Developing proteomics-based biomarkers for colorectal neoplasms for clinical practice: Opportunities and challenges

Proteomics - Clinical Applications

Volumn 7, Issue 1-2, 2013, Pages 30-41

  Luo, Yanxin ^a,b   Wang, Lei ^a   Wang, Jianping ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b Fred Hutchinson Cancer Research Center   (United States)

Author keywords

Biomarker; Colorectal cancer

Indexed keywords

ACETYLSALICYLIC ACID; B RAF KINASE; CARCINOEMBRYONIC ANTIGEN; CETUXIMAB; CISPLATIN; FLUOROURACIL; IRINOTECAN; NONSTEROID ANTIINFLAMMATORY AGENT; OXALIPLATIN; TUMOR MARKER;

ADENOMATOUS POLYP; ADVANCED CANCER; CANCER CHEMOTHERAPY; CANCER INVASION; CANCER MORTALITY; CANCER RECURRENCE; CANCER RESISTANCE; CANCER RISK; CANCER STAGING; CHROMOSOMAL INSTABILITY; CLINICAL PRACTICE; COLORECTAL ADENOMA; COLORECTAL CANCER; COLORECTAL CARCINOMA; COLORECTAL TUMOR; CPG ISLAND; DISEASE ASSOCIATION; DNA METHYLATION; DRUG SENSITIVITY; EARLY DIAGNOSIS; EPIGENETICS; GENE MUTATION; HUMAN; IMMUNOHISTOCHEMISTRY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MICROSATELLITE INSTABILITY; ONCOGENE K RAS; PERSONALIZED MEDICINE; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; REVIEW; SURVIVAL RATE; TREATMENT PLANNING; TUMOR GROWTH;

COLORECTAL NEOPLASMS; DISEASE PROGRESSION; HUMANS; MASS SPECTROMETRY; PROTEOMICS; TUMOR MARKERS, BIOLOGICAL;

EID: 84872742367     PISSN: 18628346     EISSN: 18628354     Source Type: Journal    
DOI: 10.1002/prca.201200071     Document Type: Review

References (76)

