MRC Institute of Genetics and Molecular Medicine

Metformin, a mainstay of treatment for type 2 diabetes, can cause vitamin B12 deficiency. Clinical risk factors have been identified but genetic factors remain undiscovered. Our objective was to identify and validate genetic predisposing factors and establish clinical utility. Individuals with metformin-induced vitamin B12 deficiency (n=487) and metformin-tolerant control individuals (n=6686) were identified in UK Biobank. Genome-wide association analysis was undertaken using logistic regression. Replication was undertaken in three cohorts: a Scottish cohort; the Diabetes Prevention Program Outcomes Study (DPPOS); and a separate cohort from Liverpool. In the Liverpool cohort, plasma metformin levels were also measured. Analysis identified a genome-wide significant non-synonymous SNP in the cubilin gene (CUBN, rs1801222/p.S253F) associated with metformin-induced vitamin B12 deficiency (additive model; adjusted p=1.86×10-10; OR 1.56 [95% CI 1.36, 1.79] for AG vs GG genotype; OR 2.43 [95% CI 1.85, 3.20] for AA vs GG genotype), which was replicated in both the Scottish and the DPPOS cohorts. Vitamin B12 deficiency occurred in 0.84-1.20% of non-metformin-exposed individuals regardless of rs1801222 genotype. However, a large interaction with metformin use was observed, with vitamin B12 deficiency occurring at 6.02% in GG, 7.96% in GA and 12.84% in AA genotype groups. When followed up from metformin initiation, 10% with the AA genotype were vitamin B12 deficient by 11 years vs 21 years for 10% of the GG group. The observed genetic association suggests that the rs180122 genotype should be considered a significant risk factor for metformin-induced vitamin B12 deficiency. While clinical monitoring of serum vitamin B12 levels in patients on metformin is inconsistently done, this finding highlights the potential clinical utility of targeted monitoring for certain subsets of individuals, including those genetically at high risk.

Objective Risankizumab is an interleukin-23 p19 subunit inhibitor which received approval for Crohn’s disease (CD) by UK licensing authorities in May 2023. Our aim was to evaluate the real-world outcomes of risankizumab in the UK. Design We conducted a retrospective, multicentre, cohort study of patients with CD treated with risankizumab across 25 health boards in the UK between 1 January 2021 and 1 November 2024. Our primary outcome was treatment persistence at 6 months. Our secondary endpoints were steroid-free clinical remission (Harvey-Bradshaw index <5), C-reactive protein (CRP) remission (CRP ≤5 mg) and faecal calprotectin (FCAL) remission (FCAL <250 µg/g). Results We included 763 patients with a median follow-up time of 27 weeks (IQR 18–41 weeks) with a total of 432 and 110 patients having 6-month and 12-month data available. The median number of advanced therapy exposures was 3 (2–4), with 92% (704/763) having failed anti-tumour necrosis factor therapy and 72% (548/763) having failed ustekinumab. Treatment persistence at 6 and 12 months was 95.4% and 89.2%, respectively. Unadjusted persistence rates for ustekinumab-naive versus ustekinumab-exposed patients were 92.7% vs 95.3% and 89.0% vs 74.2% at 6 and 12 months, respectively (p=0.62). Rates of clinical, CRP and FCAL remission were 52% (123/236), 53% (169/319) and 44% (69/156) at 6 months. Rates of clinical remission for ustekinumab naive versus exposed were 57% (29/51) vs 51% (94/185) (p=0.54) 6 months. Adverse events occurred in 17% (n=127) of the cohort, of which 12% (n=92) were serious. Conclusion Risankizumab was effective in a large, real-world, medically refractory CD cohort with excellent persistence and good clinical and biochemical remission rates.

