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Series GSE139900 Query DataSets for GSE139900
Status Public on Jul 19, 2021
Title Therapeutic manipulation of SRSF1 mitigates genome-wide transcriptome alterations and neuronal hyperexcitability in C9ORF72-linked amyotrophic lateral sclerosis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Loss of motor neurons in amyotrophic lateral sclerosis (ALS) leads to relentless paralysis and death usually within a few years from symptom onset. Thousands of RNA molecules with roles in multiple cellular pathways are compromised in disease challenging the identification of alterations causing pathogenesis over downstream changes consequent to neurodegeneration. We recently showed that partial depletion of SR-rich splicing factor SRSF1 inhibits the nuclear export of pathological C9ORF72-repeat transcripts and subsequent translation of dipeptide-repeat proteins in patient-derived neurons and Drosophila, providing in turn a promising strategy of neuroprotection for the most common form of ALS. While the roles of SRSF1 remain poorly characterised in neurons, its therapeutic manipulation offers a rare opportunity to identify disease-modifying gene expression changes. Here, we report diseased and neuroprotected transcriptomes from human-derived neurons and Drosophila heads. Strikingly, while the depletion of SRSF1 has limited effects on genome-wide expression, splicing and nuclear export of RNAs, reversal of 90 disease-modifying transcripts were identified over 2,000 RNA changes in human disease. Functional validation further demonstrated that conserved potassium intermediate/small conductance calcium-activated KCNN channel inhibitors mitigate C9ORF72-ALS mediated hyperexcitability and death of human motor neurons as well as Drosophila motor deficits. Our data support efficacy and safety of SRSF1 manipulation as a therapeutic approach leading to rescue of multiple biological processes without disrupting neuronal transcriptomes. In addition to a potential new therapeutic target for pharmacological inhibition, we also identified in vitro and in vivo disease-modifying gene expression signatures to guide the development of new biomarkers and novel therapeutic approaches in C9ORF72-ALS/FTD.
 
Overall design A total of 24 mRNA profiles, were sequenced using Illumina Illumina HiSeq 4000 (Paired-end, 2x150 bp sequencing, generating data from >280 M clusters per lane). 3 Whole-cell transcriptomes (WCT) and 3 cytoplasmic transcriptomes (CyT) were rofiles for both healthy control (H) and for C9ORF72-ALS (C9) patient-derived neurons treated with Ctrl-RNAi and SRSF1-RNAi lentivirus. A total of 12 samples for each group were sequenced with a total of three biological replicates.
 
Contributor(s) Milo M, Hautbergue GM, Granata I
Citation(s) 34376242
Submission date Nov 04, 2019
Last update date Aug 18, 2021
Contact name Ilaria Granata
E-mail(s) ilaria.granata@icar.cnr.it
Organization name National Research Council of Italy (CNR)
Department Institute for high performance computing and networking (ICAR)
Street address Via Pietro Catellino, 111
City Napoli
ZIP/Postal code 80131
Country Italy
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (24)
GSM4148472 Healthy1_C-RNAi_WCT
GSM4148473 Healthy1_C-RNAi_CyT
GSM4148474 Healthy1_DSRSF1_WCT
Relations
BioProject PRJNA587499
SRA SRP228554

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE139900_matrix_ExonCounts.txt.gz 6.9 Mb (ftp)(http) TXT
GSE139900_matrix_TranscriptCounts.txt.gz 5.5 Mb (ftp)(http) TXT
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