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Series GSE252200 Query DataSets for GSE252200
Status Public on Jan 02, 2024
Title Reversal of C9orf72 mutation-induced transcriptional dysregulation and pathology in cultured human neurons by allele-specific excision
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Efforts to genetically reverse C9orf72 pathology have been hampered by our incomplete understanding of the regulation of this complex locus. We generated five different genomic excisions at the C9orf72 locus in a patient-derived iPSC line and a WT line (11 total isogenic lines), and examined gene expression and pathological hallmarks of C9 FTD/ALS in motor neurons differentiated from these lines. Comparing the excisions in these isogenic series removed the confounding effects of different genomic backgrounds and allowed us to probe the effects of specific genomic changes. A coding SNP in the patient cell line allowed us to distinguish transcripts from the normal vs. mutant allele. Using ddPCR, we determined that transcription from the mutant allele is upregulated at least ten-fold, and that sense transcription is independently regulated from each allele whereas antisense transcription is regulated by the opposite allele. Surprisingly, excision of the WT allele increased pathologic dipeptide repeat expression from the mutant allele. Importantly, a single allele was sufficient to supply a normal amount of protein, suggesting that the C9orf72 gene is haplo-sufficient in induced motor neurons. Excision of the mutant repeat expansion reverted all pathology (RNA abnormalities, dipeptide repeat production and TDP-43 pathology) and improved electrophysiological function, whereas silencing sense expression did not eliminate all DPRs, presumably because of the antisense expression. These data increase our understanding of C9orf72 gene regulation and inform gene therapy approaches, including ASOs and CRISPR gene editing.
Overall design Single molecule sequencing of the C9orf72 repeat region from CRISPR edited patient iPSCs using PacBio No-Amp protocol
Contributor(s) Clelland C, Issagholian-Lewin P
Citation(s) 38621131
Submission date Dec 28, 2023
Last update date Apr 24, 2024
Contact name Claire Clelland
Organization name UCSF
Street address 1651 4th St
City San Francisco
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL28352 Sequel II (Homo sapiens)
Samples (5)
GSM7996584 C9P5 unedited
GSM7996585 C9P5 Rex
GSM7996586 C9P5 HET(Mut)x
BioProject PRJNA1058535

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Supplementary file Size Download File type/resource
GSE252200_RAW.tar 59.5 Mb (http)(custom) TAR (of BAM, BED, BW)
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