RNA sequencing provides insight into the mechanism of kinase inhibitor resistance

Alternative drug target identification based on altered gene expression profiles

  • Resistance to kinase inhibitors often manifests in patients after an initial good response.

  • Insight into the mechanism of resistance can aid in determining the next treatment regimen.

  • At Oncolines we generated cell lines resistant to the pan-FGFR inhibitor erdafitinib.

    • Erdafitinib is FDA-approved for the treatment of locally advanced or metastatic urothelial carcinoma harboring genetic FGFR2 or FGFR3 alterations.
  • The resistant cell lines were profiled by RNA sequencing and analysed for differences in gene expression by gene set enrichment analysis.

    • Myc target genes were found to be upregulated.
    • Alterations in c-Myc expression were observed by immunoblotting in a time-course of erdafitinib treatment.
    • Increased sensitivity to c-Myc inhibition was confirmed via indirect targeting with BET-Bromodomain inhibitors JQ1 and I‑BET-762.

  • Altered c-Myc expression might be a common resistance mechanism to FGFR inhibitors, because the resistant cell lines were also resistant to pemigatinib and infigratinib, two other FDA approved FGFR inhibitors.

  • Targeting Myc can be explored as alternative treatment upon FGFR inhibitor resistance.

The parental AN3 CA cell line and the erdafitinib resistant clone 05 were profiled with RNA sequencing, followed by analysis on differentially expressed genes. Left image: Gene set enrichment analysis indicated Myc target genes were upregulated in the resistant clone. Right image: the enrichment plot for Myc target gene set v1.
c-Myc expression is altered in the resistant cell lines compared to the parental cell line. c-Myc protein expression of parental and resistant cell lines were analysed by immunoblotting upon a time-course of erdafitinib treatment.
xenograft model
Increased sensitivity to c-Myc inhibition was confirmed by in vitro drug testing. Dose response curves for BET-bromodomain inhibitors JQ1 (left) and I-BET-762 (right) indirectly targeting c-Myc.