RAF inhibitors such as vemurafenib and dabrafenib block BRAF-mediated cell proliferation and achieve meaningful clinical benefit in the vast majority of patients with BRAF(V600E)-mutant melanoma. However, some patients do not respond to this regimen, and nearly all progress to therapeutic resistance. We used a pooled RNA interference screen targeting more than 16,500 genes to discover loss-of-function events that could drive resistance to RAF inhibition. The highest ranking gene was NF1, which encodes neurofibromin, a tumor suppressor that inhibits RAS activity. NF1 loss mediates resistance to RAF and mitogen-activated protein kinase (MAPK) kinase kinase (MEK) inhibitors through sustained MAPK pathway activation. However, cells lacking NF1 retained sensitivity to the irreversible RAF inhibitor AZ628 and an ERK inhibitor. NF1 mutations were observed in BRAF-mutant tumor cells that are intrinsically resistant to RAF inhibition and in melanoma tumors obtained from patients exhibiting resistance to vemurafenib, thus showing the clinical potential for NF1-driven resistance to RAF/MEK-targeted therapies.
Achilles_QC_v2.4.3.rnai.gct is the final shRNA-level file from pooled screening of 216 cancer cell lines, performed in quadruplicate. See Achilles_Analysis_README_v2.4.3 for processing steps.
Significance Oncogenic lesions give rise to genotype-specific dependencies in tumors by altering cell physiology. Understanding how oncogenes drive cell transformation will therefore help identify strategies to target tumors harboring these mutations. Although targeting certain oncogenes has led to clinical responses in some cases, PIK3CA inhibition has been disappointing to date. Here, we show that cell proliferation and tumor growth of PIK3CA mutant cancers is inhibited by suppression 2-oxoglutarate dehydrogenase, which leads to increased metabolite 2-oxoglutarate (2OG) levels. Elevated 2OG affects the function of the malate–aspartate shuttle, which is important because of the glycolytic nature of these cancers. This work provides novel insights into how mutant PIK3CA drives tumor proliferation and identifies a metabolic dependency that can be exploited in these cancers.