Identification of hallmarks of lung adenocarcinoma prognosis using whole genome sequencing

Oncotarget

Volumn 6, Issue 35, 2015, Pages 38016-38028

  Liu, Li ^a   Huang, Jiao ^a   Wang, Ke ^a   Li, Li ^a   Li, Yangkai ^a   Yuan, Jingsong ^b   Wei, Sheng ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b NewYork Presbyterian Hospital   (United States)

Author keywords

Copy number variation; Lung adenocarcinoma; Overall survival; Progression free survival; Whole genome sequencing

Indexed keywords

ADULT; AGED; ARTICLE; BRD9 GENE; CANCER GROWTH; CANCER PROGNOSIS; CANCER STAGING; CANCER SURVIVAL; CEP72 GENE; CHINESE; CHROMOSOME 3; COPY NUMBER VARIATION; FEMALE; GENE EXPRESSION; GENE LOCATION; GENOTYPE; HUMAN; LOC100506688 GENE; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MALE; ONCOGENE; OVERALL SURVIVAL; PBXIP1 GENE; PDCD6 GENE; PROGRESSION FREE SURVIVAL; SDHA GENE; SLC6A18 GENE; SLC6A19 GENE; SLC9A3 GENE; SURVIVAL TIME; TERT GENE; TPPP GENE; TRIP13 GENE; ADENOCARCINOMA; COMPARATIVE GENOMIC HYBRIDIZATION; FOLLOW UP; GENETICS; HUMAN GENOME; LUNG TUMOR; MIDDLE AGED; MORTALITY; PATHOLOGY; PROGNOSIS; SURVIVAL RATE; TUMOR RECURRENCE;

PBXIP1 PROTEIN, HUMAN; TELOMERASE; TERT PROTEIN, HUMAN; TRANSCRIPTION FACTOR; TUMOR MARKER;

ADENOCARCINOMA; AGED; BIOMARKERS, TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; FEMALE; FOLLOW-UP STUDIES; GENOME, HUMAN; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; NEOPLASM RECURRENCE, LOCAL; NEOPLASM STAGING; PROGNOSIS; SURVIVAL RATE; TELOMERASE; TRANSCRIPTION FACTORS;

EID: 84947720895     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.5697     Document Type: Article

References (43)

