Abstract
Background Autism Spectrum Disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including canonical mitochondrial pathways. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the aetiology of ASD. We examined the relationship between DNA methylation of peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α), an essential transcriptional regulator of mitochondrial homeostasis, and mitochondrial dysfunction in an ASD cohort of South African children.
Results Using targeted Next Generation bisulfite sequencing, we found 12 highly variable CpG sites in PGC-1α that were significantly differentially methylated (p<0.05) between ASD (n = 55) and controls (n = 44). In ASD, eight CpG sites were hypermethylated in the PGC-1α promotor with a putative binding site for CAMP response binding element 1 (CREB1) spanning one of these CpG sites (p = 1 × 10−6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1α promoter. There was a positive correlation between methylation at PGC-1α at CpG#1 and mtDNA copy number (Spearman’s r = 0.2, n = 49, p = 0.04) in ASD, but a negative correlation between methylation at PGC-1α at CpG#4 promoter and mtDNA copy number in controls (Spearman’s r = −0.4, n = 42, p = 0.045). While there was no relationship between mtDNA deletions and PGC-1α methylation in ASD, mtDNA deletions correlated negatively with methylation at PGC-1α at CpG#4 (Spearman’s r = −0.4, n = 42, p = 0.032) in controls. Furthermore, levels of urinary organic acids associated with mitochondrial dysfunction correlated significantly (p<0.05) with DNA methylation at PGC-1α CpG#1 and mtDNA copy number in ASD (n= 20) and controls (n= 13) with many of these metabolites involved in altered redox homeostasis and neuroendocrinology.
Conclusions These data show an association between PGC-1α promoter methylation, elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored link between DNA methylation and mitochondrial dysfunction in ASD.
Competing Interest Statement
The authors have declared no competing interest.
ABBREVIATIONS
- ADOS-2
- Autism Diagnostic Observation Schedule, Second Edition
- ASD
- Autism Spectrum Disorder
- ATP
- Adenosine 5’-triphosphate
- BCAAs
- Branched-chain amino acids
- B2M
- Beta-2-microglobulin
- CA
- Citramalic acid
- CREB1
- CAMP response binding element 1
- DM
- Differentially methylated
- DRP1
- Dynamin-related protein 1
- FIS1
- Mitochondrial fission protein 1
- GABPA
- GA-binding protein α-chain
- GC-MS
- Gas chromatography – mass spectrometry
- MFN1
- Mitofusin 1
- MFN2
- Mitofusin 2
- mtDNA
- Mitochondrial DNA
- ND1
- NADH dehydrogenase 1
- ND4
- NADH dehydrogenase 4
- Nrf-1
- Nuclear respiratory factor 1
- Nrf-2
- Nuclear respiratory factor 2
- NRF2A
- Nuclear respiratory factor 2 alpha subunit
- OPA1
- Optic atrophy 1
- OXPHOS
- Oxidative phosphorylation
- PGC-1α
- Peroxisome proliferator-activated receptor gamma coactivator -1 alpha
- ROS
- Reactive oxygen species
- RT-qPCR
- Real-time quantitative polymerase chain reaction
- STOML2
- Stomatin-like protein 2
- TFAM
- Mitochondrial transcription factor A
- TFB2M
- Mitochondrial transcription factor B2
- tNGBS
- targeted Next Generation Bisulfite Sequencing
- TSS
- Transcriptional start site
- UTR
- Untranslated region
- 3-H-3-MGA
- 3-hydroxy-3-methylglutaric acid
- 3-MGA
- 3-Methylglutaconic acid