Network cluster analysis of protein-protein interaction network identified biomarker for early onset colorectal cancer

Molecular Biology Reports

Volumn 40, Issue 12, 2013, Pages 6561-6568

  Luo, Tiancheng ^a   Wu, Shengdi ^a   Shen, Xizhong ^a   Li, Lei ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

Biomarker; Colorectal cancer (CRC); Functional modules; Protein protein interaction (PPI) network

Indexed keywords

CAVEOLIN 1; FIBRONECTIN 1; ONCOPROTEIN; PROTEIN CDC42; QUAKING; TESTIS EXPRESSED PROTEIN 11; TUMOR MARKER; UNCLASSIFIED DRUG;

APOPTOSIS; ARTICLE; CARCINOGENESIS; CELL COMMUNICATION; CELL PROLIFERATION; CELL SHAPE; COLORECTAL CANCER; CONTROLLED STUDY; EARLY CANCER; ENVIRONMENTAL ENRICHMENT; GENE EXPRESSION PROFILING; HIGH THROUGHPUT SCREENING; HUMAN; HUMAN TISSUE; MAJOR CLINICAL STUDY; MOLECULAR DYNAMICS; ONTOLOGY; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

AGE OF ONSET; CLUSTER ANALYSIS; COLORECTAL NEOPLASMS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE ONTOLOGY; HUMANS; MOLECULAR SEQUENCE ANNOTATION; PROTEIN INTERACTION MAPS; TUMOR MARKERS, BIOLOGICAL;

EID: 84890442698     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-013-2694-0     Document Type: Article

References (51)

