Journal Article

A blood-based prognostic biomarker in IBD

Biasci, Daniele, Noor, Nurulamin M, McKinney, Eoin F, Smith, Kenneth G C, Ahmad, Tariq, Lewis, Nina, Hart, Ailsa, Lee, James C, Lyons, Paul A, Hou, Monica, Parkes, Miles, Pombal, Diana R

2019

Overview

ObjectiveWe have previously described a prognostic transcriptional signature in CD8 T cells that separates patients with IBD into two phenotypically distinct subgroups, termed IBD1 and IBD2. Here we sought to develop a blood-based test that could identify these subgroups without cell separation, and thus be suitable for clinical use in Crohn’s disease (CD) and ulcerative colitis (UC).DesignPatients with active IBD were recruited before treatment. Transcriptomic analyses were performed on purified CD8 T cells and/or whole blood. Phenotype data were collected prospectively. IBD1/IBD2 patient subgroups were identified by consensus clustering of CD8 T cell transcriptomes. In a training cohort, machine learning was used to identify groups of genes (‘classifiers’) whose differential expression in whole blood recreated the IBD1/IBD2 subgroups. Genes from the best classifiers were quantitative (q)PCR optimised, and further machine learning was used to identify the optimal qPCR classifier, which was locked down for further testing. Independent validation was sought in separate cohorts of patients with CD (n=66) and UC (n=57).ResultsIn both validation cohorts, a 17-gene qPCR-based classifier stratified patients into two distinct subgroups. Irrespective of the underlying diagnosis, IBDhi patients (analogous to the poor prognosis IBD1 subgroup) experienced significantly more aggressive disease than IBDlo patients (analogous to IBD2), with earlier need for treatment escalation (hazard ratio=2.65 (CD), 3.12 (UC)) and more escalations over time (for multiple escalations within 18 months: sensitivity=72.7% (CD), 100% (UC); negative predictive value=90.9% (CD), 100% (UC)).ConclusionThis is the first validated prognostic biomarker that can predict prognosis in newly diagnosed patients with IBD and represents a step towards personalised therapy.

• Publisher: BMJ Publishing Group Ltd and British Society of Gastroenterology,BMJ Publishing Group LTD,BMJ Publishing Group
• Subject: Adult / Antigens / Bioinformatics / Biomarkers / Biomarkers - blood / Blood / Breast cancer / Cancer therapies / CD8 antigen / CD8-Positive T-Lymphocytes - metabolism / Clinical medicine / Colitis, Ulcerative - blood / Colitis, Ulcerative - diagnosis / Crohn Disease - blood / Crohn Disease - diagnosis / Crohn's disease / Diagnosis, Differential / Endoscopy / Female / Gastroenterology / Gene Expression / Gene Expression Profiling - methods / Generalized linear models / Humans / Ibd basic besearch / Ibd clinical / Inflammatory Bowel Disease / Learning algorithms / Lymphocytes / Lymphocytes T / Machine Learning / Male / Middle Aged / Patients / Phenotype / Phenotypes / Predictive Value of Tests / Prognosis / Reproducibility of Results / Sensitivity and Specificity / Severity of Illness Index / Transcription / Tumor necrosis factor-TNF / Ulcerative colitis