Introduction
Despite advances in treat-to-target strategies, a substantial proportion of ulcerative colitis (UC) patients fail to achieve endoscopic and histological remission [1]. This gap reflects the complex biological heterogeneity underlying UC pathogenesis and the limitations of current one-size-fits-all treatment algorithms. The absence of validated biomarkers predicting response to biologic therapy remains a major barrier to precision treatment selection. Pharmacogenetic studies captured by SNPs may help explain inter-individual heterogeneity in therapeutic response [2,3]. We aimed to identify SNPs signatures predictive of response to Ustekinumab in patients with moderate-to-severe UC enrolled in the Phase 3 UNIFI clinical trial [4].
Aims & Methods
Genome-wide data from 654 participants with moderate-to-severe UC were processed and analysed using PLINK v1.9 [5]. The binary genotype files generated were subjected to standard quality control (QC) parameters, including sample call rate filtering followed by variant call, minor allele frequency (MAF), and Hardy-Weinberg equilibrium (HWE) filtering. Genome-wide association analyses (GWAS) evaluated SNPs associated with Clinical remission (Mayo ≤2), endoscopic improvement and remission (Mayo endoscopic score [MES] 1 and 0, respectively), histological improvement and remission (Geboes score <3.1 and <2B.0, respectively), and mucosal healing (endoscopic and histological remission) at maintenance week 44. A multimodal logistic regression model, adjusted for relevant covariates, was applied. The threshold for identifying Single Nucleotide Polymorphism (SNP) was considered at 1 X 10-5 (suggestive threshold) for further downstream interpretations.
Results
QC filtered data generated a total of 1,528,830 variants retained for downstream analyses with an overall genotype rate of 0.9993. Table 1 summarise the identified SNPs with corresponding therapeutic outcomes. GWAS analysis with treatment response phenotypes demonstrated associations with 41 SNPs (9 protective, 32 risk‑increasing) for clinical remission, 25 SNPs for endoscopic improvement (23 protective, 2 risk‑increasing), and 5 protective SNPs for histological improvement. Additionally, SNPs signatures were associated with endoscopic remission (10 SNPs; 8 protective, 2 risk‑increasing), histological remission (4 risk‑increasing SNPs), and mucosal healing (14 SNPs; 8 protective, 6 risk‑increasing). Notably, several loci mapped to immune regulatory genes, including RGS1 and IL7R [6], suggesting a mechanistic link between host immunogenetic variation and response to IL-12/23 pathway inhibition.
Table 1: Summary of therapeutic outcomes with corresponding identified SNPs
| Therapeutic outcomes | N of patients | N of associated SNPs | Genes involved in SNPs | Biological Significance |
Clinical remission (Mayo ≤2) | 344 (52.92%) | 41 (9 protective, 32 risk-increasing) | RGS1, HLA‑DQA1 region, MAPT locus, IL7R, FHIT | Immune system regulation (T cell activation, lymphocyte trafficking), DNA damage response and epithelial integrity, microtubule stability |
Endoscopic improvement (MES 1) | 216 (33.23%) | 25 (23 protective and 2 risk increasing) | RGS1 and genes of unknown functions | Immune system regulation (lymphocyte trafficking) |
Histological improvement (Geboes < 3.1) | 237 (36.46%) | 5 (all protective) | RGS1 | Immune system regulation (lymphocyte trafficking) |
Endoscopic remission (MES 0) | 123 (18.92 %) | 10 (8 protective 2 risk-increasing) | MAPT locus, RGS1, C12orf65, SLC4A10 | Immune system regulation (T cell activation, lymphocyte trafficking, microtubule stability, regulatory function) |
Histological remission (Geboes < 2B.0) | 194 (29.84%) | 4 (all risk increasing) | RGS1, FHIT, Il7R | Immune system regulation (T cell activation, lymphocyte trafficking), microtubule stability, DNA damage response and epithelial integrity |
| Mucosal healing (endoscopic and histological remission) | 102 (15.69 %) | 14 (8 protective 6 risk-increasing) | MAPT locus, RGS1, C12orf65, SLC4A10, FHIT, Il7R | Immune system regulation (T cell activation, lymphocyte trafficking), microtubule stability, DNA damage response and epithelial integrity, regulatory function |
Conclusion
Genome-wide SNPs signatures identify patients more likely to achieve a deep response to Ustekinumab, supporting the feasibility of genetically guided biologic selection in UC. These findings represent a step towards precision therapy in IBD. Further integration with multi-Omics data is ongoing to refine this predictive framework.
References
[1] Turner D, Ricciuto A, Lewis A, et al. STRIDE-II: An Update on the Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE) Initiative of the International Organization for the Study of IBD (IOIBD): Determining Therapeutic Goals for Treat-to-Target strategies in IBD. Gastroenterology. 2021;160(5):1570-1583. doi:10.1053/j.gastro.2020.12.031
[2] Plaza J, Mínguez A, Bastida G, et al. Genetic Variants Associated with Biological Treatment Response in Inflammatory Bowel Disease: A Systematic Review. Int J Mol Sci. 2024;25(7):3717. 2024. doi:10.3390/ijms25073717
[3] van der Werf J, Fleming NI. Are single nucleotide polymorphisms underutilized for guiding treatment of inflammatory bowel disease?. Immunol Cell Biol. 2025;103(6):551-562. doi:10.1111/imcb.70029
[4] Sands BE, Sandborn WJ, Panaccione R, et al. Ustekinumab as Induction and Maintenance Therapy for Ulcerative Colitis. N Engl J Med. 2019;381(13):1201-1214. doi:10.1056/NEJMoa1900750
[5] Chang C. C., Chow C. C., Tellier L. C., et al. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015; 4(1), s13742-015.
[6] Fercoq F. & Carlin L. M. “Mind the GAP”: RGS1 hinders antitumor lymphocytes. Nature Immunology. 2021; 22(7), 802-804.