Dataset Information

Genomic Mutations of Primary and Metastatic Lung Adenocarcinoma in Chinese Patients.

ABSTRACT: Lung cancer is still the leading cause of cancer-related death worldwide. Of lung cancer, lung adenocarcinoma (LUAD) is the most common subtype. Most patients with LUAD would develop into metastasis, which limits the available treatment. Targeted therapy and immunotherapy provided options for those advanced patients. But they also broached up challenges to identify the appropriate patients. This study aims to reveal the landscapes of genomic mutations in primary and metastatic LUAD and their actionability. This study enrolled 636 patients with LUAD, of whom 85 and 551 were from patients with and without metastasis, respectively. Next-generation sequencing technology was used to retrieve their genomic information. Genomic mutations including short nucleotide variation, long variation, copy number variations, and fusions were called. The corresponding actionability was revealed. A comparison of genomic mutations and actionability between primary and metastatic LUAD was performed. In primary tumors, BRCA2 and FAT3 were significantly mutated in older patients; while in metastases, ALK and NOTCH2 were significantly mutated in younger patients. Primary tumors in male patients were significantly mutated in LRP1B and KRAS. Compared to primary tumors, metastases harbored less short nucleotide variations but more copy number variations and fusions. In metastases, chromosome 1 and chromosome 9 had less short nucleotide variations and more CNV than in primary tumors. Genomic variations of activated dendritic cells were more frequently mutated in metastases. EGFR genomic variations were negatively associated with PD-L1 and TMB. Patients with EGFR inhibitor treatment tend to have lower PD-L1 expression. The revealed discrepancy between primary and metastatic lung cancer could help guide the treatment strategies and the development of novel drugs.

SUBMITTER: Chen X

PROVIDER: S-EPMC7787720 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genomic Mutations of Primary and Metastatic Lung Adenocarcinoma in Chinese Patients.

Chen Xinyu X Bu Qing Q Yan Xuexin X Li Ye Y Yu Qian Q Zheng Haiping H Zhao Liang L Zeng Yanwu Y Lu Leilei L Lan Dong D Ma Jie J

Journal of oncology 20201208

Lung cancer is still the leading cause of cancer-related death worldwide. Of lung cancer, lung adenocarcinoma (LUAD) is the most common subtype. Most patients with LUAD would develop into metastasis, which limits the available treatment. Targeted therapy and immunotherapy provided options for those advanced patients. But they also broached up challenges to identify the appropriate patients. This study aims to reveal the landscapes of genomic mutations in primary and metastatic LUAD and their act ...[more]

PMID: 33488709

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Project description:Background Lung cancer is the most prevalent cancer worldwide and accounts for approximately 20% of cancer-related death in China every year. High-grade lung cancer poses a significant threat to patients, and developing a novel treatment for these patients requires an understanding of its underlying mechanism. Methods Chinese patients with lung cancer were enrolled. The tumor samples were collected by surgery or puncture and applied for next-generation sequencing. A panel of pan-cancer genes was targeted, and the sequencing depth was set to over 1,000 to improve the sensitivity of detecting mutations. Short-length mutations (substitution, insertion, and deletion), copy number variation, and gene fusion were called. Gene mutations were compared between low-grade, middle-grade, and high-grade tumors using Fisher’s exact test. The enriched pathways in each grade of tumors were also inferred. Results The study included 173 Chinese patients with non-small cell lung cancer, of whom 98 (56.6%) patients were female and 75 (43.4%) were male, with a mean age of 56.8 years. All patients were microsatellite stable; 66.4% were at the early stages (Stages 0, I, and II) with a tumor mutational burden of approximately 2.5 (confidence interval = [0, 48.3]). Compared to low-grade tumors, high-grade tumors had a significantly higher percentage of mutations in TP53 (75.9% vs 34.4%, p = 1.86e-3) and PIK3CA (24.1% vs. 0%, p = 3.58e-3). Pathway analysis found that high-grade tumors were enriched with mutations in bacterial invasion of epithelial cells (31% vs. 0%, p = 5.8e-4), Epstein–Barr virus infection (79.3% vs. 37.5%, p = 1.72e-3), and the Wnt signaling pathway (75.9% vs. 34.4%, p = 1.91e-3). High-grade tumors had a significantly higher tumor mutational burden than low-grade tumors (p-value = 0.0017). However, actionable mutations with high-level evidence were lower in high-grade tumors. Conclusion Patients with high-grade tumors from lung cancer may be more affected by bacteria and Epstein–Barr virus than low-grade tumors. High-grade tumors were specially mutated in TP53 and PIK3CA and may benefit more from immunotherapy. Further research on the underlying mechanism of high-grade lung cancer is necessary to develop new therapeutic options. Lung cancer, tumor grade, genomic mutations, Epstein–Barr virus, pathway analysis

