The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Habuka M, Fagerberg L, Hallström BM, Pontén F, Yamamoto T, Uhlen M

PLoS ONE 10 (12) e0145301 [2015-12-22; online 2015-12-22]

To understand functions and diseases of urinary bladder, it is important to define its molecular constituents and their roles in urinary bladder biology. Here, we performed genome-wide deep RNA sequencing analysis of human urinary bladder samples and identified genes up-regulated in the urinary bladder by comparing the transcriptome data to those of all other major human tissue types. 90 protein-coding genes were elevated in the urinary bladder, either with enhanced expression uniquely in the urinary bladder or elevated expression together with at least one other tissue (group enriched). We further examined the localization of these proteins by immunohistochemistry and tissue microarrays and 20 of these 90 proteins were localized to the whole urothelium with a majority not yet described in the context of the urinary bladder. Four additional proteins were found specifically in the umbrella cells (Uroplakin 1a, 2, 3a, and 3b), and three in the intermediate/basal cells (KRT17, PCP4L1 and ATP1A4). 61 of the 90 elevated genes have not been previously described in the context of urinary bladder and the corresponding proteins are interesting targets for more in-depth studies. In summary, an integrated omics approach using transcriptomics and antibody-based profiling has been used to define a comprehensive list of proteins elevated in the urinary bladder.

NGI Stockholm (Genomics Applications)

NGI Stockholm (Genomics Production)

Tissue Profiling [Collaborative]

QC bibliography QC xrefs

PubMed 26694548

DOI 10.1371/journal.pone.0145301

Crossref 10.1371/journal.pone.0145301

PONE-D-15-11078

pmc PMC4687928

E-MTAB-1733 [sequence reads]