CD26+ cancer cells and CD90+ tumor-associated stromal cells were sorted from tumor tissue. Dataset analysis with transcriptomes of CD26+ luminal, CD104+ basal, CD49a+ stromal and CD31+ endothelial was carried out to identify candidates: CD90, AGR2, BCMP11, CEACAM5, CRISP3. Quantitative protomics was applied to measure these proteins in urine samples.
Sort cancer cells from tumor specimens
Determine gene expression (transcriptome) by Affymetrix DNA arrays
Dataset analysis to identify cancer up-regulated genes encoding secreted or extracellular proteins
Proteomic analysis (mass spectrometry, Western blotting) to validate increased cancer expression
Genomics and proteomics. DNA microarray analysis of sorted cell types to identify cancer-specific genes encoding secreted/extracellular proteins. Mass spectrometry-based proteomics to measure protin levels in case vs. control urine samples.
Data analysis was done to evaluate data quality of Affymetrix arrays (mRNA expression correlation to protein expression by immunohistochemistry), to compare other publicly available prostate cancer datasets.
The National Cancer Institute's Division of Cancer Prevention has released a new funding opportunity to solicit organ-specific applications for Biomarker Developmental Laboratories (BDLs), one of the four scientific units of the recently funded Early Detection Research Network (EDRN). The EDRN is a national infrastructure funded to discover, develop, and validate biomarkers for risk assessment, detection, and molecular diagnosis and prognosis of early cancer. BDLs are responsible for the discovery, development, characterization, and testing of new, or the refinement of existing, biomarkers and biomarker assays for risk assessment, detection, and molecular diagnosis and prognosis of cancers.
The existing BDLs are primarily focused on ovary and gastrointestinal cancers. The proposed BDLs (to be supported under this funding opportunity) should be focused on one or more of the following cancers: breast, prostate and other genitourinary organs, or lung. In addition, cancers with rapidly rising incidence rates, e.g., endometrial, hepatocellular, kidney, thyroid, oropharyngeal cancers, and/or cancers with unique etiology, e.g., mesothelioma, will be considered.
The newly funded units of the Early Detection Research Network will be announced later in April. Successful applicants have already been notified. Those researchers who were not successful during the last round of applications are encouraged to apply to this opportunity.