Aherrahrou, Z. | bioRxiv Science

bioRxiv2021

Deficiency of ZC3HC1 increases vascular smooth muscle cell migration, proliferation and neointima formation following injury

RationaleThe ZC3HC1 gene has been linked to various cardiovascular traits. One variant, rs11556924-T, has been found to lower the risk of coronary artery disease (CAD) and blood pressure but increases carotid intima-media thickness (IMT). ObjectiveThis study aimed to determine how ZC3HC1 affects IMT using in vitro and in vivo models. We analyzed the effect of the rs11556924-T allele on ZC3HC1 expression in vascular smooth muscle cells (SMCs) from 151 multi-ethnic heart transplant donors. The results showed that rs11556924-T was associated with lower ZC3HC1 expression and faster SMC migration. ZC3HC1 knockdown (KD) experiments supported these findings, showing increased migration and proliferation. Mechanistically ZC3HC1 KD led to decreased expression of contractile marker genes and the accumulation of cyclin B1, a key cell cycle protein. Pathway analysis of differentially expressed genes between ZC3HC1 KD and controls SMCs showed decreased expression of genes in the cell division and cytoskeleton organization pathways, as well as higher expression of genes involved in extracellular matrix organization and cytokine-mediated signaling. To validate these findings in vivo, we generated and characterized knockout (Zc3hc1-/-) mice. These mice had enhanced neointima formation in response to arterial injury and faster SMCs migration ability. However, complete loss of Zc3hc1 led to a significant reduction in SMC proliferation and lower cyclin B1 protein level. In addition, immunostaining and confocal microscopy demonstrated, for the first time, that ZC3HC1 and Cyclin B1 were located at the cleavage furrow during mitotic progression of SMCs. ConclusionsCollectively, our study suggests that lower ZC3HC1/NIPA level leads to increased SMC migration and neointima formation. Moreover, we proposed a biphasic role of NIPA in proliferation. Lower levels of NIPA promote SMC proliferation, while complete loss of NIPA hampers cell division and abrogates proliferation.

genetics↗

bioRxiv2020

In silico candidate variant and gene identification using inbred mouse strains

Mice are the most widely used animal model to study genotype to phenotype relationships. Inbred mice are genetically identical, which eliminates genetic heterogeneity and makes them particularly useful for genetic studies. Many different strains have been bred over decades and a vast amount of phenotypic data has been generated. In addition, recently whole genome sequencing-based genome-wide genotype data for many widely used inbred strains has been released. Here, we present an approach for in silico fine-mapping that uses genotypic data of 37 inbred mouse strains together with phenotypic data provided by the user to propose candidate variants and genes for the phenotype under study. Public genome-wide genotype data covering more than 74 million variant sites is queried efficiently in real-time to provide those variants that are compatible with the observed phenotype differences between strains. Variants can be filtered by molecular consequences and by corresponding molecular impact. Candidate gene lists can be generated from variant lists on the fly. Fine-mapping together with annotation or filtering of results is provided in a Bioconductor package called MouseFM. In order to characterize candidate variant lists under various settings, MouseFM was applied to two expression data sets across 20 inbred mouse strains, one from neutrophils and one from CD4+ T cells. Fine-mapping was assessed for about 10,000 genes, respectively, and identified candidate variants and haplotypes for many expression quantitative trait loci (eQTLs) reported previously based on these data. For albinism, MouseFM reports only one variant allele of moderate or high molecular impact that only albino mice share: a missense variant in the Tyr gene, reported previously to be causal for this phenotype. Performing in silico fine-mapping for interfrontal bone formation in mice using four strains with and five strains without interfrontal bone results in 12 genes. Of these, three are related to skull shaping abnormality. Finally performing fine-mapping for dystrophic cardiac calcification by comparing 9 strains showing the phenotype with 8 strains lacking it, we identify only one moderate impact variant in the known causal gene Abcc6. In summary, this illustrates the benefit of using MouseFM for candidate variant and gene identification.

bioinformatics↗