P0065 Circulating cell-free DNA and mitochondrial DNA differentiate disease activity in paediatric-onset inflammatory bowel disease: Interim analysis from Scotland-wide Mini-MUSIC study (2020-26)
Authors: Wands D , Lau S Y , Chuah C S , Hall R , Whelan R , Fischer L , Kalla R , Cartlidge P , Drury B , Chalmers I , Hansen R , Wilson M , Jones G , Wilson D , Ho G T 
Published: January 2025

Abstract

Background
Mitochondrial dysfunction has been implicated in the pathogenesis of inflammatory bowel disease (IBD) particularly paediatric-onset IBD (PIBD).1,2 Circulating cell-free DNA (cfDNA) and mitochondrial DNA (mtDNA) are damage-associated molecular patterns (DAMPS) released into the bloodstream during tissue damage and cell death and can be detected in peripheral blood samples.3 Recent studies have suggested that levels of cfDNA and mtDNA may correlate with disease activity in adult IBD4 but their utility in paediatric populations remains unexplored. This study aims to present initial data on the potential use of cfDNA and mtDNA as biomarkers in PIBD.

Methods
Mini-MUSIC and GI-DAMPS are ongoing longitudinal and cross-sectional multi-centre translational research studies in Scotland (2020 – 2026) with a primary aim of investigating the inflammatory mechanisms of IBD with a focus on multi-omics, immune- and microbiome-profiling aligned to prospective clinical follow-up. We measured circulating cfDNA (GAPDH) and mtDNA (ND2), using digital droplet PCR, in the peripheral blood of patients diagnosed under 17 years of age (A1 phenotype) and correlated this with phenotypic data and disease activity scores.

Results
Sixty-five A1 patients were included (39/65 (60%) male; 51 Crohn’s disease (CD), 6 ulcerative colitis (UC), 1 inflammatory bowel disease unclassified (IBDU) and 7 symptomatic non-IBD controls) with a median (IQR) age at diagnosis of 13 (10.0-15.0) years. mtDNA levels were significantly higher in those with highly active disease compared to those in remission (median [IQR] 145.1 (89.5-673.7 ng/μl) vs 64.4 (24.3-167.5 ng/μl), p=0.008) and compared to non-IBD symptomatic controls (median [IQR] 145.1 (89.5-673.7 ng/μl) vs 28.8 (12.6 – 138.7 ng/μl), p=0.036). Circulating cell-free DNA levels were significantly higher in those with highly active disease than non-IBD controls (4.94 (1.1-9.9 ng/ul) vs median [IQR] 0.53 (0.0-1.4 ng/ul), p=0.017). mtDNA levels were positively correlated with endoscopic disease activity (SES-CD) in Crohn’s disease (Pearson r=0.7619, p=0.004).

Conclusion
Our initial data from ongoing work, demonstrate that the levels of cfDNA and mtDNA in the blood are potentially valuable biomarkers for differentiating disease activity in PIBD and to identify PIBD-patients where mitochondrial dysfunction is dominant and thereby with the potential to stratify future human mechanistic studies and mitochondrial-targeted therapies.

References
1. Haberman Y, Karns R, Dexheimer PJ, et al. Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response. Nat Commun. 2019;10(1):38. doi:10.1038/s41467-018-07841-32.
2. Mottawea W, Chiang C-K, Mühlbauer M, et al. Altered intestinal microbiota-host mitochondria crosstalk in new onset Crohn’s disease. Nat Commun. 2016;7:13419. doi:10.1038/ncomms134193.
3. Chuah CS, Fischer L, Ho G-T. Circulating Cell-Free DNA in Inflammatory Bowel Disease: Liquid Biopsies with Mechanistic and Translational Implications. Fac Rev. 2023;12:14. doi:10.12703/r/12-144.
4. Boyapati RK, Dorward DA, Tamborska A, et al. Mitochondrial DNA Is a Pro-Inflammatory Damage-Associated Molecular Pattern Released During Active IBD. Inflamm Bowel Dis. 2018;24(10). doi:10.1093/ibd/izy095