1. Jemal, A., Bray, F., Center, M. M., Ferlay, J. et al., Global cancer statistics. CA Cancer J. Clin. 2011, 61, 69-90.
2. Fearon, E. R., Vogelstein, B., A genetic model for colorectal tumorigenesis. Cell 1990, 61, 759-767.
3. Siegel, R., Naishadham, D., Jemal, A., Cancer statistics, 2012. CA Cancer J. Clin. 2012, 62, 10-29.
4. Grady, W. M., Carethers, J. M., Genomic and epigenetic instability in colorectal cancer pathogenesis. Gastroenterology 2008, 135, 1079-1099.
5. Cooper, K., Squires, H., Carroll, C., Papaioannou, D. et al., Chemoprevention of colorectal cancer: systematic review and economic evaluation. Health Technol. Assess 2010, 14, 1-206.
6. Cunningham, D., Atkin, W., Lenz, H. J., Lynch, H. T. et al., Colorectal cancer. Lancet 2010, 375, 1030-1047.
7. Dahabreh, I. J., Terasawa, T., Castaldi, P. J., Trikalinos, T. A. et al., Systematic review: Anti-epidermal growth factor receptor treatment effect modification by KRAS mutations in advanced colorectal cancer. Ann. Intern. Med. 2011, 154, 37-49.
8. Lieberman, D. A., Clinical practice. Screening for colorectal cancer. N. Engl. J. Med. 2009, 361, 1179-1187.
9. Creeden, J., Junker, F., Vogel-Ziebolz, S., Rex, D. et al., Serum tests for colorectal cancer screening. Mol. Diagn. Ther. 2011, 15, 129-141.
10. Berger, B. M., Ahlquist, D. A., Stool DNA screening for colorectal neoplasia: biological and technical basis for high detection rates. Pathology 2012, 44, 80-88.
11. Pasche, B., Absher, D., Whole-genome sequencing: a step closer to personalized medicine. JAMA 2011, 305, 1596-1597.
12. Hanahan, D., Weinberg, R. A., Hallmarks of cancer: the next generation. Cell 2011, 144, 646-674.
13. Markowitz, S. D., Bertagnolli, M. M., Molecular origins of cancer: molecular basis of colorectal cancer. N. Engl. J. Med. 2009, 361, 2449-2460.
14. Boland, C. R., Goel, A., Microsatellite instability in colorectal cancer. Gastroenterology 2010, 138, 2073-2087 e3.
15. Barderas, R., Babel, I., Casal, J. I., Colorectal cancer proteomics, molecular characterization and biomarker discovery. Proteomics Clin. Appl. 2010, 4, 159-178.
16. Jimenez, C. R., Knol, J. C., Meijer, G. A., Fijneman, R. J. et al., Proteomics of colorectal cancer: overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers. J. Proteomics 2010, 73, 1873-1895.
17. Rajcevic, U., Niclou, S. P., Jimenez, C. R., Proteomics strategies for target identification and biomarker discovery in cancer. Front. Biosci. 2009, 14, 3292-3303.
18. Marouga, R., David, S., Hawkins, E., The development of the DIGE system: 2D fluorescence difference gel analysis technology. Anal. Bioanal. Chem. 2005, 382, 669-678.
19. Luo, Y. X., Cui, J., Wang, L., Chen, D. K. et al., Identification of cancer-associated proteins by proteomics and downregulation of beta-tropomyosin expression in colorectal adenoma and cancer. Proteomics Clin. Appl. 2009, 3, 1397-1406.
20. Sugihara, Y., Taniguchi, H., Kushima, R., Tsuda, H. et al., Proteomic-based identification of the APC-binding protein EB1 as a candidate of novel tissue biomarker and therapeutic target for colorectal cancer. J. Proteomics 2012, 75, 5342-5355.
21. Alfonso, P., Canamero, M., Fernandez-Carbonie, F., Nunez, A. et al., Proteome analysis of membrane fractions in colorectal carcinomas by using 2D-DIGE saturation labeling. J. Proteome Res. 2008, 7, 4247-4255.
22. Conrotto, P., Roesli, C., Rybak, J., Kischel, P. et al., Identification of new accessible tumor antigens in human colon cancer by ex vivo protein biotinylation and comparative mass spectrometry analysis. Int. J. Cancer 2008, 123, 2856-2864.
23. Rho, J. H., Qin, S., Wang, J. Y., Roehrl, M. H. et al., Proteomic expression analysis of surgical human colorectal cancer tissues: up-regulation of PSB7, PRDX1, and SRP9 and hypoxic adaptation in cancer. J. Proteome Res. 2008, 7, 2959-2972.
