Please wait a minute...
Frontiers of Medicine

ISSN 2095-0217

ISSN 2095-0225(Online)

CN 11-5983/R

Postal Subscription Code 80-967

2018 Impact Factor: 1.847

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 Zhou1,2, 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
 Download: PDF(523 KB)   HTML
 Export: BibTeX | EndNote | Reference Manager | ProCite | RefWorks
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 Authors: 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:  
http://academic.hep.com.cn/fmd/EN/10.1007/s11684-017-0580-1
http://academic.hep.com.cn/fmd/EN/Y2018/V12/I3/280
Patient ID Gene Chr Start End Ref Alt Function Transcriptor cDNA position Amino acid
712 C10orf95 10 104210754 104210754 G C Stopgain NM_024886 c.C234G p.Y78X
CNTNAP3 9 39287976 39287976 C T Splicing NM_033655 c.85+ 1G>A
DPPA4 3 109046864 109046864 C A NS NM_018189 c.G886T p.V296F
GLB1L 2 220102416 220102416 T C NS NM_024506 c.A1507G p.I503V
MACF1 1 39913789 39913789 C A NS NM_012090 c.C13876A p.P4626T
NCL 2 232325382 232325384 TCC NF NM_005381 c.807_809del p.E271del
NCOR2 12 124810072 124810072 G A NS NM_006312 c.C7421T p.A2474V
805 IGFN1 1 201178904 201178904 A G NS NM_001164586 c.A4883G p.E1628G
MADCAM1 19 501801 501802 AG CC NS NM_130760 c.[A800C;G801C] p.K267T
ZP3 7 76069902 76069902 G C NS NM_001110354 c.G1034C p.R345T
831 ACAP3 1 1233970 1233970 G T NS NM_030649 c.C840A p.S280R
CEL 9 135947032 135947032 C A NS NM_001807 c.C2152A p.P718T
SLAMF9 1 159923185 159923185 C A NS NM_001146172 c.G305T p.W102L
MUC4 3 195513461 195513461 G A NS NM_018406 c.C4990T p.P1664S
UBE2Q1 1 154530881 154530881 G T NS NM_017582 c.C149A p.S50Y
KDM4B 19 5032981 5032981 A T NS NM_015015 c.A80T p.D27V
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.
Exonic mutations/MB Mutated genes/sample Nonsynonymous mutations/sample Synonymous mutations/sample Rearrangements/sample
Frameshift Inframe
CNC 0.5661 7.7887 6.9184 4.1339 0.3661 1.0774
Tumor 7.0671 164.8159 152.5272 53.3745 12.2950 3.1088
P value <0.0001 <0.0001 <0.0001 <0.0001 <0.0001 <0.0001
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.
1 Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, Meyerson M, Gabriel SB, Lander ES, Getz G. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 2014; 505(7484): 495–501
https://doi.org/10.1038/nature12912 pmid: 24390350
2 Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010; 11(10): 685–696
https://doi.org/10.1038/nrg2841 pmid: 20847746
3 Hecht SS. Lung carcinogenesis by tobacco smoke. Int J Cancer 2012; 131(12): 2724–2732
https://doi.org/10.1002/ijc.27816 pmid: 22945513
4 Auerbach O, Hammond EC, Kirman D, Garfinkel L. Effects of cigarette smoking on dogs. II. Pulmonary neoplasms. Arch Environ Health 1970; 21(6): 754–768
https://doi.org/10.1080/00039896.1970.10667329 pmid: 5478560
5 Herbst RS, Heymach JV, Lippman SM. Lung cancer. N Engl J Med 2008; 359(13): 1367–1380
https://doi.org/10.1056/NEJMra0802714 pmid: 18815398
6 Lemjabbar-Alaoui H, Hassan OUI, Yang YW, Buchanan P. Lung cancer: biology and treatment options. Biochim Biophys Acta 2015; 1856(2): 189–210
pmid: 26297204
7 Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 2012; 489(7417): 519–525
https://doi.org/10.1038/nature11404 pmid: 22960745
8 Li C, Gao Z, Li F, Li X, Sun Y, Wang M, Li D, Wang R, Li F, Fang R, Pan Y, Luo X, He J, Zheng L, Xia J, Qiu L, He J, Ye T, Zhang R, He M, Zhu M, Hu H, Shi T, Zhou X, Sun M, Tian S, Zhou Y, Wang Q, Chen L, Yin G, Lu J, Wu R, Guo G, Li Y, Hu X, Li L, Asan, Wang Q, Yin Y, Feng Q, Wang B, Wang H, Wang M, Yang X, Zhang X, Yang H, Jin L, Wang CY, Ji H, Chen H, Wang J, Wei Q. Whole exome sequencing identifies frequent somatic mutations in cell-cell adhesion genes in Chinese patients with lung squamous cell carcinoma. Sci Rep 2015; 5: 14237
