Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Location is important: differentiation between ileal and colonic Crohn’s disease

Abstract

Crohn’s disease can affect any part of the gastrointestinal tract; however, current European and national guidelines worldwide do not differentiate between small-intestinal and colonic Crohn’s disease for medical treatment. Data from the past decade provide evidence that ileal Crohn’s disease is distinct from colonic Crohn’s disease in several intestinal layers. Remarkably, colonic Crohn’s disease shows an overlap with regard to disease behaviour with ulcerative colitis, underlining the fact that there is more to inflammatory bowel disease than just Crohn’s disease and ulcerative colitis, and that subtypes, possibly defined by location and shared pathophysiology, are also important. This Review provides a structured overview of the differentiation between ileal and colonic Crohn’s disease using data in the context of epidemiology, genetics, macroscopic differences such as creeping fat and histological findings, as well as differences in regard to the intestinal barrier including gut microbiota, mucus layer, epithelial cells and infiltrating immune cell populations. We also discuss the translation of these basic findings to the clinic, emphasizing the important role of treatment decisions. Thus, this Review provides a conceptual outlook on a new mechanism-driven classification of Crohn’s disease.

Key points

  • Emerging data from fields including clinical behaviour, epidemiology, genetics and the gut microbiota strongly suggest that ileal and colonic Crohn’s disease should be regarded as at least two subtypes of this disease entity.

  • Creeping fat, which represents hyperplasia of the mesenteric fat and wrapping of inflamed intestinal segments, is unique to small-intestinal Crohn’s disease and absent in colonic Crohn’s disease.

  • Predictive models applying a genetic risk score are able to differentiate between ileal and colonic Crohn’s disease.

  • The ileum in Crohn’s disease is characterized by a type 1 or type 17 helper T cell profile, whereas the colon is characterized by a type 1 profile.

  • There is an observable trend that patients with Crohn’s disease with isolated ileal manifestation are less likely to respond to biological therapies than patients with colonic disease.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Site-specific changes of the mesentery in Crohn’s disease.
Fig. 2: Site-specific changes in Crohn’s disease.

Similar content being viewed by others

References

  1. Torres, J. et al. ECCO guidelines on therapeutics in Crohn’s disease: medical treatment. J. Crohns Colitis 14, 4–22 (2020).

    Article  PubMed  Google Scholar 

  2. Satsangi, J., Silverberg, M. S., Vermeire, S. & Colombel, J. F. The Montreal classification of inflammatory bowel disease: controversies, consensus, and implications. Gut 55, 749–753 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Dulai, P. S. et al. Should we divide Crohn’s disease into ileum-dominant and isolated colonic diseases? Clin. Gastroenterol. Hepatol. 17, 2634–2643 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Subramanian, S., Ekbom, A. & Rhodes, J. M. Recent advances in clinical practice: a systematic review of isolated colonic Crohn’s disease: the third IBD? Gut 66, 362–381 (2017).

    Article  CAS  PubMed  Google Scholar 

  5. Chouraki, V. et al. The changing pattern of Crohn’s disease incidence in northern France: a continuing increase in the 10- to 19-year-old age bracket (1988–2007). Aliment. Pharmacol. Ther. 33, 1133–1142 (2011).

    Article  CAS  PubMed  Google Scholar 

  6. Gunesh, S., Thomas, G. A., Williams, G. T., Roberts, A. & Hawthorne, A. B. The incidence of Crohn’s disease in Cardiff over the last 75 years: an update for 1996-2005. Aliment. Pharmacol. Ther. 27, 211–219 (2008).

    Article  CAS  PubMed  Google Scholar 

  7. Kyle, J. Crohn’s disease in the northeastern and northern Isles of Scotland: an epidemiological review. Gastroenterology 103, 392–399 (1992).

    Article  CAS  PubMed  Google Scholar 

  8. Lapidus, A., Bernell, O., Hellers, G., Persson, P. G. & Lofberg, R. Incidence of Crohn’s disease in Stockholm County 1955-1989. Gut 41, 480–486 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Cleynen, I. et al. Inherited determinants of Crohn’s disease and ulcerative colitis phenotypes: a genetic association study. Lancet 387, 156–167 (2016). In this study, by testing genotype–phenotype associations, predictive models applying a genetic risk score were able to distinguish ileal Crohn’s disease and colonic Crohn’s disease.

    Article  PubMed  PubMed Central  Google Scholar 

  10. Cleynen, I. et al. Genetic factors conferring an increased susceptibility to develop Crohn’s disease also influence disease phenotype: results from the IBDchip European Project. Gut 62, 1556–1565 (2013).

    Article  CAS  PubMed  Google Scholar 

  11. Cornish, J. A. et al. The risk of oral contraceptives in the etiology of inflammatory bowel disease: a meta-analysis. Am. J. Gastroenterol. 103, 2394–2400 (2008).

    Article  PubMed  Google Scholar 

  12. Lindberg, E., Jarnerot, G. & Huitfeldt, B. Smoking in Crohn’s disease: effect on localisation and clinical course. Gut 33, 779–782 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Aldhous, M. C. et al. Does cigarette smoking influence the phenotype of Crohn’s disease? Analysis using the Montreal classification. Am. J. Gastroenterol. 102, 577–588 (2007).

    Article  PubMed  Google Scholar 

  14. Breuer-Katschinski, B. D., Hollander, N. & Goebell, H. Effect of cigarette smoking on the course of Crohn’s disease. Eur. J. Gastroenterol. Hepatol. 8, 225–228 (1996).

    Article  CAS  PubMed  Google Scholar 

  15. Cosnes, J. et al. Effects of current and former cigarette smoking on the clinical course of Crohn’s disease. Aliment. Pharmacol. Ther. 13, 1403–1411 (1999).

