Review Article

Use of MicroRNAs to Screen for Colon Cancer

Farid E Ahmed*, Nancy C Ahmed, Mostafa Gouda and Chris Bonnerup

Published: 31 August, 2017 | Volume 1 - Issue 1 | Pages: 045-074

Colon cancer (CC) screening is important for diagnosing early stage for malignancy and therefore potentially reduces mortality from this disease because the cancer could be cured at the early disease stage. Early detection is needed if accurate and cost effective diagnostic methods are available. Mortality from colon cancer is theoretically preventable through screening. The Current screening method, the immunological fecal occult blood test, FOBTi, lacks sensitivity and requires dietary restriction, which impedes compliance. Moreover colonoscopy is invasive and costly, which decreases compliance, and in certain cases could lead to mortality. Compared to the FOBT test, a noninvasive sensitive screen that does not require dietary restriction would be more convenient. Colonoscopy screening is recommended for colorectal cancer (CRC). Although it is a reliable screening method, colonoscopy is an invasive test, often accompanied by abdominal pain, has potential complications and has high cost, which have hampered its application worldwide.

A screening approach that uses the relatively stable and nondegradable microRNA molecules when extracted from either the noninvasive human stool, or the semi-invasive blood samples by available commercial kits and manipulated thereafter, would be more preferable than a transcriptomic messenger (m)RNA-, a mutation DNA-, an epigenetic-or a proteomic-based test. That approach utilizes reverse transcriptase (RT), followed by a modified quantitative real-time polymerase chain reaction (qPCR). To compensate for exosomal miRNAs that would not be measured, a parallel test could be performed on stool or plasma’s total RNAs, and corrections for exosomal loss are made to obtain accurate results. Ultimately, a chip would be developed to facilitate diagnosis, as has been carried out for the quantification of genetically modified organisms (GMOs) in foods. The gold standard to which the miRNA test is compared to is colonoscopy. If laboratory performance criteria are met, a miRNA test in human stool or blood samples based on high throughput automated technologies and quantitative expression measurements currently employed in the diagnostic clinical laboratory, would eventually be advanced to the clinical setting, making a noticeable impact on the prevention of colon cancer.

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Bioinformatics; Diagnosis; Histopathology; Microarrays; QC, RNA, RT-qPCR, Statistics


  1. Peterson NB, Murff HJ, Ness RM, Dittus RS. Colorectal cancer screening among men and women in the United States. J Womens Health. 2007; 16: 57-65. Ref.: https://goo.gl/3EDoae
  2. Mandel JS. Screening for colorectal cancer. Gastrointestinal Clin N Ame. 2008; 37: 97-115. Ref.: https://goo.gl/oCuYge
  3. Davies RJ, Miller R, Coleman N. Colorectal cancer screening: prospects for molecular stool analysis. Nature Rev Cancer. 2005; 5: 199-209. Ref.: https://goo.gl/Pg1myj
  4. Smith RA, Cokkinides V, Brawley OW. Cancer screening in the United States, 2009. A review of current American Cancer Society Guidelines and issues in cancer screening. CA Cancer J Clin. 2009; 59: 27-41. Ref.: https://goo.gl/KcMdMa
  5. Centers for Disease Control and Prevention. Increased use of colorectal cancer test: United States, 2002 and 2004,MMWR Mortal Wkly. 2006; 55: 208-311. Ref.: https://goo.gl/dtF1qt
  6. Ahmed FE. Colon cancer: Prevalence, screening, gene expression and mutation, and risk factors and assessment. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev. 2003; 21: 65-131. Ref.: https://goo.gl/s1THQB
  7. Morikawa T, Kato J, Yamaji Y, Wada R, Mitsushima T, et al. A Comparison of the immunochemical fecal occult blood test and total colonoscopy in the asymptomatic population. Gastroenterology. 2005; 129: 422-428. Ref.: https://goo.gl/qFWRqy
  8. Kohler BA, Ward E, McCarthy BJ, Edwards BK, Jemal A, et al. Annual report to the nation on the status of cancer, 1975-2007, featuring colorectal cancer trends and impact of interventions (risk factors, screening, and treatment) to reduce future rates. Cancer. 2010; 116: 544-573. Ref.: https://goo.gl/HEU4v3
