The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling

• Published in: PloS one 2014-12, Vol.9 (12), p.e116125-e116125
• Main Authors: Habuka, Masato, Fagerberg, Linn, Hallström, Björn M, Kampf, Caroline, Edlund, Karolina, Sivertsson, Åsa, Yamamoto, Tadashi, Pontén, Fredrik, Uhlén, Mathias, Odeberg, Jacob
• Format: Article
• Language: English
• Subjects: Aged; Alpha-Crystallin; Antibodies; Base Sequence; Biology; Biology and Life Sciences; Biotechnology; Cataracts; Comparative analysis; Compartments; Dental schools; Disease; Distal tubules; Expression; Female; Gene; Gene expression; Gene Expression Profiling; Genes; Humans; Immunohistochemistry; Immunology; Kidney - cytology; Kidney - metabolism; Kidney Glomerulus - cytology; Kidney Tubules, Collecting; Kidney Tubules, Distal - cytology; Kidney Tubules, Proximal - cytology; Kidneys; Laboratories; Male; Medicin och hälsovetenskap; Medicine and Health Sciences; Metabolism; Middle Aged; Morphology; Nephrin; Nephrology; Organs; Pathology; Physiology; Proteins; Proteome - genetics; Proteomes; Proximal tubules; Review boards; Rna-Seq; Rodents; Science; Sequence Analysis, RNA; Slit Diaphragm; Stem cells; Tissue analysis; Tissues; Transcriptome - genetics; Uromodulin
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0116125

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.