1. Parkin DM, Bray F, Ferlay J, Pisani P. Global cancer statistics, 2002 CA Cancer J Clin. 2005; 55:74-108.
2. Molina JR, Yang P, Cassivi SD, Schild SE, Adjei AA. Non-small cell lung cancer: epidemiology, risk factors, treatment, and survivorship. Mayo Clin Proc. 2008; 83:584-594.
3. Hu Z, Chen J, Tian T, Zhou X, Gu H, Xu L, Zeng Y, Miao R, Jin G, Ma H, Chen Y, Shen H. Genetic variants of miRNA sequences and non-small cell lung cancer survival. Journal of Clinical Investigation. 2008; 118:2600-2608.
4. Chen G, Kim SH, King AN, Zhao L, Simpson RU, Christensen PJ, Wang Z, Thomas DG, Giordano TJ, Lin L, Brenner DE, Beer DG, Ramnath N. CYP24A1 is an independent prognostic marker of survival in patients with lung adenocarcinoma. Clin Cancer Res. 2011; 17:817-826.
5. Galvan A, Colombo F, Frullanti E, Dassano A, Noci S, Wang Y, Eisen T, Matakidou A, Tomasello L, Vezzalini M, Sorio C, Dugo M, Ambrogi F, et al. Germline polymorphisms and survival of lung adenocarcinoma patients: a genome-wide study in two European patient series. Int J Cancer. 2015; 136:E262-271.
6. Han JY, Yoon KA, Park JH, Lee YJ, Lee GK, Han JH, Yoon SJ, Yun T, Kim HT, Lee JS. DNA repair gene polymorphisms and benefit from gefitinib in never-smokers with lung adenocarcinoma. Cancer. 2011; 117:3201-3208.
7. Cappuzzo F, Varella-Garcia M, Shigematsu H, Domenichini I, Bartolini S, Ceresoli GL, Rossi E, Ludovini V, Gregorc V, Toschi L, Franklin WA, Crino L, Gazdar AF, et al. Increased HER2 gene copy number is associated with response to gefitinib therapy in epidermal growth factor receptor-positive non-small-cell lung cancer patients. J Clin Oncol. 2005; 23:5007-5018.
8. Hirsch FR, Varella-Garcia M, Bunn PA Jr., Di Maria MV, Veve R, Bremmes RM, Baron AE, Zeng C, Franklin WA. Epidermal growth factor receptor in non-small-cell lung carcinomas: correlation between gene copy number and protein expression and impact on prognosis. J Clin Oncol. 2003; 21:3798-3807.
9. Hirsch FR, Herbst RS, Olsen C, Chansky K, Crowley J, Kelly K, Franklin WA, Bunn PA Jr., Varella-Garcia M, Gandara DR. Increased EGFR gene copy number detected by fluorescent in situ hybridization predicts outcome in non-small-cell lung cancer patients treated with cetuximab and chemotherapy. J Clin Oncol. 2008; 26:3351-3357.
10. Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C, Tyler-Smith C, Carter N, Scherer SW, et al. Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science. 2007; 315:848-853.
11. Ionita-Laza I, Rogers AJ, Lange C, Raby BA, Lee C. Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis. Genomics. 2009; 93:22-26.
12. Dhawan D, Padh H. Pharmacogenetics: technologies to detect copy number variations. Curr Opin Mol Ther. 2009; 11:670-680.
13. Lee JH, Jeon JT. Methods to detect and analyze copy number variations at the genome-wide and locus-specific levels. Cytogenet Genome Res. 2008; 123:333-342.
14. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011; 144:646-674.
15. Hieronymus H, Schultz N, Gopalan A, Carver BS, Chang MT, Xiao Y, Heguy A, Huberman K, Bernstein M, Assel M, Murali R, Vickers A, Scardino PT, et al. Copy number alteration burden predicts prostate cancer relapse. Proc Natl Acad Sci U S A. 2014; 111:11139-11144.
16. Peng CH, Liao CT, Ng KP, Tai AS, Peng SC, Yeh JP, Chen SJ, Tsao KC, Yen TC, Hsieh WP. Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget. 2015; 6:19891-19906.
17. Witkiewicz AK, McMillan EA, Balaji U, Baek G, Lin WC, Mansour J, Mollaee M, Wagner KU, Koduru P, Yopp A, Choti MA, Yeo CJ, McCue P, et al. Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets. Nat Commun. 2015; 6:6744.
18. Seo AN, Yang JM, Kim H, Jheon S, Kim K, Lee CT, Jin Y, Yun S, Chung JH, Paik JH. Clinicopathologic and prognostic significance of c-MYC copy number gain in lung adenocarcinomas. Br J Cancer. 2014; 110:2688-2699.
19. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010; 11:685-696.
20. Xie C, Tammi MT. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics. 2009; 10:80.
21. Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, Kadel S, Moll I, Nagore E, Hemminki K, Schadendorf D, Kumar R. TERT promoter mutations in familial and sporadic melanoma. Science. 2013; 339:959-961.
22. Garnis C, Davies JJ, Buys TP, Tsao MS, MacAulay C, Lam S, Lam WL. Chromosome 5p aberrations are early events in lung cancer: implication of glial cell line-derived neurotrophic factor in disease progression. Oncogene. 2005; 24:4806-4812.
23. Kang JU, Koo SH, Kwon KC, Park JW, Shin SY, Kim JM, Jung SS. High frequency of genetic alterations in non-small cell lung cancer detected by multi-target fluorescence in situ hybridization. J Korean Med Sci. 2007;:S47-51.
