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Series GSE116117 Query DataSets for GSE116117
Status Public on Jul 19, 2019
Title The FAK-Inhibitor BI 853520 exerts anti-tumor effects in breast cancer
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In order to delineate the molecular mechanisms leading to the therapeutic effect of BI 853520 on primary tumor growth, mice harboring 4T1 primary tumors were treated for five days with BI 853520, and RNA extracted from total tumors was subjected to next generation sequencing. Only primary tumors with sufficient RNA quality were included into further analysis (Suppl. Fig. 2A). Gene expression correlation analysis displayed a clear separation of transcriptomic profiles derived from primary tumors of mice treated with BI 853520 or vehicle (Suppl. Fig. 2B). Comparative gene expression analysis of primary tumors of mice treated with BI 853520 versus vehicle control revealed 1293 upregulated and 475 downregulated genes (cutoffs: p-value ≤ 0.05, fold change +/- 1.5). Functional enrichment analysis for biological processes and signaling pathways indicated that the regulation of epithelial cell proliferation, positive regulation of cell cycle/cell proliferation/cell division and regulation of cell proliferation/cell division/cell growth were enriched in genes downregulated by BI 853520 treatment (Fig. 3A). In line with this finding, gene set enrichment analysis confirmed a significant reduction in the relative expression of genes important for cell cycle and positive regulation of mitotic cell cycle (including cyclin-dependent kinase 1 and 4; Cdk1: log2 fold-change= -0.4519, FDR= 4.24e-03; Cdk4: log2 fold-change= -0.3072, FDR= 0.003718), while the negative regulation of cell proliferation was increased following BI 853520 treatment (Fig. 3C; Suppl. Fig. 2C).
 
Overall design BI 853520 was administered from day 15 post injection for five consecutive days. RNA was isolated from snap-frozen 4T1 primary tumor pieces and applied to next generation sequencing.
 
Contributor(s) Bill R, Kalathur R, Ivanek R, Christofori G
Citation(s) 30237500
Submission date Jun 21, 2018
Last update date Nov 17, 2021
Contact name DBM Bioinformatics Core Facility
Phone +41612073541
Organization name University of Basel
Department Departement of Biomedicine
Street address Hebelstrasse 20
City Basel
State/province BS
ZIP/Postal code 4053
Country Switzerland
 
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (9)
GSM3209126 J4672_Natrosol_0.5perc_5d
GSM3209127 J4673_Natrosol_0.5perc_5d
GSM3209128 J4674_Natrosol_0.5perc_5d
Relations
BioProject PRJNA477312
SRA SRP151030

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
GSE116117_counts.tsv.gz 338.6 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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