Differential gene expression in colon tissue associated with diet, lifestyle, and related oxidative stress

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Slattery, Martha L ^a   Pellatt, Daniel F ^a   Mullany, Lila E ^a   Wolff, Roger K ^a  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA TOCOPHEROL; ASCORBIC ACID; BETA CAROTENE; IBUPROFEN; LYCOPENE; MITOGEN ACTIVATED PROTEIN KINASE KINASE 3; NEU DIFFERENTIATION FACTOR; XANTHOPHYLL; ZEAXANTHIN;

ADULT; ALCOHOL CONSUMPTION; ALCOHOLIC BEVERAGE; ARTICLE; BEER; CANCER PATIENT; COLON; COLON CANCER; CONTROLLED STUDY; DIET; DISEASE ASSOCIATION; DOWN REGULATION; DRUG USE; FEMALE; GENE; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE IDENTIFICATION; GENE REGULATORY NETWORK; GENETIC ASSOCIATION; HDX GENE; HUMAN; HUMAN TISSUE; LIFESTYLE; MAJOR CLINICAL STUDY; MALE; MAP2K3 GENE; MIDDLE AGED; NRG4 GENE; OXIDATIVE STRESS; RNA SEQUENCE; SMOKING; ST8SIA4 GENE; STEAP3 GENE; SYCP3 GENE; TEK GENE; TMC06 GENE; UPREGULATION; WINE; DRINKING BEHAVIOR; GENETICS; METABOLISM;

ALCOHOL DRINKING; COLON; DIET; FEMALE; GENE EXPRESSION REGULATION; HUMANS; LIFE STYLE; MALE; OXIDATIVE STRESS; SMOKING;

EID: 84942091104     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0134406     Document Type: Article

References (41)

