DNA methylation in Friedreich ataxia silences expression of frataxin isoform E

Abstract

Epigenetic silencing in Friedreich ataxia (FRDA), induced by an expanded GAA triplet-repeat in intron 1 of the FXN gene, results in deficiency of the mitochondrial protein, frataxin. A lesser known extramitochondrial isoform of frataxin detected in erythrocytes, frataxin-E, is encoded via an alternate transcript (FXN-E) originating in intron 1 that lacks a mitochondrial targeting sequence. We show that FXN-E is deficient in FRDA, including in patient-derived cell lines, iPS-derived proprioceptive neurons, and tissues from a humanized mouse model. In a series of FRDA patients, deficiency of frataxin-E protein correlated with the length of the expanded GAA triplet-repeat, and with repeat-induced DNA hypermethylation that occurs in close proximity to the intronic origin of FXN-E. CRISPR-induced epimodification to mimic DNA hypermethylation seen in FRDA reproduced FXN-E transcriptional deficiency. Deficiency of frataxin E is a consequence of FRDA-specific epigenetic silencing, and therapeutic strategies may need to address this deficiency.

Proprioceptors-enriched neuronal cultures from induced pluripotent stem cells from Friedreich ataxia patients show altered transcriptomic and proteomic profiles, abnormal neurite extension, and impaired electrophysiological properties

“…1A and B ). This agrees with the DNA methylation profile at the FXN locus highlighted in different cellular models, including hiPSC-derived sensory neurons: 22 , 23 in fact, although a higher rate of DNA methylation was observed in FRDA cells, a sort of physiological increase was observed also in non-affected cells upstream of the GAA repeats.…”

“…Our observations are in line with the DNA methylation profile at the FXN locus. 22 , 23 We also suggest the existence of a physiological silencing of the intronic region flanking the GAA repeats in CT neurons, as indicated by the combined reduced acetylation and increased trimethylation of H3K9 and H3K27 in that site. The removal of the GAA expansion mutation in ISO CT neurons was only able to induce a partial reversal of the repressive marks, which was, however, sufficient to restore frataxin expression.…”

Liquid Chromatography–Mass Spectrometry Analysis of Frataxin Proteoforms in Whole Blood as Biomarkers of the Genetic Disease Friedreich’s Ataxia

“…It is noteworthy that in the mouse, which lacks the methionine-76 start codon (AUG) for alternative splicing found in human frataxin, significant amounts of extra-mitochondrial frataxin can be detected in the brain, heart, and liver tissue. Mouse extra-mitochondrial frataxin is thought to arise from the proteolysis of frataxin rather than by the alternative splicing pathway that gives rise to human frataxin-E. , …”

“…Friedreich’s ataxia (FRDA) is an autosomal recessive disease, caused by mutations in the FXN gene that affect approximately 1 in 50,000 of the US population . The disease is caused primarily by expanded GAA repeats (up to 1300) in intron 1 of both alleles of the FXN gene, leading to transcriptional silencing and reduced expression of frataxin mRNA and protein. , FRDA is characterized by slowly progressive ataxia and cardiomyopathy . Symptoms generally appear during adolescence, and patients slowly progress to wheelchair dependency within 15 years .…”

FXNgene methylation determines carrier status in Friedreich ataxia

“…An epigenetic signature of the GAA-TRE involves DNA hypermethylation of the FRDA differentially methylated region (FRDA-DMR) in intron 1, which occurs in cis with the GAA-TRE, and is highly predictive of FXN transcriptional deficiency and age of onset in FRDA. [8][9][10] FRDA individuals homozygous for typical GAA-TREs with >500 triplets have >90% methylation in the FRDA-DMR, and non-FRDA individuals with both GAA alleles of <30 repeats have <10% methylation. 8 A minority of patients (~5%) are compound heterozygotes, having one FXN allele with a GAA-TRE and the homologous allele with another intragenic FXN pathogenic variant.…”