title: Defining the human gallbladder proteome by transcriptomics and affinity proteomics.
abstract: Global protein analysis of human gallbladder tissue is vital for identification of molecular regulators and effectors of its physiological activity. Here, we employed a genome-wide deep RNA sequencing analysis in 28 human tissues to identify the genes overrepresented in the gallbladder and complemented it with antibody-based immunohistochemistry in 48 human tissues. We characterized human gallbladder proteins and identified 140 gallbladder-specific proteins with an elevated expression in the gallbladder as compared to the other analyzed tissues. Five genes were categorized as enriched, with at least fivefold higher levels in gallbladder, 60 genes were categorized as group enriched with elevated transcript levels in gallbladder shared with at least one other tissue and 75 genes were categorized as enhanced with higher expression than the average expression in other tissues. We explored the localization of the genes within the gallbladder through cell-type specific antibody-based protein profiling and the subcellular localization of the genes through immunofluorescent-based profiling. Finally, we revealed the biological processes and metabolic functions carried out by these genes through the use of GO, KEGG Pathway, and HMR2.0 that is compilation of the human metabolic reactions. We demonstrated the results of the combined analysis of the transcriptomics and affinity proteomics.
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Caroline
authors.initials: C
authors.lastname: Kampf
authors.forename: Adil
authors.initials: A
authors.lastname: Mardinoglu
authors.forename: Linn
authors.initials: L
authors.lastname: Fagerberg
authors.forename: Björn M
authors.initials: BM
authors.lastname: Hallström
authors.forename: Angelika
authors.initials: A
authors.lastname: Danielsson
authors.forename: Jens
authors.initials: J
authors.lastname: Nielsen
authors.forename: Fredrik
authors.initials: F
authors.lastname: Pontén
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlen
mesh_terms: D005704:Gallbladder / Q000737:chemistry / Q000378:metabolism* / Q000648:ultrastructure; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D020543:Proteome / Q000032:analysis* / Q000235:genetics* / Q000378:metabolism; D040901:Proteomics / Q000379:methods; D049490:Systems Biology; D059467:Transcriptome
chemical_list: D020543:Proteome
keywords: Gallbladder; Proteome; RNA-sequencing; Systems biology; Transcriptome