1. Slattery ML, Curtin K, Anderson K, Ma KN, Ballard L, Edwards S, et al. (2000) Associations between cigarette smoking, lifestyle factors, and microsatellite instability in colon tumors. J Natl Cancer Inst 92:1831-1836. PMID: 11078760
2. Slattery ML, Potter JD, Samowitz W, Bigler J, Caan B, Leppert M (1998) NAT2, GSTM-1, cigarette smoking, and risk of colon cancer. Cancer Epidemiol Biomarkers Prev 7:1079-1084. PMID: 9865425
3. Giovannucci E, Colditz GA, Stampfer MJ, Hunter D, Rosner BA, Willett WC, et al. (1994) A prospective study of cigarette smoking and risk of colorectal adenoma and colorectal cancer in U. S. women. Journal of the National Cancer Institute 86:192-199. PMID: 8283491
4. Giovannucci E, Rimm EB, Stampfer MJ, Colditz GA, Ascherio A, Kearney J, et al. (1994) A prospective study of cigarette smoking and risk of colorectal adenoma and colorectal cancer in U. S. men. Journal of the National Cancer Institute 86:183-191. PMID: 8283490
5. Giovannucci E (2001) An updated review of the epidemiological evidence that cigarette smoking increases risk of colorectal cancer. Cancer Epidemiol Biomarkers Prev 10:725-731. PMID: 11440957
6. Chao A, Thun MJ, Jacobs EJ, Henley SJ, Rodriguez C, Calle EE (2000) Cigarette smoking and colorectal cancer mortality in the cancer prevention study II. J Natl Cancer Inst 92:1888-1896. PMID: 11106680
7. Talukder MA, Johnson WM, Varadharaj S, Lian J, Kearns PN, El-Mahdy MA, et al. (2011) Chronic cigarette smoking causes hypertension, increased oxidative stress, impaired NO bioavailability, endothelial dysfunction, and cardiac remodeling in mice. Am J Physiol Heart Circ Physiol 300:H388-396. doi: 10. 1152/ajpheart.00868.2010 PMID: 21057039
8. Chavez J, Cano C, Souki A, Bermudez V, Medina M, Ciszek A, et al. (2007) Effect of cigarette smoking on the oxidant/antioxidant balance in healthy subjects. Am J Ther 14:189-193. PMID: 17414589
9. Mena S, Ortega A, Estrela JM (2009) Oxidative stress in environmental-induced carcinogenesis. Mutat Res 674:36-44. doi: 10.1016/j.mrgentox.2008.09.017 PMID: 18977455
10. Petersen DR (2005) Alcohol, iron-associated oxidative stress, and cancer. Alcohol 35:243-249. PMID: 16054986
11. Nagamma T, Bhutia RD, Pokharel DR, Yadav S, Baxi J (2012) Influence of alcohol consumption on oxidative stress and antioxidant status in cancer patients-case-control study from Western Nepal. Asian Pac J Cancer Prev 13:3513-3517. PMID: 22994787
12. Oyesanmi O, Snyder D, Sullivan N, Reston J, Treadwell J, Schoelles KM (2010) Alcohol consumption and cancer risk: understanding possible causal mechanisms for breast and colorectal cancers. Evid Rep Technol Assess (Full Rep):1-151.
13. Slattery ML, Benson J, Curtin K, Ma KN, Schaeffer D, Potter JD (2000) Carotenoids and colon cancer. Am J Clin Nutr 71:575-582. PMID: 10648274
14. Slattery ML, Edwards SL, Anderson K, Caan B (1998) Vitamin E and colon cancer: is there an association? Nutr Cancer 30:201-206. PMID: 9631491
15. Stone WL, Papas AM (1997) Tocopherols and the etiology of colon cancer. J Natl Cancer Inst 89:1006-1014. PMID: 9230882
16. Satia-Abouta J, Galanko JA, Martin CF, Potter JD, Ammerman A, Sandler RS (2003) Associations of micronutrients with colon cancer risk in African Americans and whites: results from the North Carolina Colon Cancer Study. Cancer Epidemiol Biomarkers Prev 12:747-754. PMID: 12917206
17. Slattery ML, Lundgreen A, Welbourn B, Wolff RK, Corcoran C (2012) Oxidative balance and colon and rectal cancer: Interaction of lifestyle factors and genes. Mutation Research 734:30-40. doi: 10.1016/j. mrfmmm.2012.04.002 PMID: 22531693
18. Goodman M, Bostick RM, Gross M, Thyagarajan B, Dash C, Flanders WD (2010) Combined measure of pro- and anti-oxidant exposures in relation to prostate cancer and colorectal adenoma risk: an update. Annals of epidemiology 20:955-957. doi: 10.1016/j.annepidem.2010.08.011 PMID: 21074110
19. Goodman M, Bostick RM, Dash C, Terry P, Flanders WD, Mandel J (2008) A summary measure of proand anti-oxidant exposures and risk of incident, sporadic, colorectal adenomas. Cancer causes & control: CCC 19:1051-1064. doi: 10.1007/s10552-008-9169-y PMID: 18543072
