Cell type-specific properties and environment shape tissue specificity of cancer genes

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Schaefer, Martin H ^a,b   Serrano, Luis ^a,b,c  

^a BARCELONA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Spain)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY SPECIFICITY; BIOLOGICAL MODEL; GENETICS; HUMAN; METABOLISM; NEOPLASM; NUCLEIC ACID DATABASE; PATHOLOGY; TUMOR GENE; TUMOR MICROENVIRONMENT;

DATABASES, NUCLEIC ACID; GENES, NEOPLASM; HUMANS; MODELS, GENETIC; NEOPLASMS, GERM CELL AND EMBRYONAL; ORGAN SPECIFICITY; TUMOR MICROENVIRONMENT;

EID: 84957837730     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep20707     Document Type: Article

References (72)

1. Lawrence, M. S. et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014).
2. Friedenson, B. BRCA1 and BRCA2 pathways and the risk of cancers other than breast or ovarian. Med Gen Med 7, 60 (2005).
3. Lage, K. et al. A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes. Proc. Natl. Acad. Sci. USA 105, 20870-5 (2008).
4. Sieber, O. M., Tomlinson, S. R. & Tomlinson, I. P. M. Tissue, cell and stage specificity of (epi)mutations in cancers. Nat. Rev. Cancer 5, 649-55 (2005).
5. Monteiro, A. N. A. BRCA1: the enigma of tissue-specific tumor development. Trends Genet. 19, 312-5 (2003).
6. Young, N. P. & Jacks, T. Tissue-specific p19Arf regulation dictates the response to oncogenic K-ras. Proc. Natl. Acad. Sci. USA 107, 10184-9 (2010).
7. Gorrini, C. et al. Estrogen controls the survival of BRCA1-deficient cells via a PI3K-NRF2-regulated pathway. Proc. Natl. Acad. Sci. USA 111, 4472-7 (2014).
8. Friedberg, E. C. How nucleotide excision repair protects against cancer. Nat. Rev. Cancer 1, 22-33 (2001).
9. Wilhelm, M. et al. Mass-spectrometry-based draft of the human proteome. Nature 509, 582-587 (2014).
10. Ardlie, K. G. et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (80-.). 348, 648-660 (2015).
11. Vogelstein, B. & Kinzler, K. W. Cancer genes and the pathways they control. Nat. Med. 10, 789-99 (2004).
12. Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).
13. Leblond, C. P. & Walker, B. E. Renewal of Cell Populations. Physiol Rev 36, 255-276 (1956).
14. Lieber, M. R. Pathological and Physiological Double-Strand Breaks. Am. J. Pathol. 153, 1323-1332 (1998).
15. Tsujimoto, Y., Gorham, J., Cossman, J., Jaffe, E. & Croce, C. The t(14;18) chromosome translocations involved in B-cell neoplasms result from mistakes in VDJ joining. Science (80-.). 229, 1390-1393 (1985).
16. Liehr, J. G. Is estradiol a genotoxic mutagenic carcinogen ? Endocr. Rev. 21, 40-54 (2000).
17. Williamson, L. M. & Lees-Miller, S. P. Estrogen receptor α -mediated transcription induces cell cycle-dependent DNA double-strand breaks. Carcinogenesis 32, 279-85 (2011).
18. Savage, K. I. et al. BRCA1 deficiency exacerbates estrogen-induced DNA damage and genomic instability. Cancer Res. 74, 2773-84 (2014).
19. Slatter, T. L. et al. Smoking during pregnancy causes double-strand DNA break damage to the placenta. Hum. Pathol. 45, 17-26 (2014).
20. Jorgensen, E. D., Zhao, H., Traganos, F., Albino, A. P. & Darzynkiewicz, Z. DNA damage response induced by exposure of human lung adenocarcinoma cells to smoke from tobacco- and nicotine-free cigarettes. Cell Cycle 9, 2170-2176 (2010).
21. Albino, A. P. et al. gammaH2AX: A potential DNA damage response biomarker for assessing toxicological risk of tobacco products. Mutat. Res. 678, 43-52 (2009).
22. Albino, A. P. et al. Induction of H2AX Phosphorylation in Pulmonary Cells by Tobacco Smoke: A New Assay for Carcinogens. Cell Cycle 3, 1060-1066 (2014).
