Expert recommendations to standardize transcriptomic analysis in inflammatory bowel disease clinical trials

Linggi B, Azucena S, Steere B, Verstockt B, Alsoud D, Casero D, Mcgovern D, Chan E, Smith MI, Ungaro F, Rieder F, Aden K, Shackelton LM, Massimino L, Neurath M, Allez M, Atreya R, Snapper SB, Raine T, Ahuja V, Haberman Y, Feagan BG, Jairath V, Vande Casteele N (2025)

Publication Type: Journal article

Publication year: 2025

Journal

Journal of Crohns & Colitis Elsevier

Book Volume: 19

Article Number: jjaf068

Journal Issue: 5

DOI: 10.1093/ecco-jcc/jjaf068

Abstract

Background and aims: Substantial methodological and reporting heterogeneity confounds the interpretation and generalizability of transcriptomic data for inflammatory bowel disease (IBD) studies. We aimed to develop recommendations to standardize transcriptomic research in clinical trials. Methods: A 2-part study was undertaken. A systematic review identified reports of transcriptomic analyses utilizing samples from IBD clinical trials. Studies that used global RNA assay platforms were included. Data regarding study design, methodological approaches, and reporting of transcriptomic research were extracted. The systematic review results informed a modified Research and Development/University of California Los Angeles appropriateness methodology process and the development of survey statements focused on topics with substantial methodological heterogeneity. A panel of 16 IBD translational researchers and gastroenterologists rated the appropriateness of survey statements in 2 rounds. Results: The systematic review identified 37 reports that included transcriptomic analyses of samples from IBD patients. The appropriateness of 416 statements was rated by 15 panellists in the first survey. The final survey included 305 statements, of which 14 panellists rated 75% appropriate, 1% inappropriate, and 24% uncertain. The panel determined that transcriptomic analysis for multiple research objectives was appropriate at most phases of clinical development in patients with active disease. Recommendations regarding study sample size; biopsy number, location, preservation, and storage; and data analysis and reporting were also generated. Conclusion: The persistence of existing methodologic heterogeneity may continue to limit the value of transcriptomic research in IBD. This study provides expert recommendations to address and overcome these discrepancies and foster the inclusion of this research in clinical development.

Authors with CRIS profile

Markus Neurath Lehrstuhl für Innere Medizin I (Medizin 1) Raja Atreya Professur für Translationale Immunforschung bei chronisch entzündlichen Darmerkrankungen

Involved external institutions

Alimentiv GB United Kingdom (GB) Hospital Clínic de Barcelona ES Spain (ES) Eli Lilly and Company US United States (USA) (US) University Hospital Leuven (UZ) / Universitaire ziekenhuizen Leuven BE Belgium (BE) Katholieke Universiteit Leuven (KUL) / Catholic University of Leuven BE Belgium (BE) Cedars-Sinai Medical Center US United States (USA) (US) Ospedale San Raffaele (früher: Centro San Raffaele del Monte Tabor Foundation) IT Italy (IT) Christian-Albrechts-Universität zu Kiel DE Germany (DE) Université Sorbonne Paris Cité FR France (FR) Boston Children's Hospital US United States (USA) (US) Addenbrooke's Hospital GB United Kingdom (GB) All India Institute of Medical Sciences IN India (IN) Tel Aviv University IL Israel (IL) Cleveland Clinic US United States (USA) (US)

How to cite

APA:

Linggi, B., Azucena, S., Steere, B., Verstockt, B., Alsoud, D., Casero, D.,... Vande Casteele, N. (2025). Expert recommendations to standardize transcriptomic analysis in inflammatory bowel disease clinical trials. Journal of Crohns & Colitis, 19(5). https://doi.org/10.1093/ecco-jcc/jjaf068

MLA:

Linggi, Bryan, et al. "Expert recommendations to standardize transcriptomic analysis in inflammatory bowel disease clinical trials." Journal of Crohns & Colitis 19.5 (2025).

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