    Article  CAS  PubMed  Google Scholar 

  16. Hancock, L. et al. Clinical and molecular characteristics of isolated colonic Crohn’s disease. Inflamm. Bowel Dis. 14, 1667–1677 (2008).

    Article  PubMed  Google Scholar 

  17. Holdstock, G., Savage, D., Harman, M. & Wright, R. Should patients with inflammatory bowel disease smoke? Br. Med. J. 288, 362 (1984).

    Article  CAS  Google Scholar 

  18. Nunes, T. et al. Smoking does influence disease behaviour and impacts the need for therapy in Crohn’s disease in the biologic era. Aliment. Pharmacol. Ther. 38, 752–760 (2013).

    Article  CAS  PubMed  Google Scholar 

  19. Russel, M. G. et al. Inflammatory bowel disease: is there any relation between smoking status and disease presentation? European Collaborative IBD Study Group. Inflamm. Bowel Dis. 4, 182–186 (1998).

    Article  CAS  PubMed  Google Scholar 

  20. Somerville, K. W., Logan, R. F., Edmond, M. & Langman, M. J. Smoking and Crohn’s disease. Br. Med. J. 289, 954–956 (1984).

    Article  CAS  Google Scholar 

  21. Tobin, M. V., Logan, R. F., Langman, M. J., McConnell, R. B. & Gilmore, I. T. Cigarette smoking and inflammatory bowel disease. Gastroenterology 93, 316–321 (1987).

    Article  CAS  PubMed  Google Scholar 

  22. Chivese, T., Esterhuizen, T. M., Basson, A. R. & Watermeyer, G. The influence of second-hand cigarette smoke exposure during childhood and active cigarette smoking on Crohn’s disease phenotype defined by the Montreal classification scheme in a Western Cape population, South Africa. PLoS ONE 10, e0139597 (2015).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Prideaux, L., De Cruz, P., Ng, S. C. & Kamm, M. A. Serological antibodies in inflammatory bowel disease: a systematic review. Inflamm. Bowel Dis. 18, 1340–1355 (2012).

    Article  PubMed  Google Scholar 

  24. Linskens, R. K. et al. Evaluation of serological markers to differentiate between ulcerative colitis and Crohn’s disease: pANCA, ASCA and agglutinating antibodies to anaerobic coccoid rods. Eur. J. Gastroenterol. Hepatol. 14, 1013–1018 (2002).

    Article  CAS  PubMed  Google Scholar 

  25. Zholudev, A., Zurakowski, D., Young, W., Leichtner, A. & Bousvaros, A. Serologic testing with ANCA, ASCA, and anti-OmpC in children and young adults with Crohn’s disease and ulcerative colitis: diagnostic value and correlation with disease phenotype. Am. J. Gastroenterol. 99, 2235–2241 (2004).

    Article  PubMed  Google Scholar 

  26. Koutroubakis, I. E. et al. Anti-Saccharomyces cerevisiae mannan antibodies and antineutrophil cytoplasmic autoantibodies in Greek patients with inflammatory bowel disease. Am. J. Gastroenterol. 96, 449–454 (2001).

    CAS  PubMed  Google Scholar 

  27. Quinton, J. F. et al. Anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease: prevalence and diagnostic role. Gut 42, 788–791 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Lakatos, P. L. et al. Pancreatic autoantibodies are associated with reactivity to microbial antibodies, penetrating disease behavior, perianal disease, and extraintestinal manifestations, but not with NOD2/CARD15 or TLR4 genotype in a Hungarian IBD cohort. Inflamm. Bowel Dis. 15, 365–374 (2009).

    Article  PubMed  Google Scholar 

  29. Bacher, P. et al. Human anti-fungal Th17 immunity and pathology rely on cross-reactivity against Candida albicans. Cell 176, 1340–1355.e15 (2019).

    Article  CAS  PubMed  Google Scholar 

  30. Rodríguez-Sillke, Y. et al. Small intestinal inflammation but not colitis drives pro-inflammators nutritional antigen-specific T-cell response. J. Crohns Colitis 14, S154–S155 (2020).

    Article  Google Scholar 

  31. Jostins, L. et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119–124 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Liu, J. Z. et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat. Genet. 47, 979–986 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Hampe, J. et al. Association of NOD2 (CARD 15) genotype with clinical course of Crohn’s disease: a cohort study. Lancet 359, 1661–1665 (2002).

    Article  CAS  PubMed  Google Scholar 

  34. Hugot, J. P. et al. Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease. Nature 411, 599–603 (2001).

    Article  CAS  PubMed  Google Scholar 

  35. Ogura, Y. et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature 411, 603–606 (2001).

    Article  CAS  PubMed  Google Scholar 

  36. Ahmad, T. et al. The molecular classification of the clinical manifestations of Crohn’s disease. Gastroenterology 122, 854–866 (2002).

    Article  CAS  PubMed  Google Scholar 

  37. Cuthbert, A. P. et al. The contribution of NOD2 gene mutations to the risk and site of disease in inflammatory bowel disease. Gastroenterology 122, 867–874 (2002).

    Article  CAS  PubMed  Google Scholar 

  38. de la Concha, E. G. et al. Susceptibility to severe ulcerative colitis is associated with polymorphism in the central MHC gene IKBL. Gastroenterology 119, 1491–1495 (2000).

    Article  PubMed  Google Scholar 

  39. Economou, M., Trikalinos, T. A., Loizou, K. T., Tsianos, E. V. & Ioannidis, J. P. Differential effects of NOD2 variants on Crohn’s disease risk and phenotype in diverse populations: a metaanalysis. Am. J. Gastroenterol. 99, 2393–2404 (2004).

    Article  CAS  PubMed  Google Scholar 

  40. Newman, B. et al. CARD15 and HLA DRB1 alleles influence susceptibility and disease localization in Crohn’s disease. Am. J. Gastroenterol. 99, 306–315 (2004).

