Publications

Epigenetic changes contribute to colorectal cancer (CRC) pathogenesis. We investigated whether methylation quantitative trait loci (mQTLs) are associated with CRC risk, survival and recurrence. Using a well-characterised Scottish case-control study (6821 CRC cases, 14,692 controls), we derived 118,982 mQTLs based on the Genetics of DNA Methylation Consortium (GoDMC). Association analysis between mQTLs and CRC risk, survival and recurrence was performed using logistic regression or Cox models respectively. Additionally, colocalisation analysis was performed. 19 mQTLs within 10 distinct genomic regions were associated with CRC risk. Two novel regions were mapped to MDGA2 (p value = 3.0×10−6\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$3.0 \times\!{10}^{-6}$$\end{document}) and STARD3 (p value = 5.6×10−6\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$5.6 \times\!{10}^{-6}$$\end{document}). Four regions mapped to POU5F1B, POU2AF2 (c11orf53)/POU2AF3 (COLCA2), GREM1 and CABLES2 were previously identified. Four regions mapped to PPA2, PANDAR/LAP3P2, POU6F1 and CTIF contained SNPs previously identified by CRC GWAS but with SNPs annotated to different genes. We found no evidence that any of the 19 mQTLs associated with CRC risk influenced survival or recurrence after FDR correction. Colocalisation analysis suggested that in three of the ten regions the causal variants were shared for methylation and CRC risk. This study adds to the repertoire of CRC genes. However, we found no associations between methylation and CRC survival or recurrence.

The “omnigenic” hypothesis postulates that the polygenic effects of common variants on a typical complex trait coalesce on relatively few core genes through trans-effects on their expression. Our aim was to identify core genes for systemic lupus erythematosus (SLE) by testing for association with genome-wide aggregated trans-effects (GATE) scores for gene expression in a large genetic dataset (5267/4909 SLE cases/controls). SLE was strongly associated with upregulation of expression of eight interferon-stimulated genes driven by shared trans-effects. We estimate that trans-effects on interferon signaling account for 9% of the total genetic effect on SLE risk. Outside this pathway, GATE analysis detected twenty putative core genes for SLE. Direct protein measurements for these genes were strongly associated with SLE in UK Biobank. Two putative core genes (TNFRSF17, TNFRSF13B) encode receptors (BCMA, TACI) expressed on B cells; their ligands (BAFF, APRIL) are targeted by drugs licensed or in development for SLE. Four genes (PDCD1, LAG3, TNFRSF9, CD27) encode receptors that have been characterized as immune checkpoints, and three (CD5L, SIGLEC1, CXCL13) are biomarkers of SLE disease activity. These results provide genetic support for existing drug targets in SLE (interferon signaling, BAFF/APRIL signaling) and identify other possible therapeutic targets including immune checkpoint receptors.

The “omnigenic” hypothesis postulates that polygenic effects of common variants on typical complex traits coalesce via trans effects on the expression of a relatively sparse set of “core” effector genes and their encoded proteins in relevant tissues. The objective of this study was to identify core proteins for type 1 diabetes. We used summary statistics for single nucleotide polymorphism associations with plasma levels of 5,130 proteins in three large cohorts, including the UK Biobank, to compute genome-wide aggregated trans effects (GATE) scores for protein levels in two type 1 diabetes case-control studies (6,828 case individuals, 416,000 control individuals). GATE scores for 27 proteins were associated with type 1 diabetes. Of these, 14 were replicated between data sets, 11 had support in Mendelian randomization analysis, and 9 had experimental support in mouse models of autoimmune diabetes. The strongest associations were for immune checkpoints (PDCD1, CD5, TIGIT, and LAG3), chemokines, and innate immune system proteins (NCR1 and KLRB1). While PDCD1 is a known cause of monogenic autoimmune diabetes, neither it nor most of the core proteins identified here were previously reported as genome-wide association study hits for type 1 diabetes. These results identify possible drug targets with genetic support for causality and suggest that programmed cell death protein 1 agonists under development for other indications should be trialed for type 1 diabetes prevention. Article Highlights Demonstrating genetic evidence for a role of a protein in disease gives important support for its potential as a drug target. We aimed to identify proteins that have genetic evidence to support a causal role in the pathogenesis of type 1 diabetes. We found 27 core proteins had genetic evidence of causality for type 1 diabetes. Top hits included immune checkpoints (PDCD1, CD5, TIGIT, and LAG3) and innate immune system proteins (NCR1 and KLRB1). These results identify possible drug targets and suggest that programmed cell death protein 1 agonists should be trialed for type 1 diabetes prevention.

Abstract Background Genome-wide association studies of inflammatory bowel disease have identified hundreds of common genetic variants that are associated with inflammatory bowel disease, but few promising therapeutic targets. The “omnigenic” sparse effector hypothesis postulates that the polygenic effects of common SNPs on a typical complex trait are mediated by trans-effects that coalesce on the expression of a sparse set of core genes. The objective of this study was to identify core genes for inflammatory bowel disease. Methods Using summary statistics from studies of transcript levels in whole blood or proteins in plasma, we constructed genome-wide aggregated trans-effects (GATE) scores for predicted gene expression in the UK Biobank cohort and tested these scores for association with inflammatory bowel disease (7949 cases, 452 790 noncases). Results Inflammatory bowel disease was inversely associated with GATE scores for 5 interferon-stimulated genes—IFIT1, IFI44, HERC5, MX1, IFI44L—regulated by the same trans-expression quantitative trait locus, and with the GATE score for IFNL1. For 6 other genes, GATE score associations with inflammatory bowel disease were supported by other criteria: reported associations with nearby genetic variants, perturbation in experimental models, association with measured protein levels, or drug effects. Conclusions These results implicate down-regulation of Type III interferon signaling as a core pathway in the etiology of inflammatory bowel disease, supported by reports of monogenic inflammatory bowel disease caused by rare loss-of-function variants and by perturbation in experimental models of colitis. Deficient Type III interferon signaling may be amenable to therapeutic intervention.

The sparse effector “omnigenic” hypothesis postulates that the polygenic effects of common single nucleotide polymorphisms (SNPs) on a typical complex trait are mediated by trans effects that coalesce on expression of a relatively sparse set of core genes. The objective of this study was to identify core genes for rheumatoid arthritis by testing for association of rheumatoid arthritis with genome‐wide aggregated trans effects (GATE) scores for expression of each gene as transcript in whole blood or as circulating protein levels.

Objective Genome-wide association studies have successfully identified more than 100 loci associated with susceptibility to rheumatoid arthritis (RA). However, our understanding of the functional effects of genetic variants in causing RA and their effects on disease severity and response to treatment remains limited. Methods In this study, we conducted expression quantitative trait locus (eQTL) analysis to dissect the link between genetic variants and gene expression comparing the disease tissue against blood using RNA-Sequencing of synovial biopsies (n=85) and blood samples (n=51) from treatment-naïve patients with RA from the Pathobiology of Early Arthritis Cohort. Results This identified 898 eQTL genes in synovium and genes loci in blood, with 232 genes in common to both synovium and blood, although notably many eQTL were tissue specific. Examining the HLA region, we uncovered a specific eQTL at HLA-DPB2 with the critical triad of single-nucleotide polymorphisms (SNPs) rs3128921 driving synovial HLA-DPB2 expression, and both rs3128921 and HLA-DPB2 gene expression correlating with clinical severity and increasing probability of the lympho-myeloid pathotype. Conclusions This analysis highlights the need to explore functional consequences of genetic associations in disease tissue. HLA-DPB2 SNP rs3128921 could potentially be used to stratify patients to more aggressive treatment immediately at diagnosis.

Identified genetic loci for C-peptide and age at diagnosis (AAD) in individuals with type 1 diabetes (T1D) explain only a small proportion of their variation. Here, we aimed to perform large meta–genome-wide association studies (GWAS) of C-peptide and AAD in T1D and to identify the HLA allele/haplotypes associated with C-peptide and AAD. A total of 7,252 and 7,923 European individuals with T1D were included in C-peptide and AAD GWAS, respectively. HLA-DQB1*06:02, which is strongly protective against T1D, was associated with higher C-peptide. HLA-DQB1*03:02, HLA-DRB1*03:01, and HLA-A*24:02, which increase T1D risk, were independently associated with younger AAD. HLA-DR3-DR4 haplotype combination, the strongest T1D susceptibility factor, was associated with younger AAD. Outside the HLA region, rs115673528 on chromosome 5 (Chr5) (GABRG2) was associated with C-peptide, and an indel, rs111970692, on Chr15 within CTSH, a known T1D locus, was associated with AAD. Genetically predicted CTSH expression, methylation, and protein levels were associated with AAD. Mendelian randomization analysis suggested that higher levels of pro-cathepsin H reduced AAD. In conclusion, some HLA allele/haplotypes associated with T1D also contribute to variability of C-peptide and AAD. Outside HLA, T1D loci were generally not associated with C-peptide or AAD. CTSH could be a potential therapeutic target to delay development/progression of T1D. Article Highlights Identified genetic loci for C-peptide and type 1 diabetes (T1D) age at diagnosis (AAD) explain only a small proportion of their variation. We aimed to identify additional genetic loci associated with C-peptide and AAD. Some HLA allele/haplotypes associated with T1D also contributed to variability of C-peptide and AAD, whereas outside the HLA region, T1D loci were mostly not associated with C-peptide or AAD. Genetic variation within CTSH can affect AAD. There is still residual heritability of C-peptide and AAD outside of HLA that could benefit from larger meta–genome-wide association studies.

The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel drug targets for SLE. This study reveals possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and novel disease-specific meQTLs. Finally, novel targets for drug development were discovered.

Summary The “omnigenic” hypothesis postulates that the polygenic effects of common SNPs on a typical complex trait are mediated through trans-effects on expression of a relatively sparse set of effector (“core”) genes. We tested this hypothesis in a study of 4,964 cases of type 1 diabetes (T1D) and 7,497 controls by using summary statistics to calculate aggregated (excluding the HLA region) trans-scores for gene expression in blood. From associations of T1D with aggregated trans-scores, nine putative core genes were identified, of which three—STAT1, CTLA4 and FOXP3—are genes in which variants cause monogenic forms of autoimmune diabetes. Seven of these genes affect the activity of regulatory T cells, and two are involved in immune responses to microbial lipids. Four T1D-associated genomic regions could be identified as master regulators via trans-effects on gene expression. These results support the sparse effector hypothesis and reshape our understanding of the genetic architecture of T1D.

Current methods for Mendelian randomization studies have several limitations: to construct unlinked genetic instruments they can use only one SNP from each clump of exposure-associated SNPs, they require that weak instruments are excluded, and they rely on makeshift procedures for downweighting outliers to allow inference of causality in the presence of pleiotropic effects. This paper describes methods that overcome these limitations. A scalar instrument is constructed from all exposure-associated SNPs in each clump, and inference of causality is based on marginalizing over the distribution of pleiotropic effects. To demonstrate the approach, we tested the effect of circulating levels of adiponectin, encoded by ADIPOQ, on the risk of type 2 diabetes. Genotypic instruments were constructed from 24 unlinked trans-pQTLs detected in Icelanders using the Somalogic platform and 43 detected in the UK Biobank study using the Olink platform. These instruments were tested for association with type 2 diabetes in a non-overlapping subset of the UK Biobank cohort. In contrast to the results of earlier Mendelian randomization studies of adiponectin that used only a cis-pQTL, with multiple trans-pQTLs there was clear evidence for a causal effect: standardized log odds ratio -0.38 (95% CI -0.5 to -0.25) using DeCODE instruments and -0.33 (95% CI -0.43 to -0.23) using UK Biobank instruments. Guidelines for the design of Mendelian randomization studies that recommend exclusion of weak instruments, or restricting the instruments to cis-acting variants where the exposure under study is a gene transcript or gene product, should be reassessed.

Objective. The heterogeneity of systemic lupus erythematosus (SLE) can be explained by epigenetic alterations that disrupt transcriptional programs mediating environmental and genetic risk. This study evaluated the epigenetic contribution to SLE heterogeneity considering molecular and serological subtypes, genetics and transcriptional status, followed by drug target discovery. Methods. We performed a stratified epigenome-wide association studies of whole blood DNA methylation from 213 SLE patients and 221 controls. Methylation quantitative trait loci analyses, cytokine and transcription factor activity - epigenetic associations and methylation-expression correlations were conducted. New drug targets were searched for based on differentially methylated genes. Results. In a stratified approach, a total of 974 differential methylation CpG sites with dependency on molecular subtypes and autoantibody profiles were found. Mediation analyses suggested that SLE-associated SNPs in the HLA region exert their risk through DNA methylation changes. Novel genetic variants regulating DNAm in disease or in specific molecular contexts were identified. The epigenetic landscapes showed strong association with transcription factor activity and cytokine levels, conditioned by the molecular context. Epigenetic signals were enriched in known and novel potential drug targets for SLE. Conclusion. This study expands the number of genes associated with SLE and reveals novel pathways of disease. The findings reveal possible genetic drivers and consequences of epigenetic variability on SLE heterogeneity and disentangles the DNAm mediation role on SLE genetic risk and the genetic architecture of DNAm in different molecular contexts. Finally, novel targets for drug development were discovered.

Genome‐wide association studies (GWAS) have identified several risk loci for gallstone disease. As with most polygenic traits, it is likely that many genetic determinants are undiscovered. The aim of this study was to identify genetic variants that represent new targets for gallstone research and treatment.

Objective: Genome-wide association studies (GWAS) have identified several risk loci for gallstone disease. As with most polygenic traits, it is likely many genetic determinants are undiscovered. The aim of this study was to identify novel genetic variants that represent new targets for gallstone research and treatment. Design: We performed a GWAS of 28,627 gallstone cases and 348,373 controls in the UK Biobank and a GWA meta-analysis (43,639 cases and 506,798 controls) with the FinnGen cohort. We assessed pathway enrichment using gene-based then gene-set analysis and tissue expression of implicated genes in Genotype-Tissue Expression project data. We constructed a polygenic risk score (PRS) and evaluated phenotypic traits associated with the score. Results: Seventy-five risk loci were identified (P<5*10-8) of which forty-six were novel. Pathway enrichment revealed associations with lipid homeostasis, glucuronidation, phospholipid metabolism and gastrointestinal motility. ANO1 and TMEM147, both in novel loci, are strongly expressed in the gallbladder and gastrointestinal tract. Both regulate gastrointestinal motility. The gallstone risk allele rs7599-A leads to suppression of hepatic TMEM147 expression suggesting the protein protects against gallstone formation. Individuals in the highest decile of the PRS demonstrated a 6-fold increased risk of gallstones compared to the lowest risk category. The PRS was strongly associated with increased body mass index, serum liver enzyme and C-reactive protein concentrations and decreased lipoprotein cholesterol concentrations. Conclusion: This GWAS demonstrates the polygenic nature of gallstone risk and identifies 46 novel susceptibility loci. For the first time, we implicate genes influencing gastrointestinal motility in the pathogenesis of gallstones.

Fidelity of cell division depends on the ability of an internal cell structure called the mitotic spindle, to maintain the structural integrity of the cellular architecture despite being subject to high compressive loading. We propose a generic software tool called Spindle FEA that employs continuum mechanics and finite elements analysis (FEA) code Abaqus CAE to study the stability of mitotic spindles in various phases of mitosis. The proposed application has a modular structure which allows easy modification of any part of the analysis which is of particular importance considering that new knowledge of spindles is constantly emerging. Thanks to the highly optimised finite element solver used in Abaqus CAE, Spindle FEA is highly suitable for large multi-parametric studies which in turn may significantly benefit the planning of new experiments or identifying new key properties of the spindle. We also discuss the main physiological properties of spindles and show how they are modelled with the proposed technique as well as discuss all the essential analysis steps. We use Spindle FEA to study the buckling of a mitotic spindle in anaphase B to show how the additional stiffness of the lateral support of the spindle affects the left-right symmetry of cell division as well as to demonstrate the capacities of the proposed technique.

The article is dedicated to the discussion on the exact dynamic stiffness matrix method applied to the problems of elastic stability of engineering structures. The detailed formulation of the member dynamic stiffness matrix for beams is presented along with the general guidelines on automatisation of the assembly of member dynamic stiffness matrices into the global matrix that corresponds to the whole structure. The advantage of the dynamic stiffness matrix in case of parametric studies is explained. The problem of computing the eigenvalues of transcendental matrix is addressed. The straightforward approach as well as a powerful Witrick-Williams algorithm are discussed in details. The general guidelines on programming the DS matrix method are given as well.