https://doi.org/10.1038/srep14237 pmid: 26503331
9 Yu XJ, Yang MJ, Zhou B, Wang GZ, Huang YC, Wu LC, Cheng X, Wen ZS, Huang JY, Zhang YD, Gao XH, Li GF, He SW, Gu ZH, Ma L, Pan CM, Wang P, Chen HB, Hong ZP, Wang XL, Mao WJ, Jin XL, Kang H, Chen ST, Zhu YQ, Gu WY, Liu Z, Dong H, Tian LW, Chen SJ, Cao Y, Wang SY, Zhou GB. Characterization of somatic mutations in air pollution-related lung cancer. EBioMedicine 2015; 2(6): 583–590
https://doi.org/10.1016/j.ebiom.2015.04.003 pmid: 26288819
10 McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010; 20(9): 1297–1303
https://doi.org/10.1101/gr.107524.110 pmid: 20644199
11 Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010; 26(5): 589–595
https://doi.org/10.1093/bioinformatics/btp698 pmid: 20080505
12 Franco B, Meroni G, Parenti G, Levilliers J, Bernard L, Gebbia M, Cox L, Maroteaux P, Sheffield L, Rappold GA, Andria G, Petit C, Ballabio A. A cluster of sulfatase genes on Xp22.3: mutations in chondrodysplasia punctata (CDPX) and implications for warfarin embryopathy. Cell 1995; 81(1): 15–25
https://doi.org/10.1016/0092-8674(95)90367-4 pmid: 7720070
13 Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009; 4(1): 44–57
https://doi.org/10.1038/nprot.2008.211 pmid: 19131956
14 Saito K, Yamashiro K, Ichikawa Y, Erlmann P, Kontani K, Malhotra V, Katada T. cTAGE5 mediates collagen secretion through interaction with TANGO1 at endoplasmic reticulum exit sites. Mol Biol Cell 2011; 22(13): 2301–2308
https://doi.org/10.1091/mbc.E11-02-0143 pmid: 21525241
15 Burrows JF, McGrattan MJ, Johnston JA. The DUB/USP17 deubiquitinating enzymes, a multigene family within a tandemly repeated sequence. Genomics 2005; 85(4): 524–529
https://doi.org/10.1016/j.ygeno.2004.11.013 pmid: 15780755
16 Ooi AT, Gower AC, Zhang KX, Vick JL, Hong L, Nagao B, Wallace WD, Elashoff DA, Walser TC, Dubinett SM, Pellegrini M, Lenburg ME, Spira A, Gomperts BN. Molecular profiling of premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis. Cancer Prev Res (Phila) 2014; 7(5): 487–495
https://doi.org/10.1158/1940-6207.CAPR-13-0372 pmid: 24618292
17 Gomperts BN, Spira A, Massion PP, Walser TC, Wistuba II, Minna JD, Dubinett SM. Evolving concepts in lung carcinogenesis. Semin Respir Crit Care Med 2011; 32(1): 32–43
https://doi.org/10.1055/s-0031-1272867 pmid: 21500122
18 Kadara H, Shen L, Fujimoto J, Saintigny P, Chow CW, Lang W, Chu Z, Garcia M, Kabbout M, Fan YH, Behrens C, Liu DA, Mao L, Lee JJ, Gold KA, Wang J, Coombes KR, Kim ES, Hong WK, Wistuba II. Characterizing the molecular spatial and temporal field of injury in early-stage smoker non-small cell lung cancer patients after definitive surgery by expression profiling. Cancer Prev Res (Phila) 2013; 6(1): 8–17
https://doi.org/10.1158/1940-6207.CAPR-12-0290 pmid: 23087048
19 Wistuba II, Behrens C, Milchgrub S, Bryant D, Hung J, Minna JD, Gazdar AF. Sequential molecular abnormalities are involved in the multistage development of squamous cell lung carcinoma. Oncogene 1999; 18(3): 643–650
https://doi.org/10.1038/sj.onc.1202349 pmid: 9989814
20 Qu LW, Zhou B, Wang GZ, Chen Y, Zhou GB. Genomic variations in paired normal controls for lung adenocarcinomas. Oncotarget 2017 (in press)
