Genetic variation, transcriptomics and epigenetics in calcific aortic valve stenosis – CavsGen

Within this project, the common form of CAVS in the general population will be studied by identifying susceptibility genes thanks to a large cohort of severe CAVS cases recruited by the ‘institut du thorax’ in Nantes, in collaboration with Nantes, Rennes and Angers University hospitals. In addition, we are initiating a collaboration with the Bichat Hospital (Paris) and the ‘Institut Universitaire de Cardiologie et de Pneumologie de Québec’ to perform a meta-analysis. Furthermore, the identification of familial forms by the ‘institut du thorax’, suggests a strong genetic component for CAVS and rare Mendelian forms of the disease, and should allow the identification of the first major CAVS diseases genes. The identification of new diseases genes will also be guided by studying gene expression, splicing (the ‘transcriptome’) and miRNAs in diseased aortic valves from patients, and we will interrogate if epigenetic modifications (such as dynamic changes in DNA methylation), which can influence common diseases, could play a role in CAVS.

As of today, mining the rare and common genetic variants predisposing to CAVS, significant progress was made in the field of common variants.
An extended GWAS including addition cases and controls identified a suggestive association to CAVS occurring on tricuspid valve on chromosome 8. Of interest within the association peak, one gene, AGPAT5, encoding a protein involved in Lipid synthesis will be further investigated since par Thanassoulis et al; N Engl J Med. 2013 showed that an common genetic variant at the LPA locus (lipoprotein(a)) is also predisposing to aortic stenosis.

If the role of AGPAT5 is confirmed, this finding will reinforce the major role of the genetic background of lipid homeostasis in the developed of Aortic Stenosis and could trigger new pharmacological approaches to prevent the development or aggravation of the disease.

The difficulties arising from association analysis with rare variants underline the importance of suitable reference population cohorts, which integrate detailed spatial information. We analyzed a sample of 1684 individuals from Western France, who were genotyped at genome-wide level, from two cohorts D.E.S.I.R and CavsGen. We found that fine-scale population structure occurs at the scale of Western France, with distinct admixture proportions for individuals originating from the Brittany Region and the Vendee Department. Genetic differentiation increases with distance at a high rate in these two parts of Northwestern France and linkage disequilibrium is higher in Brittany suggesting a lower effective population size. When looking for genomic regions informative about Breton origin, we found two prominent associated regions that include the lactase region and the HLA complex. For both the lactase and the HLA regions, there is a low differentiation between Bretons and Irish, and this is also found at the genome-wide level. At a more refined scale, and within the Pays de la Loire Region, we also found evidence of fine-scale population structure, although principal component analysis showed that individuals from different departments cannot be confidently discriminated. Because of the evidence for fine-scale genetic structure in Western France, we anticipate that rare and geographically localized variants will be identified in future full-sequence analyses. Publication: Karakachoff M, et al. Fine-scale human genetic structure in Western France. Eur J Hum Genet. 2014.

The objective of this fundamental research proposal, CavsGen, is to identify genes and biological pathways involved in calcific aortic valve stenosis (CAVS), the most common valvular heart disease (2% > 65 years old). With population ageing, the number of surgical valve replacements, only therapeutic solution in the absence of preventive treatment, will increase. Despite the high prevalence of CAVS in the population, practically nothing is known about its genetic component and the pathophysiological mechanisms involved, and consequently there are no pharmacological treatments available.

High-throughput genotyping technologies allow the screening of large cohorts of patients for hundreds of thousands of markers. ‘Genome-wide association studies’, which have been focusing mostly on common variants, have been successful in identifying new biological pathways and new potential therapeutic targets for common diseases such as multiple sclerosis or rheumatoid arthritis. Nevertheless, common variants only explain a small fraction of the heritability of common diseases, and the scientific community is now turning to the characterisation of rare genetic variants, empowered by next-generation sequencing. Exome sequencing has allowed the identification of the underlying genetic cause of dozens of previously unsolved rare diseases in only three years, and can also be used to study rare familial forms of common diseases.

Within this project, the common form of CAVS in the general population will be studied by identifying susceptibility genes thanks to a large cohort of 1 800 severe CAVS cases (1 400 cases already genotyped), recruited by the ‘institut du thorax’ in Nantes, in collaboration with Nantes, Rennes and Angers University hospitals. In addition, we are initiating a collaboration with the Bichat Hospital (Paris) and the ‘Institut Universitaire de Cardiologie et de Pneumologie de Québec’ (960 cases already genotyped) to perform a meta-analysis. Furthermore, the identification of familial forms by the ‘institut du thorax’, suggests a strong genetic component for CAVS and rare Mendelian forms of the disease, and should allow the identification of the first major CAVS diseases genes. The identification of new diseases genes will also be guided by studying gene expression, splicing (the ‘transcriptome’) and miRNAs in diseased aortic valves from patients, and we will interrogate if epigenetic modifications (such as dynamic changes in DNA methylation), which can influence common diseases, could play a role in CAVS. The functional characterisation of the newly identified genes in cellular and animal models will be initiated in collaboration with French and international partners. This project will represent a major step towards understanding valve remodelling and identifying therapeutic targets by identifying the first disease genes responsible for common and rare forms of CAVS, thereby improving prevention and medical care.

Combining clinical expertise, cutting-edge genomic technologies, integrative data analyses, and functional follow-up, will not only improve the understanding of one of the most frequent cardiovascular diseases, but will also represent a step forward for genomic medicine.