Abstract
Genetic and genomic studies have provided key insights into the biology responsible for inflammatory bowel disease (IBD) susceptibility, but the biology of disease outcome remains relatively unexplored. Like most autoimmune and inflammatory diseases, IBD has a highly variable course, with the potential to have a devastating impact on patients’ lives. As a result, being able to reliably predict prognosis in IBD remains a major ambition of clinicians and patients alike.
In most fields of medicine, the goal of delivering personalised medicine has become increasingly important. For this to become a reality, however, it will first be necessary to better understand what determines disease prognosis. A major step towards this goal may lie in the emerging evidence that the biology that drives prognosis in IBD is distinct from the biology that underpins disease susceptibility. Indeed, it is hoped that by better understanding the mechanisms that determine disease progression, it might ultimately be possible to develop clinically useful biomarkers, which could be translated back to the clinic to improve patient care.
In this chapter we will review the efforts that have already been made using genetic and genomic tools to develop prognostic and predictive biomarkers in IBD. We will discuss the important requirements for such biomarkers, both in terms of their development and validation, and the evidence that will be required in order for them to be translated back into clinical practice.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Cameron D, Piccart-Gebhart MJ, Gelber RD, et al. 11 years’ follow-up of trastuzumab after adjuvant chemotherapy in HER2-positive early breast cancer: final analysis of the HERceptin Adjuvant (HERA) trial. Lancet. 2017;389:1195–205.
Cardoso F, van’t Veer LJ, Bogaerts J, et al. 70-gene signature as an aid to treatment decisions in early-stage breast cancer. N Engl J Med. 2016;375:717–29.
Sparano JA, Gray RJ, Makower DF, et al. Prospective validation of a 21-gene expression assay in breast cancer. N Engl J Med. 2015;373:2005–14.
de Lange KM, Moutsianas L, Lee JC, et al. Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease. Nat Genet. 2017;49:256–61.
Liu JZ, van Sommeren S, Huang H, et al. Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet. 2015;47:979–86.
Jostins L, Ripke S, Weersma RK, et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491:119–24.
Lee JC, Lyons PA, McKinney EF, et al. Gene expression profiling of CD8+ T cells predicts prognosis in patients with Crohn disease and ulcerative colitis. J Clin Invest. 2011;121:4170–9.
Lee JC, Biasci D, Roberts R, et al. Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn’s disease. Nat Genet. 2017;49:262–8.
Kugathasan S, Denson LA, Walters TD, et al. Prediction of complicated disease course for children newly diagnosed with Crohn’s disease: a multicentre inception cohort study. Lancet. 2017;389:1710–8.
Marigorta UM, Denson LA, Hyams JS, et al. Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn’s disease. Nat Genet. 2017;49:1517–21.
Jess T, Riis L, Vind I, et al. Changes in clinical characteristics, course, and prognosis of inflammatory bowel disease during the last 5 decades: a population-based study from Copenhagen, Denmark. Inflamm Bowel Dis. 2007;13:481–9.
D’Haens G. Top-down therapy for IBD: rationale and requisite evidence. Nat Rev Gastroenterol Hepatol. 2010;7:86–92.
Colombel JF, Sandborn WJ, Reinisch W, et al. Infliximab, azathioprine, or combination therapy for Crohn’s disease. N Engl J Med. 2010;362:1383–95.
D’Haens G, Baert F, van Assche G, et al. Early combined immunosuppression or conventional management in patients with newly diagnosed Crohn’s disease: an open randomised trial. Lancet. 2008;371:660–7.
Hamburg MA, Collins FS. The path to personalized medicine. N Engl J Med. 2010;363:301–4.
Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372:793–5.
Burki T. UK and US governments to fund personalised medicine. Lancet Oncol. 2015;16:e108.
Torres J, Caprioli F, Katsanos KH, et al. Predicting outcomes to optimize disease management in inflammatory bowel diseases. J Crohns Colitis. 2016;10:1385–94.
O’Byrne S, Kaser A, Parik A, et al. Discovery of biomarkers of response in early drug development. J Crohns Colitis. 2016;10 Suppl 2:S560–6.
Wellcome Trust Case Control Consortium. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007;447:661–78.
Franke A, McGovern DP, Barrett JC, et al. Genome-wide meta-analysis increases to 71 the number of confirmed Crohn’s disease susceptibility loci. Nat Genet. 2010;42:1118–25.
Anderson CA, Boucher G, Lees CW, et al. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet. 2011;43:246–52.
Satsangi J, Grootscholten C, Holt H, et al. Clinical patterns of familial inflammatory bowel disease. Gut. 1996;38:738–41.
Chataway J, Mander A, Robertson N, et al. Multiple sclerosis in sibling pairs: an analysis of 250 families. J Neurol Neurosurg Psychiatry. 2001;71:757–61.