Project description:BackgroundEpidermal growth factor receptor exon 20 insertions (EGFR ex20ins) occur in about 4-14% of lung adenocarcinoma (LUAD) patients with EGFR mutations. Recently some targeted drugs have been approved for the treatment of LUAD patients with EGFR ex20ins. However, the heterogeneity of EGFR ex20ins mutations and resultant challenges in identifying them have led to the underestimation of their frequency.MethodsWe investigated the molecular and clinicopathologic features of EGFR ex20ins in 3,892 Chinese LUAD patients using next-generation sequencing (NGS). The frequency and distribution of EGFR ex20ins mutations between Chinese and Western LUAD patients were also compared by integrating the data of this study and the data of previous studies.ResultsA total of 23 unique EGFR ex20ins were identified in 77 LUAD patients, accounting for 1.98% of all LUAD patients and 3.49% of EGFR mutant LUDA patients. The 2 most common EGFR ex20ins subtypes were S768_D770dup and A767_V769dup, which together accounted for 55.84% of the EGFR ex20ins cases. About 61% (14/23) of the EGFR ex20ins subtypes occurred only once. Additionally, 8 of the EGFR ex20ins subtypes were not recorded in the COSMIC database. These results showed that the EGFR ex20ins mutations were highly heterogeneous. There was no significant difference in the frequency and distribution of EGFR ex20ins mutations between Chinese and Western LUAD patients, but the frequency of EGFR ex20ins mutations was significantly lower in EGFR-mutant Chinese LUAD patients than Western LUAD patients. The co-mutation analysis showed that EGFR ex20ins occurred significantly and exclusively with certain driver genes in LUAD, including ALK fusion (χ2=7.133, P=0.008), KRAS (χ2=8.468, P=0.004), and PIK3CA (χ2=5.792, P=0.016). No gene was observed to be significantly co-mutated with EGFR ex20ins. In general, patients with EGFR ex20ins shared a similar age and gender to patients with other EGFR mutations or without EGFR ex20ins.ConclusionsOverall, our results revealed the molecular and clinicopathologic features of EGFR ex20ins in Chinese LUAD patients, which will be helpful for drug development and in clinical trials targeting EGFR ex20ins.

Project description:BackgroundAs a rare subtype of lung adenocarcinoma, the diagnosis of pulmonary enteric adenocarcinoma (PEAC) remains challenging due to overlapping morphologic spectrum with lung metastatic colorectal cancer (lmCRC). However, the molecular features of PEAC as a separate lung cancer entity are poorly understood.MethodsWe performed whole-exome sequencing and targeted bisulfite sequencing of 32 PEAC and 30 lmCRC to improve differential molecular characterization of the two diseases. We used machine learning methods to select key markers and developed a diagnostic classifier. In addition, we validated the classifier in the internal test cohort and an independently recruited external validation cohort with 17 PEAC and 7 lmCRC.FindingsOur results showed that EGFR was the key driver mutation in PEAC but at a lower prevalence compared to typical lung adenocarcinomas, whereas ERBB2 and KRAS were more frequently observed in PEAC. By contrast, we observed significant enrichment of KRAS and APC mutations in lmCRC compared with PEAC. At the chromosome arm level, copy number variations in 13q, 14q, and 18p were the major chromosomal differences observed between PEAC and lmCRC. Furthermore, by comparing differentially methylated regions (DMRs), we established a neat DNA methylation-based classifier consisting of eight DMRs. This classifier correctly classified all samples in the training cohort and 95% of the samples in the internal test cohort. An external validation cohort of 24 cases recruited from multiple centers in China also reliably agreed with pathological diagnosis.InterpretationThese results provide solid evidence of PEAC-specific genomic characteristics and demonstrate the potential utility of DNA methylation markers for auxiliary diagnosis of PEAC and lmCRC.FundingThis work was supported by National key research and development project 2019YFC1315700, CAMS Key Laboratory of Translational Research on Lung Cancer (2018PT31035), and Beijing Natural Science Foundation (7222144).

Dataset Information

Genomic Mutations of Primary and Metastatic Lung Adenocarcinoma in Chinese Patients.

Publications

Genomic Mutations of Primary and Metastatic Lung Adenocarcinoma in Chinese Patients.

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