:: Comparative Study; Journal Article; Research Support, Non-U.S. Gov't
Język:: English
Imprint Name(s):: Publication: <2015- > : Philadelphia, PA : Wolters Kluwer Health, Inc.
Original Publication: New York, Masson.
MeSH Terms:: Exome Sequencing*
Biomarkers, Tumor/*genetics
Carcinoma, Non-Small-Cell Lung/*genetics
Carcinoma, Squamous Cell/*genetics
Epstein-Barr Virus Infections/*virology
Herpesvirus 4, Human/*pathogenicity
Lung Neoplasms/*genetics
Lymphocytes, Tumor-Infiltrating/*immunology
Aged ; Carcinoma, Non-Small-Cell Lung/immunology ; Carcinoma, Non-Small-Cell Lung/pathology ; Carcinoma, Non-Small-Cell Lung/virology ; Carcinoma, Squamous Cell/immunology ; Carcinoma, Squamous Cell/pathology ; Carcinoma, Squamous Cell/virology ; DNA Copy Number Variations ; DNA Mutational Analysis ; Female ; Gene Dosage ; Humans ; Lung Neoplasms/immunology ; Lung Neoplasms/pathology ; Lung Neoplasms/virology ; Middle Aged ; Mutation ; Predictive Value of Tests ; Terminology as Topic
References:: Travis WD, Brambilla E, Burke AP, et al. WHO Classification of Tumours of the Lung, Pleura, Thymus and Heart, 4th ed. Lyon, France: IARC; 2015.
Yeh YC, Kao HL, Lee KL, et al. Epstein-Barr virus-associated pulmonary carcinoma: proposing an alternative term and expanding the histologic spectrum of lymphoepithelioma-like carcinoma of the lung. Am J Surg Pathol. 2019;43:211–219.
Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489:519–525.
Ellrott K, Bailey MH, Saksena G, et al. Scalable open science approach for mutation calling of tumor exomes using multiple genomic pipelines. Cell Syst. 2018;6:271.e7–281.e7.
Hong S, Liu D, Luo S, et al. The genomic landscape of Epstein-Barr virus-associated pulmonary lymphoepithelioma-like carcinoma. Nat Commun. 2019;10:3108.
Van der Auwera GA, Carneiro MO, Hartl C, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43:11.10.1–11.10.33.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25:1754–1760.
Li H, Handsaker B, Wysoker A, et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078–2079.
Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–219.
Kandoth C. mskcc/vcf2maf: vcf2maf, v1.6.19; 2020.
McLaren W, Gil L, Hunt SE, et al. The Ensembl variant effect predictor. Genome Biol. 2016;17:122.
Lawrence MS, Stojanov P, Polak P, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214–218.
Talevich E, Shain AH, Botton T, et al. CNVkit: Genome-wide copy number detection and visualization from targeted DNA sequencing. PLoS Comput Biol. 2016;12:e1004873.
Mermel CH, Schumacher SE, Hill B, et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12:R41.
Mayakonda A, Lin DC, Assenov Y, et al. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28:1747–1756.
Huang PJ, Chiu LY, Lee CC, et al. mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Res. 2018;46(D1):D964–D970.
Desrichard A, Kuo F, Chowell D, et al. Tobacco smoking-associated alterations in the immune microenvironment of squamous cell carcinomas. J Natl Cancer Inst. 2018;110:1386–1392.
Goodman AM, Piccioni D, Kato S, et al. Prevalence of PDL1 amplification and preliminary response to immune checkpoint blockade in solid tumors. JAMA Oncol. 2018;4:1237–1244.
Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature. 2014;513:202–209.
Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature. 2014;511:543–550.
Tong J, Zhang X, Qu H, et al. The positive correlation between tumor mutation burden and the purity of tumor samples in non–small cell lung cancer and colorectal cancer. J Clin Oncol. 2020;38(suppl):e13683.
Chau SL, Tong JH, Chow C, et al. Distinct molecular landscape of Epstein-Barr virus associated pulmonary lymphoepithelioma-like carcinoma revealed by genomic sequencing. Cancers (Basel). 2020;12:2065.