  9. Ahlquist DA. Fecal occult blood testing for colorectal cancer. Can we afford to do this? Gastroenterol Clin N Amer. 1997; 26: 41-55, Ref.: https://goo.gl/CiDZiY
  10. Davidson LA, Lupton JR, Miskovsky E, Miskovsky, Alan P. Fields, et al. Quantification of human intestinal gene expression profiling using exfoliated colonocytes: a pilot study. Biomarkers. 2003; 8: 51-61. Ref.: https://goo.gl/kam5TN
  11. Ahmed FE, Jeffries CD, Vos PW, Flake G, Nuovo GJ, et al. Diagnostic microRNA markers for screening sporadic human colon cancer and ulcerative colitis in stool and tissue. Cancer Genom Proteom. 2009; 6: 281-296. Ref.: https://goo.gl/7cKJBE
  12. Ahmed FE, Vos P, iJames S, Lysle DT, Allison RR, et al. Transcriptomic molecular markers for screening human colon cancer in stool & tissue. Cancer Genom Proteom. 2007; 4: 1-20, 2007. Ref.: https://goo.gl/7yJ3eB
  13. Ahmed FE, Ahmed NC, Vos PW, Bonnerup C, Atkins JN,et al. Diagnostic microRNA markers to screen for sporadic human colon cancer in stool: I. Proof of principle. Cancer Genom Proteom. 2013; 10:93-113. Ref.: https://goo.gl/FPuKfyc
  14. Ahmed FE, Ahmed NC, Vos PW, Bonnerup C, Atkins JN, et al. Diagnostic microRNA markers to screen for sporadic human colon cancer in blood. Cancer Genom Proteom. 2012; 9: 179-192. Ref.: https://goo.gl/EDntph
  15. Ahlquist DA. Fecal occult blood testing for colorectal cancer. Can we afford to do this? Gastroenterol Clin North Am. 1997; 26: 41-55. Ref.: https://goo.gl/htMCvJ
  16. Cheng L, Eng G, Nieman L, Kapadia AS, Du XL.Trends in colorectal cancer incidence by anatomic site and disease stage in the United States from 1976 to 2005. Am J Clin Oncol. 2011; 34: 573-580. Ref.: https://goo.gl/VkxgTB
  17. Huxley RR, Ansary-Moghaddam A, Clifton P, Czernichow S, Parr CL, et al.The impact of dietary and lifestyle risk factors on risk of colorectal cancer: a quantitative overview of the epidemiological evidence. J Natl Cancer Inst. 2009; 125: 171-180. Ref.: https://goo.gl/i4eq6N
  18. Morikawa T, Kato J, Yamaji, Wada R, Mitsushima T, et al. Comparison of the immunochemical fecal occult blood test and total colonoscopy in the asymptomatic population. Gastroenterology. 2005; 129: 422-428. Ref.: https://goo.gl/iHrxpa
  19. Newcomb PA, Storer BE, Morimoto LA, Templeton A, Potter JD. Long-term efficacy of sigmoidoscopy in the reduction of colorectal cancer incidence. J Natl Cancer Inst. 2003; 95: 622-625. Ref.: https://goo.gl/iAzxbz
  20. Yamai Y, Mitsushima T, Ikuma H, Watabe H, Okamoto M, et al.Right-sided shift of colorectal adenomas with aging. Gastrointest Endoscopy. 2006;63: 453-458. Ref.: https://goo.gl/ZPW9Cj
  21. Gatto NM, Frucht H, Sundarararjan V, Jacobson JS, Grann VR, et al. Risk of perforation after colonoscopy or sigmoidoscopy: a population based study. J Natl Cancer Inst. 2003; 95: 230-236. Ref.: https://goo.gl/QzDjNM
  22. Birkenkamp-Demtroder K, Olesen SH, Sørensen FB, Laurberg S, Laiho P, et al. Differential gene expression in colon cancer of the ceacum versus the sigmoid and rectosigmoid. Gut. 2005; 54: 374-384. Ref.: https://goo.gl/Cv6fVD
  23. Gervaz P, Bouzourene H, Gerottini JP. Dukes B colorectal cancer: distinct genetic categories and clinical outcome based on proximal or distal tumor locations. Dis Colon Rectum. 2001; 44: 364-372.
  24. Bressler B, Paszat LF, Vinden C, Li C, He J, et al. Colonoscopic miss rates for right-sided colon cancer: population-based study.Gastroenterology. 2004; 127: 452-456. Ref.: https://goo.gl/gqM49H
  25. Mulhall BP, Veerappan GR, Jackson J. Meta-analysis: Computed tomographic colonography. Ann Intern Med. 2005; 142: 635-650. Ref.: https://goo.gl/Fhefc9
  26. Kealey SM, Dodd JD, MacEneaney PM, Gibney RG, Malone DE. Minimal preparation computed tomography instead of barium enema/colonoscopy for suspected colon cancer in frail elderly patients: an outcome analysis study. Clinical Radiol. 2004; 59: 44-52. Ref.: https://goo.gl/pYJV17
  27. Mȕller H M, Oberwalder M, Fiegl H, Morandell M, Goebel G, et al. Methylation changes in fecal DNA: a marker for colorectal cancer screening. Lancet. 2004; 363: 1283-1285. Ref.: https://goo.gl/uJuByP
