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.

Single cell RNA sequencing to dissect the molecular heterogeneity in lupus nephritis

“…Tubular cell subpopulations determined. The expression of some specific tubular cell markers has previously been shown to depend on their specific location along the nephron (18). We therefore performed additional analysis of only tubular cells using PCA and t-SNE (19), which further subclustered them into 4 subtypes.…”

“…The full list of differentially expressed genes defining each tubular cell compartment is listed in Supplemental Table 2. Proximal convoluted tubular cells expressed ALDOB and MIOX (18), loop of Henle cells expressed UMOD and SLC12A1 known to be restricted to the thick ascending limb (20,21), distal convoluted tubular cells expressed CDH16 (22), and collecting duct cells selectively expressed the transcription factor KLF5 (23), as well as cell junction proteins TJP1 and CLDN4 (24).…”

Clinical and Functional Relevance of the Monocarboxylate Transporter Family in Disease Pathophysiology and Drug Therapy

“…Protein expression of human MCT9 was found in the proximal tubular epithelial cell of the kidneys. 23 Based on human mRNA expression data, MCT11 is highly expressed in the thyroid, liver, and salivary gland. 24 Peak gene expression levels of MCT12 were observed in the eyes, lungs, kidneys, and testis.…”

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

“…The tissues with the most mRNAs highly enriched (at least 5× the levels in all other tissues) are testis (999) and brain (318). Several tissue-specific HPA publications have been published, and more are expected during 2015 with tissue-specific immunohistochemical and transcript evidence to guide specimen selection for further MS studies, for example, describing the brain, 18 liver, 19 testis, 20 kidney, 21 pancreas, 22 skin, 23 adipose tissue, 24 gallbladder, 25 lung, 26 gastrointestinal tract, 27 and cardiac and skeletal muscle. 28 HPA, v14, will be released in Fall 2015 along with a novel Rodent Brain Atlas comprising immunofluorescently stained whole-mouse-brain sections.…”