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Elimination of Toxic Microsatellite Repeat Expansion RNA by RNA-Targeting Cas9.

Ranjan Batra, David A Nelles, Elaine Pirie, Steven M Blue, Ryan J Marina, Harrison Wang, Isaac A Chaim, James D Thomas, Nigel Zhang, Vu Nguyen, Stefan Aigner, Sebastian Markmiller, Guangbin Xia, Kevin D Corbett, Maurice S Swanson, Gene W Yeo

Cell · 2017 · Vol. 170 (5) · pp. 899-912.e10

PubMed ↗ DOI ↗ PMC full text ↗

Abstract

Microsatellite repeat expansions in DNA produce pathogenic RNA species that cause dominantly inherited diseases such as myotonic dystrophy type 1 and 2 (DM1/2), Huntington's disease, and C9orf72-linked amyotrophic lateral sclerosis (C9-ALS). Means to target these repetitive RNAs are required for diagnostic and therapeutic purposes. Here, we describe the development of a programmable CRISPR system capable of specifically visualizing and eliminating these toxic RNAs. We observe specific targeting and efficient elimination of microsatellite repeat expansion RNAs both when exogenously expressed and in patient cells. Importantly, RNA-targeting Cas9 (RCas9) reverses hallmark features of disease including elimination of RNA foci among all conditions studied (DM1, DM2, C9-ALS, polyglutamine diseases), reduction of polyglutamine protein products, relocalization of repeat-bound proteins to resemble healthy controls, and efficient reversal of DM1-associated splicing abnormalities in patient myotubes. Finally, we report a truncated RCas9 system compatible with adeno-associated viral packaging. This effort highlights the potential of RCas9 for human therapeutics.

Linked datasets 1

GSE100943 GSE · via ncbi_elink
GEO ↗

Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9

Homo sapiens

36 data files
FileTypeSize
Myoblast1_S1_L001_R1_001.fastq.gz RNA-Seq 1.4 GB
Myoblast1_S1_L002_R1_001.fastq.gz RNA-Seq 1.5 GB
Myoblast2_S2_L001_R1_001.fastq.gz RNA-Seq 2.4 GB
Myoblast2_S2_L002_R1_001.fastq.gz RNA-Seq 2.4 GB
Myoblast3_S3_L001_R1_001.fastq.gz RNA-Seq 2.4 GB
Myoblast3_S3_L002_R1_001.fastq.gz RNA-Seq 2.4 GB
Myoblast4_S4_L001_R1_001.fastq.gz RNA-Seq 1.4 GB
Myoblast4_S4_L002_R1_001.fastq.gz RNA-Seq 1.4 GB
Myoblast5_S5_L001_R1_001.fastq.gz RNA-Seq 1.8 GB
Myoblast5_S5_L002_R1_001.fastq.gz RNA-Seq 1.8 GB
Myotube1_S6_L001_R1_001.fastq.gz RNA-Seq 2.3 GB
Myotube1_S6_L002_R1_001.fastq.gz RNA-Seq 2.3 GB
Myotube2_S7_L001_R1_001.fastq.gz RNA-Seq 1.2 GB
Myotube2_S7_L002_R1_001.fastq.gz RNA-Seq 2.5 GB
Myotube3_S8_L001_R1_001.fastq.gz RNA-Seq 1.9 GB
Myotube3_S8_L002_R1_001.fastq.gz RNA-Seq 2.0 GB
Myotube4_S9_L001_R1_001.fastq.gz RNA-Seq 2.2 GB
Myotube4_S9_L002_R1_001.fastq.gz RNA-Seq 2.3 GB
SRR5812278_GSM2696922 RNA-Seq 1.4 GB
SRR5812279_GSM2696922 RNA-Seq 1.5 GB
SRR5812280_GSM2696923 RNA-Seq 2.4 GB
SRR5812281_GSM2696923 RNA-Seq 2.4 GB
SRR5812282_GSM2696924 RNA-Seq 2.4 GB
SRR5812283_GSM2696924 RNA-Seq 2.4 GB
SRR5812284_GSM2696925 RNA-Seq 1.4 GB
SRR5812285_GSM2696925 RNA-Seq 1.4 GB
SRR5812286_GSM2696926 RNA-Seq 1.8 GB
SRR5812287_GSM2696926 RNA-Seq 1.8 GB
SRR5812288_GSM2696927 RNA-Seq 2.3 GB
SRR5812289_GSM2696927 RNA-Seq 2.3 GB
SRR5812290_GSM2696928 RNA-Seq 1.2 GB
SRR5812291_GSM2696928 RNA-Seq 2.5 GB
SRR5812292_GSM2696929 RNA-Seq 1.9 GB
SRR5812293_GSM2696929 RNA-Seq 2.0 GB
SRR5812294_GSM2696930 RNA-Seq 2.2 GB
SRR5812295_GSM2696930 RNA-Seq 2.3 GB

Potentially related datasets 1

These accessions were text-mined from the PMC full text. They may be referenced for comparison, cited from other studies, or otherwise mentioned without being primary data for this paper.

Accession Source Title
GSE100943 GSE · GEO GEO ↗ Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9

Analysis pipelines 1

Pipeline Assay Steps Dataset
GSE100943 RNA-seq Data Processing geo_data_processing RNA-seq 7 GSE100943
Funding 5 grants
Grant Funder
R01 HG004659 NHGRI NIH HHS (United States)
R01 NS103172 NINDS NIH HHS (United States)
T32 GM008666 NIGMS NIH HHS (United States)
K12 GM068524 NIGMS NIH HHS (United States)
R01 NS075449 NINDS NIH HHS (United States)