Editors' ChoiceCellular Metabolism

Metabolic Reprogramming with a Long Noncoding RNA

Sci. Signal.  21 Jan 2014:
Vol. 7, Issue 309, pp. ec16
DOI: 10.1126/scisignal.2005088

Cells exposed to hypoxic (low oxygen) conditions mount an adaptive response mediated by the hypoxia-inducible factor (HIF) family of transcription factors. A change associated with this hypoxic reprogramming is an increased dependence on glycolysis over oxidative phosphorylation, a metabolic shift called the Warburg effect, which is associated with tumor growth. With bioinformatic analysis, Yang et al. identified six long noncoding RNAs (lncRNA or lincRNA, depending on whether they are coded within a gene or intragenically, respectively) with hypoxia response elements in their promoters, and real-time reverse transcription polymerase chain reaction (RT-PCR) analysis in several human cells lines or a primary cell culture showed that only lincRNA-p21 was increased by hypoxia. Knockdown of lincRNA-p21 prevented hypoxia-induced changes in metabolism that were rescued by ectopic expression of HIF-1α or a resistant lincRNA-p21 construct. In cells exposed to hypoxic conditions, knockdown of lincRNA-p21 decreased HIF-1α protein and triggered more rapid degradation of HIF-1α without altering the abundance of HIF-1α–encoding mRNA. HIF-1α was stabilized in cells with knockdown of both lincRNA-p21 and VHL, which is an E3 ubiquitin ligase that marks HIF-1α for degradation by the ubiquitin-proteasomal pathway, suggesting that lincRNA-p21 interferes with this degradation pathway for HIF-1α. Multiple in vitro binding assays indicated that lincRNA-p21 interacted with both HIF-1α and VHL, and experiments with VHL deletion mutants suggested that lincRNA-p21 may bind to the HIF-1α–binding regions of VHL and thus competitively inhibit the interaction between these two proteins. Knockdown of HIF-1α reduced the hypoxia-induced increase in lincRNA-p21 abundance, and chromatin immunoprecipitation experiments and promoter reporter assays confirmed that lincRNA-p21 was a direct transcriptional target of HIF-1α. In a xenograft model in which mice were injected with cells that had been exposed to hypoxia before injection, knockdown of lincRNA-p21 reduced tumor growth and changes in protein abundance associated with the Warburg effect. Thus, lincRNA-p21 functions as part of a positive feedback loop that increases HIF-1α stability in response to hypoxia.

F. Yang, H. Zhang, Y. Mei, M. Wu, Reciprocal regulation of HIF-1α and lincRNA-21 modulates the Warburg effect. Mol. Cell 53, 88–100 (2014). [PubMed]