1. Merika E, Saif M, Katz A, Syrigos C, Morse M (2010) Colon cancer vaccines: an update. In Vivo 24(5):607-628
2. Sung JJ, Lau JY, Goh KL, Leung WK (2005) Increasing incidence of colorectal cancer in Asia: implications for screening. Lancet Oncol 6(11):871-876. doi: 10.1016/S1470-2045(05)70422-8
3. Kuriki K, Tajima K (2006) The increasing incidence of colorectal cancer and the preventive strategy in Japan. Asian Pac J Cancer Prev 7(3):495-501
4. Fatemi SR, Malek FN, Shivarani S, Vahedi M, Almasi S, Maserat E, Ebrahimi M, Zali MR (2010) Prevalence of colorectal cancer in relatives of Iranian patients diagnosed with colorectal cancer. Asian Pac J Cancer Prev 11(1):91-93
5. Haggar FA, Boushey RP (2009) Colorectal cancer epidemiology: incidence, mortality, survival, and risk factors. Clin Colon Rectal Surg 22(4):191-197. doi: 10.1055/s-0029-1242458
6. Al-Jashamy K, Murad A, Zeehaida M, Rohaini M, Hasnan J (2010) Prevalence of colorectal cancer associated with Streptococcus bovis among inflammatory bowel and chronic gastrointestinal tract disease patients. Asian Pac J Cancer Prev 11(6):1765-1768
7. Rustgi AK (2007) The genetics of hereditary colon cancer. Genes Dev 21(20):2525-2538. doi: 10.1101/gad.1593107
8. Lichtenstein P, Holm NV, Verkasalo PK, Iliadou A, Kaprio J, Koskenvuo M, Pukkala E, Skytthe A, Hemminki K (2000) Environmental and heritable factors in the causation of cancer-analyses of cohorts of twins from Sweden, Denmark, and Finland. N Engl J Med 343(2):78-85. doi: 10.1056/NEJM200007133430201
9. Houlston RS, Webb E, Broderick P, Pittman AM, Di Bernardo MC, Lubbe S, Chandler I, Vijayakrishnan J, Sullivan K, Penegar S, Carvajal-Carmona L, Howarth K, Jaeger E, Spain SL, Walther A, Barclay E, Martin L, Gorman M, Domingo E, Teixeira AS, Kerr D, Cazier JB, Niittymaki I, Tuupanen S, Karhu A, Aaltonen LA, Tomlinson IP, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Cetnarskyj R, Porteous ME, Pharoah PD, Koessler T, Hampe J, Buch S, Schafmayer C, Tepel J, Schreiber S, Volzke H, Chang-Claude J, Hoffmeister M, Brenner H, Zanke BW, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG (2008) Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 40(12):1426-1435. doi: 10.1038/ng.262
10. Zanke BW, Greenwood CM, Rangrej J, Kustra R, Tenesa A, Farrington SM, Prendergast J, Olschwang S, Chiang T, Crowdy E, Ferretti V, Laflamme P, Sundararajan S, Roumy S, Olivier JF, Robidoux F, Sladek R, Montpetit A, Campbell P, Bezieau S, O'Shea AM, Zogopoulos G, Cotterchio M, Newcomb P, McLaughlin J, Younghusband B, Green R, Green J, Porteous ME, Campbell H, Blanche H, Sahbatou M, Tubacher E, Bonaiti-Pellie C, Buecher B, Riboli E, Kury S, Chanock SJ, Potter J, Thomas G, Gallinger S, Hudson TJ, Dunlop MG (2007) Genome-wide association scan identifies a colorectal cancer susceptibility locus on chromosome 8q24. Nat Genet 39(8):989-994. doi: 10.1038/ng2089
11. Tomlinson IP, Webb E, Carvajal-Carmona L, Broderick P, Howarth K, Pittman AM, Spain S, Lubbe S, Walther A, Sullivan K, Jaeger E, Fielding S, Rowan A, Vijayakrishnan J, Domingo E, Chandler I, Kemp Z, Qureshi M, Farrington SM, Tenesa A, Prendergast JG, Barnetson RA, Penegar S, Barclay E, Wood W, Martin L, Gorman M, Thomas H, Peto J, Bishop DT, Gray R, Maher ER, Lucassen A, Kerr D, Evans DG, Schafmayer C, Buch S, Volzke H, Hampe J, Schreiber S, John U, Koessler T, Pharoah P, van Wezel T, Morreau H, Wijnen JT, Hopper JL, Southey MC, Giles GG, Severi G, Castellvi-Bel S, Ruiz-Ponte C, Carracedo A, Castells A, Forsti A, Hemminki K, Vodicka P, Naccarati A, Lipton L, Ho JW, Cheng KK, Sham PC, Luk J, Agundez JA, Ladero JM, de la Hoya M, Caldes T, Niittymaki I, Tuupanen S, Karhu A, Aaltonen L, Cazier JB, Campbell H, Dunlop MG, Houlston RS (2008) A genome-wide association study identifies colorectal cancer susceptibility loci on chromosomes 10p14 and 8q23.3. Nat Genet 40(5):623-630. doi: 10.1038/ng.111