    Article  CAS  PubMed  Google Scholar 

  41. Silverberg, M. S. et al. A population- and family-based study of Canadian families reveals association of HLA DRB1*0103 with colonic involvement in inflammatory bowel disease. Inflamm. Bowel Dis. 9, 1–9 (2003).

    Article  PubMed  Google Scholar 

  42. Caruso, R., Warner, N., Inohara, N. & Nunez, G. NOD1 and NOD2: signaling, host defense, and inflammatory disease. Immunity 41, 898–908 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Hampe, J. et al. A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat. Genet. 39, 207–211 (2007).

    Article  CAS  PubMed  Google Scholar 

  44. Murthy, A. et al. A Crohn’s disease variant in Atg16l1 enhances its degradation by caspase 3. Nature 506, 456–462 (2014).

    Article  CAS  PubMed  Google Scholar 

  45. Cadwell, K. et al. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature 456, 259–263 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Kaser, A. et al. XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease. Cell 134, 743–756 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Adolph, T. E. et al. Paneth cells as a site of origin for intestinal inflammation. Nature 503, 272–276 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. VanDussen, K. L. et al. Genetic variants synthesize to produce paneth cell phenotypes that define subtypes of Crohn’s disease. Gastroenterology 146, 200–209 (2014).

    Article  CAS  PubMed  Google Scholar 

  49. Crohn, B. B., Ginzburg, L. & Oppenheimer, G. D. Regional ileitis: a pathological and clinical entity. JAMA 99, 1323–1329 (1932).

    Article  Google Scholar 

  50. Kredel, L. I. et al. T-cell composition in ileal and colonic creeping fat – separating ileal from colonic Crohn’s disease. J. Crohns Colitis 13, 79–91 (2019). This study analysed the mesenteric fat of the ileum and colon in Crohn’s disease, revealing adipocyte hyperplasia, fibrosis and a strong immune cell infiltrate as unique to ileal Crohn’s disease. In addition, the ileum is characterized by a TH1:TH17 profile, whereas the colon shows a TH1 profile in the lamina propria.

    Article  PubMed  Google Scholar 

  51. Mao, R. et al. The mesenteric fat and intestinal muscle interface: creeping fat influencing stricture formation in Crohn’s disease. Inflamm. Bowel Dis. 25, 421–426 (2019).

    Article  PubMed  Google Scholar 

  52. Batra, A. et al. Mesenteric fat – control site for bacterial translocation in colitis? Mucosal Immunol. 5, 580–591 (2012).

    Article  CAS  PubMed  Google Scholar 

  53. Peyrin-Biroulet, L. et al. Mesenteric fat as a source of C reactive protein and as a target for bacterial translocation in Crohn’s disease. Gut 61, 78–85 (2012).

    Article  CAS  PubMed  Google Scholar 

  54. Siegmund, B. Mesenteric fat in Crohn’s disease: the hot spot of inflammation? Gut 61, 3–5 (2012).

    Article  CAS  PubMed  Google Scholar 

  55. Zulian, A. et al. Visceral adipocytes: old actors in obesity and new protagonists in Crohn’s disease? Gut 61, 86–94 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Kredel, L. I. et al. Adipokines from local fat cells shape the macrophage compartment of the creeping fat in Crohn’s disease. Gut 62, 852–862 (2013).

    Article  CAS  PubMed  Google Scholar 

  57. Ha, C. W. Y. et al. Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans. Cell 183, 666–683.e17 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Rahier, J. F. et al. Decreased lymphatic vessel density is associated with postoperative endoscopic recurrence in Crohn’s disease. Inflamm. Bowel Dis. 19, 2084–2090 (2013).

    Article  PubMed  Google Scholar 

  59. Randolph, G. J. et al. Lymphoid aggregates remodel lymphatic collecting vessels that serve mesenteric lymph nodes in Crohn disease. Am. J. Pathol. 186, 3066–3073 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Randolph, G. J. & Miller, N. E. Lymphatic transport of high-density lipoproteins and chylomicrons. J. Clin. Invest. 124, 929–935 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Van Kruiningen, H. J. & Colombel, J. F. The forgotten role of lymphangitis in Crohn’s disease. Gut 57, 1–4 (2008).

    Article  PubMed  Google Scholar 

  62. Thaunat, O., Kerjaschki, D. & Nicoletti, A. Is defective lymphatic drainage a trigger for lymphoid neogenesis? Trends Immunol. 27, 441–445 (2006).

    Article  CAS  PubMed  Google Scholar 

  63. Wehkamp, J. & Stange, E. F. An update review on the paneth cell as key to ileal Crohn’s disease. Front. Immunol. 11, 646 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kobayashi, N., Takahashi, D., Takano, S., Kimura, S. & Hase, K. The roles of Peyer’s patches and microfold cells in the gut immune system: relevance to autoimmune diseases. Front. Immunol. 10, 2345 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Hold, G. L. et al. Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years? World J. Gastroenterol. 20, 1192–1210 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  66. Kostic, A. D., Xavier, R. J. & Gevers, D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146, 1489–1499 (2014).

    Article  CAS  PubMed  Google Scholar 

  67. Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 15, 382–392 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Darfeuille-Michaud, A. et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology 127, 412–421 (2004). In this study, adherent-invasive Escherichia coli previously identified in the intestinal mucosa of patients with Crohn’s disease was detected in ileal specimens of patients with Crohn’s disease.

    Article  PubMed  Google Scholar 

  69. Rhodes, J. M. The role of Escherichia coli in inflammatory bowel disease. Gut 56, 610–612 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Rolhion, N. & Darfeuille-Michaud, A. Adherent-invasive Escherichia coli in inflammatory bowel disease. Inflamm. Bowel Dis. 13, 1277–1283 (2007).

