Erratum: Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature (Journal of Clinical Investigation (2014) 124: 8 (3617-3633) DOI: 10.1172/JCI75436);Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature

Journal of Clinical Investigation

Volumn 124, Issue 8, 2014, Pages 3617-3633

  Haberman, Yael ^a   Tickle, Timothy L ^b,c   Dexheimer, Phillip J ^d   Kim, Mi Ok ^a   Tang, Dora ^a   Karns, Rebekah ^d   Baldassano, Robert N ^e   Noe, Joshua D ^f   Rosh, Joel ^g   Markowitz, James ^h   Heyman, Melvin B ⁱ   Griffiths, Anne M ^j   Crandall, Wallace V ^k   Mack, David R ^l   Baker, Susan S ^m   Huttenhower, Curtis ^b,c   Keljo, David J ⁿ   Hyams, Jeffrey S ^o   Kugathasan, Subra ^p   Walters, Thomas D ^j   Aronow, Bruce ^d   Xavier, Ramnik J ^c,q,r   Gevers, Dirk ^c   Denson, Lee A ^a   more..

^a CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER   (United States)

^b HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^c HARVARD UNIVERSITY   (United States)

^d Biomedical Informatics   (United States)

^e UNIVERSITY OF PENNSYLVANIA   (United States)

^f MEDICAL COLLEGE OF WISCONSIN   (United States)

^g Atlantic Health   (United States)

^h Hofstra Northwell Steven and Alexandra Cohen Children s Medical Center of NY Northwell Health   (United States)

ⁱ UNIVERSITY OF CALIFORNIA   (United States)

^j HOSPITAL FOR SICK CHILDREN   (Canada)

^k NATIONWIDE CHILDREN S HOSPITAL   (United States)

^l CHILDREN S HOSPITAL OF EASTERN ONTARIO   (Canada)

^m UNIVERSITY AT BUFFALO   (United States)

ⁿ CHILDREN S HOSPITAL OF PITTSBURGH   (United States)

^o Division of Pediatric Infectious Diseases   (United States)

^p EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^q HARVARD MEDICAL SCHOOL   (United States)

^r MASSACHUSETTS GENERAL HOSPITAL   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ANTIMICROBIAL DUAL OXIDASE; APOLIPOPROTEIN A1; OXIDOREDUCTASE; STEROID; TRANSCRIPTOME; UNCLASSIFIED DRUG; APOA1 PROTEIN, HUMAN; DUOX2 PROTEIN, HUMAN; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE OXIDASE;

ACTINOBACTERIA; APOA1 GENE; ARTICLE; BACTEROIDETES; CELL POLARITY; CHILD; CLINICAL FEATURE; COLON CROHN DISEASE; CONTROLLED STUDY; CROHN DISEASE; DISEASE SEVERITY; DOWN REGULATION; DUOX2 GENE; FEMALE; FIRMICUTES; FUSOBACTERIUM; GENE; GENE EXPRESSION; GENE ONTOLOGY; HUMAN; HUMAN TISSUE; ILEUM; IMMUNOHISTOCHEMISTRY; INTESTINE FLORA; INTESTINE INJURY; INTESTINE MUCOSA; INTESTINE ULCER; MAJOR CLINICAL STUDY; MALE; MEASUREMENT ACCURACY; MICROBIAL COMMUNITY; MODEL; NUCLEOTIDE SEQUENCE; OXIDATIVE STRESS; PREDICTION; PRIORITY JOURNAL; PROTEOBACTERIA; REMISSION; SCHOOL CHILD; TH1 CELL; ULCERATIVE COLITIS; UPREGULATION; VEILLONELLA; VERRUCOMICROBIUM; ADOLESCENT; CASE CONTROL STUDY; COHORT ANALYSIS; GENE EXPRESSION PROFILING; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; MICROFLORA;

ADOLESCENT; APOLIPOPROTEIN A-I; CASE-CONTROL STUDIES; CHILD; COHORT STUDIES; COLITIS, ULCERATIVE; CROHN DISEASE; FEMALE; GENE EXPRESSION PROFILING; HUMANS; ILEUM; MALE; MICROBIOTA; NADPH OXIDASE; PROTEOBACTERIA; TRANSCRIPTOME;

EID: 84905482236     PISSN: 00219738     EISSN: 15588238     Source Type: Journal    
DOI: 10.1172/JCI79657     Document Type: Erratum

References (47)

