Hypoxia induces transcriptional and translational downregulation of the type I interferon (IFN) pathway in multiple cancer cell types

Ana Miar, Esther Arnaiz, Esther Bridges, Shaunna Beedie, Adam P Cribbs, Damien J. Downes, Robert Beagrie, Jan Rehwinkel, Adrian L. Harris

Preprint posted on 25 July 2019

Article now published in Cancer Research at

Through the I of cancer; Immunosuppression via the hypoxic downregulation of IFN in multiple cancer cell types

Selected by Jonny Coates

Context and background

Escape from immune control is a defining hallmark of cancer (1,2). This escape is mediated via multiple mechanisms. Initially, cancer cells undergo immunoediting (where the cancer cells downregulate antigens recognised by the immune system in order to avoid detection) which is followed by immunosubversion (where the cancer cells actively or passively supress the immune response) (3,4). Combined, these processes enable cancer cells to evade the immune system and proliferate unchecked.

Precisely how cancer cells suppress the immune response is not clearly defined. What is clear, is that this suppression is highly complex. One method by which the tumour microenvironment can suppress the immune response is through the induction of hypoxia (considered to be less than 1% oxygen). Hypoxia is a particular issue in solid tumours where there is reduced vasculature (5) and plays a key role in promoting the hallmarks of cancer (6). Hypoxia can suppress the immune system through the downregulation of pro-inflammatory cytokines/chemokines and upregulation of anti-inflammatory mediators (7).

In this study, Miar et al investigated the impact of hypoxia on type-I IFN signalling.  Type-I IFN signalling is primarily involved in the anti-viral and anti-tumour responses (8). Miar et al find that hypoxia induces a downregulation of the type-I IFN pathway in multiple cancer cell lines. This finding reveals a novel mechanism of immunosuppression.


Key findings

  1. Hypoxia downregulates the type-I IFN pathway

The authors performed a thorough investigation into the type-I IFN pathway, investigating the sensors, transcription factors and IFN release. The authors found that hypoxia induces a wide ranging down-regulation of the IFN pathway at both the RNA and protein levels. This downregulation was found to occur in multiple breast cancer cell lines (including oestrogen receptor positive and triple negative cells). Interestingly, the triple negative cells appeared to be more resistant to the effects of hypoxia.

The authors confirmed that the downregulation of the type-I IFN pathway was due to oxygen levels by reoxygenating the cells. This reversed the mRNA downregulation observed in hypoxia but not the protein levels (although the authors only looked at 24-hours reoxygenation). The authors further confirmed that hypoxia downregulates the IFN pathway by using a strong inducer of IFN (poly I:C). Treatment with poly I:C activated the IFN pathway but this activation was lower in cells exposed to hypoxia compared to normoxia.


  1. Type-I IFN downregulation is only partially dependent on HIF-1α

To investigate the role of HIF-1α, the authors utilised HIF-1α knock-out MCF-7 cells. Stimulation of MCF-7 cells with ploy I:C in normoxia induced type-I IFN pathway components (IRF3, pIRF3, IRF7 & pSTAT1) in both MCF-7-WT and MCF-7-HIF1α-KO. The induction was higher in the HIF-1α KO cells (with the exception of pSTAT1). Under hypoxia, the expression of those proteins was attenuated to similar levels in both cell lines. This suggests that the observed effects were independent of HIF-1α.


  1. Hypoxia decreases chromatin accessibility on IRF3 containing promoters

IF HIF-1α is not responsible for the downregulation of the type-I IFN pathway then what mediates this change? To address this, the authors performed ATACseq (a sequencing approach to reveal chromatin accessibility) on MCF-7 cells that had been cultured in either normoxia or hypoxia. The authors found 5577 peaks with differential accessibility. IRF3 motifs were less represented in peaks with increased accessibility. In addition, the authors found that there was reduced accessibility at FOXA1 and GATA3 (which have roles in downstream ER signalling) sites. Overall, hypoxia appeared to induce global changes to chromatin accessibility.


Why I chose this paper

Immunoevasion has been a strong personal interest from my time as an undergraduate. My current work (based around hypoxia) also makes this paper particularly relevant for me. The current revolution of immunotherapies for cancer treatment has significantly improved outcomes for patients. With a better understanding of the impact of cancer on the immune response, these therapies can be refined and improved, leading to even better outcomes and survival rates.


Open questions

  1. The authors discuss the role of type-I IFN’s in modulating the immune response. Are the authors planning in investigating the effect of the decreased IFN expression on immune cells, perhaps through a co-culture approach? Experimentally confirming that the decreased IFN production from cancer cells can modulate immune cell activity would be a great addition and logical next step.
  2. Could the authors expand upon their ATACseq data a little more? For example it would be great to know what specific histone modifications they believe may be mediating the observed changes in chromatin accessibility.
  3. Could the authors expand on their finding that triple-negative cancers appeared to be more resistant to the effects of hypoxia? What do the authors believe is conferring this resistance and could it be utilised therapeutically/does this have an impact on prognosis?
  4. The type-I IFN pathway has a long history as a therapeutic target in cancer, how do you see your work here in relation to this? Do you envisage this to help shape future or current therapies?
  5. Did you find other immune-related pathways to be modulated by hypoxia in the RNAseq data? If so, do these complement the type-I IFN pathway actions (e.g. are all anti-tumour immune responses decreased).



  1. Hanahan D, Weinberg RA. The Hallmarks of Cancer. Cell. 2000 Jan 7;100(1):57–70.
  2. Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011 Mar 4;144(5):646–74.
  3. Dunn GP, Old LJ, Schreiber RD. The Immunobiology of Cancer Immunosurveillance and Immunoediting. Immunity. 2004 Aug;21(2):137–48.
  4. Schreiber RD, Old LJ, Smyth MJ. Cancer Immunoediting: Integrating Immunity’s Roles in Cancer Suppression and Promotion. Science. 2011 Mar 25;331(6024):1565–70.
  5. McKeown SR. Defining normoxia, physoxia and hypoxia in tumours—implications for treatment response. Br J Radiol [Internet]. 2014 Mar [cited 2019 Jun 12];87(1035). Available from:
  6. Ruan K, Song G, Ouyang G. Role of hypoxia in the hallmarks of human cancer. J Cell Biochem. 2009 Aug 15;107(6):1053–62.
  7. Petrova V, Annicchiarico-Petruzzelli M, Melino G, Amelio I. The hypoxic tumour microenvironment. Oncogenesis. 2018 Jan 24;7(1):1–13.
  8. Dunn GP, Koebel CM, Schreiber RD. Interferons, immunity and cancer immunoediting. Nat Rev Immunol. 2006 Nov;6(11):836–48.




Tags: atacseq, hypoxia, ifn

Posted on: 25 August 2019


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