    Article  PubMed  Google Scholar 

  71. Bringer, M. A., Glasser, A. L., Tung, C. H., Meresse, S. & Darfeuille-Michaud, A. The Crohn’s disease-associated adherent-invasive Escherichia coli strain LF82 replicates in mature phagolysosomes within J774 macrophages. Cell Microbiol. 8, 471–484 (2006).

    Article  CAS  PubMed  Google Scholar 

  72. De la Fuente, M. et al. Escherichia coli isolates from inflammatory bowel diseases patients survive in macrophages and activate NLRP3 inflammasome. Int. J. Med. Microbiol. 304, 384–392 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  73. Meconi, S. et al. Adherent-invasive Escherichia coli isolated from Crohn’s disease patients induce granulomas in vitro. Cell Microbiol. 9, 1252–1261 (2007).

    Article  CAS  PubMed  Google Scholar 

  74. Barnich, N. et al. CEACAM6 acts as a receptor for adherent-invasive E. coli, supporting ileal mucosa colonization in Crohn disease. J. Clin. Invest. 117, 1566–1574 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Baumgart, M. et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J. 1, 403–418 (2007).

    Article  CAS  PubMed  Google Scholar 

  76. Lopez-Siles, M. et al. Mucosa-associated Faecalibacterium prausnitzii and Escherichia coli co-abundance can distinguish irritable bowel syndrome and inflammatory bowel disease phenotypes. Int. J. Med. Microbiol. 304, 464–475 (2014).

    Article  PubMed  Google Scholar 

  77. Willing, B. et al. Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn’s disease. Inflamm. Bowel Dis. 15, 653–660 (2009).

    Article  PubMed  Google Scholar 

  78. Sokol, H. et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc. Natl Acad. Sci. USA 105, 16731–16736 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Schulthess, J. et al. The short chain fatty acid butyrate imprints an antimicrobial program in macrophages. Immunity 50, 432–445.e7 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Dicksved, J. et al. Molecular analysis of the gut microbiota of identical twins with Crohn’s disease. ISME J. 2, 716–727 (2008).

    Article  CAS  PubMed  Google Scholar 

  81. Tyler, A. D. et al. Microbiome heterogeneity characterizing intestinal tissue and inflammatory bowel disease phenotype. Inflamm. Bowel Dis. 22, 807–816 (2016).

    Article  PubMed  Google Scholar 

  82. Willing, B. P. et al. A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854.e1 (2010).

    Article  PubMed  Google Scholar 

  83. Naftali, T. et al. Distinct microbiotas are associated with ileum-restricted and colon-involving Crohn’s disease. Inflamm. Bowel Dis. 22, 293–302 (2016).

    Article  PubMed  Google Scholar 

  84. Li, E. et al. Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. PLoS ONE 7, e26284 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Rajca, S. et al. Alterations in the intestinal microbiome (dysbiosis) as a predictor of relapse after infliximab withdrawal in Crohn’s disease. Inflamm. Bowel Dis. 20, 978–986 (2014).

    PubMed  Google Scholar 

  86. Kugathasan, S. et al. Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicentre inception cohort study. Lancet 389, 1710–1718 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  87. Rehman, A. et al. Nod2 is essential for temporal development of intestinal microbial communities. Gut 60, 1354–1362 (2011).

    Article  CAS  PubMed  Google Scholar 

  88. Lavoie, S. et al. The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response. eLife 8, e39982 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  89. Imhann, F. et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 67, 108–119 (2018).

    Article  CAS  PubMed  Google Scholar 

  90. Haberman, Y. et al. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J. Clin. Invest. 124, 3617–3633 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Ouellette, A. J. & Bevins, C. L. Paneth cell defensins and innate immunity of the small bowel. Inflamm. Bowel Dis. 7, 43–50 (2001).

    Article  CAS  PubMed  Google Scholar 

  92. Tunzi, C. R. et al. Beta-defensin expression in human mammary gland epithelia. Pediatr. Res. 48, 30–35 (2000).

    Article  CAS  PubMed  Google Scholar 

  93. Johansson, M. E. & Hansson, G. C. Immunological aspects of intestinal mucus and mucins. Nat. Rev. Immunol. 16, 639–649 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Pelaseyed, T. & Hansson, G. C. Membrane mucins of the intestine at a glance. J. Cell. Sci. 133, jcs240929 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Allen, A., Hutton, D. A. & Pearson, J. P. The MUC2 gene product: a human intestinal mucin. Int. J. Biochem. Cell Biol. 30, 797–801 (1998).

    Article  CAS  PubMed  Google Scholar 

  96. Axelsson, M. A., Asker, N. & Hansson, G. C. O-Glycosylated MUC2 monomer and dimer from LS 174T cells are water-soluble, whereas larger MUC2 species formed early during biosynthesis are insoluble and contain nonreducible intermolecular bonds. J. Biol. Chem. 273, 18864–18870 (1998).

    Article  CAS  PubMed  Google Scholar 

  97. Pullan, R. D. et al. Thickness of adherent mucus gel on colonic mucosa in humans and its relevance to colitis. Gut 35, 353–359 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Buisine, M. P. et al. Abnormalities in mucin gene expression in Crohn’s disease. Inflamm. Bowel Dis. 5, 24–32 (1999).

    Article  CAS  PubMed  Google Scholar 

  99. Antoni, L. et al. Human colonic mucus is a reservoir for antimicrobial peptides. J. Crohns Colitis 7, e652–664 (2013).

    Article  PubMed  Google Scholar 

  100. Bevins, C. L. & Salzman, N. H. Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis. Nat. Rev. Microbiol. 9, 356–368 (2011).

    Article  CAS  PubMed  Google Scholar 

  101. Ostaff, M. J., Stange, E. F. & Wehkamp, J. Antimicrobial peptides and gut microbiota in homeostasis and pathology. EMBO Mol. Med. 5, 1465–1483 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  102. Schauber, J. et al. Heterogeneous expression of human cathelicidin hCAP18/LL-37 in inflammatory bowel diseases. Eur. J. Gastroenterol. Hepatol. 18, 615–621 (2006).

