Newborn mitochondrial DNA copy number is associated with changes to DNA methylation that persist into childhood and are associated with cognitive development.

Background/objectives: Mitochondrial-nuclear crosstalk is critical for cell function, and nuclear DNA methylation (DNAm) may regulate this process. Mitochondria maintain an extranuclear genome, and mitochondrial DNA copy number (mtDNA-CN) has been previously associated with DNAm. However, there is little information on this relationship in children, whose brains are particularly vulnerable to energetic perturbations during development. Our objectives were to (1) characterize associations of mtDNA-CN with nuclear DNAm at birth; (2) determine their persistence into childhood; and (3) investigate associations in relation to neurodevelopment.

Methods: We quantified mtDNA-CN with qRT-PCR and DNAm with the MethylationEPIC BeadChip array in umbilical cord leukocytes (N = 422) in newborns from the PROGRESS birth cohort in Mexico City (2007-2011). At the 48-month visit, we measured DNAm in peripheral blood leukocytes (N = 177) and assessed the McCarthy Scales of Children's Abilities (N = 290). We performed an epigenome-wide association study (EWAS) with cord mtDNA-CN in mitochondrially relevant genes (23,261 CpG sites) and across the genome (745,691 sites). We determined if our results persisted until childhood and were associated with cognitive scales. The findings were replicated in a US-based cohort (N = 130).

Results: We observed 11 and 165 differentially methylated positions (DMPs) in mitochondria-related nuclear genes and across the genome, respectively, after correction for multiple comparisons. In mitochondrial genes, two significant DMPs mapped to PRELID3A and a DMP in the promoter region of SLC25A24 replicated in our external cohort. At 48 months of age, 17 of 165 DMPs remained associated with cord mtDNA-CN, 12 were associated with child memory scales, and associations with 17 replicated in our external cohort. Several positions mapped to genes in immune activation and development.

Conclusions: In newborns, mtDNA-CN was associated with DNAm in mitochondria-related genes and throughout the genome, several of which remained associated in childhood, were associated with child memory scales, and were replicated in a US-based cohort. These findings open new avenues for future targets for children's health and disease.