Introduction
Transcriptomic analysis has potential to evaluate the molecular basis and pathophysiology of inflammatory bowel disease (IBD), discover therapeutic targets, and identify biomarkers. However, the value of this technology in clinical trials is limited by substantial methodological heterogeneity, which confounds interpretation, generalisability, and comparison of data across studies.
Aims & Methods
We conducted a 2-part study that aimed to develop recommendations for standardising transcriptomic analysis in multicentre IBD clinical trials. First, 3 public databases were searched from inception to May 2021 to identify clinical trials that included patients with IBD and transcriptomic analyses. Studies that collected blood or intestinal samples and utilised microarray, RNA sequencing, or other global RNA analysis methods were eligible. Data on study design and methodological approaches to transcriptomic research ranging from biopsy location to data analysis and reporting were extracted by 2 independent reviewers. The results of the systematic review (SR) informed the second part of the study, in which a panel of 16 IBD translational researchers participated in a modified Research and Development/University of California Los Angeles appropriateness methodology (RAM) process. A list of statements focused on topics with substantial methodological heterogeneity (Table) was developed based on the SR and panel opinion and formed the basis for creation of a formal survey. Panellists rated the appropriateness of survey statements in 2 rounds, with panel input and survey modification between rounds.
Table. Overview of RAM survey topics
| Topic | No. of statements |
| Use of blood or intestinal mucosal samples for bulk RNA transcriptomics in IBD clinical trials | 140 |
| Sampling of intestinal mucosa for bulk RNA transcriptomic analyses | 45 |
| Analysing, interpreting, and reporting transcriptomics data | 95 |
| scRNA-seq, snRNA-seq, and spatial transcriptomics | 136 |
| Abbreviations: IBD, inflammatory bowel disease; RAM, Research and Development/University of California Los Angeles appropriateness methodology; RNA, ribonucleic acid; scRNA-seq, single-cell ribonucleic acid sequencing; snRNA-seq, single nucleus ribonucleic acid sequencing. |
Results
The SR identified 37 reports (22 abstracts; 15 manuscripts) of 22 clinical trials (13 ulcerative colitis [UC]; 6 Crohn’s disease [CD]; 3 UC and CD) that included transcriptomic analyses. The earliest report was published in 2009, with most (>75%) reports published between 2017 and 2021. Most (59%) analyses were conducted at phase 1b or 2 of clinical development. The appropriateness of 416 statements were 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. In general, transcriptomic analysis for multiple research objectives using either mucosal biopsy or blood samples was considered appropriate at all phases of clinical development in patients with active disease. Validation of results with external datasets and/or orthogonal methods was considered appropriate, as was the complete reporting of individual patient metadata (ex, patient demographics, disease/treatment history, sample location, and local disease activity); the latter of which was viewed as a critical component for further analysis and utility of transcriptomic data.
Conclusion
Although inclusion of transcriptomic analysis in IBD clinical trials has increased over the past decade, persistence of existing methodologic heterogeneity will continue to limit the interpretation and generalisability of the results of this important research. This study provides an initial framework for expert recommendations to address and overcome these discrepancies and increase the value of this research in clinical development.
Disclosure
BL, EC, MIS, LS: employees of Alimentiv Inc
AS: research grants from Roche-Genentech, Abbvie, GSK, Scipher Medicine, Alimentiv Inc, Boehringer Ingelheim and Agomab (Origo Biopharma); consulting fees from Genentech, GSK, Pfizer, HotSpot Therapeutics, Alimentiv, Origo Biopharma, Thabor Therapeutics, Goodgut and Boxer Capital
BS: employee of Lilly
BV: research support from from AbbVie, Biora Therapeutics, Landos, Pfizer, Sossei Heptares and Takeda; speaker’s fees from Abbvie, Biogen, Bristol Myers Squibb, Celltrion, Chiesi, Falk, Ferring, Galapagos, Janssen, MSD, Pfizer, R-Biopharm, Takeda, Truvion and Viatris; consulting fees from Abbvie, Alimentiv, Applied Strategic, Atheneum, Biora Therapeutics, Bristol Myers Squibb, Galapagos, Guidepont, Mylan, Inotrem, Ipsos, Janssen, Pfizer, Progenity, Sandoz, Sosei Heptares, Takeda, Tillots Pharma and Viatris
DM: consulting fees from Prometheus Biosciences, Takeda, Pfizer and Prometheus Laboratories; owns stock in Prometheus Biosciences.