    Article  CAS  PubMed  Google Scholar 

  103. Chu, H. et al. Human α-defensin 6 promotes mucosal innate immunity through self-assembled peptide nanonets. Science 337, 477–481 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Raschig, J. et al. Ubiquitously expressed human beta defensin 1 (hBD1) forms bacteria-entrapping nets in a redox dependent mode of action. PLoS Pathog. 13, e1006261 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  105. Wehkamp, J. et al. NOD2 (CARD15) mutations in Crohn’s disease are associated with diminished mucosal α-defensin expression. Gut 53, 1658–1664 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Wehkamp, J. et al. Reduced Paneth cell α-defensins in ileal Crohn’s disease. Proc. Natl Acad. Sci. USA 102, 18129–18134 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Simms, L. A. et al. Reduced α-defensin expression is associated with inflammation and not NOD2 mutation status in ileal Crohn’s disease. Gut 57, 903–910 (2008).

    Article  CAS  PubMed  Google Scholar 

  108. Liu, T. C. et al. LRRK2 but not ATG16L1 is associated with Paneth cell defect in Japanese Crohn’s disease patients. JCI Insight 2, e91917 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  109. Tanabe, H. et al. Denatured human α-defensin attenuates the bactericidal activity and the stability against enzymatic digestion. Biochem. Biophys. Res. Commun. 358, 349–355 (2007).

    Article  CAS  PubMed  Google Scholar 

  110. Liu, T. C. et al. Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn’s disease. J. Clin. Invest. 128, 5110–5122 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  111. Stappenbeck, T. S. & McGovern, D. P. B. Paneth cell alterations in the development and phenotype of Crohn’s disease. Gastroenterology 152, 322–326 (2017).

    Article  CAS  PubMed  Google Scholar 

  112. Tschurtschenthaler, M. et al. Defective ATG16L1-mediated removal of IRE1α drives Crohn’s disease-like ileitis. J. Exp. Med. 214, 401–422 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Courth, L. F. et al. Crohn’s disease-derived monocytes fail to induce Paneth cell defensins. Proc. Natl Acad. Sci. USA 112, 14000–14005 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Peyrin-Biroulet, L. et al. Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon. Proc. Natl Acad. Sci. USA 107, 8772–8777 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Wehkamp, J. et al. Inducible and constitutive β-defensins are differentially expressed in Crohn’s disease and ulcerative colitis. Inflamm. Bowel Dis. 9, 215–223 (2003).

    Article  PubMed  Google Scholar 

  116. Lala, S. et al. Crohn’s disease and the NOD2 gene: a role for paneth cells. Gastroenterology 125, 47–57 (2003).

    Article  CAS  PubMed  Google Scholar 

  117. Ogura, Y. et al. Expression of NOD2 in Paneth cells: a possible link to Crohn’s ileitis. Gut 52, 1591–1597 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Wang, Y. et al. Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine. J. Exp. Med. 217, e20191130 (2020).

    Article  PubMed  CAS  Google Scholar 

  119. Gunther, C. et al. Interferon lambda promotes paneth cell death via STAT1 signaling in mice and is increased in inflamed ileal tissues of patients with Crohn’s disease. Gastroenterology 157, 1310–1322.e13 (2019). This study shows an increase in IFNλ in serum and inflamed ileum of patients with Crohn’s disease that is associated with a loss of Paneth cells. In mice, secreted IFNλ resulted in a loss of Paneth cells via STAT1 and MLKL in a caspase 8-dependent manner.

    Article  PubMed  CAS  Google Scholar 

  120. Howell, K. J. et al. DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome. Gastroenterology 154, 585–598 (2018). IECs were isolated from mucosal biopsies (ileum, ascending colon, sigmoid) of children with newly diagnosed IBD; changes in DNA methylation and transcription pattern were exclusively identified in IECs from the terminal ileum.

    Article  CAS  PubMed  Google Scholar 

  121. Pierre, N. et al. Proteomics highlights common and distinct pathophysiological processes associated with ileal and colonic ulcers in Crohn’s disease. J. Crohns Colitis 14, 205–215 (2020).

    Article  PubMed  Google Scholar 

  122. Duvoisin, G. et al. Novel biomarkers and the future potential of biomarkers in inflammatory bowel disease. Mediators Inflamm. 2017, 1936315 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  123. Kofla-Dlubacz, A., Matusiewicz, M., Krzystek-Korpacka, M. & Iwanczak, B. Correlation of MMP-3 and MMP-9 with Crohn’s disease activity in children. Dig. Dis. Sci. 57, 706–712 (2012).

    Article  CAS  PubMed  Google Scholar 

  124. Verdier, J., Begue, B., Cerf-Bensussan, N. & Ruemmele, F. M. Compartmentalized expression of Th1 and Th17 cytokines in pediatric inflammatory bowel diseases. Inflamm. Bowel Dis. 18, 1260–1266 (2012).

    Article  CAS  PubMed  Google Scholar 

  125. Becker, C. et al. Constitutive p40 promoter activation and IL-23 production in the terminal ileum mediated by dendritic cells. J. Clin. Invest. 112, 693–706 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Ivanov, I. I. et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139, 485–498 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Monteleone, G. et al. Control of matrix metalloproteinase production in human intestinal fibroblasts by interleukin 21. Gut 55, 1774–1780 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Monteleone, G. et al. Interleukin-21 enhances T-helper cell type I signaling and interferon-γ production in Crohn’s disease. Gastroenterology 128, 687–694 (2005).

