Development of novel diagnostic and prognostic molecular markers for sporadic colon cancer

Expert Review of Molecular Diagnostics

Volumn 5, Issue 3, 2005, Pages 337-352

  Ahmed, Farid E ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

Author keywords

Diagnosis; Differential display; Markers; Microarrays; Prognosis; RT PCR; SAGE; Screening; SSH

Indexed keywords

MOLECULAR MARKER;

CANCER DIAGNOSIS; CANCER GENETICS; COLON CANCER; COLON CARCINOGENESIS; DIFFERENTIAL DISPLAY; DNA FINGERPRINTING; DNA MICROARRAY; IMMUNOHISTOCHEMISTRY; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; POLYP; PROGNOSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; REVIEW; SERIAL ANALYSIS OF GENE EXPRESSION; SUPPRESSION SUBTRACTIVE HYBRIDIZATION;

COLONIC NEOPLASMS; DNA FINGERPRINTING; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 18844449182     PISSN: 14737159     EISSN: None     Source Type: Journal    
DOI: 10.1586/14737159.5.3.337     Document Type: Review

References (91)

1. Ahmed FE. Colon cancer: prevalence, screening, gene expression and mutation, and risk factors and assessment. J. Env. Sci. Health C21, 65-131 (2003). Provides an overview of environmental and genetic factors in colon cancer carcinogenesis.
2. Smith RA, von Eschenbach AC, Wender R et al. American Cancer Society guidelines for the early detection of cancer: update of the early detection guidelines for prostate, colorectal and endometrial cancers. CA Cancer J. Clin. 51, 38-75 (2001).
3. Johnson CD, Harmsen WS, Wilson LM et al. Prospective blinded evaluation of computed tomographic colonography for screen detection of colorectal polyps. Gastroenterology 125, 311-319 (2003).
4. Ahlquist DA, Shuber AP. Stool screening for colorectal cancer: evolution from occult blood to molecular markers. Clin. Chim. Acta 31, 157-168 (2002).
5. Lipton L, Halford SE, Johnson V et al. Carcinogenesis in MYH-associated polyposis following a distinct genetic pathway. Cancer Res. 63, 7595-7599 (2003).
6. Mori Y, Selaru FM, Sato F et al. The impact of microsatellite instability on the molecular phenotype of colorectal tumors. Cancer Res. 63, 4577-4582 (2003). Application of microarray expression technology to distinguish between different colon cancer phenotypes.
7. Gryfe R, Gallinger S. Microsatellite instability, mismatch repair deficiency and colorectal cancer. Surgery 130, 17-20 (2001).
8. Halford SE, Sawyer EJ, Lambros MB et al. MSI-low, a real phenomenon which varies in frequency among cancer types. J. Pathol. 201(3), 389-394 (2003).
9. Whitehall VLJ, Walsh MD, Young J et al. Methylation of O-6-methyl guanine DNA methyltransferase characterize a subset of colorectal cancer with low-level of DNA microsatellite instability. Cancer Res. 61, 827-830 (2001).
10. Toyota M, Ahuja N, Ohe-Toyota M et al. CpG island methylation phenotype in colorectal cancers. Proc. Natl Acad. Sci. USA 96, 8681-8686 (1999).
11. Iacopetta B. Aberrant DNA methylation: have we entered the era of more than one type of colorectal cancer? Am. J. Pathol. 162, 1043-1045 (2003).
12. Tsavellas G, Patel H, Allen Mersh TG. Detection and clinical significance of occult tumor cells in colorectal cancer. Br. J. Surg. 88, 1307-1320 (2001).
13. Cairns R, Sidaransky D. Molecular methods for diagnosis of cancer. Biochim. Biophys. Acta 1423, C11-C18 (1999).
14. Ahmed FE, Dobbs LJ Jr, Johnke RM et al. Isolation of circulating colon carcinoma cells for RT-PCR. Anal. Biochem. 332, 394-397 (2004). Improved method for extraction of RNA from blood followed by quantitative real-time reverse transcriptase (RT)-PCR.
15. Kusnezow W, Hoheisel JD. Antibody microarrays: promises and problems. Biotechniques 33, S14-S23 (2002).
16. Lewis RC. Gene expression profiling: a new lens on cancer. Scientist Genet. 17(Suppl.), 22-24 (2003).
17. Ahmed FE. Molecular techniques for studying gene expression in carcinogenesis. J. Env. Sci. Health C20, 77-116 (2002). Details various functional genomic techniques employed in carcinogenesis studies.