FR: consulting fees from Adiso, Adnovate, Agomab, Allergan, AbbVie, Arena,Astra Zeneca, Boehringer-Ingelheim, Celgene/BMS, CDISC,Celsius, Cowen,Ferring,Galapagos,Galmed,Genentech,Gilead,Gossamer,Granite,Guidepoint,Helmsley,Horizon Therapeutics,Image Analysis Limited, Index Pharma, Landos,Jannsen, Koutif, Mestag,Metacrine,Mopac,Morphic,Organovo,Origo,Pfizer,Pliant,Prometheus Biosciences,Receptos, RedX,Roche,Samsung,Sanofi,Surmodics,Surrozen,Takeda,Techlab,Teva,Theravance,Thetis,UCB,Ysios,89Bio
KA: grant support from Janssen, consulting fees from Johnson & Johnson/Janssen, Lilly, Takeda
MA: speaker/consultation fees or grants from Abbvie, Amgen, Biogen, Boehringer Ingelheim, Bristol Myers Squibb, Celgene, Celltrion, Ferring, Genentech, Gilead, IQVIA, Janssen, Lilly, MSD, Novartis, Pfizer, Roche, Takeda, and Tillots
RA: speaker/consultation fees or grants from AbbVie, Amgen, Arena Pharmaceuticals, Biogen, Boehringer Ingelheim, Celltrion, Dr Falk Pharma, Ferring, Galapagos, Gilead, InDex Pharmaceuticals, Janssen-Cilag, Kliniksa Pharmaceuticals, MSD Sharp & Dohme, Novartis, Pfizer, Roche Pharma, Samsung Bioepsis, Takeda, and Tillotts Pharma
SS: scientific advisory board fees from Pfizer, Pandion, Celgene, Lilly, Takeda, Cosmo Pharmaceuticals, Merck, Sonoma Biotherapeutics, and EcoR1; grant support from Pfizer, Amgen Takeda, and Novartis; consulting fees from Amgen, Kyverna, BMS, Merck, Third Rock, 89bio, GentiBio and Apple Tree Life Sciences
TR: research grants and/or speaker/consultation fees from Abbvie, Arena, Aslan, AstraZeneca, Boehringer-Ingelheim, BMS, Celgene, Ferring, Galapagos, Gilead, GSK, Heptares, LabGenius, Janssen, Mylan, MSD, Novartis, Pfizer, Roche, Sandoz, Takeda, UCB and XAP therapeutics
BFG: grant/research support from AbbVie, Amgen, AstraZeneca/MedImmune, Atlantic Pharmaceuticals, Boehringer Ingelheim, Celgene, Celltech, Genentech/Hoffmann-La Roche, Gilead Sciences, GlaxoSmithKline, Janssen Research & Development, Pfizer, Receptos/Celgene International, Sanofi, Santarus, Takeda Development Center Americas, Tillotts Pharma AG, and UCB Pharma; consulting fees from Abbott/AbbVie, Akebia Therapeutics, Allergan, Amgen, Applied Molecular Transport, Aptevo Therapeutics, AstraZeneca, Atlantic Pharmaceuticals, Avir Pharma, Biogen Idec, BiomX Israel, Boehringer Ingelheim, Bristol Myers Squibb, Calypso Biotech, Celgene, Elan/Biogen, EnGene, Ferring, Roche/Genentech, Galapagos, GiCare Pharma, Gilead, Gossamer Pharma, GlaxoSmithKline, Inception IBD, Johnson & Johnson/Janssen, Kyowa Hakko Kirin, Lexicon, Lilly, Lycera BioTech, Merck, Mesoblast Pharma, Millennium, Nestle, Nextbiotix, Novo Nordisk, Pfizer, Prometheus Therapeutics and Diagnostics, Progenity, Protagonist, Receptos, Salix Pharmaceuticals, Shire, Sienna Biologics, Sigmoid Pharma, Sterna Biologicals, Synergy Pharma, Takeda, Teva Pharmaceuticals, TiGenix, Tillotts Pharma AG, UCB Pharma, Vertex Pharmaceuticals, Vivelix Pharmaceuticals, VHsquared, and Zyngenia; speakers bureau fees from Abbott/AbbVie, Johnson&Johnson/Janssen, Lilly, Takeda, Tillotts Pharma AG, and UCB Pharma; is a scientific advisory board member for Abbott/AbbVie, Allergan, Amgen, AstraZeneca, Atlantic Pharmaceuticals, Avaxia Biologics, Boehringer Ingelheim, Bristol Myers Squibb, Celgene, Centocor, Elan/Biogen, Galapagos, Genentech/Roche, Johnson & Johnson/Janssen, Merck, Nestle, Novartis, Novo Nordisk, Pfizer, Prometheus Laboratories, Protagonist, Salix Pharmaceuticals, Sterna Biologicals, Takeda, Teva, TiGenix, Tillotts Pharma AG, and UCB Pharma; Senior Scientific Officer of Alimentiv.
VJ: consulting/advisory board fees from AbbVie, Alimentiv Inc, Arena Pharmaceuticals, Asahi Kasei Pharma, Asieris, Astra Zeneca, Bristol Myers Squibb, Celltrion, Eli Lilly, Ferring, Flagship Pioneering, Fresenius Kabi, Galapagos, GlaxoSmithKline, Genentech, Gilead, Janssen, Merck, Metacrine, Mylan, Pandion, Pendopharm, Pfizer, Protagonist, Prometheus, Reistone Biopharma, Roche, Sandoz, Second Genome, Sorriso Pharmaceuticals, Takeda, Teva, Topivert, Ventyx, and Vividion; speaker’s fees from, Abbvie, Ferring, Bristol Myers Squibb, Galapagos, Janssen, Pfizer, Shire, Takeda, and Fresenius Kabi.
NVC: grant from R-Biopharm; personal fees from AcelaBio, Alimentiv, Pfizer, ProciseDX, Ventyx.
DA, DC, FU, LM, MN, VA, YH: none