Genome-wide CRISPR screens reveal a Wnt–FZD5 signaling circuit as a druggable vulnerability of RNF43-mutant pancreatic tumors

• Published in: Nature medicine Vol. 23; no. 1; pp. 60 - 68
• Main Authors: Steinhart, Zachary, Pavlovic, Zvezdan, Chandrashekhar, Megha, Hart, Traver, Wang, Xiaowei, Zhang, Xiaoyu, Robitaille, Mélanie, Brown, Kevin R, Jaksani, Sridevi, Overmeer, René, Boj, Sylvia F, Adams, Jarrett, Pan, James, Clevers, Hans, Sidhu, Sachdev, Moffat, Jason, Angers, Stéphane
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.01.2017; Nature Publishing Group
• Subjects: 631/154/1435/2417; 692/699/1503/1504/1713; Adenocarcinoma; Adenocarcinoma - genetics; Adenocarcinoma - metabolism; Animals; Antibodies; Antibodies - pharmacology; Biomedicine; Cancer Research; Carcinoma, Pancreatic Ductal - genetics; Carcinoma, Pancreatic Ductal - metabolism; Care and treatment; Cell Cycle Checkpoints - drug effects; Cell Line, Tumor; Cell proliferation; Cell surface; Cellular signal transduction; Clustered Regularly Interspaced Short Palindromic Repeats; Colorectal cancer; Colorectal carcinoma; Colorectal Neoplasms - genetics; Colorectal Neoplasms - metabolism; CRISPR; Development and progression; DNA-Binding Proteins - genetics; Flow Cytometry; Fluorescent Antibody Technique; Frizzled protein; Frizzled Receptors - antagonists & inhibitors; Frizzled Receptors - metabolism; Genetic aspects; Genetic engineering; Genetic screening; Genome editing; Genomes; Genotypes; Health aspects; Humans; Immunoglobulins; Infectious Diseases; Innovations; Metabolic Diseases; Mice; Mice, SCID; Molecular Medicine; Molecular Targeted Therapy; Mutation; Neoplasm Transplantation; Neurosciences; Oncogene Proteins - genetics; Organoids; Organoids - drug effects; Organoids - metabolism; Pancreas; Pancreatic cancer; Pancreatic Neoplasms - genetics; Pancreatic Neoplasms - metabolism; Proteins; Real-Time Polymerase Chain Reaction; Receptors; Reverse Transcriptase Polymerase Chain Reaction; RNA, Messenger - metabolism; Signaling; Therapy; Tumors; Wnt protein; Wnt Signaling Pathway - drug effects; Wnt Signaling Pathway - genetics; Xenografts; Xenotransplantation
• ISSN: 1078-8956; 1546-170X; 1546-170X
• DOI: 10.1038/nm.4219

A genome-wide CRISPR screen reveals that FZD5, but none of the other nine Frizzled receptors encoded in the human genome, is a therapeutic vulnerability of pancreatic and colorectal tumors bearing RNF43 mutations. Forward genetic screens with CRISPR–Cas9 genome editing enable high-resolution detection of genetic vulnerabilities in cancer cells. We conducted genome-wide CRISPR–Cas9 screens in RNF43 -mutant pancreatic ductal adenocarcinoma (PDAC) cells, which rely on Wnt signaling for proliferation. Through these screens, we discovered a unique requirement for a Wnt signaling circuit: engaging FZD5, one of the ten Frizzled receptors encoded in the human genome. Our results uncover an underappreciated level of context-dependent specificity at the Wnt receptor level. We further derived a panel of recombinant antibodies that reports the expression of nine FZD proteins and confirms that FZD5 functional specificity cannot be explained by protein expression patterns. Additionally, antibodies that specifically bind FZD5 and FZD8 robustly inhibited the growth of RNF43 -mutant PDAC cells grown in vitro and as xenografts in vivo , providing orthogonal support for the functional specificity observed genetically. Proliferation of a patient-derived PDAC cell line harboring an RNF43 variant was also selectively inhibited by the FZD5 antibodies, further demonstrating their use as a potential targeted therapy. Tumor organoid cultures from colorectal carcinoma patients that carried RNF43 mutations were also sensitive to the FZD5 antibodies, highlighting the potential generalizability of these findings beyond PDAC. Our results show that CRIPSR-based genetic screens can be leveraged to identify and validate cell surface targets for antibody development and therapy.