  28. Lenhard K, Bommer GT, Asutay S, Schauer R, Brabletz T, et al. Analysis of promoter methylation in stool: a novel method for the detection of colorectal cancer. Clin Gastroenterol Hepatol. 2005; 3: 142-149. Ref.: https://goo.gl/FJi9r5
  29. Itzkowitz SH, Jandorf L, Brand R, Rabeneck L, Schroy PC 3rd, et al. Improved fecal DNA test for colorectal cancer screening. Clin Gastroenterol Hepatol. 2007; 5: 111-117. Ref.: https://goo.gl/yh4Ln5
  30. Imperiale TF, Ransohoff DF, Itzkowitz SH, Turnbull BA, Ross ME, et al. Fecal DNA versus fecal occult blood for colorectal cancer screening in an average-risk population. New Eng J Med. 2004; 351: 2704-2714. Ref.: https://goo.gl/ivNqvJ
  31. Ahmed FE. Liquid chromatography-mass spectrometry: A tool for proteome analysis & biomarker discovery and validation. Exp Opin Mol Diag. 2009; 3: 429-444. Ref.: https://goo.gl/icM5wn
  32. Osborn NK, Ahlquist DA. Stool screening for colorectal cancer: molecular approaches. Gastroenterology. 2005;128: 192-206. Ref.: https://goo.gl/ghMA4Q
  33. Ahlquist DA, Shuber AP. Stool screening for colorectal cancer: evolution from occult blood to molecular markers. Clin Chim Acta. 2002; 315: 151-157. Ref.: https://goo.gl/AJkUr2
  34. Traverso G, Shuber A, Levin B, Johnson C, Olsson L, et al. Detection of APC mutations in fecal and DNA from patients with colorectal tumors. New Engl J Med. 2002; 346: 311-320. Ref.: https://goo.gl/o5Svd1
  35. Ahlquist DA, Skoletsky JE, Boynton KA, Harrington JJ, Mahoney DW, et al. Colorectal cancer screening by detection of altered human DNA in stool: feasibility of a multitarget assay panel. Gastroenterology. 2000; 119: 1219-1227. Ref.: https://goo.gl/Zh284Z
  36. Ladabaum U and Song K. Projected national impact of colorectal cancer screening on clinical and economic outcomes and health services demand. Gastroenterology. 2005; 129: 1151-1126. Ref.: https://goo.gl/KDLhgo
  37. Polley AC, Mulholland F, Pin C, Williams EA, Bradburn DM, et al. Proteomic analysis reveals field-wide changes in protein expression in the morphologically normal mucosa of patients with colorectal neoplasia. Cancer Res. 2006; 66: 6553-6562. Ref.: https://goo.gl/vER2Ub
  38. Xin B, Platzer P, Fink SP, Reese L, Nosrati A, et al. Colon cancer secreted protein-2 (CCSP-2) a novel candidate serological marker of colon neoplasia. Oncogene. 2005; 24: 724-731. Ref.: https://goo.gl/WPSSdC
  39. Thomas SN, Zhu F, Schnaar RL, Alves CS, Konstantopoulos K. Carcinoembryonic antigen and CD44 variant isoforms cooperate to mediate colon carcinoma cell adhesion to E- and L-selectin in shear flow. J Biol Chem. 2008; 283, 15647-15655. Ref.: https://goo.gl/xRW845
  40. Koprowski H, Herlyn M, Steplewski Z, Sears HF. Specific antigen in serum of patients with colon carcinoma. Science. 1981; 212: 53-55. Ref.: https://goo.gl/X55j65
  41. 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. 2001; 51: 38-75.
  42. Ng EKO, Chong WWS, Jin H, Lam EK, Shin VY, et al. Differential expression of microRNA in plasma of patients with colorectal cancer: A potential marker for colorectal cancer screening. Gut. 2009; 58: 1375-1381.Ref.: https://goo.gl/vdrg7u
  43. Link A, Balaguer F, Shen Y, Nagasaka T, Lozano JJ, et al. Fecal miRNAs as novel biomarkers for colon cancer screening. Cancer Epidemiol Biomarkers Prev. 2010; 19: 1766-1774. Ref.: https://goo.gl/T8zM6n
  44. Koga Y, Yasunaga M, Takahashi A, Kuroda J, Moriya Y, et al. MicroRNA expression profiling of exfoliated colonocytes isolated from feces for colorectal cancer screening. Cancer Prev Res. 2010; 3: 1435-1442. Ref.: https://goo.gl/omh9cj
  45. Kalimutho M, Del Vecchio BG, Di Cecilia S, Sileri P, Cretella M, et al. Differential expression of miR-144* as a novel fecal-based diagnostic marker for colorectal cancer. J Gastroenterol. 2011; 46: 1391-1402. Ref.: https://goo.gl/8ofmSf
  46. Kalimutho M, Di Cecilia S, Del Vecchio BG, Roviello F, Sileri P, et al. Epigenetically silenced miR-34b/c as a novel faecal-based screening marker for colorectal cancer. Br J Cancer. 2011; 24: 1770-17780. Ref.: https://goo.gl/S6BHd2
