RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

Julianty Frost, Alessio Ciulli (Lead / Corresponding author), Sonia Rocha (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

10 Citations (Scopus)
186 Downloads (Pure)


Background: Hypoxia-inducible factor (HIF) transcription factors are well known to control the transcriptional response to hypoxia. Given the importance of cellular response to hypoxia, a number of pharmacological agents to interfere with this pathway have been developed and entered pre-clinical or clinical trial phases. However, how similar or divergent the transcriptional response elicited by different points of interference in cells is currently unknown.

Methods: We performed RNA-sequencing to analyse the similarities and differences of transcriptional response in HeLa cells treated with hypoxia or chemical agents that stabilise HIF by inhibiting components of the hypoxia signalling pathway - prolyl hydroxylase (PHD) inhibitor or von Hippel-Lindau (VHL) inhibitor.

Results: This analysis revealed that hypoxia produces the highest changes in gene transcription, with activation and repression of genes being in large numbers. Treatment with the PHD inhibitor IOX2 or the VHL inhibitor VH032 led mostly to gene activation, majorly via a HIF-dependent manner. These results were also confirmed by qRT-PCR using more specific and/or efficient inhibitors, FG-4592 (PHDs) and VH298 (VHL).

Conclusion: PHD inhibition and VHL inhibition mimic gene activation promoted by hypoxia via a HIF-dependent manner. However, gene repression is mostly associated with the hypoxia response and not common to the response elicited by inhibitors of the pathway.

Original languageEnglish
Article number17
Pages (from-to)1-17
Number of pages17
JournalWellcome Open Research
Publication statusPublished - 29 Jan 2019


  • FG-4592
  • HIF
  • Hypoxia
  • IOX2
  • PHDs
  • RNA-seq
  • VH298
  • VHL

ASJC Scopus subject areas

  • Medicine (miscellaneous)
  • General Biochemistry,Genetics and Molecular Biology


Dive into the research topics of 'RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response'. Together they form a unique fingerprint.

Cite this