Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Jostins L., Ripke S., Weersma RK., Duerr RH., McGovern DP., Hui KY., Lee JC., Schumm LP., Sharma Y., Anderson CA., Essers J., Mitrovic M., Ning K., Cleynen I., Theatre E., Spain SL., Raychaudhuri S., Goyette P., Wei Z., Abraham C., Achkar J-P., Ahmad T., Amininejad L., Ananthakrishnan AN., Andersen V., Andrews JM., Baidoo L., Balschun T., Bampton PA., Bitton A., Boucher G., Brand S., Büning C., Cohain A., Cichon S., D'Amato M., De Jong D., Devaney KL., Dubinsky M., Edwards C., Ellinghaus D., Ferguson LR., Franchimont D., Fransen K., Gearry R., Georges M., Gieger C., Glas J., Haritunians T., Hart A., Hawkey C., Hedl M., Hu X., Karlsen TH., Kupcinskas L., Kugathasan S., Latiano A., Laukens D., Lawrance IC., Lees CW., Louis E., Mahy G., Mansfield J., Morgan AR., Mowat C., Newman W., Palmieri O., Ponsioen CY., Potocnik U., Prescott NJ., Regueiro M., Rotter JI., Russell RK., Sanderson JD., Sans M., Satsangi J., Schreiber S., Simms LA., Sventoraityte J., Targan SR., Taylor KD., Tremelling M., Verspaget HW., De Vos M., Wijmenga C., Wilson DC., Winkelmann J., Xavier RJ., Zeissig S., Zhang B., Zhang CK., Zhao H., Silverberg MS., Annese V., Hakonarson H., Brant SR., Radford-Smith G., Mathew CG., Rioux JD., Schadt EE., Daly MJ., Franke A., Parkes M., Vermeire S., Barrett JC., Cho JH.
Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.