CPEB alteration and aberrant transcriptome-polyadenylation lead to a treatable SLC19A3 deficiency in Huntington’s disease

Abstract

Huntington's disease (HD) is a devastating hereditary neurodegenerative disorder of the basal ganglia for which disease-modifying treatments are not available. Although promising genesilencing therapies are currently being tested, new molecular mechanisms underneath the triggering mutation must be explored to identify easily druggable targets. Cytoplasmic polyadenylation element binding proteins 1-4 (CPEB1-4) are RNA-binding proteins that repress or activate translation of CPE-containing transcripts by, respectively, shortening or elongating their poly(A) tail. Here we report increased CPEB1 and decreased CPEB4 protein levels in striatum of HD patients and mouse models. This correlates with a reprogramming of polyadenylation in 17.3% of the transcriptome that markedly affects neurodegeneration-associated genes (like PSEN1, MAPT, SNCA, LRRK2, PINK1, DJ1, SOD1, TARDBP, FUS and HTT), thus suggesting a new molecular mechanism in neurodegenerative disease aetiology. Besides, we found decreased protein levels of top deadenylated transcript-genes which include striatal atrophy-linked genes not previously related to HD such as KTN1 and, remarkably, the easily druggable SLC19A3 (ThTr2 thiamine transporter). Mutations in SLC19A3 cause biotin-thiamine-responsive basal ganglia disease (BTBGD), a devastating striatal disorder that however reverts upon a vitaminbased therapy. Decreased ThTr2 in HD led to discover that, alike BTBGD patients, HD patients show decreased CSF thiamine levels. Furthermore, HD patients and mice show decreased striatal concentrations of TPP, the metabolically active form of thiamine. Remarkably, a high dose biotin+thiamine treatment used to revert BTBGD prevented the TPP deficiency of HD mice and attenuated their radiological, neuropathological and motor HD-like phenotypes, thus unveiling an easy to implement therapy for HD.

Altered m6A RNA methylation contributes to hippocampal memory deficits in Huntington’s disease mice

“…In this sense, when comparing naive WT and Hdh +/Q111 mice, we observed a differential m6A methylation in the distinct transcript regions (5´ and 3´UTR, exons and introns), which could induce such effects on downstream mRNA processing and metabolism in the HD condition. Supporting this possibility, we found several transcripts hypermethylated that have previously been described to be affected by mis-splicing or polyA changes [18,21]. Majority of the m6A peaks of the methylated transcripts that overlap with mis-spliced genes are found in introns and exons, which are more likely to undergo alternative splicing as previously described [29].…”

“…To understand this neuronal dysfunction, these studies have focused on the control of gene expression at the transcriptional level by transcription factors or epigenetic modifications of DNA or histones [14][15][16]. However, post-transcriptional mechanisms such as the regulation of miRNA expression, missplicing and altered polyadenylation [17][18][19][20][21] have also been described to be critical in the regulation of gene expression in HD. Notably, all these processes can be regulated by RNA modifications, in particular N6-methyladenosine (m6A), the most abundant internal modification in mRNA that is especially enriched in the mammalian brain [22,23].…”

“…Moreover, we found around 40% of the m6A peaks located in introns. Since m6A changes may also influence RNA splicing and polyadenylation [64][65][66][67], we next explored whether the observed alterations in methylation in Hdh +/Q111 mice could be related with known genes affected by mis-splicing or aberrant polyadenylation in HD [18,21]. We integrated our dataset with published datasets of alternative splicing and polyadenylation analysis from the R6/1 HD mouse model at symptomatic disease stages (3,5 and 7-8 months, respectively) [18,21].…”

“…Since m6A changes may also influence RNA splicing and polyadenylation [64][65][66][67], we next explored whether the observed alterations in methylation in Hdh +/Q111 mice could be related with known genes affected by mis-splicing or aberrant polyadenylation in HD [18,21]. We integrated our dataset with published datasets of alternative splicing and polyadenylation analysis from the R6/1 HD mouse model at symptomatic disease stages (3,5 and 7-8 months, respectively) [18,21]. Integration analysis showed a significant over-enrichment of genes with changes in m6A levels and genes described to be mis-spliced, both at 5 and 8 months of age (Supplementary Fig.…”

Heritability Estimation of Multiple Sclerosis Related Plasma Protein Levels in Sardinian Families with Immunochip Genotyping Data

“…The intergenic variant rs2546722 is located near the CPEB4 gene and was shown to be associated with its gene expression levels in blood [ 75 ]; in our analysis, this genetic variant resulted associated with Sod1 plasma levels. Interestingly, CPEB4 encodes for a RNA binding protein which was found to affect SOD1 transcriptome polyadenylation and potentially lead to neurodegenerative disorder etiology [ 76 , 77 ].…”