  47. Kunte DP, Delacruz M, Wali RK, Menon A, Du H, et al. Dysregulation of microRNAs in colonic field carcinogenesis: implications for screening. PLoS One. 2012; 7. Ref.: https://goo.gl/9Uv87v
  48. Wu CW, Ng SS, Dong YJ, Ng SC, Leung WW, et al. Detection of miR-92a and miR-21 in stool samples as potential screening biomarkers for colorectal cancer and polyps. Gut. 2012; 61: 739-745. Ref.: https://goo.gl/KM4KTC
  49. Cummins JM, He Y, Leary RJ, Pagliarini R, Diaz LA Jr, et al. The colorectal microRNome. Proc Natl Acad Sci USA. 2006; 103: 3687-3692. Ref.: https://goo.gl/1ffTMh
  50. Schepler T, Reinert JT, Oslenfeld MS, Christensen LL, Silahtaroglu AN, et al. Diagnostic and prognostic microRNAs in Stage II colon cancer. Cancer Res. 2008; 68: 6416-6424. Ref.: https://goo.gl/7jxmdN
  51. Barbarotto E, Schmittgen TD, Calin GA. MicroRNAs and cancer: Profile, profile, profile. Int J Cancer. 2008; 122: 969-977. Ref.: https://goo.gl/AAH3YA
  52. Schetter AJ, Leung SY, Sohn JJ, Harris HH, Calin GA, et al. MicroRNA expression profile associated with progression and therapeutic outcome in colon adenocarcinoma. J Am Med Assoc. 2008; 299: 425-436. Ref.: https://goo.gl/rG9qaK
  53. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer. 2006; 6: 857-866. Ref.: https://goo.gl/a4VaZA
  54. Lu J, Getz G, Miska EA, Eric A, Alvarez-Saavedra, Ezequiel, et al. MicroRNA expression profiles classify human cancers. Nature. 2005; 435: 834-838. Ref.: https://goo.gl/2tBaAP
  55. Yantis RK, Goodarzi M, Zhou XK, Rennert H, Pirog EC, et al Clinical, pathological, and molecular features of early-onset colorectal carcinoma. Am J Surg Pathol. 2009; 33: 572-582. Ref.: https://goo.gl/Pkcs1N
  56. Luo X, Burwinke B, Tao S, Brenner J. MicroRNA signatures: Novel biomarkers for colorectal cancers. Cancer Epidemiol Biomarkers Prev. 2011; 20: 1272-1286. Ref.: https://goo.gl/rz2aXY
  57. Ahmed FE Testing for genetically modified organisms (GMOs) in food products. Lab Plus Intern. 2002; 16: 8-16.
  58. Ahmed FE, Vos P Molecular markers for human colon cancer in stool and blood identified by RT-PCR. Anticancer Res. 2004; 24: 4127-4134.
  59. Wang K, Zhang S. Weber J, Baxter D, Galas DJ. Export of microRNAs and microRNA-protective protein by mammalian cells. Nucleic Acids Res. 2010; 38: 7248-7259. Ref.: https://goo.gl/7Z4k68
  60. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, et al. Argonaute 2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA. 2011; 108: 5003-5008. Ref.: https://goo.gl/6ithpn
  61. Vickers KC, Palmisano BT, Shoucri BM, Shamburek RD, Remaley AT. MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol. 2011; 13: 423-433. Ref.: https://goo.gl/LVkXDu
  62. Hunter MP. Detection of microRNA expression in human peripheral blood microvessicles. PLoS One. 2008; 3: e3694. Ref.: https://goo.gl/VCsF6q
  63. Shaffer J, Schlumpberger M, Lader E. miRNA profiling from blood-Challenges and recommendations. 2012; 1-10. Ref.: https://goo.gl/UzZJcA
  64. Ahmed FE, James SI, Lysle DT, Johnke RM, Flake G, et al. Improved methods for extracting RNA from exfoliated human colonocytes in stool and RT-PCR analysis. Dig Dis Sci. 2004; 49: 1889-189. Ref.: https://goo.gl/ZL3RF1
  65. Mestdagh P, Van Vlierberghe P, Weer De, Muth D, Westermann F, et al. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biology. 2009; 10: R64. Ref.: https://goo.gl/NcZsbM
  66. Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, et al. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet. 2005; 37: 766-770. Ref.: https://goo.gl/SdnC8n
  67. Balcells I, Cirera S, Busk PK. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 2011; doi: 10.1186/1472-6750-11-70. Ref.: https://goo.gl/acP9sf
  68. Resnick KE, Alder H, Hagan JP, Richardson DL, Croce CM, et al. The detection of differentially expressed microRNAs from the serum of ovarian cancer patients using a novel real-time PCR platform. Gynecol Oncol. 2009; 112: 55-59. Ref.: https://goo.gl/r3FHeQ
  69. Redshaw N, Wilkes T, Whale A, Cowen S, Huggett J, et al. A comparison of miRA isolation and RT-qPCR technologies and their effects on quantification accuracy and repeatability. BioTechniques. 2013; 54: 155-164. Ref.: https://goo.gl/odZL4n
  70. Lee EJ, Gusev Y, Jiang J, Nuovo GJ, Lerner MR, et al. Expression profiling identifies distinct microRNA signature in pancreatic cancer. Int J Cancer.2007; 120: 1046-1054. Ref.: https://goo.gl/GkjLKn
  71. Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 2006; 9: 189-198. Ref.: https://goo.gl/iaXvCV
  72. Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005; 65: 7065-7070. Ref.: https://goo.gl/gRnTYF
  73. Miska EA, Alvarez-Saavedra E, Townsend M, Yoshii A, Rakic P, et al. Microarray analysis of microRNA expression in the developing mammalian brain. Genome Biol. 2004;5: R68. Ref.: https://goo.gl/aGnWQi
  74. Kim J, Krichevsky A, Grad Y, Gabriel D, Kenneth S, et al. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci USA. 2004; 101: 360-365. Ref.: https://goo.gl/g4rd6K
  75. Volinia S, Calin GA, Liu CG, Cimmino A, Petrocca F, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA. 2006; 103: 2257-2261. Ref.: https://goo.gl/tdtGu8
  76. Aandrés E, Cubedo E, Agirre X, Malumbres R, Navarro A, et al. Identification by real-time PCR of 13 mature microRNAs differentially expressed in colorectal cancer and non-tumor tissues. Mol Cancer. 2006;5: 29. Ref.: https://goo.gl/QsXhHD
  77. Jiang J, Lee EJ, Gusev Y, Schmittgen TD. Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res. 2005; 33: 5394-5403. Ref.: https://goo.gl/hYNyXD
  78. Shi B, Stepp-Lorenzino L, Prisco M, Linsley P, Baserga R, et al. MicroRNA 145 targets the insulin receptor substrate-1 and inhibits the growth of colon cancer cells. J Biol Chem. 2007; 282: 32582-32590. Ref.: https://goo.gl/fx31Av
  79. Calin GA, Ferracin M, Cimmino A, Shimizu M, Visone R, et al. A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Eng J Med. 2005; 353: 1793-1801. Ref.: https://goo.gl/9xaxAH
  80. Eis PS, Tam W, Sun L, Chadburn A, Li Z, et al. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc Natl Acad Sci USA. 2003; 102: 3627-3632. Ref.: https://goo.gl/3tiZ6j
  81. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, et al. Frequent deletions and downregulation of microRNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acas Sci USA. 2002; 99: 15524-15529. Ref.: https://goo.gl/k8rtMh
  82. Nybo K, Lo PCH. Optimal miRNA RT-qPCR. BioTechniques. 2013;54: 113.
  83. Ahmed FE, Vos PW, Clark J, Wiley JE, Weidner DA, et al. Differences in mRNA and microRNA expression profiles in human colon adenocarcinoma HT-29 cells treated with either intensity-modulated radiation therapy (IMRT), or conventional radiation therapy (RT). Cancer Genom Proteom. 2009; 6: 109-127. Ref.: https://goo.gl/PQodJ6
  84. Wu F, Zikusoka M, Trindade A, Dassopoulos T, Chakravarti S, et al. MicroRNAs are differentially expressed in ulcerative colitis and alter expression of macrophage inflammatory particle 2-α. Gastroenterology. 2008; 135: 1626-1635. Ref.: https://goo.gl/edUJbv
  85. Lu M, Zhang Q, Deng M, Miao, Cui Q, et al. An analysis of human microRNA and disease associations. PLoS One. 2008; 3: e3420. Ref.: https://goo.gl/YQYE4V
  86. Ahmed FE Expression microarray proteomics and the search for cancer biomarkers. Curr Genomics. 2006; 7: 399-426. Ref.: https://goo.gl/fvhGMA
  87. Ahmed FE. Quantitative real-time RT-PCR: Application to carcinogenesis. Cancer Genom Proteom. 2005; 2: 317-332. Ref.: https://goo.gl/6WZE5f
  88. Lewis BP, Shih IH, Jones-Rhodes MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell. 2003; 115: 787-789. Ref.: https://goo.gl/EQCSzC
  89. Gusev Y. Computational methods for analysis of cellular functions and pathways collectively targeted by differentially expressed microRNA. Methods. 2008; 44: 61-72. Ref.: https://goo.gl/BgFKoA
  90. Gusev Y, Schmittgen TD, Lerner M, Postier R, Brackett D. Computational analysis of biological functions and pathways collectively targeted by coexpressed microRNAs in cancer. BMC Bioinformatics. 2007; 8(Suppl 7): S16. Ref.: https://goo.gl/4wsGK5
  91. Ahmed FE. The role of microRNA in carcinogenesis and biomarker selection: a methodological perspective. Exp Rev Mol Diag. 2007; 7: 569-603. Ref.: https://goo.gl/krV5s9
  92. Sobin LH, Wittekind CH. eds UICC TNM Classification of Malignant Tumors, 6th Edition. New York, John Wiley. 2002; 170-173.