18. Ahmed FE, James S, Lysle DT et al. Improved methods for extracting RNA from exfoliated human colonocytes in stool and RT-PCR analysis. Dig. Dis. Sci. 49, 1889-1898 (2004). Use of commercially available kits to extract high-quality RNA from stool suitable for subsequent RT-PCR.
19. Giordano TJ, Shedder KA, Schwanz DR et al. Organ-specific molecular classification of primary lung, colon and ovarian adenocarcinomas using gene expression profiles. Am. J. Pathol. 159, 1231-1238 (2001).
20. Velculesvu VE, Zhang L, Vogelstein B et al. Serial analysis of gene expression. Science 270, 484-487 (1995). Pioneering serial analysis of gene expression (SAGE) method for studying gene expression.
21. Yamamoto M, Wakatsuki T, Hada A et al. Use of serial analysis of gene expression (SAGE) technology. J. Immunol. Methods 250, 45-66 (2001).
22. Ruijter JM, Van Kampen AH, Baas F. Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol. Genomics 11, 37-44 (2002).
23. Liang P. SAGE Genie: a suite with panoramic view of gene expression. Proc. Natl Acad. Sci. USA 99, 11547-11548 (2002).
24. Ahmed FE. Serial analysis of gene expression (SAGE) technology. In: Encyclopedia of Diagnostic Genomics and Proteomics. Fuchs J, Podda M (Eds), Marcel Dekker, NY, USA, 1191-1196 (2004).
25. Liang PA. A decade of differential display. Biotechniques 33, 338-346 (2002). Provides an overview of differential display gene expression analysis methods.
26. Rompf R, Kahl G. mRNA differential display in agarose gel. Biotechniques 23, 28-32 (1997).
27. Crawford DR, Kochheiser JC, Schools GP et al. Differential display: a critical analysis. Gene Expr. 10, 101-107 (2002).
28. Welsh J, Chada K, Dahl SS et al. Arbitrary primed PCR fingerprinting of RNA. Nucleic Acids Res. 20, 4965-49700 (1992). Pioneering arbitrary primed PCR fingerprinting method for analysis of gene expression.
29. Ahmed FE. Differential display (DD) analysis. In: Encyclopedia of Diagnostic Genomics and Proteomics. Fuchs J, Podda M (Eds), Marcel Dekker, NY, USA, 331-335 (2004).
30. Diatchenko L, Lau Y-F C, Campbell AP et al. Suppression subtraction hybridization: a method for generating differentially regulated or tissue specific cDNA probes. Proc. Natl Acad. Sci. USA 93, 6025-6030 (1996). Original suppression PCR method for analysis of gene expression.
31. Broude NE. Differential display in the time of microarrays. Expert Rev. Mol. Diagn. 2, 89-96 (2002). Compares microarray technology with other open systems of gene expression.
32. Weckx S, De Rijk P, Van Breckhoven C et al. SSH Suite: an integrated software package for analysis of large-scale suppression subtractive hybridization data. Biotechniques 36, 1043-1045 (2004).
33. Diatchenko L, Lukyanov S, Lau YFC et al. Suppression subtraction hybridization: a versatile method for identifying differentially expressed genes. Methods Enzymol. 20, 349-380 (1999).
34. Ahmed FE. Molecular markers for early cancer detection. J. Env. Sci. Health C18, 75-126 (2000).
35. Holst-Jensen A, Rønning SB, Løvseth A et al. PCR technology for screening and quantification of genetically modified organisms (GMOs). Anal. Bioanal. Chem. 375, 985-993 (2003).
36. Bustin SA. Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol. 29, 23-39 (2002). Overview of real-time RT-PCR in quantitative gene expression analysis.
37. Gibson G. Microarrays in ecology and evolution: a preview. Mol. Ecol. 11, 17-24 (2002).
38. Ye RW, Wan T, Bedzyk L et al. Applications of DNA microarrays in microbial systems. J. Microbiol. 47, 257-272 (2001).
39. Novak JP, Sladek R, Hudson TJ. Characterization of variability in large scale gene expression data: implications for study design. Genomics. 79, 104-113 (2002).
40. Hitt E. One chip, one gene. Scientist 18, 38-39 (2004).
41. Etienne W, Meyer MH, Peppers J et al. Comparison of mRNA gene expression by RT-PCR and DNA microarray. Biotechniques 36, 618-626 (2004). Discusses causes of agreement and disagreement between RT-PCR and microarray expression data.
42. Satagopan J, Panageas KS. A statistical perspective on gene expression data analysis. Stat. Med. 22, 481-499 (2003).
43. Wilson CL, Pepper SD, Hey Y et al. Amplification protocols introduce systematic but reproducible error into gene expression studies. Biotechniques 36, 498-506 (2004).
