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An RNA-targeting CRISPR-Cas13d system alleviates disease-related phenotypes in Huntington's disease models.

Kathryn H Morelli, Qian Wu, Maya L Gosztyla, Hongshuai Liu, Minmin Yao, Chuangchuang Zhang, Jiaxu Chen, Ryan J Marina, Kari Lee, Krysten L Jones, Megan Y Huang, Allison Li, Charlene Smith-Geater, Leslie M Thompson, Wenzhen Duan, Gene W Yeo
Nature neuroscience · 2023 · Vol. 26 (1) · pp. 27-38
PubMed DOI PMC Full Text

Abstract

Huntington's disease (HD) is a fatal, dominantly inherited neurodegenerative disorder caused by CAG trinucleotide expansion in exon 1 of the huntingtin (HTT) gene. Since the reduction of pathogenic mutant HTT messenger RNA is therapeutic, we developed a mutant allele-sensitive CAG<sup>EX</sup> RNA-targeting CRISPR-Cas13d system (Cas13d-CAG<sup>EX</sup>) that eliminates toxic CAG<sup>EX</sup> RNA in fibroblasts derived from patients with HD and induced pluripotent stem cell-derived neurons. We show that intrastriatal delivery of Cas13d-CAG<sup>EX</sup> via an adeno-associated viral vector selectively reduces mutant HTT mRNA and protein levels in the striatum of heterozygous zQ175 mice, a model of HD. This also led to improved motor coordination, attenuated striatal atrophy and reduction of mutant HTT protein aggregates. These phenotypic improvements lasted for at least eight months without adverse effects and with minimal off-target transcriptomic effects. Taken together, we demonstrate proof of principle of an RNA-targeting CRISPR-Cas13d system as a therapeutic approach for HD, a strategy with implications for the treatment of other dominantly inherited disorders.

Publication Types

["Journal Article", "Research Support, U.S. Gov't, Non-P.H.S.", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't"]

Keywords

[]

MeSH Terms

["Mice", "Animals", "Huntington Disease", "RNA", "Clustered Regularly Interspaced Short Palindromic Repeats", "Corpus Striatum", "RNA, Messenger", "Phenotype", "Huntingtin Protein", "Disease Models, Animal"]

Funding

U24 HG009889 NHGRI NIH HHS (United States)
S10 OD026929 NIH HHS (United States)
R01 HG004659 NHGRI NIH HHS (United States)
R01 NS103172 NINDS NIH HHS (United States)
U41 HG009889 NHGRI NIH HHS (United States)
P01 AI132122 NIAID NIH HHS (United States)
S10 OD025052 NIH HHS (United States)
U19 MH107367 NIMH NIH HHS (United States)
T32 GM008666 NIGMS NIH HHS (United States)
F32 NS112654 NINDS NIH HHS (United States)
R01 NS082338 NINDS NIH HHS (United States)
P50 HD103538 NICHD NIH HHS (United States)
R01 NS099397 NINDS NIH HHS (United States)
R01 EY029166 NEI NIH HHS (United States)
R01 NS124084 NINDS NIH HHS (United States)
F31 NS111859 NINDS NIH HHS (United States)
R56 NS124084 NINDS NIH HHS (United States)
R21 NS118079 NINDS NIH HHS (United States)

Linked Datasets (3)

GSE214108 GSE via ncbi_elink
GEO

RNA-Targeting CRISPR/Cas13d System Alleviates Disease-Related Phenotypes in Pre-clinical Models of Huntington’s Disease (Human).

