Clinical Gene Networks AB

Stockholm, Sweden

Clinical Gene Networks AB

Stockholm, Sweden
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Miller C.L.,Stanford University | Pjanic M.,Stanford University | Wang T.,Stanford University | Nguyen T.,Stanford University | And 21 more authors.
Nature Communications | Year: 2016

Coronary artery disease (CAD) is the leading cause of mortality and morbidity, driven by both genetic and environmental risk factors. Meta-analyses of genome-wide association studies have identified >150 loci associated with CAD and myocardial infarction susceptibility in humans. A majority of these variants reside in non-coding regions and are co-inherited with hundreds of candidate regulatory variants, presenting a challenge to elucidate their functions. Herein, we use integrative genomic, epigenomic and transcriptomic profiling of perturbed human coronary artery smooth muscle cells and tissues to begin to identify causal regulatory variation and mechanisms responsible for CAD associations. Using these genome-wide maps, we prioritize 64 candidate variants and perform allele-specific binding and expression analyses at seven top candidate loci: 9p21.3, SMAD3, PDGFD, IL6R, BMP1, CCDC97/TGFB1 and LMOD1. We validate our findings in expression quantitative trait loci cohorts, which together reveal new links between CAD associations and regulatory function in the appropriate disease context.

Talukdar H.A.,Karolinska Institutet | Asl H.,Karolinska Institutet | Jain R.K.,University of Tartu | Ermel R.,University of Tartu | And 22 more authors.
Cell Systems | Year: 2016

Inferring molecular networks can reveal how genetic perturbations interact with environmental factors to cause common complex diseases. We analyzed genetic and gene expression data from seven tissues relevant to coronary artery disease (CAD) and identified regulatory gene networks (RGNs) and their key drivers. By integrating data from genome-wide association studies, we identified 30 CAD-causal RGNs interconnected in vascular and metabolic tissues, and we validated them with corresponding data from the Hybrid Mouse Diversity Panel. As proof of concept, by targeting the key drivers AIP, DRAP1, POLR2I, and PQBP1 in a cross-species-validated, arterial-wall RGN involving RNA-processing genes, we re-identified this RGN in THP-1 foam cells and independent data from CAD macrophages and carotid lesions. This characterization of the molecular landscape in CAD will help better define the regulation of CAD candidate genes identified by genome-wide association studies and is a first step toward achieving the goals of precision medicine. Well-established atherosclerosis risk factors and pathways are shown to operate through regulatory gene networks, active both within and across vascular and metabolic tissues, to cause coronary artery disease (CAD). Within these CAD-causal networks, the hierarchical order and connectivity patterns of both established and new genes in CAD, including so-called key disease driver genes, advance not only our global understanding of the molecular landscape in CAD but also reveal new candidate genes that may serve as suitable drug targets. © 2016 The Authors.

Foroughi Asl H.,Cardiovascular Genomics Group | Talukdar H.A.,Cardiovascular Genomics Group | Kindt A.S.D.,University of Edinburgh | Jain R.K.,University of Tartu | And 21 more authors.
Circulation: Cardiovascular Genetics | Year: 2015

Background-Despite recent discoveries of new genetic risk factors, the majority of risk for coronary artery disease (CAD) remains elusive. As the most proximal sensor of DNA variation, RNA abundance can help identify subpopulations of genetic variants active in and across tissues mediating CAD risk through gene expression. Methods and Results-By generating new genomic data on DNA and RNA samples from the Stockholm Atherosclerosis Gene Expression (STAGE) study, 8156 cis-acting expression quantitative trait loci (eQTLs) for 6450 genes across 7 CAD-relevant tissues were detected. The inherited risk enrichments of tissue-defined sets of these eQTLs were assessed using 2 independent genome-wide association data sets. eQTLs acting across increasing numbers of tissues were found increasingly enriched for CAD risk and resided at regulatory hot spots. The risk enrichment of 42 eQTLs acting across 5 to 6 tissues was particularly high (≤7.3-fold) and confirmed in the combined genome-wide association data from Coronary Artery Disease Genome Wide Replication And Meta-Analysis Consortium. Sixteen of the 42 eQTLs associated with 19 master regulatory genes and 29 downstream gene sets (n>30) were further risk enriched comparable to that of the 153 genome-wide association risk single-nucleotide polymorphisms established for CAD (8.4-fold versus 10-fold). Three gene sets, governed by the master regulators FLYWCH1, PSORSIC3, and G3BP1, segregated the STAGE patients according to extent of CAD, and small interfering RNA targeting of these master regulators affected cholesterol-ester accumulation in foam cells of the THP1 monocytic cell line. Conclusions-eQTLs acting across multiple tissues are significant carriers of inherited risk for CAD. FLYWCH1, PSORSIC3, and G3BP1 are novel master regulatory genes in CAD that may be suitable targets. © 2015 American Heart Association, Inc.

Schadt E.E.,Mount Sinai School of Medicine | Bjorkegren J.L.M.,Cardiovascular Genomics | Bjorkegren J.L.M.,University of Tartu | Bjorkegren J.L.M.,Clinical Gene Networks AB
Science Translational Medicine | Year: 2012

Complete repertoires of molecular activity in and between tissues provided by new high-dimensional "omics"technologies hold great promise for characterizing human physiology at all levels of biological hierarchies. The combined effects of genetic and environmental perturbations at any level of these hierarchies can lead to vicious cycles of pathology and complex systemic diseases. The challenge lies in extracting all relevant information from the rapidly increasing volumes of omics data and translating this information first into knowledge and ultimately into wisdom that can yield clinically actionable results. Here, we discuss how molecular networks are central to the implementation of this new biology in medicine and translation to preventive and personalized health care.

Franzen O.,Mount Sinai School of Medicine | Franzen O.,Clinical Gene Networks AB | Ermel R.,University of Tartu | Cohain A.,Mount Sinai School of Medicine | And 25 more authors.
Science | Year: 2016

Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown.We genotyped and RNAsequenced vascular and metabolic tissues from 600 coronary artery disease patients in the Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task study (STARNET). Gene expression traits associated with CMD risk single-nucleotide polymorphism (SNPs) identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs. In contrast, the regulatory effects of other GWAS risk SNPs were tissue-specific; abdominal fat emerged as an important gene-regulatory site for blood lipids, such as for the low-density lipoprotein cholesterol and coronary artery disease risk gene PCSK9. STARNET provides insights into gene-regulatory mechanisms for CMD risk loci, facilitating their translation into opportunities for diagnosis, therapy, and prevention.

Shang M.-M.,Karolinska Institutet | Shang M.-M.,Clinical Gene Networks AB | Talukdar H.A.,Karolinska Institutet | Hofmann J.J.,Karolinska Institutet | And 23 more authors.
Arteriosclerosis, Thrombosis, and Vascular Biology | Year: 2014

OBJECTIVE - Using a multi-tissue, genome-wide gene expression approach, we recently identified a gene module linked to the extent of human atherosclerosis. This atherosclerosis module was enriched with inherited risk for coronary and carotid artery disease (CAD) and overlapped with genes in the transendothelial migration of leukocyte (TEML) pathway. Among the atherosclerosis module genes, the transcription cofactor Lim domain binding 2 (LDB2) was the most connected in a CAD vascular wall regulatory gene network. Here, we used human genomics and atherosclerosis-prone mice to evaluate the possible role of LDB2 in TEML and atherosclerosis. APPROACH AND RESULTS - mRNA profiles generated from blood macrophages in patients with CAD were used to infer transcription factor regulatory gene networks; LdlrApob mice were used to study the effects of Ldb2 deficiency on TEML activity and atherogenesis. LDB2 was the most connected gene in a transcription factor regulatory network inferred from TEML and atherosclerosis module genes in CAD macrophages. In LdlrApob mice, loss of Ldb2 increased atherosclerotic lesion size ≈2-fold and decreased plaque stability. The exacerbated atherosclerosis was caused by increased TEML activity, as demonstrated in air-pouch and retinal vasculature models in vivo, by ex vivo perfusion of primary leukocytes, and by leukocyte migration in vitro. In THP1 cells, migration was increased by overexpression and decreased by small interfering RNA inhibition of LDB2. A functional LDB2 variant (rs10939673) was associated with the risk and extent of CAD across several cohorts. CONCLUSIONS - As a key driver of the TEML pathway in CAD macrophages, LDB2 is a novel candidate to target CAD by inhibiting the overall activity of TEML. © 2014 American Heart Association, Inc.

Hagg S.,Karolinska Institutet | Hagg S.,Clinical Gene Networks AB | Salehpour M.,Uppsala University | Noori P.,Karolinska Institutet | And 12 more authors.
PLoS ONE | Year: 2011

Background: The stability of atherosclerotic plaques determines the risk for rupture, which may lead to thrombus formation and potentially severe clinical complications such as myocardial infarction and stroke. Although the rate of plaque formation may be important for plaque stability, this process is not well understood. We took advantage of the atmospheric 14C-declination curve (a result of the atomic bomb tests in the 1950s and 1960s) to determine the average biological age of carotid plaques. Methodology/Principal Finding: The cores of carotid plaques were dissected from 29 well-characterized, symptomatic patients with carotid stenosis and analyzed for 14C content by accelerator mass spectrometry. The average plaque age (i.e. formation time) was 9.6±3.3 years. All but two plaques had formed within 5-15 years before surgery. Plaque age was not associated with the chronological ages of the patients but was inversely related to plasma insulin levels (p = 0.0014). Most plaques were echo-lucent rather than echo-rich (2.24±0.97, range 1-5). However, plaques in the lowest tercile of plaque age (most recently formed) were characterized by further instability with a higher content of lipids and macrophages (67.8±12.4 vs. 50.4±6.2, p = 0.00005; 57.6±26.1 vs. 39.8±25.7, p<0.0005, respectively), less collagen (45.3±6.1 vs. 51.1±9.8, p<0.05), and fewer smooth muscle cells (130±31 vs. 141±21, p<0.05) than plaques in the highest tercile. Microarray analysis of plaques in the lowest tercile also showed increased activity of genes involved in immune responses and oxidative phosphorylation. Conclusions/Significance: Our results show, for the first time, that plaque age, as judge by relative incorporation of 14C, can improve our understanding of carotid plaque stability and therefore risk for clinical complications. Our results also suggest that levels of plasma insulin might be involved in determining carotid plaque age. © 2011 Hägg et al.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH-2007-2.1.2-5 | Award Amount: 3.83M | Year: 2009

Background. Parkinson Disease is the second most common progressive neurodegenerative disorder. The selective degeneration of subsets of midbrain dopaminergic neurons is believed to be the primary cause for disruption of the ability to control movements. Objective. We propose to apply a highly interdisciplinary approach to construct complex networks consisting of protein coding genes, non-protein-coding genes and cis-regulatory elements within dopaminergic neurons in the brain across three chordate organisms (Mouse, Zebrafish and Ciona) to identify and compare gene regulatory networks in these neurons. This will be achieved by: Expression profiling of genes on single dopaminergic neurons via laser microdissection and transgenic lines in Mouse, Ciona and Zebrafish HT-Sequencing of microCAGE assays on dopaminergic neurons, providing TSS usage and transcript discovery Microscopy HTS of cis-regulatory elements siRNA and morpholino network perturbation experiments Innovative systems biology approaches to decipher and define molecular networks Data generated by microCAGE and microarray will define a set of key genes in dopaminergic neurons, in which cis-regulatory elements will be predicted and screened utilizing HTS in zebrafish. The data will aid network reconstruction, which will be validated by perturbation experiments. This project relies also on the availability of data produced through the many existing collaborations among consortium partners such as FP6 funded TRANSCODE project as well as the international Fantom3 consortium. Potential impact: The prevalence of PD in Europe today is ~2 million people. Within the next 50 years, the number is expected to rise to 5 million. Thus, the burden placed by dementia on the working-age population will rise dramatically. No treatments are known to slow the progression of the disease. Deciphering the basic networks of dopaminergic neurons will generate novel diagnostic and therapeutic candidates.

Agency: European Commission | Branch: FP7 | Program: CP-FP | Phase: HEALTH.2013.2.4.2-1 | Award Amount: 7.88M | Year: 2013

Atherosclerosis and its most disabling sequelae, coronary artery disease (CAD) and stroke, are leading causes of death in Europe. Until now, preventive and therapeutic interventions for these diseases aim at ameliorating the effects of established cardiovascular risk factors. More recently, results of genome-wide association (GWA) studies added to our perception of mechanisms leading to atherosclerosis. At present, over 40 CAD and several genomic risk loci have been identified, the majority through efforts led by the applicants. Some genes at these loci work through known risk factors such as lipids and, in fact, are already established or evolving treatment targets. However, this is not true for the majority of risk variants, which implies that key pathways leading to atherosclerosis are yet to be exploited for therapeutic intervention. This EU network (CVgenes@target), which brings together an equal number of SME- and academic partners, will utilize genomic variants affecting atherosclerosis risk for identification of both underlying genes and affected pathways in order to identify, characterize, and validate novel therapeutically relevant targets for prevention and treatment of CAD and stroke. In programme 1 we will investigate molecular mechanisms at the genomic loci in order to further unravel causal genes, in programme 2 we will explore in vitro and in vivo whether the pathways disturbed by causal genes are suitable for therapeutic intervention, and in programme 3 we will establish assays and initiate high throughput screens to tackle therapeutically attractive targets. Our resources including large OMICs and state-of-the-art bioinformatics platforms as well as multiple, already established in vitro and in vivo models support the feasibility of the approach. In fact, two genomic risk loci (ADAMTS7 (CAD); HDAC9 (stroke and CAD)), both identified in GWA studies under direction of the applicants, already revealed attractive targets for therapeutic intervention.

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