Transcriptomics

Dataset Information

31

Gene expression down-regulation in prostate tumor-associated stromal cells involves organ-specific genes


ABSTRACT: The prostate stroma is a key mediator of epithelial differentiation and development, and potentially plays a role in the initiation and progression of prostate cancer. Isolation and characterization of viable populations of the constituent cell types of prostate tumors could provide valuable insight into the biology of cancer. The CD90+ stromal fibromuscular cells from tumor specimens were isolated by cell-sorting and analyzed by DNA microarray. Dataset analysis was used to compare gene expression between normal and tumor-associated reactive stromal cells. Reactive stroma is characterized by smooth muscle differentiation, prostate down-regulation of SPOCK3, MSMB, CXCL13, and PAGE4, bladder down-regulation of TRPA1, HSD17B2, IL24, and SALL1, and an up-regulation of CXC-chemokines. This study identified a group of differentially expressed genes in CD90+ reactive stromal cells that are potentially involved in organ development and smooth muscle cell differentiation. Overall design: A total of 15 arrays were run for the following sample types obtained from 10 patients: 2 CD90+ prostate tumor-associated stromal: Patient 1: CP_Str_08-028_CD90posi Patient 2: 08-032_CP_strom_CD90posi 2 CD13+ normal bladder stromal: Patient 3: 06-125_NB_CD13posi Patient 4: 06-070_NB_str_CD13posi 1 CD13+ bladder tumor-associated stromal: Patient 5: 07-008_CB_str_CD13posi 5 whole tissue prostate cancer and 5 normal tissue from matched pairs: Patient 6: 05-206_CaP, 05-206_NP Patient 7: 05-213_CaP, 05-213_NP Patient 8: 05-214_CaP, 05-214_NP Patient 9: 05-218_CaP, 05-218_NP Patient 10: 05-220_CaP, 05-220_NP Additionally, 8 arrays were run for the following sample types obtained from 7 patients: 5 CD49a+ normal prostate stromal (PMID 16638148): Patient 1: CD49a_01-26-04 Patient 2: CD49a_03-23-04 Patient 3: CD49a_03-04-04 Patient 4: CD49a-1_06-02-04 Patient 5: CD49a-4_06-02-04 3 CD26+ prostate cancer (2 biological replicates, 1 sample run twice): Patient 6: 05-179_CD26t Patient 6: 05-179_CD26t_2 Patient 7: 08-032_CP_epi_CD26posi The following two prostate cancer samples were also included in the analyses: CD26+ cancer cell, replicate 1 CD26+ cancer cell, replicate 2 The tissue samples consisted of prostate tissue specimens obtained from patients undergoing radical prostatectomy under approval by the University of Washington Institutional Review Board. The same approach was used for both cancer-free and cancer-enriched (where at least 85% of the cells in the corresponding frozen section were of cancer) samples. To obtain bladder stromal cells for analysis, tissue specimens were obtained from cystoprostatectomy surgeries. For cell sorting, the collected specimens were processed within hours. Cell types were sorted using monoclonal antibodies specific for tumor-associated prostate stromal cells (CD90), tumor-associated bladder stromal cells (CD13) and normal bladder stromal cells (CD13) with MACS.

REANALYSED by: GSE20125GSE119128

INSTRUMENT(S): [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array

ORGANISM(S): Homo sapiens  

SUBMITTER: Ricardo Z.N. Vêncio 

PROVIDER: GSE17906 | GEO |

SECONDARY ACCESSION(S): PRJNA119977

REPOSITORIES: GEO

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