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

doi:10.1007/s11684-017-0580-1

Front. Med.

2018, Vol. 12

Issue (3) : 280-288 https://doi.org/10.1007/s11684-017-0580-1

RESEARCH ARTICLE

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

Dalin Zhang¹, Liwei Qu¹, Bo Zhou^1,², Guizhen Wang¹, Guangbiao Zhou¹(

)

¹. Division of Molecular Carcinogenesis and Targeted Therapy for Cancer, State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
². University of the Chinese Academy of Sciences, Beijing 100049, China

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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

Corresponding Author(s): Guangbiao Zhou

Just Accepted Date: 09 October 2017 Online First Date: 29 November 2017 Issue Date: 04 May 2018

Cite this article:

Dalin Zhang,Liwei Qu,Bo Zhou, et al. Genomic variations in the counterpart normal controls of lung squamous cell carcinomas[J]. Front. Med., 2018, 12(3): 280-288.

URL:

https://academic.hep.com.cn/fmd/EN/10.1007/s11684-017-0580-1
https://academic.hep.com.cn/fmd/EN/Y2018/V12/I3/280

Tab.1 Genomic variations in the normal lung tissues of three patients with LUSCs

Fig.1 Validation of genomic variations in normal lung tissues. Genomic variations were identified through the analyses of whole-genome sequencing data. Polymerase chain reaction and Sanger capillary sequencing were performed using the primers listed in Table S1and genomic DNA samples from three patients with LUSC. (A) NCOR2 in the normal lung and tumor samples of a patient with LUSC. Two sets of primers were used. (B) GLB1L in the normal lung and tumor samples of a patient with LUSC. Two sets of primers were used. (C) MACF1 in the normal lung and tumor samples of a patient with LUSC. Two sets of primers were used. (D) C10orf95 in the normal lung and tumor samples of a patient with LUSC. (E) DPPA4 in the normal lung and tumor samples of a patient with LUSC. (F) NCL in the normal lung and tumor samples of a patient with LUSC.

Tab.2 Somatic mutations in CNCs and the tumor samples of TCGA LUSCs

Fig.2 Genomic variations in the CNCs of 478 patients with LUSC. (A) Frequency of each type of single base substitution in CNC and tumor samples of 478 patients with LUSC. (B) Proportion of nucleotide changes in the CNCs of nonsmokers, current smokers, and reformed smokers. (C) Frequency of base substitution in the CNCs of male and female patients with LUSC. (D) Altered genes in the CNCs of patients with LUSC. CNC samples are arranged from left to right in the top track.

Fig.3 CNC variations in nine representative genes. Schematic representations of proteins encoded by the genes are shown. Numbers refer to amino acid residues. Each “+” corresponds to an independent, mutated CNC sample, and mutations in a nonred “+” with the same color are found in the same patient. (A) Variations in ARSD. (B) Variations in MUC4. (C) Variations in RBMX. (D) Variations in MUC5B. (E) Variations in RP1L1. (F) Variations in CDC27. (G) Variations in MADCAM1. (H) Variations in ANKRD36. (I) Variations in KRTAP5-5.

Fig.4 CNC variations associated with poor patient prognosis. (A) Variations of CTAGE5 in CNC samples and Kaplan–Meier curve for the overall survival of the patients. (B) Variations of USP17L7 in the CNCs and overall survival of the patients.

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