Tissue-specific microRNA signatures in pediatric inflammatory bowel disease with juvenile idiopathic arthritis: differential expression and cross-platform evaluation

Background & Aim Development of extraintestinal manifestations in pediatric inflammatory bowel disease (pIBD) is associated with a more severe disease course; juvenile idiopathic arthritis (JIA) is the most frequent extraintestinal manifestation in pIBD. We investigated whether intestinal mucosal microRNAs measured at pIBD diagnosis could predict subsequent JIA (pIBD-JIA) before symptoms emerge.

We analyzed formalin-fixed, paraffin-embedded diagnostic intestinal biopsies from 101 pediatric patients under 18 years of age: a discovery cohort (n=62; 27 pIBD, 25 pIBD-JIA, 10 non-IBD controls) and a validation cohort (n=39; 29 pIBD, 10 non-IBD; pIBD-JIA cases reused from discovery cohort). Discovery profiling used Affymetrix GeneChip™ miRNA 4.0. Significant probe sets were cross-referenced in MirGeneDB 2.1 and literature-curated to nominate candidates for RT-qPCR validation.

We identified 532 differentially expressed probe sets across groups (adjusted p2. Thirteen microRNAs exhibited the clearest separation between pIBD and pIBD-JIA; 11 achieved AUC>0.70 in discovery. Four candidates (miR-663a, miR-3197, miR-4463, miR-92a-3p) were advanced to RT-qPCR validation. Two assays (miR-3197, miR-4463) failed technical criteria; differences in miR-663a and miR-92a-3p were reproduced within a discovery subset but did not replicate in the pIBD/non-IBD validation cohort.

Diagnostic mucosal microRNA profiles distinguished pIBD patients who later developed JIA in discovery, but selected microRNA candidates were not general across cohorts. These findings underscore both the potential of tissue microRNAs as prognostic markers and the need for larger, fully independent, standardized studies before clinical translation. Competing Interest Statement I have read the journal’s policy and the authors of this manuscript have the following competing interests: Maria Dorn-Rasmussen: None Jaslin P James: None Mikkel Malham: None Thea A Hvidtfeldt: None Boye S Nielsen: None Johan Burisch: Reports grants from AbbVie, Janssen-Cilag, MSD, Takeda, Tillots Pharma, Bristol Myers Squibb, and Novo Nordisk Foundation personal fees from AbbVie, Janssen-Cilag, Celgene, MSD, Pfizer, Takeda, Tillots Pharma, Bristol Myers Squibb, Samsung Bioepis, Pharmacosmos, Ferring, Galapagos, Eli Lilly, Dr Falk Pharma, Celltrion, Zealand Pharma and Orion Pharma. JB is supported by the EU Horizon Europe Program grant miGut-Health: Personalised blueprint of intestinal health (101095470). Helene A S Ingels: None Estrid V S Høgdall: None Lene B Riis: None Vibeke Wewer: None Funding Statement Yes Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: This study was approved by the Danish National Ethical Committee (reference number H-20065831) and the Danish Data Protection Agency (reference number P-2020-1065). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes DISCLOSURES: Maria Dorn-Rasmussen: None Jaslin P James: None, Mikkel Malham: None Thea A Hvidtfeldt: None Boye S Nielsen: None, Johan Burisch: Reports grants from AbbVie, Janssen-Cilag, MSD, Takeda, Tillots Pharma, Bristol Myers Squibb, and Novo Nordisk Foundation; personal fees from AbbVie, Janssen-Cilag, Celgene, MSD, Pfizer, Takeda, Tillots Pharma, Bristol Myers Squibb, Samsung Bioepis, Pharmacosmos, Ferring, Galapagos, Eli Lilly, Dr Falk Pharma, Celltrion, Zealand Pharma and Orion Pharma. JB is supported by the EU Horizon Europe Program grant miGut-Health: Personalised blueprint of intestinal health (101095470). Helene A S Ingels: None Estrid V S Høgdall: None Lene B Riis: None Vibeke Wewer: None Data Availability Microarray expression data have been deposited in ArrayExpress at the European Bioinformatics Institute (EMBL-EBI) under the accession number E-MTAB-15807.