Jawaheer D, Lum RF, Amos CI, et al. Clustering of disease features within 512 multicase rheumatoid arthritis families. Arthritis Rheum. 2004;50:736–41.
Fowler SA, Ananthakrishnan AN, Gardet A, et al. SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn’s disease. J Crohns Colitis. 2014;8:845–51.
Latiano A, Palmieri O, Cucchiara S, et al. Polymorphism of the IRGM gene might predispose to fistulizing behavior in Crohn’s disease. Am J Gastroenterol. 2009;104:110–6.
Cleynen I, Boucher G, Jostins L, et al. Inherited determinants of Crohn’s disease and ulcerative colitis phenotypes: a genetic association study. Lancet. 2016;387:156–67.
Helio T, Halme L, Lappalainen M, et al. CARD15/NOD2 gene variants are associated with familially occurring and complicated forms of Crohn’s disease. Gut. 2003;52:558–62.
Onnie CM, Fisher SA, Prescott NJ, et al. Diverse effects of the CARD15 and IBD5 loci on clinical phenotype in 630 patients with Crohn’s disease. Eur J Gastroenterol Hepatol. 2008;20:37–45.
Haritunians T, Taylor KD, Targan SR, et al. Genetic predictors of medically refractory ulcerative colitis. Inflamm Bowel Dis. 2010;16:1830–40.
Lee JC, Espeli M, Anderson CA, et al. Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway. Cell. 2013;155:57–69.
Candore G, Cigna D, Todaro M, et al. T-cell activation in HLA-B8, DR3-positive individuals. Early antigen expression defect in vitro. Hum Immunol. 1995;42:289–94.
Sambo F, Trifoglio E, Di Camillo B, et al. Bag of Naive Bayes: biomarker selection and classification from genome-wide SNP data. BMC Bioinf. 2012;13 Suppl 14:S2.
de Los Campos G, Vazquez AI, Fernando R, et al. Prediction of complex human traits using the genomic best linear unbiased predictor. PLoS Genet. 2013;9:e1003608.
Yang SK, Hong M, Baek J, et al. A common missense variant in NUDT15 confers susceptibility to thiopurine-induced leukopenia. Nat Genet. 2014;46:1017–20.
Heap GA, Weedon MN, Bewshea CM, et al. HLA-DQA1-HLA-DRB1 variants confer susceptibility to pancreatitis induced by thiopurine immunosuppressants. Nat Genet. 2014;46:1131–4.
Heap GA, So K, Weedon M, et al. Clinical features and HLA association of 5-Aminosalicylate (5-ASA)-induced nephrotoxicity in inflammatory bowel disease. J Crohns Colitis. 2016;10:149–58.
Lee JC. Beyond disease susceptibility-Leveraging genome-wide association studies for new insights into complex disease biology. HLA. 2017;90:329–34.
Lyons PA, Koukoulaki M, Hatton A, et al. Microarray analysis of human leucocyte subsets: the advantages of positive selection and rapid purification. BMC Genomics. 2007;8:64.
Flint SM, McKinney EF, Lyons PA, et al. The contribution of transcriptomics to biomarker development in systemic vasculitis and SLE. Curr Pharm Des. 2015;21:2225–35.
West NR, Hegazy AN, Owens BMJ, et al. Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease. Nat Med. 2017;23:579–89.
Vermeire S, O’Byrne S, Keir M, et al. Etrolizumab as induction therapy for ulcerative colitis: a randomised, controlled, phase 2 trial. Lancet. 2014;384:309–18.
Kabakchiev B, Turner D, Hyams J, et al. Gene expression changes associated with resistance to intravenous corticosteroid therapy in children with severe ulcerative colitis. PLoS One. 2010;5:e13085.
McKinney EF, Lyons PA, Carr EJ, et al. A CD8+ T cell transcription signature predicts prognosis in autoimmune disease. Nat Med. 2010;16:586–91, 581p following 591.
McKinney EF, Lee JC, Jayne DR, et al. T-cell exhaustion, co-stimulation and clinical outcome in autoimmunity and infection. Nature. 2015;523:612–6.
Lee JC, Biasci D, Noor NM, et al. PROFILE trial: predicting outcomes for Crohn’s disease using a molecular biomarker. Gut. 2017;66:A22–3.
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Noor, N.M., Parkes, M., Lee, J.C. (2019). Genetic and Genomic Markers for Prognostication. In: Sheng Ding, N., De Cruz, P. (eds) Biomarkers in Inflammatory Bowel Diseases. Springer, Cham. https://doi.org/10.1007/978-3-030-11446-6_27
Download citation
DOI: https://doi.org/10.1007/978-3-030-11446-6_27
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-11445-9
Online ISBN: 978-3-030-11446-6
eBook Packages: MedicineMedicine (R0)