  93. Greene FL, Page DL, Fleming ID. Eds AJCC Cancer Staging Manual. 6th Edition. Springer-Verlag, New York. 2002.
  94. DeBakey ME, Yang L, Belaguli N. MicroRNA and colorectal cancer. World J Surg. (2009); 33: 638-646. Ref.: https://goo.gl/pHHkda
  95. Zhou X, Ruan J, Wang G, Zhang W. Characterization and identification of microRNA core promoters in trout model species. PLoS Comput Biol. 2005; 3: e37. Ref.: https://goo.gl/QeaCdV
  96. Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNA using deep-sequencing data. Nucleic Acids Res. 2014; 42: D68-D73. Ref.: https://goo.gl/725cpz
  97. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism and function. Cell. 2004;116: 281-297. Ref.: https://goo.gl/dzyaTz
  98. Reinhart BJ, Slack FJ, Basson M et al RNA regulates developmental timing in Caenorhabditis elegans. Nature. 2000; 403: 901-906. Ref.: https://goo.gl/t4bGUJ
  99. Xu P, Guo M, Hay BA. MicroRNAs and the regulation of cell death. Trend Genet. 2004; 20: 617-624. Ref.: https://goo.gl/rek2Ao
  100. Chang-Zheng C. MicroRNAs as oncogenes and tumor supressors. N Eng J Med. 2005; 353: 1768- 1771. Ref.: https://goo.gl/1jXDzK
  101. Calin GA, Sevignai C, Dumitru CD, Hyslop T, Noch E, et al. Human microRNAs are frequently located at fragile sites and genomic regions involved in cancer. Proc Natl Acad Sci USA. 2004; 101: 2999-3004. Ref.: https://goo.gl/8S2Ut9
  102. Ahmed FE. Molecular markers that predict response to colon cancer therapy. Exp Rev Mol Diag. 2005; 5: 353-375. Ref.: https://www.ncbi.nlm.nih.gov/pubmed/15934813
  103. Lanza G, Ferracin M, Gafà R, Veronese A, Spizzo R, et al. mRNA/microRNA gene expression profile in microsatellite unstable colorectal cancer. Molecular Cancer. 2007; 6: 54. Ref.: https://goo.gl/EKzZ3r
  104. Kiriakidou M, Nelson PT, Kouranov A, Fitziev P, Bouyioukos C, et al. A combined computational-experimental approach predicts human microRNA targets. Genes Dev. 2004; 18: 1165-1178. Ref.: https://goo.gl/fipMMv
  105. John BB, Enright AJ, Aravin A, Tuschl T, Sander C, et al. Human microRNA target. PloS Biol. 2004; 2: e363. Ref.: https://goo.gl/2mFVB9
  106. Krek A, Grun D, Poy MN, Wolf R, Rosenberg L, et al.Combinational microRNA target predictions. Nature Genet. 2005; 37: 495-500. Ref.: https://goo.gl/4zo78L
  107. Stark A, Brennecke J, Bushati N, Russell RB, Cohen SM. Animal microRNAs confers robustness to gene expression and have a significant impact on 3’UTR evaluation. Cell. 2005; 123: 1133-1146. Ref.: https://goo.gl/p3Gvna
  108. Oberg AL, French AJ, French AJ, Subramanian S, Morlan BW et al. MiRNA expression in colon polyps provide evidence for a multihit model of colon cancer. PLoS ONE. 2011; 6: e20465. Ref.: https://goo.gl/h6uvVY
  109. Valadi H, Elkstrom K, Bossios A,Sjöstrand M, Lee JJ, et al. Exosome mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol. 2007; 9: 654-659. Ref.: https://goo.gl/hPT9bm
  110. Ahmed FE. Laser microdissection: application to carcinogenesis. Cancer Genom. Proteom. 2006; 3: 217-226.
  111. Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inbibitors. Proc Natl Acas Sci USA. 1977; 74: 5463-5467. Ref.: https://goo.gl/dTJRbo
  112. Morozova O, Marra MA. Application of next-generation sequencing technologies in functional genomics. Genomics. 2008; 92: 255-264. Ref.: https://goo.gl/n7gTfz
  113. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1988; 8: 186-194. Ref.: https://goo.gl/aefkk9
  114. Margulies M, Engholm M, Altman WE, Attiya S, Bader JS, et al. Genome sequencing in microfabricated high-density picoliter reactors. Nature. 2005; 437: 376-380. Ref.: https://goo.gl/8txWVi
  115. Bentley DR. Whole-genome re-sequencing. Curr Opin Genet Dev. 2006; 16: 545-552. Ref.: https://goo.gl/rnJPes
  116. Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. Accurate multiplex polony sequencing at an evolved bacterial genome. Science. 2005; 309: 1728-1732. Ref.: https://goo.gl/QMz8kk
  117. Jensen SG, Lamy P, Rasmussen MH, Ostenfeld MS, Dyrskjøt L, et al. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics. 2011; 12: 435. Ref.: https://goo.gl/pSZgPA
  118. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res. 2005; 33: e179. Ref.: https://goo.gl/U6PHMc