23. Kamburov, A., Stelzl, U., Lehrach, H. & Herwig, R. The Consensus PathDB interaction database: 2013 update. Nucleic Acids Res. 41, D793-800 (2013).
24. Futreal, P. A. et al. A census of human cancer genes. Nat. Rev. Cancer 4, 177-83 (2004).
25. Montgomery, R. I., Warner, M. S., Lum, B. J. & Spear, P. G. Herpes simplex virus-1 entry into cells mediated by a novel member of the TNF/NGF receptor family. Cell 87, 427-36 (1996).
26. Kim, Y. J. et al. Association of TNF-alpha promoter polymorphisms with the clearance of hepatitis B virus infection. Hum. Mol. Genet. 12, 2541-6 (2003).
27. Allam, A., Swiecki, M., Vermi, W., Ashwell, J. D. & Colonna, M. Dual function of CD70 in viral infection: modulator of early cytokine responses and activator of adaptive responses. J. Immunol. 193, 871-8 (2014).
28. Johnson, J. M. et al. Free major histocompatibility complex class I heavy chain is preferentially targeted for degradation by human T-cell leukemia/lymphotropic virus type 1 p12(I) protein. J. Virol. 75, 6086-94 (2001).
29. Calderone, A., Licata, L. & Cesareni, G. Virus Mentha: a new resource for virus-host protein interactions. Nucleic Acids Res. (2014). doi: 10.1093/nar/gku830
30. Klein, G., Klein, E. & Kashuba, E. Interaction of Epstein-Barr virus (EBV) with human B-lymphocytes. Biochem. Biophys. Res. Commun. 396, 67-73 (2010).
31. Dolcetti, R. & Carbone, A. Epstein-Barr virus infection and chronic lymphocytic leukemia: a possible progression factor? Infect. Agent. Cancer 5, 22 (2010).
32. Schiffman, M., Castle, P. E., Jeronimo, J., Rodriguez, A. C. & Wacholder, S. Human papillomavirus and cervical cancer. Lancet 370, 890-907 (2007).
33. Shanmughapriya, S. et al. Viral and bacterial aetiologies of epithelial ovarian cancer. Eur. J. Clin. Microbiol. Infect. Dis. 31, 2311-7 (2012).
34. Li, N. et al. Human papillomavirus infection and bladder cancer risk: a meta-analysis. J. Infect. Dis. 204, 217-23 (2011).
35. Simões, P. W. et al. Prevalence of human papillomavirus in breast cancer: a systematic review. Int. J. Gynecol. Cancer 22, 343-7 (2012).
36. Grulich, A. E., van Leeuwen, M. T., Falster, M. O. & Vajdic, C. M. Incidence of cancers in people with HIV/AIDS compared with immunosuppressed transplant recipients: a meta-analysis. Lancet 370, 59-67 (2007).
37. Engels, E. A. et al. Cancer risk in people infected with human immunodeficiency virus in the United States. Int. J. Cancer 123, 187-94 (2008).
38. Guirimand, T., Delmotte, S. & Navratil, V. Vir HostNet 2.0: surfing on the web of virus/host molecular interactions data. Nucleic Acids Res. 43, D583-7 (2015).
39. Davis, A. P. et al. The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. Nucleic Acids Res. 43, D914-D920 (2014).
40. Selikoff, I. J., Churg, J. & Hammond, E. C. Asbestos Exposure and Neoplasia. JAMA 188, 22-26 (1964).
41. Wu, S., Wei, X., Jiang, J., Shang, L. & Hao, W. Effects of bisphenol A on the proliferation and cell cycle of HBL-100 cells. Food Chem. Toxicol. 50, 3100-5 (2012).
42. Dairkee, S. H. et al. Bisphenol A induces a profile of tumor aggressiveness in high-risk cells from breast cancer patients. Cancer Res. 68, 2076-80 (2008).
43. Yang, M., Ryu, J.-H., Jeon, R., Kang, D. & Yoo, K.-Y. Effects of bisphenol A on breast cancer and its risk factors. Arch. Toxicol. 83, 281-5 (2009).
44. Polak, P. et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360-364 (2015).
45. Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415-21 (2013).
46. Kandoth, C. et al. Mutational landscape and significance across 12 major cancer types. Nature 502, 333-339 (2013).