    Article  CAS  PubMed  Google Scholar 

  129. Neurath, M. F. Cytokines in inflammatory bowel disease. Nat. Rev. Immunol. 14, 329–342 (2014).

    Article  CAS  PubMed  Google Scholar 

  130. Pickert, G. et al. STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing. J. Exp. Med. 206, 1465–1472 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  131. Leung, J. M. et al. IL-22-producing CD4+ cells are depleted in actively inflamed colitis tissue. Mucosal Immunol. 7, 124–133 (2014).

    Article  CAS  PubMed  Google Scholar 

  132. Ouyang, W., Kolls, J. K. & Zheng, Y. The biological functions of T helper 17 cell effector cytokines in inflammation. Immunity 28, 454–467 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Sonnenberg, G. F., Fouser, L. A. & Artis, D. Border patrol: regulation of immunity, inflammation and tissue homeostasis at barrier surfaces by IL-22. Nat. Immunol. 12, 383–390 (2011).

    Article  CAS  PubMed  Google Scholar 

  134. Brand, S. et al. IL-22 is increased in active Crohn’s disease and promotes proinflammatory gene expression and intestinal epithelial cell migration. Am. J. Physiol. Gastrointest. Liver Physiol. 290, G827–G838 (2006).

    Article  CAS  PubMed  Google Scholar 

  135. Allez, M. et al. T cell clonal expansions in ileal Crohn’s disease are associated with smoking behaviour and postoperative recurrence. Gut 68, 1961–1970 (2019). A T cell receptor (TCR) analysis was performed of the ileum of patients with Crohn’s disease before and after ileocaecal resection, identifying a subgroup with a persistence of similar TCR repertoire, which was associated with smoking and recurrent disease.

    Article  CAS  PubMed  Google Scholar 

  136. Cosnes, J. et al. Long-term evolution of disease behavior of Crohn’s disease. Inflamm. Bowel Dis. 8, 244–250 (2002).

    Article  PubMed  Google Scholar 

  137. Feagan, B. G. et al. Ustekinumab as induction and maintenance therapy for Crohn’s disease. N. Engl. J. Med. 375, 1946–1960 (2016).

    Article  CAS  PubMed  Google Scholar 

  138. Sandborn, W. J. et al. Vedolizumab as induction and maintenance therapy for Crohn’s disease. N. Engl. J. Med. 369, 711–721 (2013).

    Article  CAS  PubMed  Google Scholar 

  139. Sandborn, W. J. et al. Adalimumab for maintenance treatment of Crohn’s disease: results of the CLASSIC II trial. Gut 56, 1232–1239 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Schmitt, H. et al. Expansion of IL-23 receptor bearing TNFR2+ T cells is associated with molecular resistance to anti-TNF therapy in Crohn’s disease. Gut 68, 814–828 (2019).

    Article  CAS  PubMed  Google Scholar 

  141. Visekruna, A. et al. Intestinal development and homeostasis require activation and apoptosis of diet-reactive T cells. J. Clin. Invest. 129, 1972–1983 (2019). In this study, a decreased frequency of apoptotic CD4+ T cells was observed in Peyer’s patches of patients with Crohn’s disease, revealing a potential disease mechanism unique to the ileum.

    Article  PubMed  PubMed Central  Google Scholar 

  142. Habtezion, A., Nguyen, L. P., Hadeiba, H. & Butcher, E. C. Leukocyte trafficking to the small intestine and colon. Gastroenterology 150, 340–354 (2016).

    Article  CAS  PubMed  Google Scholar 

  143. Hynes, R. O. Integrins: bidirectional, allosteric signaling machines. Cell 110, 673–687 (2002).

    Article  CAS  PubMed  Google Scholar 

  144. Shattil, S. J., Kim, C. & Ginsberg, M. H. The final steps of integrin activation: the end game. Nat. Rev. Mol. Cell Biol. 11, 288–300 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Zundler, S., Becker, E., Schulze, L. L. & Neurath, M. F. Immune cell trafficking and retention in inflammatory bowel disease: mechanistic insights and therapeutic advances. Gut 68, 1688–1700 (2019).

    Article  CAS  PubMed  Google Scholar 

  146. Berlin, C. et al. α4β7 integrin mediates lymphocyte binding to the mucosal vascular addressin MAdCAM-1. Cell 74, 185–195 (1993).

    Article  CAS  PubMed  Google Scholar 

  147. Elices, M. J. et al. VCAM-1 on activated endothelium interacts with the leukocyte integrin VLA-4 at a site distinct from the VLA-4/fibronectin binding site. Cell 60, 577–584 (1990).

    Article  CAS  PubMed  Google Scholar 

  148. Taniguchi, T. et al. Effects of the anti-ICAM-1 monoclonal antibody on dextran sodium sulphate-induced colitis in rats. J. Gastroenterol. Hepatol. 13, 945–949 (1998).

    Article  CAS  PubMed  Google Scholar 

  149. Salmi, M. et al. Immune cell trafficking in uterus and early life is dominated by the mucosal addressin MAdCAM-1 in humans. Gastroenterology 121, 853–864 (2001).

    Article  CAS  PubMed  Google Scholar 

  150. Ley, K., Laudanna, C., Cybulsky, M. I. & Nourshargh, S. Getting to the site of inflammation: the leukocyte adhesion cascade updated. Nat. Rev. Immunol. 7, 678–689 (2007).

    Article  CAS  PubMed  Google Scholar 

  151. Kinashi, T. Intracellular signalling controlling integrin activation in lymphocytes. Nat. Rev. Immunol. 5, 546–559 (2005).

    Article  CAS  PubMed  Google Scholar 

  152. Denucci, C. C., Mitchell, J. S. & Shimizu, Y. Integrin function in T-cell homing to lymphoid and nonlymphoid sites: getting there and staying there. Crit. Rev. Immunol. 29, 87–109 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  153. Svensson, M. et al. CCL25 mediates the localization of recently activated CD8αβ+ lymphocytes to the small-intestinal mucosa. J. Clin. Invest. 110, 1113–1121 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  154. Fischer, A. et al. Differential effects of α4β7 and GPR15 on homing of effector and regulatory T cells from patients with UC to the inflamed. gut in vivo. Gut 65, 1642–1664 (2016).

