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Series GSE165505 Query DataSets for GSE165505
Status Public on Sep 15, 2021
Title Genome-wide CRISPR screen identifies cell cycle as a synthetic lethal pathway with SRSF2P95H mutation
Organism Mus musculus
Experiment type Other
Summary Current strategies to target RNA splicing mutant myeloid cancers propose disruption of normal splicing activity by targeting the splicing apparatus therapeutically. This approach is only modestly sensitizing and is also toxic to non-mutant bearing wild-type cells. To explore potentially exploitable genetic interactions with spliceosome mutations, we combined data mining and functional screening for synthetic lethal interactions with an Srsf2P95H/+ mutation. Analysis of mis-splicing events in a series of both human and murine SRSF2P95H mutant samples across multiple myeloid diseases (AML, MDS, CMML) was first performed to identify conserved mis-splicing events. From this analysis, we identified that the DNA repair and cell cycle pathways were overrepresented within the conserved mis-spliced transcript sets. In parallel, to functionally define pathways essential for survival and proliferation Srsf2P95H/+ cells, we performed a genome-wide pooled CRISPR loss of function screen using Hoxb8 immortalised R26-CreERki/+ Srsf2P95H/+ and R26-CreERki/+ Srsf2+/+ cell lines. We assessed for loss of sgRNA representation at three timepoints: immediately after Srsf2P95H/+ activation, and at one week and two weeks post Srsf2P95H/+ mutation. Pathway analysis demonstrated that the DNA damage response and cell cycle pathways were amongst the top synthetic lethal pathways with Srsf2P95H/+ mutation., Based on the loss of guide RNAs targeting Cdk6, we identified that Palbocilib, a CDK6 inhibitor, showed preferential sensitivity in Srsf2P95H/+ cell lines and in primary non-immortalised lin-cKIT+Sca-1+ cells compared to wild type controls. Our data strongly suggest that cell cycle and DNA damage response pathways are required for Srsf2P95H/+ cell survival, and that Palbociclib could be an alternative therapeutic option for targeting SRSF2 mutant myeloid cancers.
 
Overall design Crispr screen using Hoxb8 imortalised GM-CSF cell line, tamoxifen treated. 3 * R26-CreERT2 Srsf2+/+ (WT) vs 3 * R26-CreERT2 Srsf2P95H/+ (P95H). Each replicate was measured at 0, 4, 11 and 18 days post tamoxifen.
 
Contributor(s) Xu JJ, Chalk AM, Nikolic I, Simpson KJ, Smeets MF, Walkley CR
Citation(s) 34464972
Submission date Jan 25, 2021
Last update date Sep 15, 2021
Contact name Alistair Morgan Chalk
E-mail(s) achalk@svi.edu.au, alistair.chalk@gmail.com
Organization name St Vincent's Institute of Medical Research
Department Stem Cell Regulation Unit
Lab Walkley
Street address 9 Princes st, Fitzroy
City Melbourne
State/province VIC
ZIP/Postal code 3065
Country Australia
 
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (24)
GSM5034785 CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 0 rep 1 (S144)
GSM5034786 CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 4 rep 1 (S144)
GSM5034787 CRISPR screen, Hoxb8 imortalised GM-CSF cell line, R26-CreERT2 Srsf2+/+ Day 11 rep 1 (S144)
This SubSeries is part of SuperSeries:
GSE165506 Transcriptome analysis and genome-wide CRISPR screen of Hoxb8 imortalised GM-CSF cell lines
Relations
BioProject PRJNA694743
SRA SRP303233

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
GSE165505_CEG2_n684.txt.gz 4.3 Kb (ftp)(http) TXT
GSE165505_SRSF2_Screen_count_data.txt.gz 3.5 Mb (ftp)(http) TXT
GSE165505_carl_w_broadgpp_brie_crispr_library.txt.gz 1.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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