20. Ornish D, Magbanua MJ, Weidner G, Weinberg V, Kemp C, Green C, et al. (2008) Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention. Proc Natl Acad Sci USA 105:8369-8374. doi: 10.1073/pnas.0803080105 PMID: 18559852
21. Morel Y, Barouki R (1999) Repression of gene expression by oxidative stress. Biochem J 342 Pt 3:481-496.
22. Slattery ML, Edwards SL, Palmer L, Curtin K, Morse J, Anderson K, et al. (2000) Use of archival tissue in epidemiologic studies: collection procedures and assessment of potential sources of bias. Mutat Res 432:7-14. PMID: 10729707
23. Samowitz WS, Curtin K, Lin HH, Robertson MA, Schaffer D, Nichols M, et al. (2001) The colon cancer burden of genetically defined hereditary nonpolyposis colon cancer. Gastroenterology 121:830-838. PMID: 11606497
24. Edwards S, Slattery ML, Mori M, Berry TD, Caan BJ, Palmer P, et al. (1994) Objective system for interviewer performance evaluation for use in epidemiologic studies. Am J Epidemiol 140:1020-1028. PMID: 7985650
25. Liu K, Slattery M, Jacobs D Jr, Cutter G, McDonald A, Van Horn L, et al. (1994) A study of the reliability and comparative validity of the cardia dietary history. Ethn Dis 4:15-27. PMID: 7742729
26. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society 57:289-300.
27. Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. PMID: 25516281
28. QIAGEN's Ingenuity Pathway Analysis
29. Kramer A, Green J, Pollard J Jr, Tugendreich S (2014) Causal analysis approaches in Ingenuity Pathway Analysis. Bioinformatics 30:523-530. doi: 10.1093/bioinformatics/btt703 PMID: 24336805
30. Llinas L, Peinado VI, Ramon Goni J, Rabinovich R, Pizarro S, Rodriguez-Roisin R, et al. (2011) Similar gene expression profiles in smokers and patients with moderate COPD. Pulm Pharmacol Ther 24:32-41. doi: 10.1016/j.pupt.2010.10.010 PMID: 20970515
31. Mossman BT, Lounsbury KM, Reddy SP (2006) Oxidants and signaling by mitogen-activated protein kinases in lung epithelium. Am J Respir Cell Mol Biol 34:666-669. PMID: 16484683
32. Arredondo J, Chernyavsky AI, Jolkovsky DL, Pinkerton KE, Grando SA (2007) Receptor-mediated tobacco toxicity: alterations of the NF-kappaB expression and activity downstream of alpha7 nicotinic receptor in oral keratinocytes. Life Sci 80:2191-2194. PMID: 17291542
33. Nielsen OH, Bjerrum JT, Csillag C, Nielsen FC, Olsen J (2009) Influence of smoking on colonic gene expression profile in Crohn's disease. PLoS One 4:e6210. doi: 10.1371/journal.pone.0006210 PMID: 19603079
34. Arredondo J, Chernyavsky AI, Jolkovsky DL, Pinkerton KE, Grando SA (2008) Receptor-mediated tobacco toxicity: acceleration of sequential expression of alpha5 and alpha7 nicotinic receptor subunits in oral keratinocytes exposed to cigarette smoke. FASEB J 22:1356-1368. doi: 10.1096/fj.07-9965.com PMID: 18450646
35. He B, Luo B, Chen Q, Zhang L (2013) Cigarette smoke extract induces the expression of GRP78 in A549 cells via the p38/MAPK pathway. Mol Med Rep 8:1683-1688. doi: 10.3892/mmr.2013.1724 PMID: 24126384
36. Bai SK, Lee SJ, Na HJ, Ha KS, Han JA, Lee H, et al. (2005) beta-Carotene inhibits inflammatory gene expression in lipopolysaccharide-stimulated macrophages by suppressing redox-based NF-kappaB activation. Exp Mol Med 37:323-334. PMID: 16155409
37. Rafi MM, Kanakasabai S, Gokarn SV, Krueger EG, Bright JJ (2014) Dietary Lutein Modulates Growth and Survival Genes in Prostate Cancer Cells. J Med Food.
38. Dorr C, Wu B, Guan W, Muthusamy A, Sanghavi K, Schladt DP, et al. (2015) Differentially expressed gene transcripts using RNA sequencing from the blood of immunosuppressed kidney allograft recipients. PLoS One 10:e0125045. doi: 10.1371/journal.pone.0125045 PMID: 25946140
39. Guo Y, Sheng Q, Li J, Ye F, Samuels DC, Shyr Y (2013) Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data. PLoS One 8:e71462. doi: 10.1371/journal.pone. 0071462 PMID: 23977046
40. Mestdagh P, Hartmann N, Baeriswyl L, Andreasen D, Bernard N, Chen C, et al. (2014) Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nat Methods 11:809-815. doi: 10.1038/nmeth.3014 PMID: 24973947
41. Fonseca NA, Marioni J, Brazma A (2014) RNA-Seq gene profiling-a systematic empirical comparison. PLoS One 9:e107026. doi: 10.1371/journal.pone.0107026 PMID: 25268973