George J, Lim JS, Jang SJ, et al. Comprehensive genomic profiles of small cell lung cancer. Nature. 2015;524:47–53.
Alexandrov LB, Stratton MR. Mutational signatures: the patterns of somatic mutations hidden in cancer genomes. Curr Opin Genet Dev. 2014;24:52–60.
Alexandrov LB, Ju YS, Haase K, et al. Mutational signatures associated with tobacco smoking in human cancer. Science. 2016;354:618–622.
Alexandrov LB, Jones PH, Wedge DC, et al. Clock-like mutational processes in human somatic cells. Nat Genet. 2015;47:1402–1407.
Bobrovnitchaia I, Valieris R, Drummond RD, et al. APOBEC-mediated DNA alterations: a possible new mechanism of carcinogenesis in EBV-positive gastric cancer. Int J Cancer. 2020;146:181–191.
Zheng H, Dai W, Cheung AK, et al. Whole-exome sequencing identifies multiple loss-of-function mutations of NF-kappaB pathway regulators in nasopharyngeal carcinoma. Proc Natl Acad Sci USA. 2016;113:11283–11288.
Wakae K, Kondo S, Pham HT, et al. EBV-LMP1 induces APOBEC3s and mitochondrial DNA hypermutation in nasopharyngeal cancer. Cancer Med. 2020;9:7663–7671.
Saito R, Abe H, Kunita A, et al. Overexpression and gene amplification of PD-L1 in cancer cells and PD-L1(+) immune cells in Epstein-Barr virus-associated gastric cancer: the prognostic implications. Mod Pathol. 2017;30:427–439.
Miliotis C, Slack F. Multi-layered control of PD-L1 expression in Epstein-Barr virus-associated gastric cancer. J Cancer Metastasis Treat. 2020;6:13.
Substance Nomenclature:: 0 (Biomarkers, Tumor)
Entry Date(s):: Date Created: 20210430 Date Completed: 20211025 Latest Revision: 20230922
Update Code:: 20240104
DOI:: 10.1097/PAS.0000000000001722
PMID:: 33927156
: Czasopismo naukowe

Pulmonary lymphoepithelioma-like carcinoma (LELC) is a distinct type of Epstein-Barr virus (EBV)-associated non-small cell carcinoma characterized by a syncytial growth pattern with heavy lymphocytic infiltration. We recently identified a group of non-small cell carcinomas, which are also associated with EBV but lack significant lymphocytic infiltration. These EBV-associated pulmonary carcinomas with low lymphocytic infiltration morphologically resemble nonkeratinizing squamous cell carcinoma, but their patient characteristics are more similar to those of LELC, including female sex and nonsmoking status. To clarify the relationships between these disease entities, in this study, we explored the molecular characteristics of the EBV-associated carcinomas with low lymphocytic infiltration using whole-exome sequencing and compared their molecular profiles with those of classic LELC and pulmonary squamous cell carcinoma. We demonstrate that the molecular characteristics of EBV-associated carcinomas with low lymphocytic infiltration are highly similar to those of classic LELC. Both show low tumor mutational burden, lack of commonly mutated driver genes in other types of non-small cell lung cancer, similar mutational signature involving APOBEC-related mutations, and enrichment of CD274 (programmed death-ligand 1) amplification. These molecular characteristics are very different from those of pulmonary squamous cell carcinoma. The unique patient demographics and molecular characteristics shared by EBV-associated carcinomas with low lymphocytic infiltration and classic LELC suggest that these tumors represent one single disease entity defined by EBV association. This study supports the proposal for the usage of the term "EBV-associated pulmonary carcinoma" to encompass the entire morphologic spectrum of this distinct EBV-associated disease entity.
Competing Interests: Conflicts of Interest and Sources of Funding: Supported by the Ministry of Science and Technology, Taiwan (MOST 109-2320-B-075-004-MY3) and Taipei Veterans General Hospital, Taiwan (V109C-110). The authors have disclosed that they have no significant relationships with, or financial interest in, any commercial companies pertaining to this article.
(Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Informacja