Publicly Available Datasets

Gene expression microarray data from 2 previously published adult patient cohorts were included. For adult cohort 1 ({"type":"entrez-geo","attrs":{"text":"GSE87650","term_id":"87650"}}GSE87650),¹⁵ a total of 52 CD8⁺ T-cell–specific genome-wide transcriptomes (profiled on Illumina HumanHT-12, version 4) were available (n = 14 healthy controls, n = 19 CD, n = 19 UC). A summary of this patient cohort is provided in Supplementary Table 3. Adult cohort 2 included a total of 67 CD8⁺ T-cell–specific transcriptomes (profiled on Affymetrix Human Gene ST, versions 1.0 and 1.1) with samples derived from patients diagnosed with CD (n = 35) and UC (n = 32) (E-MTAB-331).⁶ Clinical phenotype data available for the latter cohort included age, sex, and disease severity classed as either severe (IBD1) or mild (IBD2). We obtained publicly available CD8⁺ T-cell–derived genome-wide DNA methylation profiles (K450 Illumina DNA methylation arrays) from 2 previously published adult patient cohorts. Adult cohort 1 ({"type":"entrez-geo","attrs":{"text":"GSE87640","term_id":"87640"}}GSE87640)¹⁵ contained a total of 56 CD8⁺ T-cell samples—18 CD, 19 UC, and 19 healthy control individuals (age range, 18–63 years). Adult cohort 3 included samples obtained from a younger (age range, 22–34 years, n = 50) and older (age range, 73–84 years, n = 50) group of healthy adults ({"type":"entrez-geo","attrs":{"text":"GSE59065","term_id":"59065"}}GSE59065).¹⁶

Data analyses were performed separately in each dataset following the same analytical approach as outlined below, with adjustments made to account for differences in array type. Datasets derived from different studies were never combined or analyzed together.