12. Tenesa A, Farrington SM, Prendergast JG, Porteous ME, Walker M, Haq N, Barnetson RA, Theodoratou E, Cetnarskyj R, Cartwright N, Semple C, Clark AJ, Reid FJ, Smith LA, Kavoussanakis K, Koessler T, Pharoah PD, Buch S, Schafmayer C, Tepel J, Schreiber S, Volzke H, Schmidt CO, Hampe J, Chang-Claude J, Hoffmeister M, Brenner H, Wilkening S, Canzian F, Capella G, Moreno V, Deary IJ, Starr JM, Tomlinson IP, Kemp Z, Howarth K, Carvajal-Carmona L, Webb E, Broderick P, Vijayakrishnan J, Houlston RS, Rennert G, Ballinger D, Rozek L, Gruber SB, Matsuda K, Kidokoro T, Nakamura Y, Zanke BW, Greenwood CM, Rangrej J, Kustra R, Montpetit A, Hudson TJ, Gallinger S, Campbell H, Dunlop MG (2008) Genome-wide association scan identifies a colorectal cancer susceptibility locus on 11q23 and replicates risk loci at 8q24 and 18q21. Nat Genet 40(5):631-637. doi: 10.1038/ng.133
13. Tomlinson I, Webb E, Carvajal-Carmona L, Broderick P, Kemp Z, Spain S, Penegar S, Chandler I, Gorman M, Wood W, Barclay E, Lubbe S, Martin L, Sellick G, Jaeger E, Hubner R, Wild R, Rowan A, Fielding S, Howarth K, Silver A, Atkin W, Muir K, Logan R, Kerr D, Johnstone E, Sieber O, Gray R, Thomas H, Peto J, Cazier JB, Houlston R (2007) A genome-wide association scan of tag SNPs identifies a susceptibility variant for colorectal cancer at 8q24.21. Nat Genet 39(8):984-988. doi: 10.1038/ng2085
14. Mourra N, Zeitoun G, Buecher B, Finetti P, Lagarde A, Adelaide J, Birnbaum D, Thomas G, Olschwang S (2007) High frequency of chromosome 14 deletion in early-onset colon cancer. Dis Colon Rectum 50(11):1881-1886. doi: 10.1007/s10350-007-9040-3
15. Zhou LP, Luan H, Dong XH, Jin GJ, Man DL, Shang H (2011) Vascular endothelial growth factor gene polymorphisms and colorectal cancer risk: a meta-analysis. Genet Mol Res 10(4):3674-3688. doi: 10.4238/2011.October.31.13
16. Papadopoulos N, Nicolaides NC, Wei YF, Ruben SM, Carter KC, Rosen CA, Haseltine WA, Fleischmann RD, Fraser CM, Adams MD et al (1994) Mutation of a mutL homolog in hereditary colon cancer. Science 263(5153):1625-1629
17. Wilmink AB (1997) Overview of the epidemiology of colorectal cancer. Dis Colon Rectum 40(4):483-493
18. Houlston RS, Tomlinson IP (2001) Polymorphisms and colorectal tumor risk. Gastroenterology 121(2):282-301
19. Wang Y, Jatkoe T, Zhang Y, Mutch MG, Talantov D, Jiang J, McLeod HL, Atkins D (2004) Gene expression profiles and molecular markers to predict recurrence of Dukes' B colon cancer. J Clin Oncol 22(9):1564-1571. doi: 10.1200/JCO.2004.08.186JCO.2004.08.186
20. Wang YC, Chen BS (2011) A network-based biomarker approach for molecular investigation and diagnosis of lung cancer. BMC Med Genomics 4:2. doi: 10.1186/1755-8794-4-2
21. Ein-Dor L, Zuk O, Domany E (2006) Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA 103(15):5923-5928. doi: 10.1073/pnas.0601231103
22. Hong Y, Ho KS, Eu KW, Cheah PY (2007) A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis. Clin Cancer Res 13(4):1107-1114. doi: 10.1158/1078-0432.CCR- 06-1633
23. Ceol A, Chatr Aryamontri A, Licata L, Peluso D, Briganti L, Perfetto L, Castagnoli L, Cesareni G (2010) MINT, the molecular interaction database: 2009 update. Nucleic Acids Res 38(Database issue):D532-D539. doi: 10.1093/nar/gkp983
24. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34(Database issue):D535-D539. doi: 10.1093/nar/gkj109
25. Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A (2009) Human Protein Reference Database: 2009 update. Nucleic Acids Res 37(Database issue):D767-D772. doi: 10.1093/nar/gkn892
26. Team RC (2008) R: a language and environment for statistical computing Version 2.7.1. R Foundation for Statistical Computing, Vienna, Austria
27. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2):249-264. doi: 10.1093/biostatistics/4.2.2494/2/249
28. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol doi. doi: 10.2202/1544-6115.1027
29. Benjamini YH, Hochberg Y (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. J R Stat Soc Series B (Methodol) 57:289-300
30. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13(11):2498-2504. doi: 10.1101/gr.123930313/11/2498
31. Bader GD, Hogue CW (2003) An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2
32. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44-57. doi: 10.1038/nprot.2008.211
