Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers

The adaptive response of cancer cells to hypoxia, a key microenvironmental factor in solid tumors, is orchestrated by Hypoxia-inducible factor 1 (HIF-1). Recent evidence indicate that oxygen tension in tumor is dynamic, with hypoxia being frequently unstable, or cycling. Cycling hypoxia is associated with specific phenotypic outcomes for the cancers. Transcriptomic analysis shows that for most genes, expression changes in cycling hypoxia lie expectedly in between the change caused by stable hypoxia, suggesting multi-cycle averaging of dosage in the oxygen tension, and likely HIF-1 induced transcription. However, a small subset of genes show an oscillation/cycling hypoxia specific response, suggesting that the transcriptional machinery of these genes may interpret cycling HIF-1 activity differently from stably high HIF-1 activity. Here, we model a gene regulatory circuit, the incoherent feed-forward loops (IFFLs) to illustrate that there are parameter regimes in such genetic circuits where oscillatory specific transcription is plausible. In these IFFL models, HIF-1 regulates gene transcription of a target gene directly, as well indirectly via another transcription factor with an opposite effect on gene transcription. This IFFL circuit is able to generate gene expression of certain target genes that is more extreme than either normoxia or stable hypoxia, and this nonlinear IFFL behavior can result from either the dynamic nature or even the intermediate, time averaged hypoxic signal Supplementary Information 1 (Steady state analysis of IFFL circuits). This gene circuit also allows us to search for plausible signaling intermediaries involved in the IFFL mediated cycling hypoxic response. Finally, we present experimental evidence suggesting that HIF-1 can form IFFLs with two key transcription factors p53, and Notch1, resulting in cycling hypoxia-specific gene expression linked to breast cancer progression and poor prognosis. Our work aims to draw attention to genetic circuits as plausible mechanisms where temporal fluctuations in the tumor microenvironment may directly inform downstream transcription. These ideas could identify hitherto unknown HIF-1 driven mechanism of cancer progression contributing to emergent tumor heterogeneity.