An insufficient level of oxygen – known as hypoxia – can occur in tumours, where excessive cell proliferation outstrips oxygen supply from the blood. In these conditions, hypoxia pathways are activated, which drive many of the well-known hallmarks of cancer, including cell proliferation, genomic instability, and metastasis. The Hypoxia-Inducible Factor (HIF) family of transcription factors are key regulators of these pathways, and activate genes which either increase oxygen delivery to the cell, or decrease oxygen consumption.
In this study published in Cell Reports, Olivia Lombardi and colleagues aim to better understand these pathways by defining a HIF “metagene”. A metagene is a set of genes whose expression is functionally correlated; in this case to activation of the HIF pathway. The use of such an ensemble of genes is a more powerful way to study cell pathways than investigating genes on an individual basis, where they may be missed. To produce this HIF metagene, they used a dual approach; combining transcriptional profiling (using RNA-seq) and whole-genome HIF binding assays (using ChIP-seq) across cell lines from various common cancer types subjected to identical hypoxic conditions. Integrative analysis of these results then allowed them to produce the final “HIF metagene”, which is composed of 48 pan-cancer HIF target genes.
In this work, they demonstrate the utility of the HIF metagene as a marker of HIF pathway activation in bulk RNA-seq as well as single cell RNA-seq analysis. Both the cells within a tumour and their surrounding microenvironment display high levels of heterogeneity, and the application of this HIF metagene to single cell data will allow researchers to track and compare the activation of HIF pathways throughout the diverse array of cells that make up a tumour.