Genomic and immune profiling of pre-invasive lung adenocarcinoma

Adenocarcinoma in situ and minimally invasive adenocarcinoma are the pre-invasive forms of lung adenocarcinoma. The genomic and immune profiles of these lesions are poorly understood. Here we report exome and transcriptome sequencing of 98 lung adenocarcinoma precursor lesions and 99 invasive adenocarcinomas. We have identified EGFR, RBM10, BRAF, ERBB2, TP53, KRAS, MAP2K1 and MET as significantly mutated genes in the pre/minimally invasive group. Classes of genome alterations that increase in frequency during the progression to malignancy are revealed. These include mutations in TP53, arm-level copy number alterations, and HLA loss of heterozygosity. Immune infiltration is correlated with copy number alterations of chromosome arm 6p, suggesting a link between arm-level events and the tumor immune environment.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 10 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001005479	Whole-exome sequencing coupled with RNA-seq of preinvasive (n=98) and invasive (n=99) lung adenocarcinoma samples.	HiSeq X Ten	394

Publications	Citations
Genomic and immune profiling of pre-invasive lung adenocarcinoma. Chen H, Carrot-Zhang J, Zhao Y, Hu H, Freeman SS, Yu S, Ha G, Taylor AM, Berger AC, Westlake L, Zheng Y, Zhang J, Ramachandran A, Zheng Q, Pan Y, Zheng D, Zheng S, Cheng C, Kuang M, Zhou X, Zhang Y, Li H, Ye T, Ma Y, Gao Z, Tao X, Han H, Shang J, Yu Y, Bao D, Huang Y, Li X, Zhang Y, Xiang J, Sun Y, Li Y, Cherniack AD, Campbell JD, Shi L, Meyerson M. Nat Commun 10: 2019 5472	116
Evolution of DNA methylome from precancerous lesions to invasive lung adenocarcinomas. 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 JJ, Zhang J. Nat Commun 12: 2021 687	37
A seven-gene prognostic signature predicts overall survival of patients with lung adenocarcinoma (LUAD). Al-Dherasi A, Huang QT, Liao Y, Al-Mosaib S, Hua R, Wang Y, Yu Y, Zhang Y, Zhang X, Huang C, Mousa H, Ge D, Sufiyan S, Bai W, Liu R, Shao Y, Li Y, Zhang J, Shi L, Lv D, Li Z, Liu Q. Cancer Cell Int 21: 2021 294	19
Allele frequency deviation (AFD) as a new prognostic model to predict overall survival in lung adenocarcinoma (LUAD). Al-Dherasi A, Liao Y, Al-Mosaib S, Hua R, Wang Y, Yu Y, Zhang Y, Zhang X, Jalayta R, Mousa H, Al-Danakh A, Alnadari F, Almoiliqy M, Baldi S, Shi L, Lv D, Li Z, Liu Q. Cancer Cell Int 21: 2021 451	3
Increased Tumor Intrinsic Growth Potential and Decreased Immune Function Orchestrate the Progression of Lung Adenocarcinoma. 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. Front Immunol 13: 2022 921761	2
Elevated Mast Cell Abundance Is Associated with Enrichment of CCR2+ Cytotoxic T Cells and Favorable Prognosis in Lung Adenocarcinoma. Fan F, Gao J, Zhao Y, Wang J, Meng L, Ma J, Li T, Han H, Lai J, Gao Z, Li X, Guo R, Cao Z, Zhang Y, Zhang X, Chen H. Cancer Res 83: 2023 2690-2703	8
Identifying New Contributors to Brain Metastasis in Lung Adenocarcinoma: A Transcriptomic Meta-Analysis. Souza VGP, Forder A, Telkar N, Stewart GL, Carvalho RF, Mur LAJ, Lam WL, Reis PP. Cancers (Basel) 15: 2023 4526	1
Identification of a coagulation-related signature correlated with immune infiltration and their prognostic implications in lung adenocarcinoma. Yang S, Chen S, Zhao Y, Wu T, Wang Y, Li T, Fu L, Ye T, Hu YQ, Chen H. Thorac Cancer 14: 2023 3295-3308	2
Evolutionary proteogenomic landscape from pre-invasive to invasive lung adenocarcinoma. Zhang Y, Fu F, Zhang Q, Li L, Liu H, Deng C, Xue Q, Zhao Y, Sun W, Han H, Gao Z, Guo C, Zheng Q, Hu H, Sun Y, Li Y, Ding C, Chen H. Cell Rep Med 5: 2024 101358	2
An immune cell map of human lung adenocarcinoma development reveals an anti-tumoral role of the Tfh-dependent tertiary lymphoid structure. Liu W, You W, Lan Z, Ren Y, Gao S, Li S, Chen WW, Huang C, Zeng Y, Xiao N, Wang Z, Xie H, Ma H, Chen Y, Wang G, Chen C, Li H. Cell Rep Med 5: 2024 101448	15