24. Zhou, J., Belov, L., Solomon, M. J., Chan, C. et al., Colorectal cancer cell surface protein profiling using an antibody microarray and fluorescence multiplexing. J. Visualized Exp. 2011, 55, e3322.
25. de Wit, M., Jimenez, C. R., Carvalho, B., Belien, J. A. et al., Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut 2012, 61, 855-864.
26. Roth, U., Razawi, H., Hommer, J., Engelmann, K. et al., Differential expression proteomics of human colorectal cancer based on a syngeneic cellular model for the progression of adenoma to carcinoma. Proteomics 2010, 10, 194-202.
27. Ghosh, D., Yu, H., Tan, X. F., Lim, T. K. et al., Identification of key players for colorectal cancer metastasis by iTRAQ quantitative proteomics profiling of isogenic SW480 and SW620 cell lines. J. Proteome Res. 2011, 10, 4373-4387.
28. Yao, L., Lao, W. F., Zhang, Y., Tang, X. R. et al., Identification of EFEMP2 as a serum biomarker for the early detection of colorectal cancer with lectin affinity capture assisted secretome analysis of cultured fresh tissues. J. Proteome Res. 2012, 11, 3281-3294.
29. Ma, Y. L., Peng, J. Y., Zhang, P., Huang, L. et al., Heterogeneous nuclear ribonucleoprotein A1 is identified as a potential biomarker for colorectal cancer based on differential proteomics technology. J. Proteome Res. 2009, 8, 4525-4535.
30. Ma, Y. L., Peng, J. Y., Liu, W. J., Zhang, P. et al., Proteomics identification of desmin as a potential oncofetal diagnostic and prognostic biomarker in colorectal cancer. Mol. Cell. Proteomics 2009, 8, 1878-1890.
31. Kim, H. J., Kang, H. J., Lee, H., Lee, S. T. et al., Identification of S100A8 and S100A9 as serological markers for colorectal cancer. J. Proteome Res. 2009, 8, 1368-1379.
32. Thierolf, M., Hagmann, M. L., Pfeffer, M., Berntenis, N. et al., Towards a comprehensive proteome of normal and malignant human colon tissue by 2-D-LC-ESI-MS and 2-DE proteomics and identification of S100A12 as potential cancer biomarker. Proteom Clin. Appl. 2008, 2, 11-22.
33. O'Dwyer, D., Ralton, L. D., O'Shea, A., Murray, G. I. et al., The proteomics of colorectal cancer: identification of a protein signature associated with prognosis. PLoS One 2011, 6, e27718.
34. Tweedle, E. M., Khattak, I., Ang, C. W., Nedjadi, T. et al., Low molecular weight heat shock protein HSP27 is a prognostic indicator in rectal cancer but not colon cancer. Gut 2010, 59, 1501-1510.
35. May, D., Pan, S., Crispin, D. A., Lai, K. et al., Investigating neoplastic progression of ulcerative colitis with label-free comparative proteomics. J. Proteome Res. 2011, 10, 200-209.
36. Brentnall, T. A., Pan, S., Bronner, M. P., Crispin, D. A. et al., Proteins that underlie neoplastic progression of ulcerative colitis. Proteom Clin. Appl. 2009, 3, 1326-1337.
37. Sakai, A., Otani, M., Miyamoto, A., Yoshida, H. et al., Identification of phosphorylated serine-15 and -82 residues of HSPB1 in 5-fluorouracil-resistant colorectal cancer cells by proteomics. J. Proteomics 2012, 75, 806-818.
38. Gong, F. M., Peng, X. C., Tan, B. X., Ge, J. et al., Comparative proteomic analysis of irinotecan-sensitive colorectal carcinoma cell line and its chemoresistant counterpart. Anticancer Drugs 2011, 22, 500-506.
39. Van Houdt, W. J., Emmink, B. L., Pham, T. V., Piersma, S. R. et al., Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target. Mol. Cell Proteomics 2011, 10, M111 011353.
40. Nibbe, R. K., Markowitz, S., Myeroff, L., Ewing, R. et al., Discovery and scoring of protein interaction subnetworks discriminative of late stage human colon cancer. Mol. Cell. Proteomics 2009, 8, 827-845.
