Kadhim, A. Z. | bioRxiv Science

bioRxiv2026

Characterisation of Genetically-Derived Patient Clusters Highlights Genetic Heterogeneity of Inflammatory Bowel Disease

Background and aims. Inflammatory Bowel Disease (IBD) is a complex immune-mediated condition with a strong genetic contribution. The genetics of IBD are highly complex, with inflammation, autoimmunity, and mucosal immunity pathways involved in its pathogenicity. GenePy is a gene-level disease burden metric. The integration of clinical and genetic data and the application of machine learning methods can aid patient stratification for personalised care. Methods. Lists of consensus IBD pathway genes were curated. GenePy scores were computed from whole exome sequencing data. A K-Means algorithm was optimised using clustering quality and stability metrics on the GenePy scores of genes in each IBD pathway, and the results replicated in three independent IBD cohorts (SPARC IBD, MSCCR IBD, and Southampton IBD). Chi-square tests assessed the association between cluster assignment and phenotypic features, and were multiple test corrected via Benjamini-Hochberg FDR. Results. A strong association was replicated for NOD signalling genes driving IBD subtype, Crohns disease behaviour, and IBD surgery across all cohorts, as well as granuloma in Southampton IBD. This was mainly driven by NOD2. Similar genetic clustering patterns were observed across all cohorts, with additional phenotypic enrichment in clusters driven by NLRP1 (surgery in MSCCR IBD), and nominally significant enrichment for disease behaviour linked to BIRC2 (B2 in Southampton IBD and B2B3 in SPARC IBD). Conclusions. This analysis identified a common genetic architecture across NOD signalling genes across IBD cohorts, replicated a signal for NOD2 as a monogenic driver of disease with a strong phenotypic enrichment, and identified other putative genetic drivers of IBD, such as the NLRP1 gene.

bioinformatics↗

bioRxiv2019

Mediator subunit MDT-15/MED15 and Nuclear Receptor HIZR-1/HNF4 cooperate to regulate toxic metal stress responses in Caenorhabditis elegans

Zinc is essential for cellular functions as it is a catalytic and structural component of many proteins. In contrast, cadmium is not required in biological systems and is toxic. Zinc and cadmium levels are closely monitored and regulated as their excess causes cell stress. To maintain homeostasis, organisms induce metal detoxification gene programs through stress responsive transcriptional regulatory complexes. In Caenorhabditis elegans, the MDT-15 subunit of the evolutionarily conserved Mediator transcriptional coregulator is required to induce genes upon exposure to excess zinc and cadmium. However, the regulatory partners of MDT-15 in this response, its role in cellular and physiological stress adaptation, and the putative role mammalian for MED15 in the metal stress responses remain unknown. Here, we show that MDT-15 interacts physically and functionally with the Nuclear Hormone Receptor HIZR-1 to promote molecular, cellular, and organismal adaptation to excess metals. Using gain- and loss-of-function mutants and qPCR and reporter analysis, we find that mdt-15 and hizr-1 cooperate to induce zinc and cadmium responsive genes. Moreover, the two proteins interact physically in yeast-two-hybrid assays and this interaction is enhanced by the addition of zinc or cadmium, the former a known ligand of HIZR-1. Functionally, mdt-15 and hizr-1 mutants show defective storage of excess zinc in the gut, and at the organismal level, mdt-15 mutants are hypersensitive to zinc- and cadmium-induced reductions in egg-laying. Lastly, mammalian MDT-15 orthologs bind genomic regulatory regions of metallothionein and zinc transporter genes in a metal-stimulated fashion, and human MED15 is required to induce a metallothionein gene in lung adenocarcinoma cells exposed to cadmium. Collectively, our data show that mdt-15 and hizr-1 cooperate to regulate metal detoxification and zinc storage and that this mechanism appears to be at least partially conserved in mammals.

genetics↗