  119. Tellman G. The E-method: a highly accurate technique for gene-expression analysis. Nature Methods. 2006; 3: 1-2.
  120. Light Cycler Software®, Version 3.5, Roche Molecular Biochemicals, Mannheim, Germany, 2001; 64-79.
  121. Luu-The V, Paquet N, Calvo E, Cumps J. Improved real-time RT-PCR method for high-throughput measurements using second derivative calculation and double correction. Biotechniques. 2005; 38: 287-293. Ref.: https://goo.gl/uTwGx8
  122. Thellin O, Zorzi W, Lakaye B, De Borman B, Coumans B, et al. Housekeeping genes as internal standards: use and limits. J Biotechnol. 1999; 75: 291-295. Ref.: https://goo.gl/CHj4EB
  123. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, et al. Accurate normalization of real-time quantitative RT-PCR by geometric average of multiple internal control genes. Genome Biol. 2002; 3. Ref.: https://goo.gl/ywZczE
  124. DeMuth JP, Jackson CM, Weaver DA, Erin L Crawford, Dennis S, et al. The gene expression index cmyc x E2F-1/p21 is highly predictive of malignant phenotype in human bronchial epithelial cells. Am J Respir Cell Mol Biol. 1998; 19: 18-29. Ref.: https://goo.gl/YH5yrc
  125. Nagan CY, Yamamoto H, Seshimo I, Ezumi K, Terayama M, et al. A multivariate analysis of adhesion molecules expression in assessment of colorectal cancer. J Surg Oncol. 2007; 95: 652-662. Ref.: https://goo.gl/jKs2S9
  126. Pepe MS, Feng Z, Janes H, Bossuyt PM, Potter JD. Pivotal evaluation of the occurance of a biomarker used for classification or prediction: standards for study design of Cancer. J.Natl Cancer Inst. 2008; 100: 1432-1438. Ref.: https://goo.gl/Z7zdpA
  127. Ein-Dor L, Zuk O, Domany E. Thousands of samples are needed to generate a robust gene list for predicting outcome in cancer. Proc Natl Acad Sci USA. 2006; 103: 5923-5928. Ref.: https://goo.gl/koxRNC
  128. Schwarzenbach H, da Silva A A, Calin G, Pantel K. DNA normalization strategies for microRNA quantification. Clinical Chem. 2015; 61: 1333-1342. Ref.: https://goo.gl/9LB8DZ
  129. Bustin SA, ed. A-Z of Quantitative PCR. International University Line, La Jolla, CA, 2004.
  130. Yau TO, Wu CW, Dong Y, Tang CM, Ng SS, et al. MicroRNA-221 and microRNA-18a identification in stool as biomarkers for the non-invasive diagnosis of colorectal carcinoma. Br J Cancer. 2014; 111: 1765-1771. Ref.: https://goo.gl/AUAvH2
  131. Tichopad A, Dilger M, Schwarz G, Pfaffl MW. Standardised determination of real-time PCR efficiency from a single reaction setup. Nucleic Acids Res. 2003; 31. Ref.: https://goo.gl/eNTPgw
  132. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. The MIQUE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55: 611-622. Ref.: https://goo.gl/fhjcRN
  133. Cornell RG, Ed. Statistical models for cancer studies. In Models to Analyze Strategies in the General Population, 346-347, Marcel Dekker, NY, 1984.
  134. Sureh KP, Chandrashekare S. Sample size estimation and power analysis for clinical research studies. J Hum Reprod Sci. 2012; 5: 7-13. Ref.: https://goo.gl/UDoWY6
  135. Moore DS, McCabe GP, Craig B. Introducrion to the Practice of Statistics, 6th edition. W.H. Freeman & Company, St. Louis, MO, 2009.
  136. Tang Y, Ghosal S, Roy A. Nonparametric Bayesian estimation of positive false discovery rates. Biometrics. 2007; 63: 1126-1134. Ref.: https://goo.gl/fhT11d
  137. Nagan CY, Yamamoto H, Seshimo I, Ezumi K, Terayama M, et al. A multivariate analysis of adhesion molecules expression in assessment of colorectal cancer. J Surg Oncol. 2007; 95: 652-662. Ref.: https://goo.gl/5Wr9zQ
  138. Yildiz OY, Aslan A, Alpagdin E. Multivariate statistical tests for comparing classification algorithms. In Learning and Intelligence Optimization. Springer. 2011.
  139. Reiner A, Yekutieli D, Benjamini Y. Identyfying differentially expressed genes using false discovery rate controlling procedures. Bioinformatics. 2003; 19: 368-375. Ref.: https://goo.gl/zdjwUe
  140. Pawitan Y, Michiels S, Kosciely S, Gusnato A, Polner A. False discovery rate, sensitivity and sample size for microarray studies. Bioinformatics. 2005; 21: 3017-3024. Ref.: https://goo.gl/MDCtsB
  141. Choi H, Nesvizhskii AI. False discovery rates and related statistical concepts in mass spectrometry-based proteomics. J Proteome Res. 2008; 7: 47-50. Ref.: https://goo.gl/jEKHGT
  142. Earl-Slatter A. Cross Validation, In the Handbookmof Clinical Trials and Other Research. Radcliff Medical Press Ltd. 2002.