41. Volkel, P., Le Faou, P., Angrand, P. O., Interaction proteomics: characterization of protein complexes using tandem affinity purification-mass spectrometry. Biochem. Soc. T 2010, 38, 883-887.
42. Choi, D. S., Yang, J. S., Choi, E. J., Jang, S. C. et al., The protein interaction network of extracellular vesicles derived from human colorectal cancer cells. J. Proteome Res. 2012, 11, 1144-1151.
43. Popovici, V., Budinska, E., Tejpar, S., Weinrich, S. et al., Identification of a poor-prognosis BRAF-mutant-like population of patients with colon cancer. J. Clin. Oncol. 2012, 30, 1288-1295.
44. F Lam, F., Jankova, L., Dent, O. F., Molloy, M. P. et al., Identification of distinctive protein expression patterns in colorectal adenoma. Proteomics Clin. Appl. 2010, 4, 60-70.
45. Zhao, L., Wang, H., Sun, X., Ding, Y. et al., Comparative proteomic analysis identifies proteins associated with the development and progression of colorectal carcinoma. FEBS J. 2010, 277, 4195-4204.
46. Ma, Y., Zhao, M., Zhong, J., Shi, L. et al., Proteomic profiling of proteins associated with lymph node metastasis in colorectal cancer. J. Cell Biochem. 2010, 110, 1512-1519.
47. Ma, Y. L., Peng, J. Y., Huang, L., Liu, W. J. et al., Searching for serum tumor markers for colorectal cancer using a 2-D DIGE approach. Electrophoresis 2009, 30, 2591-2599.
48. Kim, H. J., Kang, U. B., Lee, H., Jung, J. H. et al., Profiling of differentially expressed proteins in stage IV colorectal cancers with good and poor outcomes. J. Proteomics 2012, 75, 2983-2997.
49. Sprung, R. W., Brock, J. W. C., Tanksley, J. P., Li, M. et al., Equivalence of protein inventories obtained from formalin-fixed paraffin-embedded and frozen tissue in multidimensional liquid chromatography-tandem mass spectrometry shotgun proteomic analysis. Mol. Cell. Proteomics 2009, 8, 1988-1998.
50. Nirmalan, N. J., Hughes, C., Peng, J., McKenna, T. et al., Initial development and validation of a novel extraction method for quantitative mining of the formalin-fixed, paraffin-embedded tissue proteome for biomarker investigations. J. Proteome Res. 2011, 10, 896-906.
51. Corless, C. L., Barnett, C. M., Heinrich, M. C., Gastrointestinal stromal tumours: origin and molecular oncology. Nat. Rev. Cancer 2011, 11, 865-878.
52. Demetri, G. D., von Mehren, M., Antonescu, C. R., DeMatteo, R. P. et al., NCCN Task Force report: update on the management of patients with gastrointestinal stromal tumors. J. Natl. Compr. Canc. Netw. 2010, 8 (Suppl 2), S1-S41.
53. Kaserer, K., Schmaus, J., Bethge, U., Migschitz, B. et al., Staining patterns of p53 immunohistochemistry and their biological significance in colorectal cancer. J. Pathol. 2000, 190, 450-456.
54. de Jong, K. P., Gouw, A. S., Peeters, P. M., Bulthuis, M. et al., P53 mutation analysis of colorectal liver metastases: relation to actual survival, angiogenic status, and p53 overexpression. Clin. Cancer Res. 2005, 11, 4067-4073.
55. Chen, W. D., Han, Z. J., Skoletsky, J., Olson, J. et al., Detection in fecal DNA of colon cancer-specific methylation of the nonexpressed vimentin gene. J. Natl. Cancer Inst. 2005, 97, 1124-1132.
56. Giusti, L., Iacconi, P., Da Valle, Y., Ciregia, F. et al., A proteomic profile of washing fluid from the colorectal tract to search for potential biomarkers of colon cancer. Mol. Biosyst. 2012, 8, 1088-1099.
57. Heresbach, D., Barrioz, T., Lapalus, M. G., Coumaros, D. et al., Miss rate for colorectal neoplastic polyps: a prospective multicenter study of back-to-back video colonoscopies. Endoscopy 2008, 40, 284-290.
58. van Rijn, J. C., Reitsma, J. B., Stoker, J., Bossuyt, P. M. et al., Polyp miss rate determined by tandem colonoscopy: a systematic review. Am. J. Gastroenterol. 2006, 101, 343-350.