Homo sapiens
49 data files
FileTypeSize
109-L_1_S1_L001_R1_001.fastq.gz RNA-Seq 5.4 GB
109-L_2_S2_L001_R1_001.fastq.gz RNA-Seq 4.9 GB
109-L_3_S3_L001_R1_001.fastq.gz RNA-Seq 106.6 MB
109-L_4_S4_L001_R1_001.fastq.gz RNA-Seq 6.3 GB
109-T_1_S5_L001_R1_001.fastq.gz RNA-Seq 1.7 GB
109-T_2_S6_L001_R1_001.fastq.gz RNA-Seq 3.3 GB
109-T_3_S7_L001_R1_001.fastq.gz RNA-Seq 3.0 GB
109-T_4_S8_L001_R1_001.fastq.gz RNA-Seq 1.4 GB
66-L_1_S13_L001_R1_001.fastq.gz RNA-Seq 6.0 GB
66-L_2_S14_L001_R1_001.fastq.gz RNA-Seq 3.5 GB
66-L_3_S15_L001_R1_001.fastq.gz RNA-Seq 1.5 GB
66-L_4_S16_L001_R1_001.fastq.gz RNA-Seq 5.0 GB
66-T_1_S17_L001_R1_001.fastq.gz RNA-Seq 1.6 GB
66-T_2_S18_L001_R1_001.fastq.gz RNA-Seq 3.7 GB
66-T_3_S19_L001_R1_001.fastq.gz RNA-Seq 2.8 GB
66-T_4_S20_L001_R1_001.fastq.gz RNA-Seq 4.2 GB
71-L_1_S25_L001_R1_001.fastq.gz RNA-Seq 2.5 GB
71-L_2_S26_L001_R1_001.fastq.gz RNA-Seq 908.9 MB
71-L_3_S27_L001_R1_001.fastq.gz RNA-Seq 989.3 MB
71-L_4_S28_L001_R1_001.fastq.gz RNA-Seq 1.7 GB
71-T_1_S29_L001_R1_001.fastq.gz RNA-Seq 1020.7 MB
71-T_2_S30_L001_R1_001.fastq.gz RNA-Seq 1.8 GB
71-T_3_S31_L001_R1_001.fastq.gz RNA-Seq 4.2 GB
71-T_4_S32_L001_R1_001.fastq.gz RNA-Seq 2.8 GB
C1-L_1_S37_L001_R1_001.fastq.gz RNA-Seq 2.3 GB
C1-L_2_S38_L001_R1_001.fastq.gz RNA-Seq 1.1 GB
C1-L_3_S39_L001_R1_001.fastq.gz RNA-Seq 1.1 GB
C1-L_4_S40_L001_R1_001.fastq.gz RNA-Seq 1.8 GB
C1-T_1_S41_L001_R1_001.fastq.gz RNA-Seq 1.4 GB
C1-T_2_S42_L001_R1_001.fastq.gz RNA-Seq 4.6 GB
C1-T_3_S43_L001_R1_001.fastq.gz RNA-Seq 711.2 MB
C1-T_4_S44_L001_R1_001.fastq.gz RNA-Seq 2.5 GB
C2-L_1_S49_L001_R1_001.fastq.gz RNA-Seq 1.7 GB
C2-L_2_S50_L001_R1_001.fastq.gz RNA-Seq 2.1 GB
C2-L_3_S51_L001_R1_001.fastq.gz RNA-Seq 747.6 MB
C2-L_4_S52_L001_R1_001.fastq.gz RNA-Seq 2.3 GB
C2-T_1_S53_L001_R1_001.fastq.gz RNA-Seq 2.3 GB
C2-T_2_S54_L001_R1_001.fastq.gz RNA-Seq 2.9 GB
C2-T_3_S55_L001_R1_001.fastq.gz RNA-Seq 1.3 GB
C2-T_4_S56_L001_R1_001.fastq.gz RNA-Seq 3.5 GB
C3-L_1_S61_L001_R1_001.fastq.gz RNA-Seq 1.5 GB
C3-L_2_S62_L001_R1_001.fastq.gz RNA-Seq 1.6 GB
C3-L_3_S63_L001_R1_001.fastq.gz RNA-Seq 1.2 GB
C3-L_4_S64_L001_R1_001.fastq.gz RNA-Seq 1.5 GB
C3-T_1_S65_L001_R1_001.fastq.gz RNA-Seq 2.5 GB
C3-T_2_S66_L001_R1_001.fastq.gz RNA-Seq 1.7 GB
C3-T_3_S67_L001_R1_001.fastq.gz RNA-Seq 3.3 GB
C3-T_4_S68_L001_R1_001.fastq.gz RNA-Seq 4.0 GB
SRR21696966.lite RNA-Seq 1.5 GB
GSE214109 GSE via ncbi_elink
GEO

RNA-Targeting CRISPR/Cas13d System Alleviates Disease-Related Phenotypes in Pre-clinical Models of Huntington’s Disease (Mouse).

Mus musculus
19 data files
FileTypeSize
287_S10_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.… RNA-Seq 521.0 MB
291_S9_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.S… RNA-Seq 698.5 MB
338_S11_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.… RNA-Seq 428.7 MB
343_S12_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.… RNA-Seq 1.6 GB
351_S13_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.… RNA-Seq 1.5 GB
378_S15_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.… RNA-Seq 499.2 MB
392_S6_L002_R1_001.fastqTr.sorted.STARUnmapped.out.sorted.S… RNA-Seq 1002.5 MB
mHTT_10_S50_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sor… RNA-Seq 791.5 MB
mHTT_11_S51_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sor… RNA-Seq 696.5 MB
mHTT_12_S52_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sor… RNA-Seq 895.8 MB
mHTT_16_S56_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sor… RNA-Seq 1023.1 MB
mHTT_18_S58_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sor… RNA-Seq 451.1 MB
mHTT_1_S41_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 679.4 MB
mHTT_2_S42_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 2.6 GB
mHTT_3_S43_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 1.7 GB
mHTT_7_S47_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 1.2 GB
mHTT_8_S48_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 1.2 GB
mHTT_9_S49_L004_R1_001.fastqTr.sorted.STARUnmapped.out.sort… RNA-Seq 846.9 MB
TCTGCAAG_AAGGTGAA_385_S1_L002_R1_001.fastqTr.sorted.STARUnm… RNA-Seq 483.7 MB
GSE214110 GSE via ncbi_elink
GEO

RNA-Targeting CRISPR/Cas13d System Alleviates Disease-Related Phenotypes in Pre-clinical Models of Huntington’s Disease

Mus musculus

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.

GSE214110 GSE GEO
GEO

RNA-Targeting CRISPR/Cas13d System Alleviates Disease-Related Phenotypes in Pre-clinical Models of Huntington’s Disease

Analysis Pipelines (3)

GSE214108 RNA-seq Data Processing 3 steps
RNA-seq geo_data_processing GSE214108
GSE214109 RNA-seq Data Processing 5 steps
RNA-seq geo_data_processing GSE214109
GSE214110 RNA-seq Data Processing 3 steps
RNA-seq geo_data_processing GSE214110