Genomic variations in the counterpart normal controls of lung squamous cell carcinomas

Abstract

Lung squamous cell carcinoma (LUSC) causes approximately 400 000 deaths each year worldwide. The occurrence of LUSC is attributed to exposure to cigarette smoke, which induces the development of numerous genomic abnormalities. However, few studies have investigated the genomic variations that occur only in normal tissues that have been similarly exposed to tobacco smoke as tumor tissues. In this study, we sequenced the whole genomes of three normal lung tissue samples and their paired adjacent squamous cell carcinomas. We then called genomic variations specific to the normal lung tissues through filtering the genomic sequence of the normal lung tissues against that of the paired tumors, the reference human genome, the dbSNP138 common germline variants, and the variations derived from sequencing artifacts. To expand these observations, the whole exome sequences of 478 counterpart normal controls (CNCs) and paired LUSCs of The Cancer Genome Atlas (TCGA) dataset were analyzed. Sixteen genomic variations were called in the three normal lung tissues. These variations were confirmed by Sanger capillary sequencing. A mean of 0.5661 exonic variations/Mb and 7.7887 altered genes per sample were identified in the CNC genome sequences of TCGA. In these CNCs, C:G→T:A transitions, which are the genomic signatures of tobacco carcinogen N-methyl-N-nitro-N-nitrosoguanidine, were the predominant nucleotide changes. Twenty five genes in CNCs had a variation rate that exceeded 2%, including ARSD (18.62%), MUC4 (8.79%), and RBMX (7.11%). CNC variations in CTAGE5 and USP17L7 were associated with the poor prognosis of patients with LUSC. Our results uncovered previously unreported genomic variations in CNCs, rather than LUSCs, that may be involved in the development of LUSC.

Keywords

lung cancer / counterpart normal control / genomic variations

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Acknowledgements

This work was supported by the National Natural Science Funds of China for Distinguished Young Scholar (No. 81425025), the National Key Research and Development Program of China (No. 2016YFC0905500), the National Natural Science Foundation of China (No. 81672765), the Strategic Priority Research Program of the Chinese Academy of Sciences (No. XDA12010307), and grants from the State Key Laboratory of Membrane Biology. The funders had no role in the design, data collection, and analysis of the study or in the preparation of and the decision to publish the manuscript. The results shown here are partly based on the data generated by The Cancer Genome Atlas, which is managed by the NCI and NHGRI. Information about TCGA can be found at http://cancergenome.nih.gov. The dbGaP accession number is phs000178.v9.p8.

Compliance with ethics guidelines

Liwei Qu, Bo Zhou, Guizhen Wang, and Guangbiao Zhou declare that they have no conflict of interest. All procedures followed were in accordance with the ethical standards of the responsible committee on human experimentation (institutional and national) and with the Helsinki Declaration of 1975, as revised in 2000. Additional informed consent was obtained from all patients for which identifying information is included in this article.

Electronic Supplementary Material

Supplementary material is available in the online version of this article at https://doi.org/10.1007/s11684-017-0580-1 and is accessible for authorized users.

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