59. Ma, Y., Zhang, P., Wang, F., Liu, W. et al., An integrated proteomics and metabolomics approach for defining oncofetal biomarkers in the colorectal cancer. Ann. Surg. 2012, 255, 720-730.
60. Zhang, X., Xiao, Z., Liu, X., Du, L. et al., The potential role of ORM2 in the development of colorectal cancer. PLoS One 2012, 7, e31868.
61. Murakoshi, Y., Honda, K., Sasazuki, S., Ono, M. et al., Plasma biomarker discovery and validation for colorectal cancer by quantitative shotgun mass spectrometry and protein microarray. Cancer Sci. 2011, 102, 630-638.
62. Chen, W. T., Chang, S. C., Ke, T. W., Chiang, H. C. et al., Identification of biomarkers to improve diagnostic sensitivity of sporadic colorectal cancer in patients with low preoperative serum carcinoembryonic antigen by clinical proteomic analysis. Clin. Chim. Acta 2011, 412, 636-641.
63. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012, 487, 330-337.
64. Yang, H. Y., Kwon, J., Park, H. R., Kwon, S. O. et al., Comparative proteomic analysis for the insoluble fractions of colorectal cancer patients. J. Proteomics 2012, 75, 3639-3653.
65. Besson, D., Pavageau, A. H., Valo, I., Bourreau, A. et al., A quantitative proteomic approach of the different stages of colorectal cancer establishes OLFM4 as a new nonmetastatic tumor marker. Mol. Cell Proteomics 2011, 10, M111 009712.
66. Shi, H., Hood, K. A., Hayes, M. T., Stubbs, R. S. et al., Proteomic analysis of advanced colorectal cancer by laser capture microdissection and two-dimensional difference gel electrophoresis. J. Proteomics 2011, 75, 339-351.
67. Xie, L. Q., Zhao, C., Cai, S. J., Xu, Y. et al., Novel proteomic strategy reveal combined alpha1 antitrypsin and cathepsin D as biomarkers for colorectal cancer early screening. J. Proteome Res. 2010, 9, 4701-4709.
68. Chen, D. B., Chen, F. L., Lu, X. R., Yang, X. S. et al., Identification of prohibitin as a potential biomarker for colorectal carcinoma based on proteomics technology. Int. J. Oncol. 2010, 37, 355-365.
69. Chen, J. S., Chen, K. T., Fan, C. W., Han, C. L. et al., Comparison of membrane fraction proteomic profiles of normal and cancerous human colorectal tissues with gel-assisted digestion and iTRAQ labeling mass spectrometry. FEBS J. 2010, 277, 3028-3038.
70. Li, S. Y., An, P., Cai, H. Y., Bai, X. et al., Proteomic analysis of differentially expressed proteins involving in liver metastasis of human colorectal carcinoma. Hepatobiliary Pancreat Dis. Int. 2010, 9, 149-153.
71. Liu, W. J., Ma, Y. L., Huang, L., Peng, J. Y. et al., Identification of HSP27 as a potential tumor marker for colorectal cancer by the two-dimensional polyacrylamide gel electrophoresis. Mol. Biol. Rep. 2010, 37, 3207-3216.
72. Kang, B., Hao, C. Y., Wang, H. Y., Zhang, J. et al., Evaluation of hepatic-metastasis risk of colorectal cancer upon the protein signature of PI3K/AKT pathway. J. Proteome Res. 2008, 7, 3507-3515.
73. Watanabe, M., Takemasa, I., Kawaguchi, N., Miyake, M. et al., An application of the 2-nitrobenzenesulfenyl method to proteomic profiling of human colorectal carcinoma: a novel approach for biomarker discovery. Proteomics Clin. Appl. 2008, 2, 925-935.
74. Zhao, L., Liu, Y., Sun, X., Peng, K. et al., Serum proteome analysis for profiling protein markers associated with lymph node metastasis in colorectal carcinoma. J. Comp. Pathol. 2011, 144, 187-194.
75. He, Y. J., Mou, Z. R., Li, W. L., Liu, B. H. et al., Identification of IMPDH2 as a tumor-associated antigen in colorectal cancer using immunoproteomics analysis. Int. J. Colorectal Dis. 2009, 24, 1271-1279.
76. De Monte, L., Sanvito, F., Olivieri, S., Vigano, F. et al., Serological immunoreactivity against colon cancer proteorne varies upon disease progression. J. Proteome Res. 2008, 7, 504-514.