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Series GSE131387 Query DataSets for GSE131387
Status Public on May 18, 2019
Title Editing the Sickle Cell Disease Mutation in Primary Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Site-specific correction of a point mutation causing a monogenic disease in autologous hematopoietic stem and progenitor cells (HSPCs) can be used as a treatment of inherited disorders of the blood cells. Sickle Cell Disease (SCD) is an ideal model to investigate the potential use of gene editing to transvert a single point mutation at the β-globin locus (HBB). We compared the activity of ZFNs and CRISPR/Cas9 for editing and homologous donor templates delivered as single-stranded oligodeoxynucleotides (ssODN), adeno-associated virus serotype 6 (AAV6), integrase-deficient lentiviral vectors (IDLV) and adenovirus 5/35 serotype (Ad5/35) to transvert the base-pair responsible for SCD in HBB in primary human CD34+ HSPCs. We found that the ZFNs and Cas9 directed similar frequencies of nuclease activity. In vitro, AAV6 led to the highest frequencies of homology-directed repair (HDR), but levels of base-pair transversions were significantly reduced when analyzing cells in vivo in immune-deficient mouse xenografts, with similar frequencies achieved with either AAV6 or ssODN. AAV6 also caused significant impairment of colony-forming progenitors and human cell engraftment. Gene correction in engrafting hematopoietic stem cells may be limited by the capacity of the cells to mediate HDR, suggesting additional manipulations may be needed for high efficiency gene correction in HSPCs
Overall design To assess effects of the reagents involved in editing on gene expression profiles of CD34+ PBSCs, we performed RNA-sequencing (RNA-Seq) of total RNA isolated from cells 24 hours post-editing.

Mock - Control
RNP - ribonucleoprotein, Cas9 + sgRNA
ssODN - DNA donor template, single-stranded oligodeoxynucleotides
AAV6_BG - DNA donor template, AAV6 based vector, version 1
AAV6_BG_HRPT - DNA donor template, AAV6 based vector, version 2
Contributor(s) Romero Z, Kohn DB
Citation(s) 31178391
Submission date May 17, 2019
Last update date Aug 18, 2019
Contact name Yerbol Z. Kurmangaliyev
Organization name University of California, Los Angeles
Street address 675 Charles E. Young Drive South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (24)
GSM3772956 Mock rep1
GSM3772957 Mock rep2
GSM3772958 Mock rep3
BioProject PRJNA543467
SRA SRP198749

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
GSE131387_cpm.txt.gz 2.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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