Quantitative methods to monitor RNA biomarkers in myotonic dystrophy

Abstract

Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are human neuromuscular disorders associated with mutations of simple repetitive sequences in affected genes. The abnormal expansion of CTG repeats in the 3′-UTR of the DMPK gene elicits DM1, whereas elongated CCTG repeats in intron 1 of ZNF9/CNBP triggers DM2. Pathogenesis of both disorders is manifested by nuclear retention of expanded repeatcontaining RNAs and aberrant alternative splicing. The precise determination of absolute numbers of mutant RNA molecules is important for a better understanding of disease complexity and for accurate evaluation of the efficacy of therapeutic drugs. We present two quantitative methods, Multiplex Ligation-Dependent Probe Amplification and droplet digital PCR, for studying the mutant DMPK transcript (DMPK exp RNA) and the aberrant alternative splicing in DM1 and DM2 human tissues and cells. We demonstrate that in DM1, the DMPK exp RNA is detected in higher copy number than its normal counterpart. Moreover, the absolute number of the mutant transcript indicates its low abundance with only a few copies per cell in DM1 fibroblasts. Most importantly, in conjunction with fluorescence in-situ hybridization experiments, our results suggest that in DM1 fibroblasts, the vast majority of nuclear RNA foci consist of a few molecules of DMPK exp RNA.Myotonic dystrophy type 1 (DM1) and type 2 (DM2) are adult onset muscular dystrophies leading to disability and shortened lifespan. Both belong to a larger group of human disorders associated with mutational expansions of simple repetitive sequences within specific genes. The mutation that causes DM1 results from the expansion of CTG repeats in the 3′-UTR of the DMPK gene; whereas DM2 is associated with intronic elongation of CCTG repeats in ZNF9/CNBP gene 1,2 . Pathogenesis of both diseases is mediated by a toxic RNA gain-of-function mechanism manifested by nuclear retention of expanded CUG-and CCUG-harboring RNAs which aggregate within nucleoprotein foci 3 . Their adverse effects are mediated through sequestration of various proteins including the muscleblind-like (MBNL) family of splicing factors. These proteins are functionally depleted by the expanded repeats in DM1 and DM2 which leads to abnormalities in many pathways of RNA metabolism including alternative splicing, a molecular hallmark of DM [4][5][6][7][8] . In DM adult skeletal muscle abnormal expression of embryonic splicing isoforms has been reported for a few hundred genes 4 . Given the importance of alternative splicing as one of the biomarkers of disease severity and therapeutic response, accurate quantification of splicing variants could facilitate their refinement for clinical applications. Specific oligonucleotide-based microarrays and next-generation sequencing have been used for profiling and identification of many aberrantly spliced transcripts. However, their routine application for precise quantification remains limited due to low quantitative parameters of these methods, restriction to highly expressed genes, high costs a...

CDK12 inhibition reduces abnormalities in cells from patients with myotonic dystrophy and in a mouse model

“…This is consistent with the data observed in DM1 fibroblast lines. To assess any beneficial effect on missplicing, we studied nine transcripts, known to be dysregulated in DM1 (31)(32)(33)(34)(35)(36)(37). Across the panel of genes, we consistently observed improvements in dinaciclib-treated mice (Fig.…”

Allele-specific quantitation of ATXN3 and HTT transcripts in polyQ disease models

“…One possible solution to overcome these limitations is to utilize heterozygous SNP variants present in transcripts. Droplet digital PCR (ddPCR) utilizes droplet-based microfluidics and compartmentalization to provide absolute quantification of analyzed molecules and has been used for allele-selective quantification of transcripts [22][23][24][25].…”

A potential role of extended simple sequence repeats in competing endogenous RNA crosstalk

“…3B, C). Based on experimentally verified transcript copy numbers in DM1 patient myoblasts [25,26], we assumed the existence of 15 copies per cell of a mutant DMPK transcript with the CUG tract expansion. In healthy individuals, a DMPK transcript exhibits up to~20 CUG repeats, which equates to~2 MREs, whereas approximately 40 repeats (~5 MREs) are present in healthy carriers of premutation alleles that are unstable and can lead to large expansions in progeny.…”