Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

Nielson T. Baxter1, Mack T. Ruffin2, Mary A.M. Rogers3, Patrick Schloß1
1Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
2Department of Family Medicine, University of Michigan, Ann Arbor, MI, USA
3Department of Internal Medicine, University of Michigan, Ann Arbor, MI/USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Siegel R, DeSantis C, Jemal A. Colorectal cancer statistics, 2014. CA Cancer J Clin. 2014;64:104–17.

Imperiale TF, Ransohoff DF, Itzkowitz SH, Levin TR, Lavin P, Lidgard GP, et al. Multitarget stool DNA testing for colorectal-cancer screening. N Engl J Med. 2014;370:1287–97.

Jones RM, Devers KJ, Kuzel AJ, Woolf SH. Patient-reported barriers to colorectal cancer screening: a mixed-methods analysis. Am J Prev Med. 2010;38:508–16.

Hsia J, Kemper E, Kiefe C, Zapka J, Sofaer S, Pettinger M, et al. The importance of health insurance as a determinant of cancer screening: evidence from the Women’s Health Initiative. Prev Med. 2000;31:261–70.

Centers for Disease Control and Prevention. Vital signs: Colorectal cancer screening test use–United states, 2012. MMWR Morb Mortal Wkly Rep. 2013;62:881.

Hundt S, Haug U, Brenner H. Comparative evaluation of immunochemical fecal occult blood tests for colorectal adenoma detection. Ann Intern Med. 2009;150:162–9.

Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X, et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J. 2012;6:320–9.

Chen H-M, Yu Y-N, Wang J-L, Lin Y-W, Kong X, Yang C-Q, et al. Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma. Am J Clin Nutr. 2013;97:1044–52.

Chen W, Liu F, Ling Z, Tong X, Xiang C. Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One. 2012;7:e39743.

Shen XJ, Rawls JF, Randall TA, Burcall L, Mpande C, Jenkins N, et al. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes. 2010;1:138–47.

Kostic AD, Gevers D, Pedamallu CS, Michaud M, Duke F, Earl AM, et al. Genomic analysis identifies association of Fusobacterium with colorectal carcinoma. Genome Res. 2012;22:292–8.

Feng Q, Liang S, Jia H, Stadlmayr A, Tang L, Lan Z, et al. Gut microbiome development along the colorectal adenoma–carcinoma sequence. Nat Commun. 2015;6:6528.

Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, et al. The gut microbiome modulates colon tumorigenesis. MBio. 2013;4:e00692–13.

Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, et al. Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe. 2013;14:207–15.

Wu S, Rhee K-J, Albesiano E, Rabizadeh S, Wu X, Yen H-R, et al. A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med. 2009;15:1016–22.

Arthur JC, Perez-Chanona E, Mühlbauer M, Tomkovich S, Uronis JM, Fan T-J, et al. Intestinal inflammation targets cancer-inducing activity of the microbiota. Science. 2012;338:120–3.

Zackular JP, Rogers MA, Ruffin MT, Schloss PD. The human gut microbiome as a screening tool for colorectal cancer. Cancer Prev Res. 2014;7:1112–21.

Zeller G, Tap J, Voigt AY, Sunagawa S, Kultima JR, Costea PI, et al. Potential of fecal microbiota for early-stage detection of colorectal cancer. Mol Syst Biol. 2014;10:766.

Liaw A, Wiener M. Classification and regression by randomForest. R News. 2002;2:18–22.

O’Brien CL, Allison GE, Grimpen F, Pavli P. Impact of colonoscopy bowel preparation on intestinal microbiota. PLoS One. 2013;8:e62815.

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol. 2013;79:5112–20.

Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75:7537–41.

Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007;73:5261–7.

Calle ML, Urrea V, Boulesteix A-L, Malats N. AUC-RF: A new strategy for genomic profiling with random forest. Hum Hered. 2011;72:121–32.