1. Aujnarain A, Mack DR, Benchimol EI. The role of the environment in the development of pediatric inflammatory bowel disease. Curr Gastroenterol Rep. 2013;15(6):326.
2. Molodecky NA, et al. Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. Gastroenterology. 2012;142(1):46-54.e42
3. Kim SC, Tonkonogy SL, Karrasch T, Jobin C, Sartor RB. Dual-association of gnotobiotic IL-10-/-mice with 2 nonpathogenic commensal bacteria induces aggressive pancolitis. Inflamm Bowel Dis. 2007;13(12):1457-1466.
4. Jostins L, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491(7422):119-124.
5. Morgan XC, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13(9):R79.
6. Gevers D, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15(3):382-392.
7. Hotte NS, et al. Patients with inflammatory bowel disease exhibit dysregulated responses to microbial DNA. PLoS One. 2012;7(5):e37932.
8. Colombel JF, et al. Infliximab, azathioprine, or combination therapy for Crohn's disease. N Engl J Med. 2010;362(15):1383-1395.
9. Sandborn WJ, et al. Ustekinumab induction and maintenance therapy in refractory Crohn's disease. N Engl J Med. 2012;367(16):1519-1528.
10. Parikh A, et al. Vedolizumab for the treatment of active ulcerative colitis: a randomized controlled phase 2 dose-ranging study. Inflamm Bowel Dis. 2012;18(8):1470-1479.
11. Walters TD, et al. Increased effectiveness of early therapy with anti-tumor necrosis factor-α vs an immunomodulator in children with Crohn's disease. Gastroenterology. 2014;146(2):383-391.
12. Arijs I, et al. Predictive value of epithelial gene expression profiles for response to infliximab in Crohn's disease. Inflamm Bowel Dis. 2010;16(12):2090-2098.
13. Gullberg E, Soderholm JD. Peyer's patches and M cells as potential sites of the inflammatory onset in Crohn's disease. Ann N Y Acad Sci. 2006;1072:218-232.
14. Jung C, Hugot JP, Barreau F. Peyer's patches: the immune sensors of the intestine. Int J Inflam. 2010;2010:823710.
15. Larsson E, et al. Analysis of gut microbial regulation of host gene expression along the length of the gut and regulation of gut microbial ecology through MyD88. Gut. 2012;61(8):1124-1131.
16. Zhang T, et al. An ileal Crohn's disease gene signature based on whole human genome expression profiles of disease unaffected ileal mucosal biopsies. PLoS One. 2012;7(5):e37139.
17. Zhang T, et al. Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition. PLoS One. 2012;7(6):e30044.
18. Clark PM, Dawany N, Dampier W, Byers SW, Pestell RG, Tozeren A. Bioinformatics analysis reveals transcriptome and microRNA signatures and drug repositioning targets for IBD and other autoimmune diseases. Inflamm Bowel Dis. 2012;18(12):2315-2333.
19. Noble CL, et al. Characterization of intestinal gene expression profiles in Crohn's disease by genome-wide microarray analysis. Inflamm Bowel Dis. 2010;16(10):1717-1728.
20. Chen J, Bardes EE, Aronow BJ, Jegga AG. Topp-Gene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 2009;37(Web Server issue):W305-W311.
21. Kaimal V, Bardes EE, Tabar SC, Jegga AG, Aronow BJ. ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems. Nucleic Acids Res. 2010;38(Web Server issue):W96-W102.
22. Schwartz S, et al. A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol. 2012;13(4):r32.
23. Lipinski S, et al. DUOX2-derived reactive oxygen species are effectors of NOD2-mediated antibacterial responses. J Cell Sci. 2009;122(pt 19):3522-3530.
24. Esworthy RS, Kim BW, Rivas GE, Leto TL, Doroshow JH, Chu FF. Analysis of candidate colitis genes in the Gdac1 locus of mice deficient in glutathione peroxidase-1 and -2. PLoS One. 2012;7(9):e44262.
25. Levy E, et al. Altered lipid profile, lipoprotein composition, and oxidant and antioxidant status in pediatric Crohn disease. Am J Clin Nutr. 2000;71(3):807-815.
26. Allez M, Lemann M, Bonnet J, Cattan P, Jian R, Modigliani R. Long term outcome of patients with active Crohn's disease exhibiting extensive and deep ulcerations at colonoscopy. Am J Gastroenterol. 2002;97(4):947-953.
27. Saito R, et al. A travel guide to Cytoscape plugins. Nat Methods. 2012;9(11):1069-1076.
28. Seeley EH, Washington MK, Caprioli RM, M'Koma AE. Proteomic patterns of colonic mucosal tissues delineate Crohn's colitis and ulcerative colitis. Proteomics Clin Appl. 2013;7(7-8):541-549.
29. Schnitzler F, et al. Mucosal healing predicts long-term outcome of maintenance therapy with infliximab in Crohn's disease. Inflamm Bowel Dis. 2009;15(9):1295-1301.
30. Kuhn R, Lohler J, Rennick D, Rajewsky K, Muller W. Interleukin-10- deficient mice develop chronic enterocolitis. Cell. 1993;75(2):263-274.
31. Taurog JD, et al. The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats. J Exp Med. 1994;180(6):2359-2364.
32. Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A. 2007;104(34):13780-13785.
33. Bornigen D, et al. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013;5(7):65.
34. Chappert P, Bouladoux N, Naik S, Schwartz RH. Specific gut commensal flora locally alters T cell tuning to endogenous ligands. Immunity. 2013;38(6):1198-1210.
35. Markle JG, et al. Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity. Science. 2013;339(6123):1084-1088.
36. Maslowski KM, Mackay CR. Diet, gut microbiota and immune responses. Nat Immunol. 2011;12(1):5-9.
37. Darsigny M, et al. Loss of hepatocyte-nuclearfactor-4α affects colonic ion transport and causes chronic inflammation resembling inflammatory bowel disease in mice. PLoS One. 2009;4(10):e7609.
38. Winter SE, et al. Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science. 2013;339(6120):708-711.
39. Alexander EK, et al. Preoperative diagnosis of benign thyroid nodules with indeterminate cytology. N Engl J Med. 2012;367(8):705-715.
40. Trapnell C, Salzberg SL. How to map billions of short reads onto genomes. Nat Biotechnol. 2009;27(5):455-457.
41. Carey R, et al. Activation of an IL-6:STAT3-dependent transcriptome in pediatric-onset inflammatory bowel disease. Inflamm Bowel Dis. 2008;14(4):446-457.
42. Caporaso JG, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J. 2012;6(8):1621-1624.
43. Caporaso JG, et al. QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010;7(5):335-336.
44. McDonald D, et al. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J. 2012;6(3):610-618.
45. Knights D, et al. Supervised classification of microbiota mitigates mislabeling errors. ISME J. 2011;5(4):570-573.
46. Knights D, et al. Bayesian community-wide cultureindependent microbial source tracking. Nat Methods. 2011;8(9):761-763.
47. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2002;30(1):207-210.