Vitamin D status is influenced by genetic and environmental factors—primarily sun exposure. Using satellite weather data, we estimated an ambient UVB dose for each participant based on residential address and date of sampling. We conducted genome-wide tests in 338,977 UK Biobank White British participants, adjusted for age, sex, supplements, UVB dose, and 10 principal components to account for population structure. We applied three models to test for genetic effects: marginal only, main and interaction, and joint effects. We identified 307 variants associated with standardised log-transformed 25-hydroxyvitamin D (25OHD) concentration, 162 of which were not previously identified in GWAS. We identify an increase in SNP-heritability by increasing ambient UVB exposure quintiles (h2Q1 = 8.48% vs. h2Q5 = 15.56%). Downstream annotation implicated genes in the 25OHD pathway, including the circadian regulator, BMAL1. This and further findings suggest that vitamin D status and circadian rhythm may be entangled and that vitamin D metabolites may have a role as mediators of seasonal physiological fluctuations, including metabolism, and in turn explain the established associations with lipid metabolism pathways.

Pericentromeric heterochromatin (PCH) is delineated by the enrichment of repressive epigenetic modifications, specifically trimethylated histone H3 at lysine 9 (H3K9me3) and DNA methylation (5-methylcytosine), which establish and maintain a condensed, transcriptionally silenced chromatin state. Depletion of either H3K9me3 or DNA methylation in mouse embryonic stem cells (mESCs) induces a permissive chromatin configuration that permits de novo recruitment and deposition of normally excluded Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2), characterized by H2AK119ub1 and H3K27me3 modifications, respectively, at PCH. Here, we demonstrate that H2AK119ub1 and H3K27me3 are independently recruited to hypomethylated PCH using a doxycycline-inducible mESC model allowing modulation of Dnmt1 expression levels and catalytic activity. We further investigate the roles of proposed mediators of PRC1/2 targeting, including SCML2, BEND3, KDM2b, and TET enzymes, in this context, our findings indicate that neither PRC1 nor PRC2 recruitment at hypomethylated PCH depends on these factors. Additionally, our data suggest that the permissive chromatin environment resulting from DNA hypomethylation is the principal facilitator of Polycomb complex spreading, offering novel insights into the mechanisms governing epigenetic modifier dynamics and interactions during periods of DNA methylation reprogramming.

Human facial appearance is a highly variable morphological trait, with both rare and common genetic variants shaping craniofacial morphology between individuals and in disease. Deletions encompassing an enhancer cluster 1.45 megabases upstream of SOX9 (EC1.45) cause Pierre Robin sequence, a craniofacial disorder characterised by underdevelopment of the lower jaw and associated with cleft palate. We hypothesised therefore that single nucleotide variants within EC1.45 may cause more subtle alterations in facial form. Leveraging recent human evolution, and the distinct jaw morphology of Neanderthals, we investigated the impact of three Neanderthal-derived variants on EC1.45 function. Using zebrafish dual enhancer-reporters, we observed higher activity of Neanderthal EC1.45 in neural crest-derived progenitor cells during a specific developmental window. These EC1.45-active cells reside proximal to and are transcriptionally related to precartilaginous condensations that contribute to craniofacial skeletal development. Mimicking the observed increase in enhancer activity, we overexpressed human SOX9 in EC1.45-active cells and detected an expanded volume of developing cartilaginous precursors. Our work implicates Neanderthal-derived variants in increasing regulatory activity for a disease-associated enhancer, with the potential to impact craniofacial morphology across recent hominin evolution.

Polygenic indexes (PGIs) — DNA-based predictors of individual phenotypes — have become essential tools across biomedical and social sciences. We introduce Version 2 of the Polygenic Index Repository, which expands phenotype coverage from 47 to 61, increases the number of participating datasets from 11 to 20, and adopts a more consistent and improved methodology for PGI construction. For 16 phenotypes, we leverage summary statistics from an updated GWAS meta-analysis with greater statistical power compared to the original release, thereby improving the PGI’s predictive power. To improve power for family-based analyses, we provide imputed parental PGIs in all datasets with first-degree relatives and offer a framework for interpreting results from analyses that control for parental PGIs. We illustrate the utility of parental PGIs using two applications: (1) comparing PGI associations with and without parental PGI controls for all phenotypes in two Repository datasets with family data, and (2) for BMI and diastolic blood pressure, exploring the contribution of causal versus non-causal components of PGI associations to the imperfect portability of PGIs across subgroups within a genetic ancestry. Collectively, the updates enhance predictive performance, broaden the Repository’s scope, and introduce novel resources that reduce confounding bias and improve interpretability.

