The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature
Open accessAbstract
Interactions between the host and gut microbial community likely contribute to Crohn disease (CD) pathogenesis; however, direct evidence for these interactions at the onset of disease is lacking. Here, we characterized the global pattern of ileal gene expression and the ileal microbial community in 359 treatment-naive pediatric patients with CD, patients with ulcerative colitis (UC), and control individuals. We identified core gene expression profiles and microbial communities in the affected CD ilea that are preserved in the unaffected ilea of patients with colon-only CD but not present in those with UC or control individuals; therefore, this signature is specific to CD and independent of clinical inflammation. An abnormal increase of antimicrobial dual oxidase (DUOX2) expression was detected in association with an expansion of Proteobacteria in both UC and CD, while expression of lipoprotein APOA1 gene was downregulated and associated with CD-specific alterations in Firmicutes. The increased DUOX2 and decreased APOA1 gene expression signature favored oxidative stress and Th1 polarization and was maximally altered in patients with more severe mucosal injury. A regression model that included APOA1 gene expression and microbial abundance more accurately predicted month 6 steroid-free remission than a model using clinical factors alone. These CD-specific host and microbe profiles identify the ileum as the primary inductive site for all forms of CD and may direct prognostic and therapeutic approaches.
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Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
Edgar, R. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.1.207 · Cited by 13,288
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
The International IBD Genetics Consortium (IIBDGC), Jostins, L., Ripke, S., Weersma, R. K., Duerr, R. H., McGovern, D. P., Hui, K. Y., Lee, J. C., Philip Schumm, L., Sharma, Y., et al. (2012) · Nature · doi:10.1038/nature11582 · Cited by 4,722
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Markle, J. G. M., Frank, D. N., Mortin-Toth, S., Robertson, C. E., Feazel, L. M., Rolle-Kampczyk, U., von Bergen, M., McCoy, K. D., Macpherson, A. J., & Danska, J. S. (2013) · Science · doi:10.1126/science.1233521 · Cited by 2,025
Diet, gut microbiota and immune responses
Maslowski, K. M., & Mackay, C. R. (2011) · Nature Immunology · doi:10.1038/ni0111-5 · Cited by 1,261
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Metadata
- Authors
- Haberman, Y., Tickle, T. L., Dexheimer, P. J., Kim, M.-O., Tang, D., Karns, R., Baldassano, R. N., Noe, J. D., Rosh, J., Markowitz, J., Heyman, M. B., Griffiths, A. M., Crandall, W. V., Mack, D. R., Baker, S. S., Huttenhower, C., Keljo, D. J., Hyams, J. S., Kugathasan, S., Walters, T. D., Aronow, B., Xavier, R. J., Gevers, D., & Denson, L. A.
- Venue
- Journal of Clinical Investigation
- Published
- 2014-07-08
- Volume
- 124
- Issue
- 8
- Pages
- 3617-3633
- ISSN
- 0021-9738 (ISSN-L)
- OpenAlex
- W2024192805
- Cited by
- 519
- References
- 5
- FWCI
- 24.77
- Type
- journal article
- Language
- en
- Open access
- green
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- Haberman, Y., Tickle, T. L., Dexheimer, P. J., Kim, M.-O., Tang, D., Karns, R., Baldassano, R. N., Noe, J. D., Rosh, J., Markowitz, J., Heyman, M. B., Griffiths, A. M., Crandall, W. V., Mack, D. R., Baker, S. S., Huttenhower, C., Keljo, D. J., Hyams, J. S., Kugathasan, S., . . . Denson, L. A. (2014). Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. Journal of Clinical Investigation. https://doi.org/10.1172/jci75436
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