33. Horvath S, Zhang B, Carlson M, Lu KV, Zhu S, Felciano RM, Laurance MF, Zhao W, Qi S, Chen Z, Lee Y, Scheck AC, Liau LM, Wu H, Geschwind DH, Febbo PG, Kornblum HI, Cloughesy TF, Nelson SF, Mischel PS (2006) Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc Natl Acad Sci USA 103(46):17402-17407. doi: 10.1073/pnas.0608396103
34. Bishop AL, Hall A (2000) Rho GTPases and their effector proteins. Biochem J 348(Pt 2):241-255
35. Fritz G, Brachetti C, Bahlmann F, Schmidt M, Kaina B (2002) Rho GTPases in human breast tumours: expression and mutation analyses and correlation with clinical parameters. Br J Cancer 87(6):635-644. doi: 10.1038/sj.bjc.6600510
36. Kamai T, Yamanishi T, Shirataki H, Takagi K, Asami H, Ito Y, Yoshida K (2004) Overexpression of RhoA, Rac1, and Cdc42 GTPases is associated with progression in testicular cancer. Clin Cancer Res 10(14):4799-4805. doi: 10.1158/1078-0432.CCR-0436-0310/14/4799
37. Abraham MT, Kuriakose MA, Sacks PG, Yee H, Chiriboga L, Bearer EL, Delacure MD (2001) Motility-related proteins as markers for head and neck squamous cell cancer. Laryngoscope 111(7):1285-1289. doi: 10.1097/00005537- 200107000-00027
38. Gomez Del Pulgar T, Valdes-Mora F, Bandres E, Perez-Palacios R, Espina C, Cejas P, Garcia-Cabezas MA, Nistal M, Casado E, Gonzalez-Baron M, Garcia-Foncillas J, Lacal JC (2008) Cdc42 is highly expressed in colorectal adenocarcinoma and downregulates ID4 through an epigenetic mechanism. Int J Oncol 33(1):185-193
39. Wang PJ, McCarrey JR, Yang F, Page DC (2001) An abundance of X-linked genes expressed in spermatogonia. Nat Genet 27(4):422-426. doi: 10.1038/8692786927
40. Yang F, Gell K, van der Heijden GW, Eckardt S, Leu NA, Page DC, Benavente R, Her C, Hoog C, McLaughlin KJ, Wang PJ (2008) Meiotic failure in male mice lacking an X-linked factor. Genes Dev 22(5):682-691. doi: 10.1101/gad.1613608
41. Ryder SP, Williamson JR (2004) Specificity of the STAR/GSG domain protein Qk1: implications for the regulation of myelination. RNA 10(9):1449-1458. doi: 10.1261/rna.7780504
42. Aberg K, Saetre P, Jareborg N, Jazin E (2006) Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia. Proc Natl Acad Sci USA 103(19):7482-7487. doi: 10.1073/pnas.0601213103
43. Lakiza O, Frater L, Yoo Y, Villavicencio E, Walterhouse D, Goodwin EB, Iannaccone P (2005) STAR proteins quaking-6 and GLD-1 regulate translation of the homologues GLI1 and tra-1 through a conserved RNA 3′UTR-based mechanism. Dev Biol 287(1):98-110. doi: 10.1016/j.ydbio.2005.08.038
44. Yang G, Fu H, Zhang J, Lu X, Yu F, Jin L, Bai L, Huang B, Shen L, Feng Y, Yao L, Lu Z (2010) RNA-binding protein quaking, a critical regulator of colon epithelial differentiation and a suppressor of colon cancer. Gastroenterology 138(1):231-240. doi: 10.1053/j.gastro.2009.08.001 e231-235
45. Martin S, Parton RG (2005) Caveolin, cholesterol, and lipid bodies. Semin Cell Dev Biol 16(2):163-174. doi: 10.1016/j.semcdb.2005.01.007
46. Henkhaus RS, Roy UK, Cavallo-Medved D, Sloane BF, Gerner EW, Ignatenko NA (2008) Caveolin-1-mediated expression and secretion of kallikrein 6 in colon cancer cells. Neoplasia 10(2):140-148
47. Williams TM, Lisanti MP (2005) Caveolin-1 in oncogenic transformation, cancer, and metastasis. Am J Physiol Cell Physiol 288(3):C494-C506. doi: 10.1152/ajpcell.0.0458.2004
48. Schwencke C, Braun-Dullaeus RC, Wunderlich C, Strasser RH (2006) Caveolae and caveolin in transmembrane signaling: implications for human disease. Cardiovasc Res 70(1):42-49. doi: 10.1016/j.cardiores.2005.11.029
49. Yokomizo A, Takakura M, Kanai Y, Sakuma T, Matsubara J, Honda K, Naito S, Yamada T, Ono M (2011) Use of quantitative shotgun proteomics to identify fibronectin 1 as a potential plasma biomarker for clear cell carcinoma of the kidney. Cancer Biomark 10(3-4):175-183. doi: 10.3233/CBM-2012-0243
50. Meeh PF, Farrell CL, Croshaw R, Crimm H, Miller SK, Oroian D, Kowli S, Zhu J, Carver W, Wu W, Pena E, Buckhaults PJ (2009) A gene expression classifier of node-positive colorectal cancer. Neoplasia 11(10):1074-1083
51. Fearon ER, Vogelstein B (1990) A genetic model for colorectal tumorigenesis. Cell 61(5):759-767