Characterization of Potential Driver Mutations Involved in Human Breast Cancer by Computational Approaches

Overview

Journal Oncotarget

Specialty Oncology

Date 2017 May 7

PMID 28477017

Citations 38

Authors

Barani Kumar Rajendran

Chu-Xia Deng

Affiliations

Soon will be listed here.

Abstract

Breast cancer is the second most frequently occurring form of cancer and is also the second most lethal cancer in women worldwide. A genetic mutation is one of the key factors that alter multiple cellular regulatory pathways and drive breast cancer initiation and progression yet nature of these cancer drivers remains elusive. In this article, we have reviewed various computational perspectives and algorithms for exploring breast cancer driver mutation genes. Using both frequency based and mutational exclusivity based approaches, we identified 195 driver genes and shortlisted 63 of them as candidate drivers for breast cancer using various computational approaches. Finally, we conducted network and pathway analysis to explore their functions in breast tumorigenesis including tumor initiation, progression, and metastasis.

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References

Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M . Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2014; 136(5):E359-86. DOI: 10.1002/ijc.29210. View

Haber D, Settleman J . Cancer: drivers and passengers. Nature. 2007; 446(7132):145-6. DOI: 10.1038/446145a. View

Ehrich M, Field J, Liloglou T, Xinarianos G, Oeth P, Nelson M . Cytosine methylation profiles as a molecular marker in non-small cell lung cancer. Cancer Res. 2006; 66(22):10911-8. DOI: 10.1158/0008-5472.CAN-06-0400. View

Easton D, Ford D, Bishop D . Breast and ovarian cancer incidence in BRCA1-mutation carriers. Breast Cancer Linkage Consortium. Am J Hum Genet. 1995; 56(1):265-71. PMC: 1801337. View

Giacomazzi J, Selistre S, Rossi C, Alemar B, Santos-Silva P, Pereira F . Li-Fraumeni and Li-Fraumeni-like syndrome among children diagnosed with pediatric cancer in Southern Brazil. Cancer. 2013; 119(24):4341-9. DOI: 10.1002/cncr.28346. View

Takaku M, Grimm S, Wade P . GATA3 in Breast Cancer: Tumor Suppressor or Oncogene?. Gene Expr. 2015; 16(4):163-8. PMC: 4758516. DOI: 10.3727/105221615X14399878166113. View

Chen Y, Hao J, Jiang W, He T, Zhang X, Jiang T . Identifying potential cancer driver genes by genomic data integration. Sci Rep. 2013; 3:3538. PMC: 3866686. DOI: 10.1038/srep03538. View

Petroziello J, Yamane A, Westendorf L, Thompson M, McDonagh C, Cerveny C . Suppression subtractive hybridization and expression profiling identifies a unique set of genes overexpressed in non-small-cell lung cancer. Oncogene. 2004; 23(46):7734-45. DOI: 10.1038/sj.onc.1207921. View

Ford D, Easton D, Stratton M, Narod S, Goldgar D, Devilee P . Genetic heterogeneity and penetrance analysis of the BRCA1 and BRCA2 genes in breast cancer families. The Breast Cancer Linkage Consortium. Am J Hum Genet. 1998; 62(3):676-89. PMC: 1376944. DOI: 10.1086/301749. View

10.

Sommer S, Jiang Z, Feng J, Buzin C, Zheng J, Longmate J . ATM missense mutations are frequent in patients with breast cancer. Cancer Genet Cytogenet. 2003; 145(2):115-20. DOI: 10.1016/s0165-4608(03)00119-5. View

11.

Stratton M, Campbell P, Futreal P . The cancer genome. Nature. 2009; 458(7239):719-24. PMC: 2821689. DOI: 10.1038/nature07943. View

12.

Katagiri T, Kasumi F, Yoshimoto M, Nomizu T, Asaishi K, Abe R . High proportion of missense mutations of the BRCA1 and BRCA2 genes in Japanese breast cancer families. J Hum Genet. 1998; 43(1):42-8. DOI: 10.1007/s100380050035. View

13.

Clocchiatti A, Di Giorgio E, Ingrao S, Meyer-Almes F, Tripodo C, Brancolini C . Class IIa HDACs repressive activities on MEF2-depedent transcription are associated with poor prognosis of ER⁺ breast tumors. FASEB J. 2012; 27(3):942-54. DOI: 10.1096/fj.12-209346. View

14.

Shapiro I, Cheng A, Flytzanis N, Balsamo M, Condeelis J, Oktay M . An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 2011; 7(8):e1002218. PMC: 3158048. DOI: 10.1371/journal.pgen.1002218. View

15.

Darcy D, Chiaroni-Clarke R, Murphy J, Honeyman J, Bhanot U, LaQuaglia M . The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients. Oncotarget. 2015; 6(2):755-70. PMC: 4359253. DOI: 10.18632/oncotarget.2712. View

16.

Youn A, Simon R . Identifying cancer driver genes in tumor genome sequencing studies. Bioinformatics. 2010; 27(2):175-81. PMC: 3018819. DOI: 10.1093/bioinformatics/btq630. View

17.

Walsh T, King M . Ten genes for inherited breast cancer. Cancer Cell. 2007; 11(2):103-5. DOI: 10.1016/j.ccr.2007.01.010. View

18.

Zhao J, Xu H, He M, Wang Z, Wu Y . Rho GTPase-activating protein 35 rs1052667 polymorphism and osteosarcoma risk and prognosis. Biomed Res Int. 2014; 2014:396947. PMC: 4124850. DOI: 10.1155/2014/396947. View

19.

Zhao H, Wang J, Han Y, Huang Z, Ying J, Bi X . ARID2: a new tumor suppressor gene in hepatocellular carcinoma. Oncotarget. 2011; 2(11):886-91. PMC: 3259997. DOI: 10.18632/oncotarget.355. View

20.

Brouwer A, De Laere B, Peeters D, Peeters M, Salgado R, Dirix L . Evaluation and consequences of heterogeneity in the circulating tumor cell compartment. Oncotarget. 2016; 7(30):48625-48643. PMC: 5217044. DOI: 10.18632/oncotarget.8015. View