Distinct mitochondrial DNA single-nucleotide variant signatures in TOP3A-deficient cardiomyocytes

The human heart has a continuous and exceptionally high demand for energy, which is met primarily through mitochondrial oxidative phosphorylation. This dependence places the maintenance and integrity of mitochondrial DNA (mtDNA) for proper mitochondrial function at the center of cardiac health, as mtDNA instability has been shown to cause mitochondrial dysfunction, which can ultimately impair cardiac function leading to cardiomyopathy (CM) and heart failure. However, the contribution of mtDNA instability to cardiac disease remains poorly understood. A growing number of nuclear-encoded proteins have emerged as essential regulators of mtDNA maintenance, organization and segregation. DNA Topoisomerase 3 (TOP3A) is expressed as two isoforms: one is a nuclear-related isoform involved in nuclear genome maintenance while the other localizes to the mitochondria to preserve mtDNA integrity. Recently, individuals bearing biallelic loss-of-function variants in TOP3A manifested phenotypic traits, including CM, typical for mitochondrial dysfunction, supporting a potential mechanistic link between mitochondrial genome instability and TOP3A-related cardiac disease. Here, we investigated the effects of TOP3A deficiency on mtDNA maintenance and stability in the context of TOP3A-associated CM. We employed isogenic wild-type, TOP3A-knockout and BLM-knockout induced pluripotent stem cells (iPSCs) to generate cardiomyocytes (iPSC-CMs) and established a high-throughput, ultra-deep mtDNA sequencing strategy achieving approximately 500,000X coverage to characterize low-frequency mtDNA mutational patterns. Loss of TOP3A triggered an early burst of low-frequency de novo mtDNA single-nucleotide variants during cardiac differentiation, with a striking enrichment within the mitochondrial ribosomal RNA genes, accompanied by a progressive increase in the heteroplasmy of low-frequency mtDNA variants inherited from the common isogenic background. These unique mtDNA signatures were associated with defective mtDNA copy-number expansion and impaired mitochondrial respiration in mature iPSC-CMs. Together, our approach uncovered a previously uncharacterized consequence of TOP3A deficiency and established a link between impaired mtDNA maintenance and mitochondrial dysfunction in TOP3A-associated CM.