DNAMethylation Associated with Mitochondrial Dysfunction in a South African Autism Spectrum Disorder Cohort

Abstract

Autism spectrum disorder (ASD) is characterized by phenotypic heterogeneity and a complex genetic architecture which includes distinctive epigenetic patterns. We report differential DNA methylation patterns associated with ASD in South African children. An exploratory whole‐epigenome methylation screen using the Illumina 450 K MethylationArray identified differentially methylated CpG sites between ASD and controls that mapped to 898 genes ( P ≤ 0.05) which were enriched for nine canonical pathways converging on mitochondrial metabolism and protein ubiquitination. Targeted Next Generation Bisulfite Sequencing of 27 genes confirmed differential methylation between ASD and control in our cohort. DNA pyrosequencing of two of these genes, the mitochondrial enzyme Propionyl‐CoA Carboxylase subunit Beta ( PCCB ) and Protocadherin Alpha 12 ( PCDHA12 ), revealed a wide range of methylation levels (9–49% and 0–54%, respectively) in both ASD and controls. Three CpG loci were differentially methylated in PCCB ( P ≤ 0.05), while PCDHA12 , previously linked to ASD, had two significantly different CpG sites ( P ≤ 0.001) between ASD and control. Differentially methylated CpGs were hypomethylated in ASD. Metabolomic analysis of urinary organic acids revealed that three metabolites, 3‐hydroxy‐3‐methylglutaric acid ( P = 0.008), 3‐methyglutaconic acid ( P = 0.018), and ethylmalonic acid ( P = 0.043) were significantly elevated in individuals with ASD. These metabolites are directly linked to mitochondrial respiratory chain disorders, with a putative link to PCCB , consistent with impaired mitochondrial function. Our data support an association between DNA methylation and mitochondrial dysfunction in the etiology of ASD. Autism Res 2020, 13 : 1079‐1093. © 2020 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. Lay Summary Epigenetic changes are chemical modifications of DNA which can change gene function. DNA methylation, a type of epigenetic modification, is linked to autism. We examined DNA methylation in South African children with autism and identified mitochondrial genes associated with autism. Mitochondria are power‐suppliers in cells and mitochondrial genes are essential to metabolism and energy production, which are important for brain cells during development. Our findings suggest that some individuals with ASD also have mitochondrial dysfunction.

The Mitochondrial Dysfunction Hypothesis in Autism Spectrum Disorders: Current Status and Future Perspectives

“…ASD is probably the result of a genetic predisposition and epigenetic mechanisms. The work of Stathopoulos et al [48] showed how the methylation of mitochondrial DNA plays an important role in the etiology of ASD. Therefore, understanding the mitochondrial mechanisms involved in ASD could be important for the identification of new targets in the treatment of pathology.…”

DNA methylation of PGC-1α is associated with elevated mtDNA copy number and altered urinary metabolites in Autism Spectrum Disorder

“…BCAAs provide nitrogen to the glutamate-glutamine cycle and have been implicated as important regulators of glutamatergic neurotransmission (82), which contribute to ASD aetiology (83). Two metabolites (3-H-3-MGA and 3-methylglutaconic acid (3-MGA)) were significantly elevated in our ASD cohort (22) and are characterized as urinary biomarkers of mitochondrial respiratory chain deficiencies (75,84). Altered BCAA metabolism has also been linked to oxidative stress resulting from perturbed NAD + /NADH redox ratios (85).…”

“…The observation that congenital errors of mitochondrial metabolism contribute to > 5% of ASD cases (17) first implied a role for mitochondrial dysfunction in ASD. This has since been supported by clinical (18), biochemical (19,20), molecular (21) and more recently, epigenetic data (22). Citrigno et al (23) comprehensively reviewed the recent experimental data that support the Mitochondrial Dysfunction Hypothesis in ASD.…”

“…We investigated whether the differential methylation of PGC-1α and elevated mtDNA copy number observed in ASD were associated with metabolomic evidence of mitochondrial dysfunction. We examined the correlation between PGC-1α methylation, mtDNA copy number and levels of urinary organic acids which had previously been measured (n= 20 ASD, n= 13 controls) using gas chromatography −mass spectrometry (GC-MS) (22). DNA methylation at PGC-1α CpG#1, which is DM in our samples, correlated significantly with three of the 55 urinary organic acids tested (Table S3b, Additional File 1) MtDNA copy number correlated with 22 urinary metabolites associated with mitochondrial dysfunction (Table S3a, Additional File 1).…”

Clustered Protocadherins Emerge as Novel Susceptibility Loci for Mental Disorders

“…Aging Pcdh clusters Differential methylation Rakyan et al, 2010;Bell et al, 2012;Salpea et al, 2012;Hannum et al, 2013;McClay et al, 2014;Slieker et al, 2016;Kim et al, 2018a Alzheimer's disease Pcdhγc5 Altered expression Li et al, 2012(rat) Li et al, 2017 Pcdh clusters Altered expression Nativio et al, 2018Meyer et al, 2019 Antipsychotic medication Pcdh clusters Differential methylation Melka et al, 2014;Nakazawa et al, 2017 Autism Pcdhα cluster SNP Anitha et al, 2013 Pcdh clusters De novo mutations Iossifov et al, 2014 Pcdh clusters SNV, CNV Krumm et al, 2015 Pcdhα12 Differential methylation Stathopoulos et al, 2020 Bipolar disorder Pcdh clusters Association Hong et al, 2004;Herzberg et al, 2006 Pcdhα cluster SNP Pedrosa et al, 2008 Child Schwab et al, 1997;Straub et al, 1997;Schizophrenia Working Group of the Psychiatric Genomics Consortium, 2014;Pardinas et al, 2018;Walker et al, 2019 Pcdh clusters 3D genome Rajarajan et al, 2018 Pcdh clusters Altered Pcdh pathway Shao et al, 2019 Pcdhα7, α8 Altered expression Hall et al, 2020Hall et al, et al, 2018. Interestingly, APOE4, a prominent genetic risk allele for late-onset AD, causes cPcdh gene upregulation in iPSCderived cerebral organoids (Meyer et al, 2019).…”