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The kidney transcriptome, from single cells to whole organs and back

Huang, Shizheng*; Sheng, Xin*; Susztak, Katalin

Current Opinion in Nephrology and Hypertension: May 2019 - Volume 28 - Issue 3 - p 219–226
doi: 10.1097/MNH.0000000000000495

Purpose of review Transcriptome analysis of human kidney samples provides an integrated output of genetic, physiological, or environmental inputs. This review summarizes recent findings including gene expression and genetic variation integration, bulk and single cell gene expression analysis, and describes how such studies have improved our understanding of kidney disease development.

Recent findings Bulk or whole tissue analysis of patient kidney samples identified a large number of genes, whose levels correlate with kidney function and/or structural damage. These genes were enriched for metabolic and immune functions. Using expression quantitative trait analysis, genetic variations-driven gene expression can be identified. Recent developments in single cell sequencing defined cell-type-specific gene expression changes and highlighted specific cell types for disease development.

Summary Recent advancement in whole tissue transcriptomics, specifically incorporating genotype information and single cell data have been powerful to identify kidney disease-associated genes, pathways, and cell types.

Department of Medicine, Renal Electrolyte and Hypertension Division, University of Pennsylvania, Philadelphia, Pennsylvania, USA

Correspondence to Katalin Susztak, MD, PhD, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, 12-123 Smilow Translational Building, Philadelphia, PA 19104, USA. Tel: +1 215 898 2009; e-mail:

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