DeLong ER, DeLong DM, Clarke-Pearson DL. Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach. Biometrics. 1988;44:837–45.

Youden WJ. Index for rating diagnostic tests. Cancer. 1950;3:32–5.

Pepe M, Longton G, Janes H. Estimation and comparison of receiver operating characteristic curves. Stata J. 2009;9:1.

Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez J-C, et al. PROC: An open-source package for r and s + to analyze and compare rOC curves. BMC Bioinformatics. 2011;12:1.

Dixon P, Palmer M. VEGAN, a package of r functions for community ecology. J Vegetation Sci. 2003;14:927–30.

Warren RL, Freeman DJ, Pleasance S, Watson P, Moore RA, Cochrane K, et al. Co-occurrence of anaerobic bacteria in colorectal carcinomas. Microbiome. 2013;1:16.

Yu J, Feng Q, Wong SH, Zhang D, Liang Q yi, Qin Y, Tang L, Zhao H, Stenvang J, Li Y, et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut. 2015 ;0:1–9. doi: 10.1136/gutjnl-2015-309800 .

Rex DK, Johnson DA, Anderson JC, Schoenfeld PS, Burke CA, Inadomi JM. American College of Gastroenterology guidelines for colorectal cancer screening 2008. Am J Gastroenterol. 2009;104:739–50.

Heitman SJ, Ronksley PE, Hilsden RJ, Manns BJ, Rostom A, Hemmelgarn BR. Prevalence of adenomas and colorectal cancer in average risk individuals: a systematic review and meta-analysis. Clin Gastroenterol Hepatol. 2009;7:1272–8.

Symonds EL, Osborne JM, Cole SR, Bampton PA, Fraser RJ, Young GP. Factors affecting faecal immunochemical test positive rates: demographic, pathological, behavioural and environmental variables. J Med Screen. 2015;22:187-193.

Kapidzic A, van der Meulen MP, Hol L, van Roon AH, Looman CW, Lansdorp-Vogelaar I, et al. Gender differences in fecal immunochemical test performance for early detection of colorectal neoplasia. Clin Gastroenterol Hepatol. 2015;13(8):1464–71.e4.

Levi Z, Rozen P, Hazazi R, Vilkin A, Waked A, Maoz E, et al. Sensitivity, but not specificity, of a quantitative immunochemical fecal occult blood test for neoplasia is slightly increased by the use of low-dose aspirin, NSAIDs, and anticoagulants. Am J Gastroenterol. 2009;104:933–8.

Schubert AM, Sinani H, Schloss PD. Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. MBio. 2015;6:e00974.

Pryde SE, Duncan SH, Hold GL, Stewart CS, Flint HJ. The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett. 2002;217:133–9.

Segain J, De La Blétiere DR, Bourreille A, Leray V, Gervois N, Rosales C, et al. Butyrate inhibits inflammatory responses through nFκB inhibition: Implications for Crohn’s disease. Gut. 2000;47:397–403.

D’Argenio G, Cosenza V, Delle Cave M, Iovino P, Delle Valle N, Lombardi G, et al. Butyrate enemas in experimental colitis and protection against large bowel cancer in a rat model. Gastroenterology. 1996;110:1727–34.

Hague A, Elder DJ, Hicks DJ, Paraskeva C. Apoptosis in colorectal tumour cells: Induction by the short chain fatty acids butyrate, propionate and acetate and by the bile salt deoxycholate. Int J Cancer. 1995;60:400–6.

Gallimidi AB, Fischman S, Revach B, Bulvik R, Maliutina A, Rubinstein AM, et al. Periodontal pathogens porphyromonas gingivalis and fusobacterium nucleatum promote tumor progression in an oral-specific chemical carcinogenesis model. Oncotarget. 2015;6:22613–23.

Ding T, Schloss PD. Dynamics and associations of microbial community types across the human body. Nature. 2014;509:357–60.