21 Olivier M, Weninger A, Ardin M, Huskova H, Castells X, Vallée MP, McKay J, Nedelko T, Muehlbauer KR, Marusawa H, Alexander J, Hazelwood L, Byrnes G, Hollstein M, Zavadil J. Modelling mutational landscapes of human cancers in vitro. Sci Rep 2014; 4: 4482
https://doi.org/10.1038/srep04482 pmid: 24670820
22 Dollé MET, Snyder WK, Dunson DB, Vijg J. Mutational fingerprints of aging. Nucleic Acids Res 2002; 30(2): 545–549
https://doi.org/10.1093/nar/30.2.545 pmid: 11788717
23 Govindan R, Ding L, Griffith M, Subramanian J, Dees ND, Kanchi KL, Maher CA, Fulton R, Fulton L, Wallis J, Chen K, Walker J, McDonald S, Bose R, Ornitz D, Xiong D, You M, Dooling DJ, Watson M, Mardis ER, Wilson RK. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 2012; 150(6): 1121–1134
https://doi.org/10.1016/j.cell.2012.08.024 pmid: 22980976
24 Qiu L, Wu J, Pan C, Tan X, Lin J, Liu R, Chen S, Geng R, Huang W. Downregulation of CDC27 inhibits the proliferation of colorectal cancer cells via the accumulation of p21Cip1/Waf1. Cell Death Dis 2016; 7(1): e2074
https://doi.org/10.1038/cddis.2015.402 pmid: 26821069
25 Wang J, Ma L, Tang X, Zhang X, Qiao Y, Shi Y, Xu Y, Wang Z, Yu Y, Sun F. Doxorubicin induces apoptosis by targeting Madcam1 and AKT and inhibiting protein translation initiation in hepatocellular carcinoma cells. Oncotarget 2015; 6(27): 24075–24091
https://doi.org/10.18632/oncotarget.4373 pmid: 26124182
26 Wang W, Song XW, Bu XM, Zhang N, Zhao CH. PDCD2 and NCoR1 as putative tumor suppressors in gastric gastrointestinal stromal tumors. Cell Oncol (Dordr) 2016; 39(2): 129–137
https://doi.org/10.1007/s13402-015-0258-0 pmid: 26589942
[1] FMD-17065-OF-ZGB_suppl_1 Download
[1] Hongbing Shen. Low-dose CT for lung cancer screening: opportunities and challenges[J]. Front. Med., 2018, 12(1): 116-121.
[2] Alexandra Urman,H. Dean Hosgood. Curbing the burden of lung cancer[J]. Front. Med., 2016, 10(2): 228-232.
[3] Li Bian,Yonghua Ruan,Liju Ma,Hairong Hua,Li Zhou,Xiaoyu Tuo,Zheyan Zhou,Ting Li,Shiyue Liu,Kewei Jin. Pathogenesis sequences in Gejiu miners with lung cancer: an introduction[J]. Front. Med., 2015, 9(3): 344-349.
[4] Douglas D. Fang, Joan Cao, Jitesh P. Jani, Konstantinos Tsaparikos, Alessandra Blasina, Jill Kornmann, Maruja E. Lira, Jianying Wang, Zuzana Jirout, Justin Bingham, Zhou Zhu, Yin Gu, Gerrit Los, Zdenek Hostomsky, Todd VanArsdale. Combined gemcitabine and CHK1 inhibitor treatment induces apoptosis resistance in cancer stem cell-like cells enriched with tumor spheroids from a non-small cell lung cancer cell line[J]. Front Med, 2013, 7(4): 462-476.
[5] Yue Yu, Jie He. Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis[J]. Front Med, 2013, 7(2): 157-171.
[6] Yize Xiao, Ying Shao, Xianjun Yu, Guangbiao Zhou. The epidemic status and risk factors of lung cancer in Xuanwei City, Yunnan Province, China[J]. Front Med, 2012, 6(4): 388-394.
[7] Ji Qi, David Mu. MicroRNAs and lung cancers: from pathogenesis to clinical implications[J]. Front Med, 2012, 6(2): 134-155.
[8] Min ZHU, Xiang-Ning FU, Xiao-Ping CHEN. Lobectomy by video-assisted thoracoscopic surgery (VATS) for early stage of non-small cell lung cancer[J]. Front Med, 2011, 5(1): 53-60.
[9] Dian-Ke YU PhD, Chen WU MD, Wen TAN MD, Dong-Xin LIN MD, . Functional XPF polymorphisms associated with lung cancer susceptibility in a Chinese population[J]. Front. Med., 2010, 4(1): 82-89.
[10] Bo PENG BA , Jinnong ZHANG MD , Jamile S. WOODS MD , Wei PENG MD, PhD . Molecular markers and pathogenically targeted therapy in non-small cell lung cancer[J]. Front. Med., 2009, 3(3): 245-255.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed