Work Package 1 Target Discovery
Partners in the CarTarDis consortium has collected and processed large-scale omics data (transcriptomic, metabolomic, whole-genome common variants, exome arrays, gene-clinical trait correlations and molecular networks) in large human population-based cohorts comprehensively measured for CVD-related clinical data. To enable different layers of the collaboration to work across institutional boundaries we will generate a shared database of various datasets within the consortium for integrating and analysing the molecular datasets with genotype and phenotypic data, a pre-requisite to developing improved disease models for CVD. For instance, genetic variants that are associated with expression traits, metabolite biomarkers and disease-associated gene networks provide functional bridges that may be used to find novel pathophysiological pathways and drug targets for CVD.
Three population-based human cohorts (KORA, AGES, REFINE), and three case-control studies (CardioGenX, Bike, Socrates) from Germany, Iceland, the Netherlands and Sweden will be the basis of drug target identification. These studies have a strong longitudinal component (2-14 years from baseline) and are comprehensively measured for CVD-related endpoints and measured risk factors at various time points, thus allowing us to assess the effect of markers on CVD progression. Through WP1 novel candidate CVD drug targets will be discovered via the application of high-dimensional datasets collected in a large human sampling together with drug targets identified in the context of cellular, tissue and/or animal model studies in WP2 and WP3. Targets will be ranked for chemical tractability and relevance to CVD pathology using guidance from WP4 and a subset of high confidence targets prioritized for downstream validation in in vitro and in vivo CVD model studies. The roles of the participants reside in: analysis of data from cohort studies by Helmholtz Zentrum München , Icelandic Heart Asscociation and CardiogenX, the analysis of biobank data by LUMC and Karolinska Institute, and comprehensive data analysis and target selection predominantly by Molecular Profiling Consultancy and AstraZeneca.
Work Package 2 Target validation – in vitro and in vivo models
In this WP the consortium partners will develop innovative (human) cell culture and animal models in which the selected target genes through WP1 and the drugability funnel in WP4 are overexpressed or silenced in a controlled manner on a background of established translational CVD models, to obtain mechanistic confirmation of the target’s role in CVD development, to correlate them to the clinical phenotypes from WP1 and WP3, and to validate them in pharmacological studies, using clinically relevant read-out parameters and sophisticated imaging techniques.
PolyGene will develop tissue culture models and generate genetically modified mouse strains using sophisticated technology for swift introduction of targeted changes to induce or silence targets filtered in WP1 and WP4. Simultaneously, innovative beyond-state-of-art technology will be developed to accomplish modulation of gene expression in a spatial (tissue-specific) temporal (inducible) manner resulting in controlled quantitatively adjustable gene expression in order to analyse to which extent a gene needs to be down/upregulated to affect the pre(clinical) outcome.
The Umeå University has expertise with a number of non-invasive imaging modalities to analyse cardiac function, atherosclerotic plaque development and vessel formation in vivo (including high frequency ultrasound, cryo-probe MRI and micro-PET/CT). These modalities are highly translatable to clinical medicine. In addition, Umeå has co-developed two ex vivo imaging techniques (including CARS non-linear spectroscopy and ESR) to characterize atherosclerotic plaques and reactive oxidative species. These novel techniques will be combined with standard histology for optimal characterization of the newly developed CVD animal models together with CardioGenX and TNO.
Work Package 3 Target validation – clinical tissue
Atherosclerotic disease reflects a chronic process that proceeds though successive and clearly distinct phases. In order to address the dynamics of the disease the consortium includes two independent and complementary clinical CVD biobanks: Socrates (LUMC) and BiKE (Karolinska Institute). Socrates biobank contains over 500 aortic wall patches from organ transplantation (coronary and aorta wall samples), and therefore contains material from asymptomatic, relatively healthy individuals. Socrates covers the full life span and the full spectrum of atherosclerotic disease. BiKE biobank contains over 600 surgical specimens from symptomatic CVD patients, consisting primarily of carotid endarteriectomies from unstable and stable lesions and this material therefore largely reflects symptomatic end-stage disease. Collectively, these two well annotated high quality biobanks uniquely cover the full spectrum of human atherosclerotic disease for the relevant vascular beds. Tissue biobank samples will be investigated using targeted molecular analysis techniques with high spatial resolution, in order to address the highly localized character of processes involved in cardiovascular disease. Dedicated partners involved share a distinctive expertise to analyse proteins (immunohistochemistry; Morphisto), RNA (in-situ hybridization; Bioneer) and small molecules (mass spectrometry-imaging; ImaBiotech). To further investigate mechanistic pathways, we will optimize laser capture microdissection (LCM) and padlock probe-based rolling circle amplification (RCA) on human vessel wall sections in combination with highly targeted transcriptomic and proteomic evaluation of areas of special interest (Karolinska Institute). In addition, to enable mechanistic ex vivo functional analysis, human vascular tissue explant systems will be developed and applied where needed (LUMC).
Work Package 4 Drug target prioritisation
Identification and reviewing of candidate drug targets will be carried out within the framework provided by the definitions used in the pharmaceutical industry and agreed upon within the consortium. Target validation requires a demonstration that a molecular target is directly involved in a human disease process, and that modulation of the target is likely to provide a beneficial effect in the chosen therapeutic area. By molecular target we define a macromolecule or molecules involved in pathways whose function can be modulated to cure a disease and improve health more generally. The members of WP will guide the process of drug target selection, prioritisation and validation through WP1, 2 and 3, using the best practice experience in pharmaceutical drug development for cardiovascular disease.
The tasks in this WP will be performed in collaboration between six from the indicated institutes that will work together as pharmaceutical expert group, and thus steer the focus and prioritisation of studies by other scientists within the consortium. Prof Eva Hurt-Camejo will lead the expert group to combine and apply her expertise in best practice. Other members are Prof Alain van Gool (TNO), Dr. Valur Emilsson (Iceland Heart Association), Dr. Maarten Sollewijn Gelpke (Molecular Profiling Consultancy) and Dr. Hans Princen (TNO). Each of the expert group members has over 10 years of experience in pharmaceutical research and development in cardiovascular disease and other therapeutic areas.