MicroRNA signatures of endogenous Huntingtin CAG repeat expansion in mice

<div><p>In Huntington's disease (HD) patients and in model organisms, messenger RNA transcriptome has been extensively studied; in contrast, comparatively little is known about expression and potential role of microRNAs. Using RNA-sequencing, we have quantified microRNA expression in four brain regions and liver, at three different ages, from an allelic series of HD model mice with increasing CAG length in the endogenous Huntingtin gene. Our analyses reveal CAG length-dependent microRNA expression changes in brain, with 159 microRNAs selectively altered in striatum, 102 in cerebellum, 51 in hippocampus, and 45 in cortex. In contrast, a progressive CAG length-dependent microRNA dysregulation was not observed in liver. We further identify microRNAs whose transcriptomic response to CAG length expansion differs significantly among the brain regions and validate our findings in data from a second, independent cohort of mice. Using existing mRNA expression data from the same animals, we assess the possible relationships between microRNA and mRNA expression and highlight candidate microRNAs that are negatively correlated with, and whose predicted targets are enriched in, CAG-length dependent mRNA modules. Several of our top microRNAs (<i>Mir212</i>/<i>Mir132</i>, <i>Mir218</i>, <i>Mir128</i> and others) have been previously associated with aspects of neuronal development and survival. This study provides an extensive resource for CAG length-dependent changes in microRNA expression in disease-vulnerable and -resistant brain regions in HD mice, and provides new insights for further investigation of microRNAs in HD pathogenesis and therapeutics.</p></div

MicroRNA whose DE validates in Series 1 and Series 2.

<p>The heatmap represents differential expression Z statistics in all binary genotype comparisons for those microRNAs whose association with Q (as a numeric variable) passes the threshold FDR<0.05 in both Series 1 and Series 2. Top left and right panels show validated down- and up-regulated striatum microRNAs, respectively; bottom left and right panels show all validated microRNAs in cortex and cerebellum, respectively.</p

Network plots of top hub genes in CAG length-dependent modules and their putative regulator microRNAs.

<p>Each panel shows the top hub genes in one of the CAG length-dependent modules and microRNAs that are negatively correlated with the module eigengene and whose predicted targets are significantly enriched in the module. Predicted microRNA-target relationships are indicated by turquoise lines while the gene-gene co-expression relationships are indicated by red lines (thicker and wider lines indicate higher Topological Overlap). Only modules and microRNAs from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190550#pone.0190550.t001" target="_blank">Table 1</a> are shown whose correlations are less than -0.4; correlations of all mRNA-microRNA pairs shown in this figure are negative.</p

MicroRNA-module pairs with strongest negative correlations and significant (FDR<0.05) enrichment of the module in predicted microRNA targets.

<p>MicroRNA-module pairs with strongest negative correlations and significant (FDR<0.05) enrichment of the module in predicted microRNA targets.</p

Differential expression analysis with respect to CAG length in Series 2.

<p>Bars show numbers of significantly (FDR<0.05) differentially expressed microRNAs in the 4 tissues studied in Series 2; the numbers are also shown next to each bar. Numbers in parentheses represent the counts of distinct microRNA clusters in which the significant microRNAs fall into. Blue and red bars represent microRNAs significantly down- and up-regulated, respectively, with increasing CAG length (Q).</p