Mitochondrial DNA Copy Number (mtDNA-CN) Can Influence Mortality and Cardiovascular Disease via Methylation of Nuclear DNA CpGs

Abstract

Background: Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation. Methods: To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European American (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study. To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1,995). We further assessed the effect of experimental modification of mtDNA-CN through knockout of TFAM, a regulator of mtDNA replication, via CRISPR-Cas9. Results: Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5x10 -8 ). Meta-analysis across all cohorts identified six mtDNA-CN associated CpGs at genome-wide significance (P<5x10 -8 ). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including coronary heart disease, cardiovascular disease, and mortality. Experimental modification of mtDNA-CN demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the 'neuroactive ligand receptor interaction' KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24x10 -12 ), as well as the TFAM knockout methylation (P=4.41x10 -4 ) and expression (P=4.30x10 -4 ) studies. Conclusions: These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential expression of specific genes that may impact human health and disease via altered cell signaling.

Association of mitochondrial DNA copy number with cardiometabolic diseases in a large cross-sectional study of multiple ancestries

“…40 Functional assessment demonstrated that modification of mtDNA CN levels resulted in changes in DNA methylation at specific CpGs and expression levels of nearby genes through knockout of the mitochondrial transcription factor, the protein that regulates mtDNA replication in CRISPR-Cas9. 40 These results provided evidence that mtDNA CN may impact cardiovascular health through DNA methylation and differential expression of specific genes that may impact cell signaling. Further studies are needed to investigate whether DNA methylation and gene expression mediate the effects of mtDNA CN on cardiovascular risks.…”

Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease

“…In cancer cells, mtDNA-CN alters gene expression through modifying DNA methylation [13,14]. Recent work from our lab has shown that mtDNA-CN is also associated with nuclear DNA methylation in noncancer settings [15]. Given that DNA methylation can modify gene expression, the current study seeks to explore the potential association between blood-derived mtDNA-CN and gene expression.…”

Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease

“…In cancer cells, mtDNA-CN alters gene expression through modifying DNA methylation (Reznik et al 2016;Sun and St John 2018). Recent work from our lab has shown that mtDNA-CN is also associated with nuclear DNA methylation in noncancer settings (Castellani et al 2020a). Given that DNA methylation can modify gene expression, the current study seeks to explore the potential association between blood-derived mtDNA-CN and gene expression.…”