A Genome-Scale RNA Interference Screen Implicates NF1 Loss in Resistance to RAF Inhibition

1Cancer Program, The Broad Institute of Harvard and MIT.
Cancer Discovery (Impact Factor: 19.45). 01/2013; 3(3). DOI: 10.1158/2159-8290.CD-12-0470
Source: PubMed


RAF inhibitors such as vemurafenib and dabrafenib block B-RAF-mediated cell proliferation and achieve meaningful clinical benefit in the vast majority of patients with B-RAFV600E-mutant melanoma. However, some patients do not respond to this regimen, and nearly all progress to therapeutic resistance. We employed a pooled RNA interference screen targeting >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 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 B-RAF-mutant tumor cells that are intrinsically resistant to RAF inhibition and in melanoma tumors obtained from patients exhibiting resistance to vemurafenib, thus demonstrating the clinical potential for NF1-driven resistance to RAF/MEK-targeted therapies.

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    • "not involving the MAPK pathway, have been found as well, including up-regulation of IGF-1R (Villanueva et al, 2010), PDGFRb (Nazarian et al, 2010), FOXD3 (Basile et al, 2012), EGFR (Girotti et al, 2013; Sun et al, 2014) or FGFR3 (Yadav et al, 2012) signaling. Overexpression of COT (Johannessen et al, 2010), Cyclin D1 (Smalley et al, 2008) and AEBP1 (Hu et al, 2013), amplification of MET and CTNNB1 (Vergani et al, 2011) and loss of NF1 (Whittaker et al, 2013) can also confer resistance to vemurafenib. The micro-environment can play a role in resistance, as it was found that up-regulation of HGF by the surrounding stromal cells occurs during resistance (Straussman et al, 2012). "
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    • "To rule out that some of the known offtarget effects of RAF265 (Su et al., 2012) could contribute to explain its synergy with MEK inhibition, we repeated the cell proliferation assays with AZ628. This compound has been previously reported to be more selective for wild-type RAF kinases and has been widely used for in vitro studies (Montagut et al., 2008; Whittaker et al., 2013). The results obtained with AZ628 in combination with selumetinib are consistent with the observations made with RAF265 (Figure S4A). "
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    • "The finding of concomitant genomic alterations in a tumor sample collected before systemic therapy can have important biological and therapeutic implications (in the setting of BRAF V600E mutant melanoma, NF1 loss predicts resistance to single-agent BRAF inhibitors; identification of BRAF V600E and MEK P124S in melanoma does not predict resistance to BRAF inhibitors; in KRAS mutant lung cancer, loss-of-function STK11 mutations engender resistance to the combination of MEK inhibitors and docetaxel). (Chen et al., 2012; Shi et al., 2012; Wagle et al., 2011; Whittaker et al., 2013) 2. In relapsed samples after targeted therapies, identification of " acquired " genomic alterations may be linked to resistance mechanisms and help define subsequent therapies (in EGFR-mutant lung cancer progressing to erlotinib, the finding of MET amplification directs to combination therapy with EGFR and MET blockade). "
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