DOP049Transcriptomic profiling reveals divergent molecular pathways underlying Ulcerative Colitis disease activity and prognostic severity

Abstract Background Ulcerative colitis (UC) patients show substantial heterogeneity in inflammatory activity, treatment response and long-term disease severity. Endoscopic scores capture current inflammation, but not future disease course. Identifying molecular mechanisms that distinguish various degrees of disease severity, may enable earlier prognostication and personalised disease trajectories. This study examined transcriptomic differences between UC phenotypes to uncover molecular pathways and potential prognostic markers. Methods Inflamed (Mayo endoscopic sub score, MES ≥2) mucosal colonic biopsies were obtained at diagnosis or prior to the first advanced therapy from 37 UC patients later failing ≥2 advanced therapies (S1), 50 UC patients with long-term remission (2 years) after first-line advanced therapy (S2) and 16 UC patients with sustained remission with 5-ASA alone (S3). RNA sequencing was performed using Illumina NovaSeq X Plus. Weighted gene co-expression network analysis (WGCNA) was applied to identify phenotype-associated modules. Pathway enrichment was assessed using Ingenuity Pathway Analysis (IPA) and Gene Set Enrichment Analysis (GSEA). Results Baseline MES were significantly higher in both S1 and S2 compared to S3 (p = 0.0013; p = 0.037). Multiple WGCNA modules correlated with MES, confirming a transcriptomic link to disease activity. None were correlated with disease duration. However, two modules were uniquely upregulated in both S1 and S2 phenotypes, enriched for TNFα signalling (M1, p = 4.9x10-47) and epithelial mesenchymal transition (EMT) (M2, p = 5.9x10-8), suggesting shared tissue repair and inflammatory pathways. Predicted upstream regulators included TNF and EGF for M1 (p = 6.9x10-46 and p = 6.6x10-51), and SOX10 and WNT3A for M2 (p = 1.2x10-12 and p = 3.0x10-5). A distinct module, exclusively associated with S1 (M3), showed strong enrichment in MYC targets genes (p = 9.7x10-30) and mitochondrial translation (p = 1.3 × 10−7), protein import (p = 2.4 × 10−5) and degradation (p = 1.7 × 10−4) pathways, implicating dysregulated cell proliferation and survival. Key upstream regulators included HNF4A and IL3 (p = 2.9x10-8 and p = 2.3x10-4). Conclusion Although S1 and S2 show similarly high baseline inflammation, their long-term disease trajectories are shaped by distinct molecular programs, already in place before the start of the first advanced therapy. EMT pathway activation may reflect beneficial tissue repair in responders but could contribute to fibrosis in refractory cases.1 MYC and mitochondrial pathways enrichment in S1 suggest a transcriptional signature of poor prognosis and treatment resistance.2 These findings underscore the importance of separating inflammatory activity from molecular severity, and may inform future biomarker development. References: 1.Youssef KK, Nieto MA. Epithelial-mesenchymal transition in tissue repair and degeneration. Nat Rev Mol Cell Biol 2024;25(9):720-39. doi: 10.1038/s41580-024-00733-z published Online First: 20240429 2.Sipos F, Firneisz G, Muzes G. Therapeutic aspects of c-MYC signaling in inflammatory and cancerous colonic diseases. World J Gastroenterol 2016;22(35):7938-50. doi: 10.3748/wjg.v22.i35.7938 Conflict of interest: D’hooghe, Anna-Teresa: No conflicts. Abdurahiman, Saeed: None to declare Verstockt, Sare: Grant: Postdoctoral fellowship of the Research foundation – Flanders (FWO), Belgium Giorio, Lorenzo: Research support from Galapagos NV Arnauts, Kaline: Research support by Galapagos NV Cuvry, Arno: No conflicts of interest to declare. Ferrante, Marc: Research grants from AbbVie, EG Pharma, Celltrion, Janssen, Pfizer, Takeda and Viatris Consultancy fees from AbbVie, AgomAb Therapeutics, Boehringer Ingelheim, Celgene, Celltrion, Eli Lilly, Janssen-Cilag, MRM Health, Merck Sharp and Dohme, Pfizer, Takeda and ThermoFisher Speakers’ fees from AbbVie, Biogen, Boehringer Ingelheim, Dr Falk Pharma, Ferring, Janssen-Cilag, Merck Sharp and Dohme, Pfizer, Takeda, Truvion Healthcare and Viatris Guedelha Sabino, João: Speaker’s fees: Lilly, Pfizer, Abbvie, Ferring, Falk, Takeda, Janssen, Fresenius, and Galapagos. Consultancy fees: Takeda, Pfizer, Janssen, Ferring, Fresenius, Abbvie, Galapagos, Celltrion, Pharmacosmos, and Pharmanovia. Research support: Galapagos, Viatris, and Eurogenerics. JS is supported by a Senior Clinical researcher grant from the Research foundation – Flanders. Vermeire, Séverine: No conflict of interest Verstockt, Bram: - Research support from AbbVie, Biora Therapeutics, Celltrion, Landos, Pfizer, Sanofi, Sossei Heptares/Nxera and Takeda. - Speaker’s fees from Abbvie, Agomab, Alfasigma, Biogen, Bristol Myers Squibb, Celltrion, Eli Lily, Falk, Ferring, Galapagos, Materia Prima, Johnson and Johnson, Pfizer, Sandoz, Takeda, Tillots Pharma, Truvion and Viatris. - Consultancy fees from Abbvie, Alfasigma, Alimentiv, Anaptys Bio, Applied Strategic, Astrazeneca, Atheneum, BenevolentAI, Biora Therapeutics, Boxer Capital, Bristol Myers Squibb, Domain Therapeutics, Eli Lily, Galapagos, Guidepont, Landos, Merck, Mirador Therapeutics, Mylan, Nxera, Inotrem, Ipsos, Johnson and Johnson, Pfizer, Sandoz, Sanofi, Santa Ana Bio, Sapphire Therapeutics, Sosei Heptares, Takeda, Tillots Pharma and Viatris. - Stock options Vagustim and Thethis Pharma.