NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE248761 Query DataSets for GSE248761
Status Public on Dec 01, 2023
Title Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Desmoplastic Small Round Cell Tumor (DSRCT) is an aggressive pediatric cancer caused by the EWSR1-WT1 fusion oncoprotein. The tumor is refractory to treatment with a 5-year survival rate of only 15-25%, necessitating the development of novel therapeutics, especially those able to target chemoresistant subpopulations. Novel in vitro cancer stem cell-like (CSC-like) culture conditions increase the expression of stemness markers (SOX2, NANOG) and reduce DSRCT cell line susceptibility to chemotherapy, while maintaining the ability of DSRCT cells to form xenografts. To gain insights into this chemoresistant model, RNA-seq was performed to elucidate transcriptional alterations between DSRCT cells grown in CSC-like spheres and normal 2-dimensional adherent state. Commonly upregulated and downregulated genes were identified and utilized in pathway analysis revealing upregulation of pathways related to chromatin assembly and disassembly and downregulation of pathways including cell junction assembly and extracellular matrix organization. Alterations in chromatin assembly suggest a role for epigenetics in the DSRCT CSC-like state which was further investigated with ATAC-seq, identifying over 10,000 differentially accessible peaks including 4,444 sphere accessible peaks and 6,120 adherent accessible peaks. Accessible regions were associated with higher gene expression including increased accessibility of the CSC marker SOX2 in CSC-like culture conditions. These analyses were further utilized to identify potential CSC therapeutic targets, leading to the identification of B-lymphocyte kinase (BLK) as a CSC-enriched, EWSR1-WT1 regulated, druggable target. BLK inhibition and knockdown reduced CSC-like properties including abrogation of tumorsphere formation and stemness marker expression. Importantly, BLK knockdown reduced DSRCT CSC-like cell chemoresistance making its inhibition a promising target for future combination therapy.
 
Overall design DSRCT cell lines were cultured in sphere or adherent culture conditions for 4-days and then harvested for analysis by RNA-seq (JN-DSRCT-1, BER-DSRCT, BOD-DSRCT), ATAC-seq (BER-DSRCT), or scRNA-seq (JN-DSRCT-1, BER-DSRCT).
 
Contributor(s) Lee SB, Magrath JW
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Nov 27, 2023
Last update date Dec 01, 2023
Contact name Sean Bong Lee
E-mail(s) slee30@tulane.edu
Organization name Tulane University School of Medicine
Department Pathology
Lab Lee Lab
Street address 1700 Tulane Ave
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (12)
GSM7919571 JN-DSRCT-1, Adherent Culture, Rep 1
GSM7919572 JN-DSRCT-1, Adherent Culture, Rep 2
GSM7919573 JN-DSRCT-1, Sphere Culture, Rep 1
This SubSeries is part of SuperSeries:
GSE248857 Transcriptomic Analysis Identifies B-Lymphocyte Kinase as a Therapeutic Target for Desmoplastic Small Round Cell Tumor Cancer Stem Cell-Like Cells
Relations
BioProject PRJNA1045716

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
GSE248761_BER_Sphere_vs_Adherent_rsem_DGE_results.xlsx 4.6 Mb (ftp)(http) XLSX
GSE248761_BOD_Sphere_vs_Adherent_rsem_DGE_results.xlsx 8.5 Mb (ftp)(http) XLSX
GSE248761_JN_Sphere_vs_Adherent_rsem_DGE_results.xlsx 3.0 Mb (ftp)(http) XLSX
GSE248761_RAW.tar 26.3 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap