GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE176178 Query DataSets for GSE176178
Status Public on Jun 05, 2021
Title Genomic Analysis of Response to Bacillus Calmette-Guerin (BCG) Treatment in High-Grade Stage 1 Bladder Cancer Patients
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Background: Intravesical bacillus Calmette-Guérin (BCG) therapy is standard treatment for high-risk non-muscle invasive bladder cancer (NMIBC) but overall efficacy is low, and no reliable predictive biomarkers currently exist to refine patient selection. We performed genomic analysis on high-grade (HG) T1 NMIBCs to determine if response to therapy is predicted by certain mutational and/or expressional changes.
Methods: Patients with HG T1 NMIBC treated with induction BCG were stratified by response into durable and non-durable responders. Tumor samples were subjected to whole-exome RNA sequencing. Gene expression and variant analysis were performed on RNA sequencing to identify changes between BCG durable responders and those that did not respond.
Results: Differentially expressed genes in durable responders were input into IPA and identified associated immune related pathways: MIF-mediated Glucocorticoid Regulation, MIF Regulation of Innate Immunity, and p38 MAPK Signaling. The differentially expressed genes were crossed with RNAseq variant analysis to identify genes that had significant changes in both. This analysis identified JCHAIN, S100A7, CLECB, and ANXA10 genes that had snps in non-durable responders vs durable responders and also had significant change in gene expression between these two groups.
Conclusions: Differences in the genomic profiles of HG T1 NMIBC tumors exist between those who show durable response to BCG and those who do not. Using pathway analysis, those differences imply upregulation of several interconnected inflammatory pathways among responders. Specific variants identified here are candidates for further study and, if clinically validated, may serve as useful biomarkers in the future.
Overall design RNA sequencing of stage 1 bladder cancer tumor samples in patients treated with BCG treatment.
Contributor(s) Sanders JA, Frasier C, Matulay JT, Steuerwald NM, Zhu J, Grigg CM, Kearns JT, Riggs S, Gaston KE, Brouwer CR, Burks RT, Hartman AL, Foureau DM, Burgess EF, Clark PE
Citation(s) 34430403
Submission date Jun 04, 2021
Last update date Sep 13, 2021
Contact name Peter E Clark
Organization name Atrium Health Levine Cancer Institute
Department Urology
Street address 1021 Morehead Medical Dr Suite 5201
City Charlotte
State/province North Carolina
ZIP/Postal code 28204
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (40)
GSM5359407 1A
GSM5359408 2A
GSM5359409 3A
BioProject PRJNA735225
SRA SRP322746

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
GSE176178_RNA.featurecounts.txt.gz 6.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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