title: The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.
abstract: 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.
authors.affiliation: Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.|Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, 1-757, Asahimachi-dori Niigata, 951-8510, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Habuka
authors.affiliation: Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.
authors.forename: Linn
authors.initials: L
authors.lastname: Fagerberg
authors.affiliation: Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.
authors.forename: Björn M
authors.initials: BM
authors.lastname: Hallström
authors.affiliation: Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Pontén
authors.affiliation: Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, 1-757, Asahimachi-dori Niigata, 951-8510, Japan.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Science for Life Laboratory, KTH - Royal Institute of Technology, SE-171 21, Stockholm, Sweden.|Department of Proteomics, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlen
mesh_terms: D000906:Antibodies / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D006801:Humans; D009928:Organ Specificity; D040901:Proteomics / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods; D046888:Tissue Array Analysis / Q000379:methods; D015854:Up-Regulation; D001743:Urinary Bladder / Q000378:metabolism*; D019459:Urothelium / Q000378:metabolism*
chemical_list: D000906:Antibodies