Journal Article

Tumor Mutational Burden and Genomic Alterations in Chinese Small Cell Lung Cancer Measured by Whole-Exome Sequencing

Huang, Hui-Yi, Zhang, Xian-Lan, Su, Shan, Cen, Wen-Chang, Zeng, Yun-Yun, Zhao, Zhen-Gang, Zhou, Wei, Zou, Jian-Jun, Su, Duo-Hua, Liu, Yan, Huang, Zhi-Hao, Xie, Ya-Lin, Jin, Yun, Liu, Jian-Xiong, Li, Lei, Su, Ning, Lei, An

2019

Overview

Purpose. Studies on genetic alterations of the heterogenous small cell lung cancer (SCLC) are rare. We carried out the present study to clarify the genomic alterations and TMB levels of Chinese SCLC patients by whole-exome sequencing. Materials and Methods. Whole-exome sequencing by next-generation sequencing technique was implemented on twenty SCLC samples. Significant somatic mutations and copy number variations were screened, followed by comparison with the data extracted from COSMIC. Besides, altered signaling pathways were examined in order to figure out actionable targets. Results. A total of 8,062 nonsynonymous mutations were defined. The number of mutations for each case ranged from 98 to 864. As for base substitutions, a total of 15,817 substitutions were detected with C > A conversion which was correlated to smoking occupying 25.57%. The TMB values ranged from 2.51/Mb to 22.1/Mb with a median value of 9.95/Mb. RB1 was the most frequently mutated gene altered in 18 (90%) cases, followed by TP53 altered in 17 (85%) cases. Other commonly changed genes were PTEN, and RBL1, with frequencies of 55% and 50%, respectively. SOX2 significantly amplified in 6 (30%) cases and MYCN amplified in 1 (5%) patient. Notch signaling pathway and PI3K/AKT/mTOR signaling pathway were universally and significantly changed. Major genomic alterations were in consistency with data from COSMIC, but frequencies of less common mutations were different. Conclusion. TP53 and RB1 inactivations were universally detected in SCLC. The Notch and PI3K/AKT/mTOR signaling pathways were both significantly altered, implying potential actionable targets.

• Publisher: Hindawi Publishing Corporation,Hindawi,John Wiley & Sons, Inc
• Subject: 1-Phosphatidylinositol 3-kinase / AKT protein / Analysis / Biomarkers / Biomarkers, Tumor - genetics / Cancer / Cancer therapies / Chemotherapy / Copy number / Deoxyribonucleic acid / DNA / DNA Copy Number Variations - genetics / Female / Gene mutations / Gene sequencing / Genetic aspects / Genomes / Genomics - methods / Humans / Kinases / Lung cancer / Lung cancer, Small cell / Lung Neoplasms - genetics / Male / Medical prognosis / Medical research / Middle Aged / Mutation / Mutation - genetics / Neuroendocrine tumors / Next-generation sequencing / Oncology / p53 Protein / Phosphatidylinositol 3-Kinases - genetics / PTEN Phosphohydrolase - genetics / PTEN protein / Signal transduction / Signal Transduction - genetics / Signaling / Small cell lung carcinoma / Small Cell Lung Carcinoma - genetics / Smoking / TOR protein / TOR Serine-Threonine Kinases - genetics / Tumor proteins / Tumor Suppressor Protein p53 - genetics / Tumors / Whole Exome Sequencing - methods