44. Wu TD. Analysis of gene expression data for DNA microarrays to identify candidate genes. J. Pathol. 195, 53-65 (2001).
45. Mandaokar A, Kumar VD, Amway M et al. Microarray and differential display identify genes involved in jasmonata-dependent anther development. Plant Mol. Biol. 52, 775-786 (2003).
46. Trenkle T, Welsh J, McClellan M. Differential display probes for cDNA arrays. Biotechniques 27, 554-564 (1999).
47. Fuchs BK, Zhang K, Bolander MF et al. Identification of differentially expressed genes by mutually subtracted RNA fingerprinting. Anal. Biochem. 286, 91-98 (2000).
48. Yang GP, Ross DT, Kuang WW et al. Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes. Nucleic Acids Res. 27, 1517-1523 (1999).
49. von Stein OD, Thies W-G, Hofmann M. A high-throughput screening for rarely transcribed differentially expressed genes. Nucleic Acids Res. 25, 2598-2602 (1997).
50. Srivastava S, Verma M, Henson DE et al. Biomarkers for early detection of colon cancer. Clin. Cancer Res. 71, 1118-1126 (2001).
51. Grizzle WE, Manne U, Jhala NC et al. Molecular characterization of colorectal neoplasms in translational research. Arch. Pathol. Lab. Med. 25, 91-98 (2001).
52. Duffy MJ, van Dalen A, Haglund C et al. Clinical utility of clinical markers in colorectal cancer: European Group on Tumor Markers (EGTM) guidelines. Eur. J. Cancer 39, 718-727 (2003).
53. Ahmed FE. Molecular markers that predict response to colon cancer therapy. Expert Rev. Mol. Diagn. 5(3), 353-375 (2005).
54. Lechner S, Müller-Lander U, Neumann E et al. Use of simplified transcriptors for the analysis of gene expression profiles in laser-microdissected cell populations. Lab. Invest. 81, 1233-1242 (2001).
55. Lechner S, Müller-Lander U, Renke B et al. Gene expression patterns of laser microdissected colonic crypts of adenomas with a low grade dysplasia. Gut 52, 1148-1153 (2003).
56. Emmert-Buck MR, Roth MJ, Zhuang Z et al. Laser capture microdissection. Science 274, 998-1001 (1996). Pioneering article on the development of a method to purify cells from surrounding tissue.
57. Pfeifer U, Noonan D, Albini A. Microarray studies challenge theories of metastasis. J. Natl Cancer Inst. 95(11), 829 (2003).
58. Hanahan D, Weinberger RA. The hallmark of cancer. Cell 100, 57-70 (2000).
59. Webb T. Microarray studies challenge theories of metastasis. J. Natl Cancer Inst. 95, 350-351 (2003).
60. Ahmed FE. Colorectal cancer: molecular staging models that characterize risk and enhance prognosis. Cancer Genom. Proteom. 1, 295-310 (2004). Detailed review of staging models of colon cancer progression.
61. Alexander R, Raicht RE. Purification of total RNA from human stool samples. Dig. Dis. Sci. 43, 2652-2658 (1998).
62. Zhang L, Zhou W, Velculescu VE et al. Gene expression profiles in normal and cancer cells. Science 276, 1268-1272 (1997). Comprehensive analysis of gene expression in colon cancer using SAGE technology.
63. Ojala P, Sundström J, Grönroos JM et al. mRNA differential display of gene expression in colonic carcinoma. Electrophoresis 23, 1667-1676 (2002).
64. Hufton SE, Moerkerk PT, Brandwijk R et al. A profile of differentially expressed genes in primary colorectal cancers using suppressive subtractive hybridization. FEBS Lett. 463, 77-82 (1999). Illustrates the application of suppression PCR for molecular analysis of colorectal cancer.
65. Davidson LA, Lupton JR, Miskovsky E et al. Quantification of human intestinal gene expression profiling using exfoliated colonocytes: a pilot study. Biomarkers 8, 51-61 (2003).
66. Birkenkamp-Demtroder K, Christensen LL, Harder S et al. Gene expression in colorectal cancer. Cancer Res. 62, 4352-4363 (2002).
67. Backert S, Gelos M, Kobalz U et al. Differential expression in colon carcinoma cells and tissues detected with cDNA array. Int. J. Cancer 52, 868-874 (1999).
68. Notterman DA, Alon U, Sierk AJ et al. Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide array. Cancer Res. 61, 3124-3130 (2001). Application of oligonucleotide microarrays to study differential gene expression in colorectal cancer.