    CAS  PubMed  Google Scholar 

  155. Kim, S. V. et al. GPR15-mediated homing controls immune homeostasis in the large intestine mucosa. Science 340, 1456–1459 (2013). This study identified GPR15, an orphan heterotrimeric guanine nucleotide-binding protein (G-protein)-coupled receptor as the homing receptor in particular for T cells to the lamina propria of the colon.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Nguyen, L. P. et al. Role and species-specific expression of colon T cell homing receptor GPR15 in colitis. Nat. Immunol. 16, 207–213 (2015).

    Article  CAS  PubMed  Google Scholar 

  157. Ocon, B. et al. A mucosal and cutaneous chemokine ligand for the lymphocyte chemoattractant receptor GPR15. Front. Immunol. 8, 1111 (2017).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  158. Suply, T. et al. A natural ligand for the orphan receptor GPR15 modulates lymphocyte recruitment to epithelia. Sci. Signal 10, eaal0180 (2017).

    Article  PubMed  Google Scholar 

  159. Zundler, S. et al. Blockade of αEβ7 integrin suppresses accumulation of CD8(+) and Th9 lymphocytes from patients with IBD in the inflamed gut in vivo. Gut 66, 1936–1948 (2017).

    Article  CAS  PubMed  Google Scholar 

  160. Kotze, P. G. et al. Real-world clinical, endoscopic and radiographic efficacy of vedolizumab for the treatment of inflammatory bowel disease. Aliment. Pharmacol. Ther. 48, 626–637 (2018).

    Article  CAS  PubMed  Google Scholar 

  161. Louis, E. et al. Early development of stricturing or penetrating pattern in Crohn’s disease is influenced by disease location, number of flares, and smoking but not by NOD2/CARD15 genotype. Gut 52, 552–557 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Thia, K. T., Sandborn, W. J., Harmsen, W. S., Zinsmeister, A. R. & Loftus, E. V. Jr. Risk factors associated with progression to intestinal complications of Crohn’s disease in a population-based cohort. Gastroenterology 139, 1147–1155 (2010).

    Article  PubMed  Google Scholar 

  163. Guizzetti, L. et al. Development of clinical prediction models for surgery and complications in Crohn’s disease. J. Crohns Colitis 12, 167–177 (2018).

    Article  PubMed  Google Scholar 

  164. Ott, C. & Scholmerich, J. Extraintestinal manifestations and complications in IBD. Nat. Rev. Gastroenterol. Hepatol. 10, 585–595 (2013).

    Article  CAS  PubMed  Google Scholar 

  165. Vavricka, S. R. et al. Extraintestinal manifestations of inflammatory bowel disease. Inflamm. Bowel Dis. 21, 1982–1992 (2015).

    Article  PubMed  Google Scholar 

  166. Ardizzone, S., Puttini, P. S., Cassinotti, A. & Porro, G. B. Extraintestinal manifestations of inflammatory bowel disease. Dig. Liver Dis. 40 (Suppl. 2), S253–S259 (2008).

    Article  PubMed  Google Scholar 

  167. Farhi, D. et al. Significance of erythema nodosum and pyoderma gangrenosum in inflammatory bowel diseases: a cohort study of 2402 patients. Medicine 87, 281–293 (2008).

    Article  PubMed  Google Scholar 

  168. Bhagat, S. & Das, K. M. A shared and unique peptide in the human colon, eye, and joint detected by a monoclonal antibody. Gastroenterology 107, 103–108 (1994).

    Article  CAS  PubMed  Google Scholar 

  169. Boonstra, K. et al. Primary sclerosing cholangitis is associated with a distinct phenotype of inflammatory bowel disease. Inflamm. Bowel Dis. 18, 2270–2276 (2012).

    Article  PubMed  Google Scholar 

  170. Iny, O. et al. Crohn’s disease behavior and location is altered when associated with primary sclerosing cholangitis. Isr. Med. Assoc. J. 20, 25–29 (2018).

    PubMed  Google Scholar 

  171. Hanauer, S. B. et al. Maintenance infliximab for Crohn’s disease: the ACCENT I randomised trial. Lancet 359, 1541–1549 (2002).

    Article  CAS  PubMed  Google Scholar 

  172. Targan, S. R. et al. A short-term study of chimeric monoclonal antibody cA2 to tumor necrosis factor α for Crohn’s disease. N. Engl. J. Med. 337, 1029–1036 (1997).

    Article  CAS  PubMed  Google Scholar 

  173. Hanauer, S. B. et al. Human anti-tumor necrosis factor monoclonal antibody (adalimumab) in Crohn’s disease: the CLASSIC-I trial. Gastroenterology 130, 323–333 (2006).

    Article  CAS  PubMed  Google Scholar 

  174. Sandborn, W. J. et al. Certolizumab pegol for active Crohn’s disease: a placebo-controlled, randomized trial. Clin. Gastroenterol. Hepatol. 9, 670–678.e3 (2011).

    Article  CAS  PubMed  Google Scholar 

  175. Arnott, I. D., McNeill, G. & Satsangi, J. An analysis of factors influencing short-term and sustained response to infliximab treatment for Crohn’s disease. Aliment. Pharmacol. Ther. 17, 1451–1457 (2003).

    Article  CAS  PubMed  Google Scholar 

  176. Laharie, D. et al. Predictors of response to infliximab in luminal Crohn’s disease. Gastroenterol. Clin. Biol. 29, 145–149 (2005).

