title: The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling.
abstract: To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease.
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan.
authors.forename: Masato
authors.initials: M
authors.lastname: Habuka
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Linn
authors.initials: L
authors.lastname: Fagerberg
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Björn M
authors.initials: BM
authors.lastname: Hallström
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.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Karolina
authors.initials: K
authors.lastname: Edlund
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Åsa
authors.initials: Å
authors.lastname: Sivertsson
authors.affiliation: Department of Structural Pathology, Institute of Nephrology, Medical and Dental School, Niigata University, Asahimachi-dori Niigata, Japan.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yamamoto
authors.affiliation: Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Pontén
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
authors.forename: Mathias
authors.initials: M
authors.lastname: Uhlén
authors.affiliation: School of Biotechnology, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Medicine, Karolinska Institutet and Centre for Hematology, Karolinska University Hospital, Stockholm, Sweden.
authors.forename: Jacob
authors.initials: J
authors.lastname: Odeberg
mesh_terms: D000368:Aged; D001483:Base Sequence; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007668:Kidney / Q000166:cytology / Q000378:metabolism*; D007678:Kidney Glomerulus / Q000166:cytology; D007685:Kidney Tubules, Collecting; D007686:Kidney Tubules, Distal / Q000166:cytology; D007687:Kidney Tubules, Proximal / Q000166:cytology; D008297:Male; D008875:Middle Aged; D020543:Proteome / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics*
chemical_list: D020543:Proteome