  143. Efron B, Tibshirani RJ. An introduction to the Bootstrap, Chapman and Hall. 1993.
  144. Hanley JA, McNeil BJ. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology. 1982; 143: 29-36. Ref.: https://goo.gl/rWnWhk
  145. Ringer M. What is principal component analysis? Nature Biotechnol. 2008; 26: 303-304. Ref.: https://goo.gl/F3nW3g
  146. Wegman E. Hyperdimensional data analysis using parallel coordinate. J Am Stat Assoc. 1990; 85: 644-675. Ref.: https://goo.gl/rZjzfv
  147. Gabriel KR, Odoroff CL. Biplots in biomedical research. Stat Med. 1990; 9: 469-485. Ref.: https://goo.gl/BCWcBJ
  148. Huang da W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protocol. 2009; 4: 44-57. Ref.: https://goo.gl/Ef9K2k
  149. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, et al. The human colon cancer methylome shows similar hypo- and hypermethylation at conserveds tissue-specific CpG island shores. Nat Genet. 2009; 41: 178-186. Ref.: https://goo.gl/5tpHH5
  150. Herman JG, Baylin SB. Gene silencing in association with promoter hypermethylation. N Eng J Med. 2003; 349: 2042-2054. Ref.: https://goo.gl/CwmWdN
  151. Hansen KD, Timp W, Corrada H, Sabunciyan S, Langmead B, et al. Increased methylation variation in epigenetic domains across cancer types. Nature Genet. 2011; 43: 768-775. Ref.: https://goo.gl/d4heLS
  152. Sarver AL, French AJ, Borralho PM, Thayanithy V, Oberg AL, et al. Human colon cancer profiles show differential microRNA expression depending on mismatch repair status and are characteristic of undifferentiated proliferative states. BMC Cancer. 2009; 9: 401. Ref.: https://goo.gl/r48pYJ
  153. Earle JS, Luthra R, Romans A, Abraham R, Ensor J, et al. Association of microRNA expression with microsatellite instability status in colorectal adenocarcinoma. J Mol Diag. 2010; 12: 433-440. Ref.: https://goo.gl/Mzn7aC
  154. Balaguer F, Moreira L, Lozano JJ, Link A, Ramirez G, et al. Colorectal cancers with microsatellite instability display unique miRNA profiles. Clin Cancer Res. 2011; 17: 6239-6249. Ref.: https://goo.gl/Xj5m2D
  155. Tuddenham L, Wheeler G, Ntounia-Fousara S, Waters J, Hajihosseini MK, et al. The cartlidge specific microRNA-140 targets histone deacetylase 4 in mouse cells. FEBS Lett. 2006; 580: 4214-4217. Ref.: https://goo.gl/uCPD9h
  156. Costa Y, Speed RM, Gautier P, Semple CA, Maratou K, et al. Mouse MAELSTROM: the link between miotic silencing of unsynapsed chromatin and microRNA pathways? Hum Mol Genet. 2006; 15: 2324-2334. Ref.: https://goo.gl/g5ApSb
  157. Rajewsky N. microRNA target predictions in animals. Nat Genet. 2006; 38: S8-S13. Ref.: https://goo.gl/1Y3BRr
  158. Saito Y, Liang G, Egger G, Friedman JM, Chuang JC, et al. Specific activation of microRNA-127 with downregulation of the protooncogene BCL6 by chromatin-modifying drugs in human cancer cells. Cancer Cell. 2006; 9: 435-443. Ref.: https://goo.gl/4CvfGe
  159. Lujambio A, Calin GA, Villanueva A, Ropero S, Sánchez-Céspedes M, et al. A microRNA DNA methylation signature for human cancer metastasis. Proc Natl Acad Sci USA. 2008; 105: 13556-13561. Ref.: https://goo.gl/czoFWV
  160. Dews M, Homayouni A, Yu D, Murphy D, Sevignani C, et al. Augmentation of tumor angiogenesis by a myc-activated microRNA cluster. Nature Genet. 2006; 38: 1060-1065. Ref.: https://goo.gl/P2kXXb
  161. Fazi F, Rosa A, Fatica A, Gelmetti V, De Marchis ML, et al. A minicircuitry comprised of microRNA-223 and transcription factors NFI-A and C/EBPalpha regulates human granulopoiesis. Cell. 2005; 123: 819-831. Ref.: https://goo.gl/c2ogai
  162. Koss LG, Melamed MR, Eds. Koss’ Diagnostic Cytology and Histopathologic Bases, 5th edition, Lippincott, Williams & Wilkins, 2005.
  163. Winter MJ, Nagtegaal ID, van Krieken JH, Litvinov SV. The epithelial cell adhesion molecule (Ep-CAM) as a morphoregulatory molecule is a tool in surgical pathology. Am J Pathol. 2003; 163: 2139-2148. Ref.: https://goo.gl/9qiDgf
  164. Petrelli NJ, Letourneau R, Weber T, Nava ME, Rodriguez-Bigas M. Accuracy of biopsy and cytology for the preoperative diagnosis of colorectal adenocarcinoma. J Surg Oncol. 1999; 71: 46-49. Ref.: https://goo.gl/KsPfWB
  165. Matsushita HM, Matsumura Y, Moriya Y, Akasu T, Fujita S, et al. A new method for isolating colonocytes from naturally evacuated feces and its clinical application to colorectal cancer diagnosis. Gastroenterology. 2005; 129: 1918 - 1927. Ref.: https://goo.gl/mZAy84
  166. Simpson RJ, Lim JE, Moritz RL, Mathivanan S. Exosomes: proteomic insights and diagnostic potential. Expert Rev Proteomics. 2009; 6: 267-283. Ref.: https://goo.gl/RR1Xtf
  167. Baker M. Digital PCR hits its stride. Nature Methods. 2012; 9: 541-544. Ref.: https://goo.gl/FQfNH5
  168. McShane LM, Altman DG, Sauerbrei W, Sheila E. Taube, Massimo Gion, et al. Reporting recommendations for tumor marker prognostic studies (REMARK). J Natl Cancer Inst. 2005; 97: 1180-1184. Ref.: https://goo.gl/nGLTAy


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