    Article  CAS  PubMed  Google Scholar 

  177. Vermeire, S. et al. Demographic and clinical parameters influencing the short-term outcome of anti-tumor necrosis factor (infliximab) treatment in Crohn’s disease. Am. J. Gastroenterol. 97, 2357–2363 (2002).

    Article  CAS  PubMed  Google Scholar 

  178. Reinisch, W. et al. Characterisation of mucosal healing with adalimumab treatment in patients with moderately to severely active Crohn’s disease: results from the EXTEND trial. J. Crohns Colitis 11, 425–434 (2017).

    PubMed  Google Scholar 

  179. Takenaka, K. et al. Small bowel healing detected by endoscopy in patients with Crohn’s disease after treatment with antibodies against tumor necrosis factor. Clin. Gastroenterol. Hepatol. 18, 1545–1552 (2020).

    Article  CAS  PubMed  Google Scholar 

  180. Danese, S. et al. Endoscopic, radiologic, and histologic healing with vedolizumab in patients with active Crohn’s disease. Gastroenterology 157, 1007–1018 e1007 (2019). This prospective, open-label, phase 3b study evaluated endoscopic, radiological and histological healing in the ileum and colon upon vedolizumab treatment in patients with Crohn’s disease.

    Article  CAS  PubMed  Google Scholar 

  181. Feagan, B. G. et al. Induction therapy with the selective interleukin-23 inhibitor risankizumab in patients with moderate-to-severe Crohn’s disease: a randomised, double-blind, placebo-controlled phase 2 study. Lancet 389, 1699–1709 (2017).

    Article  CAS  PubMed  Google Scholar 

  182. Visvanathan, S. et al. Selective IL-23 inhibition by risankizumab modulates the molecular profile in the colon and ileum of patients with active Crohn’s disease: results from a randomised phase II biopsy sub-study. J. Crohns Colitis 12, 1170–1179 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  183. Atreya, R. & Neurath, M. F. Mechanisms of molecular resistance and predictors of response to biological therapy in inflammatory bowel disease. Lancet Gastroenterol. Hepatol. 3, 790–802 (2018).

    Article  PubMed  Google Scholar 

  184. Atreya, R., Neurath, M. F. & Siegmund, B. Personalizing treatment in IBD: hype or reality in 2020? Can we predict response to anti-TNF? Front. Med. 7, 517 (2020).

    Article  Google Scholar 

  185. Gisbert, J. P. & Chaparro, M. Predictors of primary response to biologic treatment [anti-TNF, vedolizumab, and ustekinumab] in patients with inflammatory bowel disease: from basic science to clinical practice. J. Crohns Colitis 14, 694–709 (2020).

    Article  PubMed  Google Scholar 

  186. Arijs, I. et al. Predictive value of epithelial gene expression profiles for response to infliximab in Crohn’s disease. Inflamm. Bowel Dis. 16, 2090–2098 (2010).

    Article  PubMed  Google Scholar 

  187. Arijs, I. et al. Mucosal gene signatures to predict response to infliximab in patients with ulcerative colitis. Gut 58, 1612–1619 (2009).

    Article  CAS  PubMed  Google Scholar 

  188. Brubaker, D. K. et al. An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. Sci. Signal 13, eaay3258 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Belarif, L. et al. IL-7 receptor influences anti-TNF responsiveness and T cell gut homing in inflammatory bowel disease. J. Clin. Invest. 129, 1910–1925 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  190. Zundler, S. et al. The α4β1 homing pathway is essential for ileal homing of Crohn’s disease effector T cells in vivo. Inflamm. Bowel Dis. 23, 379–391 (2017). This study indicates that homing of effector T cells to the ileum through the α4β1–VCAM1 axis presents an essential and non-redundant pathway for Crohn’s disease in vivo.

    Article  PubMed  Google Scholar 

  191. Tew, G. W. et al. Association between response to etrolizumab and expression of integrin αE and granzyme A in colon biopsies of patients with ulcerative colitis. Gastroenterology 150, 477–487.e9 (2016).

    Article  PubMed  Google Scholar 

  192. Ichikawa, R. et al. AlphaE integrin expression is increased in the ileum relative to the colon and unaffected by inflammation. J. Crohns Colitis 12, 1191–1199 (2018). This study demonstrates markedly higher numbers of ileal compared to colonic αE+ cells, which might serve as a predictive biomarker for effectiveness of etrolizumab therapy.

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

R.A. and B.S. are supported by the research initiatives CRC-TRR 241, SI 749/10-1 and SPP1656 (B.S.), CRC1181 (R.A.), and CRC1340 and CRC1449 (B.S.) of the German Research Foundation (DFG). The DFG funds the Heisenberg Professorship of R.A.

Author information

Authors and Affiliations

Authors

Contributions

The authors contributed equally to all aspects of this article.

Corresponding author

Correspondence to Britta Siegmund.

Ethics declarations

Competing interests

B.S. has served as a consultant for Abbvie, Boehringer, Celgene, Falk, Janssen, Lilly, Pfizer, Prometheus, Takeda and has received speaker’s fees from Abbvie, CED Service GmbH, Falk, Ferring, Janssen, Novartis and Takeda as a representative of Charité – Universitätsmedizin Berlin. R.A. has served as a speaker, or consultant, or received research grants from AbbVie, Biogen, Boehringer Ingelheim, Celgene, Dr. Falk Pharma, Ferring, InDex Pharmaceuticals, Janssen-Cilag, MSD Sharp & Dome, Pfizer, Roche Pharma, Samsung Bioepis and Takeda.

Additional information

Peer review information

Nature Reviews Gastroenterology & Hepatology thanks the anonymous reviewers for their contribution to the peer review of this work.

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Atreya, R., Siegmund, B. Location is important: differentiation between ileal and colonic Crohn’s disease. Nat Rev Gastroenterol Hepatol 18, 544–558 (2021). https://doi.org/10.1038/s41575-021-00424-6

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41575-021-00424-6

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing