Transcriptomes of Major Proximal Tubule Cell Culture Models

Significance Statement Transformed cultured cell lines are widely used for research on the physiology, pathophysiology, toxicology, and pharmacology of the renal proximal tubule. The lines most appropriate for a given use depend upon the set of expressed genes. The authors have used RNA-sequencing techniques to identify the gene expression profiles of 14 different cell lines, representing six species, plus primary cultures of mouse proximal tubule and compared them with transcriptomes of native mouse kidney proximal tubule. None of the cell lines fully matched transcriptomes of native proximal tubule cells, but all expressed certain gene groups that make them suitable for studying specific cellular processes that occur in the proximal tubule. An online resource allows researchers to identify optimal cell lines to address specific experimental goals. Background Cultured cell lines are widely used for research in the physiology, pathophysiology, toxicology, and pharmacology of the renal proximal tubule. The lines that are most appropriate for a given use depend upon the genes expressed. New tools for transcriptomic profiling using RNA sequencing (RNA-Seq) make it possible to catalog expressed genes in each cell line. Methods Fourteen different proximal tubule cell lines, representing six species, were grown on permeable supports under conditions specific for the respective lines. RNA-Seq followed standard procedures. Results Transcripts expressed in cell lines variably matched transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45% of proximal marker genes [TPM threshold =15]), with pig kidney cells (LLC-PK1) close behind (39%). Lower-percentage matches were seen for various human lines, including HK-2 (26%), and lines from rodent kidneys, such as NRK-52E (23%). Nominally, identical OK cells from different sources differed substantially in expression of proximal tubule markers. Mapping cell line transcriptomes to gene sets for various proximal tubule functions (sodium and water transport, protein transport, metabolic functions, endocrine functions) showed that different lines may be optimal for experimentally modeling each function. An online resource (https://esbl.nhlbi.nih.gov/JBrowse/KCT/) has been created to interrogate cell line transcriptome data. Proteomic analysis of NRK-52E cells confirmed low expression of many proximal tubule marker proteins. Conclusions No cell line fully matched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particular metabolic and transport processes seen in the proximal tubule.