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Series GSE247589 Query DataSets for GSE247589
Status Public on Apr 22, 2024
Title Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Precise genome editing is crucial for establishing isogenic human disease models and ex vivo stem cell therapy from the patient-derived human pluripotent stem cells (hPSCs). Unlike Cas9-mediated knock-in, cytosine base editor (CBE) and prime editor (PE) achieve the desirable gene correction without inducing DNA double strand breaks. However, hPSCs possess highly active DNA repair pathways and are particularly susceptible to p53-dependent cell death. These unique characteristics impede the efficiency of gene editing in hPSCs. Here, we demonstrate that dual inhibition of p53-mediated cell death and distinct activation of the DNA damage repair system upon DNA damage by CBE or PE additively enhanced editing efficiency in hPSCs. The BE4stem system comprised of dominant negative p53 (p53DD) and three UNG inhibitor (UGI), engineered to specifically diminish base excision repair (BER), improved CBE efficiency in hPSCs. Addition of dominant negative MLH1 to inhibit mismatch repair activity and p53DD in the conventional PE system also significantly enhanced PE efficiency in hPSCs. Thus, combined inhibition of the unique cellular cascades engaged in hPSCs upon gene editing could significantly enhance precise genome editing in these cells.
 
Overall design To investigate off-target effects on transcriptome level after gene editing, we established RNA of EP(Electroporation only, control group) and BE4max, BEStem, PE4, PEStem treated sample.
 
Contributor(s) Park J, Kim Y, Hwang G, Kang C, Bae S, Cha H
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Submission date Nov 13, 2023
Last update date Apr 22, 2024
Contact name Hyuk-Jin Cha
E-mail(s) yunjkim36@gmail.com
Organization name Seoul National University
Street address 215-20 Gwan-ak ro Gwan-ak gu
City Seoul
ZIP/Postal code 08826
Country South Korea
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (5)
GSM7893389 EP [RNA-seq]
GSM7893390 BE4 [RNA-seq]
GSM7893391 BESTEM [RNA-seq]
This SubSeries is part of SuperSeries:
GSE248191 Enhancing Precise Genome Editing in Human Pluripotent Stem Cells through Dual Inhibition of DNA Damage Response and Repair Pathways
Relations
BioProject PRJNA1039785

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Supplementary file Size Download File type/resource
GSE247589_RAW.tar 630.0 Kb (http)(custom) TAR (of CSV)
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Raw data are available in SRA

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