69. Kitahara O, Furukawa Y, Tanaka T et al. Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissue and normal epithelia. Cancer Res. 61, 3544-3549 (2001).
70. Nishizuka S, Furukawa Y, Tanaka T et al. Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic and tissue array profiling. Cancer Res. 63, 5243-5250 (2003).
71. Bertucci F, Salas S, Eysteries S et al. Gene expression profiling of colon cancer by DNA microarrays and correlation with histoclinical parameters. Oncogene 23, 1377-1391 (2004).
72. Zou TT, Selaru FM, Xu Y et al. Application of cDNA microarrays to generate a molecular taxonomy capable of distinguishing between colon cancer and normal colon. Oncogene 21, 4855-4862 (2002).
73. Lin YM, Furukawa Y, Tsunoda T et al. Molecular diagnosis of colorectal tumor by expression profiles of 50 genes expressed differentially in adenomas and carcinomas. Oncogene 21, 4120-4128 (2002).
74. Frederiksen CM, Knudsen S, Laurberg S et al. Classification of Dukes' B and C colorectal cancer using expression arrays. J. Cancer Res. Clin. Oncol. 129, 263-271 (2003).
75. Wang Y, Jatkoe T, Zhang Y et al. Gene expression profiles and molecular markers to predict recurrence of Dukes' C colon cancer. J. Clin. Oncol. 22, 1564-1571 (2004).
76. Yanagawa R, Furukawa Y, Tsunoda T et al. Genome-wide screening of genes showing altered expression in liver metastasis of human colorectal cancer by cDNA microarray. Neoplasia 3, 395-401 (2001).
77. Li M, Lin Y-M, Hasegawa S et al. Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray. Int. J. Oncol. 24, 305-312 (2004).
78. Li SR, Banerjea A, Ahmed S et al. Differential expression patterns of the insulin-like factor 2 gene in human colorectal cancer. Tumor Biol. 25(1-2), 62-68 (2004).
79. Biemer-Hüttmann A-E, Walsh MD, McGuckin MA et al. Mucicone protein expression in colorectal cancer with high levels of microsatellite instability indicates a normal pathway of morphogenesis. Clin. Cancer Res. 6, 1909-1916 (2000).
80. Koketsu S, Watanabe T, Nagawa H. Expression of DNA repair proteins MYH, NTH1, and MTH1 in colorectal cancer. Hepato-Gastroenterology 51, 638-642 (2004).
81. Toyota M, Ahuja N, Ohe Toyota M et al. Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype. Proc. Natl Acad. Sci. USA 97, 710-715 (2000).
82. Fric P, Sovova V, Šloncova E et al. Different expression of some marker molecules in sporadic cancer of the left and right colon. Eur. J. Cancer Prevent. 9, 265-268 (2000).
83. Nelson AR, Fingleton B, Rothenberg ML et al. Matrix metalloproteinase: biological activity and clinical implications. J. Clin. Oncol. 18, 1135-1149 (2000).
84. Duffy MJ. The urokinase plasminogen activator system: role in malignancy. Curr. Pharmaceut. Des. 10, 39-49 (2004).
85. Carmelete P, Jhala NC, Jones J et al. Urokinase-generated plasma activates matrix metalloproteinase during aneurysm formation. Nature Genet. 17, 439-444 (1997).
86. Grizzle WE, Mann U, Weiss H et al. Molecular staging of colorectal cancer in African-American and Caucasian patients using phenotypic expression of p53, Bcl3, MUC-1 and p27KIP1. Int. J. Cancer 97, 403-409 (2002).
87. Catalano V, Baldelli MA, Giordani P et al. Molecular markers predictive of response to chemotherapy in gastrointestinal tumors. Clin. Rev. Oncol. Hematol. 38, 93-104 (2001).
88. Novotny L, Szekeres T. Cancer therapy: new targets for chemotherapy. Hematology 8, 129-137 (2003).
89. Stremmel C, Wein W, Hohenberger W et al. DNA microarrays: a new diagnostic tool and its implications in colorectal cancer. Int. J. Colorectal Dis. 17, 131-136 (2002).
90. Ahmed FE. A functional genomic approach for screening preneoplastic stages of sporadic colon cancer. Cancer Genom. Proteom. 2, 71-84 (2005). Reviews a strategy for screening early preneoplastic stages of colon cancer.
91. Ahmed FE, Vos P. Molecular markers for human colon cancer in stool and blood identified by RT-CR. AntiCancer Res. 24 (6), 4127-4134 (2004). Illustrates the application of a real-time RT-PCR to quantify expression of colon cancer-specific genes in minimally or noninvasive samples.