P0918 Identification of a serum proteomics signature linked with anti-TNF therapy response outcomes in Inflammatory Bowel Disease
Authors: Bourgery M , Bernardes J P , Wittig M , Kimmig F , Mishra N , Franke A , Aden K , Schreiber S , Rosenstiel P , Tran F 
Published: January 2025

Abstract

Background
While treatment options for active disease in IBD become diverse, the choice of therapies is mostly based on patient characteristics, disease course and severity but restrained by economic rationales. To maximize treatment effectiveness, predictive biomarkers are needed to guide therapies either ex ante or at the earliest possible time point after therapy initiation. Previously, we identified dynamic blood-based RNA and DNA methylation signatures that are linked with therapy response to anti-TNF in IBD1. Here, we aim to identify serum proteome biomarkers associated with therapeutic outcomes in IBD patients receiving anti-TNF treatment.

Methods
31 ulcerative colitis (UC) and 27 Crohn’s disease (CD) patients with active clinical and endoscopic disease were recruited and followed at baseline (W0) and at weeks 2 (W2), 6 (W6), and 14 (W14) after initiating infliximab therapy. The clinical endpoint of interest was defined as a combination of clinical remission (partial Mayo ≤ 2/CDAI &lt; 150) and endoscopic response (reduction in endoscopic Mayo ≥ 1/SES-CD ≥ 50%) at W14. Serum was collected at each time point and subjected to proximity extension assays (Olink® Explore 3072 panel) to screen for 2,944 proteins. Linear mixed models (LMM) were applied to identify differentially expressed proteins (DEPs) between endpoint achievers/non-achievers over time. Additionally, post-analysis of DEPs was performed using cv.glmnet with least absolute shrinkage and selection operator (LASSO) regression to identify candidate predictive marker sets.

Results
A total of 229 DEPs were identified over time between UC responders and non-responders: 8 at W0, 22 at W2, 181 at W6, and 78 at W14. In CD patients, 23 DEPs were identified: 9 at W0, 7 at W2, 13 at W6, and 13 at W14. These DEPs were disease-specific and linked to Gene Ontology (GO) terms related to inflammatory response and cell differentiation. Using LMM and machine learning, we identified 5 baseline proteins in UC and 6 in CD patients that differentiated combined endpoint achievers from non-achievers (AUROC: UC: 0.958, CD: 0.800). Additionally, we identified dynamic changes from W0 to W2 in 7 proteins associated with immune regulation in UC patients (1 in CD), which were linked to therapeutic outcomes at W14.

Conclusion
Detecting specific ex ante biomarkers or early dynamic molecular signatures are critical for precision medicine in IBD. Our data suggest that serum proteomics profiling enables the differentiation of patients who will attain therapeutic success under anti-TNF therapy from those who will not. This study warrants further investigations in larger, independent datasets to confirm the potential clinical utility of the proteomics signature.

References
(1) Mishra N, et al. Longitudinal multi-omics analysis identifies early blood-based predictors of anti-TNF therapy response in inflammatory bowel disease. Genome Med. 2022 Sep 24;14(1):110. doi: 10.1186/s13073-022-01112-z. PMID: 36153599; PMCID: PMC9509553.
This project has received funding from the DFG Cluster of Excellence 2167 "Precision medicine in chronic inflammation", the BMBF (e:Med Network iTREAT 01ZX2202A, and GUIDE-IBD 031L0188A), and the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 831434 (3TR) and No 853995 (ImmUniverse).The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The content provided in this publication reflects the author’s views only. Neither the Innovative Medicines Initiative (IMI JU) nor the European Commission are responsible for any use that may be made of the information it contains.