ABSTRACTBackgroundThe impact of advanced therapy prescribing on colectomy rates in ulcerative colitis (UC) is unknown with conflicting published evidence.AimTo describe advanced therapy prescribing trends and colectomy rates for patients with UC in Lothian, UK between January 1st, 2004 and December 31st, 2023.MethodsWe obtained incidence and prevalence data from the Lothian IBD Registry, a rigorously validated population cohort. We report advanced therapy prescribing and colectomy data as raw numbers and annual incidence rates. We used piecewise linear regression analyses to identify temporal trends in prescription and colectomy rates.ResultsThe prevalence of UC increased from 216 to 441 per 100,000 population in the 20 years from 2004, culminating in a total of 4115 patients with UC in 2023. We identified 720 patients who had received an advanced therapy. Prescribing of first‐line advanced therapy increased from 0 in 2004 to 115 in 2023, equating to 0.00 and 2.82 per 100 patients with UC. We identified 563 patients of the prevalent UC population who had colectomy, of whom 68% were performed as emergencies. Absolute colectomy numbers decreased from 42 in 2004 to 7 in 2023, equating to 2.48 and 0.22 per 100 patients with UC. A join point in 2013 was found for both increased advanced therapy prescribing and decreased colectomy rates.ConclusionThe incidence of colectomy in the UC population has decreased over time while the use of advanced therapies has greatly increased.

Perturbation studies using gene knockouts have become a key tool for understanding the roles of regulatory genes in development. However, large-scale studies dissecting the molecular role of development master regulators in every cell type throughout the embryo are technically challenging and scarce. Here, we systematically characterize the knockout effects of the key developmental regulators T/Brachyury and Mixl1 in gastrulation and early organogenesis using single-cell profiling of chimeric mouse embryos. For the analysis of these experimental data, we present COSICC, an effective suite of statistical tools to characterize perturbation effects in complex developing cell populations. We gain insights into T's role in lateral plate mesoderm, limb development, and posterior intermediate mesoderm specification. Furthermore, we generate Mixl1 -/- embryonic chimeras and reveal the role of this key transcription factor in discrete mesoderm lineages, in particular concerning developmental dysregulation of the recently identified juxta-cardiac field.

Mutations in the non-coding RNA gene RNU4ATAC are associated with growth restriction and complications related to antibody deficiency. Here, we report that innate immune dysfunction is a previously unrecognised feature of this disorder. In particular, painful chilblain-like lesions are common in RNU4ATAC patients and are linked to dysregulated type I interferon signalling.

Despite massive sequencing efforts, understanding the difference between human pathogenic and benign variants remains a challenge. Computational variant effect predictors (VEPs) have emerged as essential tools for assessing the impact of genetic variants, although their performance varies. Initially, sequence-based methods dominated the field, but recent advances, particularly in protein structure prediction technologies like AlphaFold, have led to an increased utilization of structural information by VEPs aimed at scoring human missense variants. This review highlights the progress in integrating structural information into VEPs, showcasing novel models such as AlphaMissense, PrimateAI-3D, and CPT-1 that demonstrate improved variant evaluation. Structural data offers more interpretability, especially for non-loss-of-function variants, and provides insights into complex variant interactions in vivo. As the field advances, utilizing biomolecular complex structures will be pivotal for future VEP development, with recent breakthroughs in protein-ligand and protein-nucleic acid complex prediction offering new avenues.