Data from: Inherent single-cell heterogeneity of the transcriptional response to hypoxia in cancer cells

Hypoxia-inducible factor (HIF) is a master regulator of cancer cell
adaptation to tumor hypoxia and is involved in cancer progression.
Single-cell (sc) differences in the HIF response allow for tumor evolution
and cause therapy resistance. These sc-differences are usually ascribed to
tumor microenvironmental differences and/or clonal (epi)genetic
variability. However, the sc-heterogeneity of the HIF response in
otherwise identical cells cultured under defined in vitro conditions has
not yet been addressed. Therefore, we analyzed the sc-response to hypoxia
in nonclonal cell lines and multiple clonal derivatives, including HIF-1a
or HIF-2a knockouts. While HIF-1a and HIF-1 target mRNA sc-heterogeneity
was slightly higher than global transcription or specific housekeeping
mRNAs, HIF-2a and especially HIF-2 target mRNA sc-heterogeneity was
extraordinary, and remained in independent clones and following HIFa
knockouts. Unexpectedly, neither HIF-2a mRNA nor nuclear protein levels
correlated with target mRNA levels. Unsupervised but not supervised HIF
target gene dimensionality reduction revealed the initial sample
composition after scRNAseq, demonstrating that, owing to sc-heterogeneity,
individual HIF target genes are not sufficient to unequivocally identify
hypoxic cancer cells. In conclusion, the pronounced intrinsic
sc-heterogeneity of the HIF response represents a hitherto unrecognized
feature of cancer cells that impairs clinical HIF pathway-dependent cancer
cell identification and targeting.