A systems genetics approach to uncover mitochondrial drivers of heart failure reveals mitochondria-nuclear cross talk in genetically diverse mouse strains

The contribution of mitochondrial genetics to heart failure is thought to be reciprocal. Its complex traits are influenced by genetic and environmental factors. Genetically diverse mouse strains form a vital repository to uncover the interaction between the mitochondrial and nuclear genomes underlying heart failure due to their traceable genetic origins, maternal lineages and controlled genetic variation. Using systems genetics, we studied this cross-talk in the Collaborative Cross (CC) mice challenged with heart failure (HF). We used 63 strains of CC-mice that grouped into 8 mitochondrial haplotypes and subjected them to HF using isoproterenol (Iso), a beta-adrenergic stimulant that mimics progressive stress induced HF in humans. The Alzet osmotic pumps delivered a consistent dose of the drug for 21 days following which the mice were euthanized for organ collection. A group of mice with saline loaded pumps acted as control (Ctrl). Baseline and end of study echocardiography were recorded for these mice. Bulk RNA sequencing was carried out on the left ventricles and data analyzed on R-studio. The CC-strains showed differences across the haplotypes for organ weights and heart function. Noticeable treatment specific gene expression differences were observed for 34 nuclear encoded genes from MitoCarta3.0 unlike mt-DNA encoded genes that were insignificant after correcting for sex and haplotypes. These genes were associated with multiple metabolic pathways in the cell. Trait-GWAS associations with markers from the mitochondrial genome were observed only for mice from Iso group with cell surface area (p = 6.19e-06) and change in ejection fraction (p = 9.22e-05) as top hits under FWER threshold of 0.01. Cyfip2 was the top candidate gene (p = 2.66e-07) among the 831 hits (47-MitoCarta & 784 other nuclear) based on our trans-eQTL analysis. The eQTL genes influenced critical pathways of OXPHOS, myogenesis, apoptosis etc. Our approach uncovered 24 gene candidates associated with mt-DNA and HF that overlapped with our previous mi-eQTL reports. CC-mice revealed ancestry dependent effects underlying HF for studying mito-nuclear interactions. Despite establishing differences, modeling these interaction needs development of complex cybrid systems to evaluate the bidirectional impact on HF. Author SummaryThe Collaborative Cross (CC) mouse is a genetically diverse population that has been used to study complex diseases. Recently, our group has comprehensively characterized the heart from 63 strains of the CC and reported genetic associations with heart failure (HF). Traditionally, genetic abnormalities underlying a disease are related to the nuclear genome but there exists an alternate genome within the cells, the mitochondrial DNA (mt-DNA), whose contribution is understudied. The mt-DNA of CC mice is maternally derived from the 8 founder strains, and our sequencing data holds this information, allowing us the ability to use them to study the contribution of mitochondrial ancestry (haplotypes) to HF. We found haplotype differences in terms of cardiac function and gene expression (both nuclear and mitochondrial) that were associated with HF. It revealed stress induced changes in the heart (trait and gene expression) linked with regions in the mt-DNA that encode genes involved in oxidative phosphorylation and metabolism. We uncovered 24 high-confidence nuclear gene candidates that agreed with our previous analyses and were associated with regions on the mt-DNA. These findings open up new opportunities to study the CC and advance the understanding of Mito-nuclear interactions in HF pathophysiology.