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Abstract: FR-PO995

Genomic Analysis of Primary Human Kidney Podocytes Reveals Numerous Differences from Widely Used Podocyte Cell Lines

Session Information

Category: Bioengineering and Informatics

  • 101 Bioengineering and Informatics


  • Sieber, Karsten B, GlaxoSmithKline, King of Prussia, Pennsylvania, United States
  • Akilesh, Shreeram, University of Washington, Seattle, Washington, United States

Kidney disease is a major and increasing burden on society, affecting ~10% of adults worldwide and causing increased risk of all-cause mortality. The glomerular podocyte is an important cell type with limited proliferative/regenerative potential that is the target of many proteinuric kidney diseases. Despite extensive cell biological characterization, very few studies have focused on characterizing the podocyte-specific epigenetic architecture and transcriptome. Such studies promise to shed light on the mechanisms of genome regulation in this important cell type and to calibrate and improve commonly used and emerging (e.g. iPSC-derived) podocyte cell culture systems.


We generated high resolution chromatin accessibility (DNase-seq) and gene expression (RNA-seq) data for primary cultures of human podocytes (n=4), and compared them to similar datasets generated from a widely used conditionally immortalized human podocyte cell line cultured under growth-permissive and differentiation-inducing conditions.


Initial transcriptomic analyses revealed that nearly 2000 genes are differentially expressed between the primary podocytes and a widely-used podocyte cell line. Of these genes, more than 100 transcription factors are differentially expressed; notably, primary podocytes retain strong expression of the lineage-defining transcription factor WT1, in contrast to the podocyte cell line which has weak expression of this gene. Many of the other differentially expressed transcription factors have not been specifically studied in podocytes. To understand their functional consequence, we are analyzing recently generated chromatin accessibility data to elucidate the transcription factor regulatory networks that drive the unique podocyte phenotype.


Compared to primary podocytes, these findings indicate widespread genome regulatory differences in the conditionally immortalized podocyte cell lines and suggest caution in their use. Ongoing studies are focusing on the impact of these differentially expressed transcription factors on the unique chromatin accessibility landscape of primary podocytes.


  • NIDDK Support