hTERT and SV40LgT Renal Cell Lines Adjust Their Transcriptional Responses After Copy Number Changes from the Parent Proximal Tubule Cells

TL;DR

This study compares how two types of immortalized kidney cell lines respond differently to chemical challenges due to changes in their gene copy numbers and transcriptional profiles.

Contribution

The study reveals how gene copy number changes during immortalization affect transcriptional responses in renal cell lines.

Findings

LgT cells showed increased injury and repair responses compared to hTERT cells after chemical challenge.

Genomic changes in LgT cells included increased gene copy numbers in chromosome 5, while hTERT cells had copy losses in chromosomes 4 and 9.

Transcriptomic differences included altered pathways in energy metabolism for hTERT and cell cycle/DNA repair for LgT cells.

Abstract

Primary mouse renal proximal tubule epithelial cells (moRPTECs) were immortalized by lentivirus transduction to create hTERT or SV40LgT (LgT) cell lines. Prior work showed a more pronounced injury and repair response in LgT versus hTERT cells after chemical challenge. We hypothesized that unique genomic changes occurred after immortalization, altering critical genes and pathways. RNA-seq profiling and whole-genome sequencing (WGS) of parent, hTERT, and LgT cells showed that 92.5% of the annotated transcripts were shared, suggesting a conserved proximal tubule expression pattern. However, the cell lines exhibited unique transcriptomic and genomic profiles different from the parent cells. Three transcript classes were quite relevant for chemical challenge response—Cyps, ion channels, and metabolic transporters—each important for renal function. A pathway analysis of the hTERT cells suggested alterations in intermediary and energy metabolism. LgT cells exhibited pathway activation in cell cycle and DNA repair that was consistent with replication stress. Genomic karyotyping by combining WGS and RNA-seq data showed increased gene copy numbers in chromosome 5 for LgT cells, while hTERT cells displayed gene copy losses in chromosomes 4 and 9. These data suggest that the exaggerated transcriptional responses of LgT cells versus hTERT cells result from differences in gene copy numbers, replication stress, and the unique selection processes underlying LgT or hTERT immortalization.

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