24. Shen H, Gao W, Wu YJ, Qiu HR, Shu YQ. Multicolor fluorescence in situ hybridization and comparative genomic hybridization reveal molecular events in lung adenocarcinomas and squamous cell lung carcinomas. Biomed Pharmacother. 2009; 63:396-403.
25. Iwakawa R, Kohno T, Kato M, Shiraishi K, Tsuta K, Noguchi M, Ogawa S, Yokota J. MYC amplification as a prognostic marker of early-stage lung adenocarcinoma identified by whole genome copy number analysis. Clin Cancer Res. 2011; 17:1481-1489.
26. Huang YT, Heist RS, Chirieac LR, Lin X, Skaug V, Zienolddiny S, Haugen A, Wu MC, Wang Z, Su L, Asomaning K, Christiani DC. Genome-wide analysis of survival in early-stage non-small-cell lung cancer. J Clin Oncol. 2009; 27:2660-2667.
27. Aviel-Ronen S, Coe BP, Lau SK, da Cunha Santos G, Zhu CQ, Strumpf D, Jurisica I, Lam WL, Tsao MS. Genomic markers for malignant progression in pulmonary adenocarcinoma with bronchioloalveolar features. Proc Natl Acad Sci U S A. 2008; 105:10155-10160.
28. Huang FW, Hodis E, Xu MJ, Kryukov GV, Chin L, Garraway LA. Highly recurrent TERT promoter mutations in human melanoma. Science. 2013; 339:957-959.
29. Eldholm V, Haugen A, Zienolddiny S. CTCF mediates the TERT enhancer-promoter interactions in lung cancer cells: identification of a novel enhancer region involved in the regulation of TERT gene. Int J Cancer. 2014; 134:2305-2313.
30. Lantuejoul S, Soria JC, Moro-Sibilot D, Morat L, Veyrenc S, Lorimier P, Brichon PY, Sabatier L, Brambilla C, Brambilla E. Differential expression of telomerase reverse transcriptase (hTERT) in lung tumours. Br J Cancer. 2004; 90:1222-1229.
31. Wang L, Soria JC, Kemp BL, Liu DD, Mao L, Khuri FR. hTERT expression is a prognostic factor of survival in patients with stage I non-small cell lung cancer. Clin Cancer Res. 2002; 8:2883-2889.
32. Azad AK, Qiu X, Boyd K, Kuang Q, Emami M, Perera N, Palepu P, Patel D, Chen Z, Cheng D, Feld R, Leighl NB, Shepherd FA, et al. A genetic sequence variant (GSV) at susceptibility loci of 5p15.33 (TERT-CLPTM1L) is associated with survival outcome in locally advanced and metastatic non-small-cell lung cancer (NSCLC). Lung Cancer. 2014; 84:289-294.
33. Bugide S, David D, Nair A, Kannan N, Samanthapudi VS, Prabhakar J, Manavathi B. Hematopoietic PBX-interacting protein (HPIP) is over expressed in breast infiltrative ductal carcinoma and regulates cell adhesion and migration through modulation of focal adhesion dynamics. Oncogene. 2014.
34. Wang X, Yang Z, Zhang H, Ding L, Li X, Zhu C, Zheng Y, Ye Q. The estrogen receptor-interacting protein HPIP increases estrogen-responsive gene expression through activation of MAPK and AKT. Biochim Biophys Acta. 2008; 1783:1220-1228.
35. van Vuurden DG, Aronica E, Hulleman E, Wedekind LE, Biesmans D, Malekzadeh A, Bugiani M, Geerts D, Noske DP, Vandertop WP. Pre-B-cell leukemia homeobox interacting protein 1 is overexpressed in astrocytoma and promotes tumor cell growth and migration. Neuro Oncol. 2014; 16:946-959.
36. Okada S, Irie T, Tanaka J, Yasuhara R, Yamamoto G, Isobe T, Hokazono C, Tachikawa T, Kohno Y, Mishima K. Potential role of hematopoietic pre-B-cell leukemia transcription factor-interacting protein in oral carcinogenesis. J Oral Pathol Med. 2015; 44:115-125.
37. Xu X, Jiang C, Wang S, Tai Y, Wang T, Kang L, Fan Z, Li S, Li L, Fu J, Liu J, Ji Q, Wang X, et al. HPIP is upregulated in liver cancer and promotes hepatoma cell proliferation via activation of G2/M transition. IUBMB Life. 2013; 65:873-882.
38. Silveira SM, Villacis RA, Marchi FA, Barros Filho Mde C, Drigo SA, Neto CS, Lopes A, da Cunha IW, Rogatto SR. Genomic signatures predict poor outcome in undifferentiated pleomorphic sarcomas and leiomyosarcomas. PLoS One. 2013; 8:e67643.
39. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR. A method and server for predicting damaging missense mutations. Nat Methods. 2010; 7:248-249.
40. Wood HM, Belvedere O, Conway C, Daly C, Chalkley R, Bickerdike M, McKinley C, Egan P, Ross L, Hayward B, Morgan J, Davidson L, MacLennan K, et al. Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Res. 2010; 38:e151.
41. Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M. Detecting copy number variation with mated short reads. Genome Res. 2010; 20:1613-1622.
42. Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, Lee E, Zhang J, Johnson MD, Muzny DM, Wheeler DA, Gibbs RA, Kucherlapati R, Park PJ. Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. Proc Natl Acad Sci U S A. 2011; 108:E1128-1136.
43. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19:1639-1645.