47. Barker, N. et al. Crypt stem cells as the cells-of-origin of intestinal cancer. Nature 457, 608-11 (2009).
48. Barshir, R., Shwartz, O., Smoly, I. Y. & Yeger-Lotem, E. Comparative analysis of human tissue interactomes reveals factors leading to tissue-specific manifestation of hereditary diseases. PLoS Comput. Biol. 10, e1003632 (2014).
49. Powell, C. L., Swenberg, J. A. & Rusyn, I. Expression of base excision DNA repair genes as a biomarker of oxidative DNA damage. Cancer Lett. 229, 1-11 (2005).
50. Dion, V. Tissue specificity in DNA repair: lessons from trinucleotide repeat instability. Trends Genet. 30, 220-9 (2014).
51. Chao, E. C. & Lipkin, S. M. Molecular models for the tissue specificity of DNA mismatch repair-deficient carcinogenesis. Nucleic Acids Res. 34, 840-52 (2006).
52. Blighe, K. Cancer Mutations and their Tissue-specific Nature. J. Cancer Sci. Ther. 6, 009-011 (2014).
53. Rahman, N. Realizing the promise of cancer predisposition genes. Nature 505, 302-8 (2014).
54. Weiss, R. A. HIV receptors and cellular tropism. IUBMB Life 53, 201-205 (2002).
55. Schaefer, M. H., Yang, J.-S., Serrano, L. & Kiel, C. Protein Conservation and Variation Suggest Mechanisms of Cell Type-Specific Modulation of Signaling Pathways. PLoS Comput. Biol. 10, e1003659 (2014).
56. Furlong, L. I. Human diseases through the lens of network biology. Trends Genet. 29, 150-9 (2013).
57. Gulbahce, N. et al. Viral perturbations of host networks reflect disease etiology. PLoS Comput. Biol. 8, e1002531 (2012).
58. Schaefer, M. H., Serrano, L. & Andrade-Navarro, M. A. Correcting for the study bias associated with protein-protein interaction measurements reveals differences between protein degree distributions from different cancer types. Front. Genet. (2015). doi: 10.3389/fgene.2015.00260.
59. Bos, J. L. ras Oncogenes in Human Cancer: A Review. Cancer Res. 49, 4682-4689 (1989).
60. Weinstein, J. N. et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113-20 (2013).
61. Supek, F., Miñana, B., Valcárcel, J., Gabaldón, T. & Lehner, B. Synonymous mutations frequently act as driver mutations in human cancers. Cell 156, 1324-35 (2014).
62. Zhao, J., Lee, S. H., Huss, M. & Holme, P. The network organization of cancer-associated protein complexes in human tissues. Sci. Rep. 3, 1583 (2013).
63. Park, S. & Lehner, B. Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types. Mol. Syst. Biol. 11, 824 (2015).
64. Subramanian, A. et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-50 (2005).
65. The UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42, D191-8 (2014).
66. Resnik, P. Using Information Content to Evaluate Semantic Similarity in a Taxonomy. In Proc. 14th Int. Jt. Conf. Artif. Intell. - Vol. 1 448-453 (Morgan Kaufmann Publishers Inc., 1995).
67. Fröhlich, H., Speer, N., Poustka, A. & Beissbarth, T. GOSim-an R-package for computation of information theoretic GO similarities between terms and gene products. BMC Bioinformatics 8, 166 (2007).
68. Brown, G. R. et al. Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 43, D36-42 (2015).
69. Bhat, K. P. et al. Estrogenic and antiestrogenic properties of resveratrol in mammary tumor models. Cancer Res. 61, 7456-63 (2001).
70. Resseguie, M. et al. Phosphatidylethanolamine N-methyltransferase (PEMT) gene expression is induced by estrogen in human and mouse primary hepatocytes. FASEB J. 21, 2622-32 (2007).
71. Singh, B. et al. Dietary quercetin exacerbates the development of estrogen-induced breast tumors in female ACI rats. Toxicol. Appl. Pharmacol. 247, 83-90 (2010).
72. Rosado, J. L. Zinc and copper: proposed fortification levels and recommended zinc compounds. J. Nutr. 133, 2985S-9S (2003).