An iron-dependent metabolic vulnerability underlies VPS34-dependence in RKO cancer cells

PLoS One. 2020 Aug 24;15(8):e0235551. doi: 10.1371/journal.pone.0235551. eCollection 2020.

Abstract

VPS34 is a key regulator of endomembrane dynamics and cargo trafficking, and is essential in cultured cell lines and in mice. To better characterize the role of VPS34 in cell growth, we performed unbiased cell line profiling studies with the selective VPS34 inhibitor PIK-III and identified RKO as a VPS34-dependent cellular model. Pooled CRISPR screen in the presence of PIK-III revealed endolysosomal genes as genetic suppressors. Dissecting VPS34-dependent alterations with transcriptional profiling, we found the induction of hypoxia response and cholesterol biosynthesis as key signatures. Mechanistically, acute VPS34 inhibition enhanced lysosomal degradation of transferrin and low-density lipoprotein receptors leading to impaired iron and cholesterol uptake. Excess soluble iron, but not cholesterol, was sufficient to partially rescue the effects of VPS34 inhibition on mitochondrial respiration and cell growth, indicating that iron limitation is the primary driver of VPS34-dependency in RKO cells. Loss of RAB7A, an endolysosomal marker and top suppressor in our genetic screen, blocked transferrin receptor degradation, restored iron homeostasis and reversed the growth defect as well as metabolic alterations due to VPS34 inhibition. Altogether, our findings suggest that impaired iron mobilization via the VPS34-RAB7A axis drive VPS34-dependence in certain cancer cells.

MeSH terms

  • Cell Hypoxia
  • Cell Line, Tumor
  • Cell Proliferation
  • Cholesterol / biosynthesis
  • Cholesterol / genetics
  • Class III Phosphatidylinositol 3-Kinases / genetics
  • Class III Phosphatidylinositol 3-Kinases / metabolism*
  • Endosomes / metabolism
  • HEK293 Cells
  • Humans
  • Iron / metabolism*
  • Lysosomes / metabolism
  • Neoplasms / metabolism*
  • Receptors, LDL / metabolism
  • Transferrin / metabolism
  • rab GTP-Binding Proteins / genetics
  • rab GTP-Binding Proteins / metabolism
  • rab7 GTP-Binding Proteins

Substances

  • Receptors, LDL
  • Transferrin
  • rab7 GTP-Binding Proteins
  • Cholesterol
  • Iron
  • Class III Phosphatidylinositol 3-Kinases
  • rab GTP-Binding Proteins

Grants and funding

The funder, Novartis Pharma AG, provided support in the form of salaries for authors MJK, JMG, ZBK, JWA, SH, EO, GM, JR, QW, JA, CR, AL, MB, GR, WC, JK, JL, CA, DW, LOM, SM, and BN, but did not have any additional role in the study design, data collection and analysis, or preparation of the manuscript. The manuscript was assessed by the Novartis legal department to ascertain that release of this manuscript did not contravene Novartis policy regarding release of proprietary information, but this was limited only to approval for release of the material and was not related to the results or interpretations/conclusions contained in the manuscript.