A multiplexed in vivo approach to identify driver genes in small cell lung cancer
Myung Chang Lee,
Hongchen Cai,
Christopher W. Murray,
Chuan Li,
Yan Ting Shue,
Laura Andrejka,
Andy L. He,
Alessandra M.E. Holzem,
Alexandros P. Drainas,
Julie H. Ko,
Garry L. Coles,
Christina Kong,
Shirley Zhu,
ChunFang Zhu,
Jason Wang,
Matt van de Rijn,
Dmitri A. Petrov,
Monte M. Winslow,
Julien Sage
Affiliations
Myung Chang Lee
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Hongchen Cai
Department of Genetics, Stanford University, Stanford, CA 94305, USA
Christopher W. Murray
Department of Genetics, Stanford University, Stanford, CA 94305, USA
Chuan Li
Department of Biology, Stanford University, Stanford, CA 94305, USA
Yan Ting Shue
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Laura Andrejka
Department of Genetics, Stanford University, Stanford, CA 94305, USA
Andy L. He
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Alessandra M.E. Holzem
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Alexandros P. Drainas
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Julie H. Ko
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Garry L. Coles
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
Christina Kong
Department of Pathology, Stanford University, Stanford, CA 94305, USA
Shirley Zhu
Department of Pathology, Stanford University, Stanford, CA 94305, USA
ChunFang Zhu
Department of Pathology, Stanford University, Stanford, CA 94305, USA
Jason Wang
Department of Pathology, Stanford University, Stanford, CA 94305, USA
Matt van de Rijn
Department of Pathology, Stanford University, Stanford, CA 94305, USA
Dmitri A. Petrov
Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
Monte M. Winslow
Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
Julien Sage
Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Corresponding author
Summary: Small cell lung cancer (SCLC) is a lethal form of lung cancer. Here, we develop a quantitative multiplexed approach on the basis of lentiviral barcoding with somatic CRISPR-Cas9-mediated genome editing to functionally investigate candidate regulators of tumor initiation and growth in genetically engineered mouse models of SCLC. We found that naphthalene pre-treatment enhances lentiviral vector-mediated SCLC initiation, enabling high multiplicity of tumor clones for analysis through high-throughput sequencing methods. Candidate drivers of SCLC identified from a meta-analysis across multiple human SCLC genomic datasets were tested using this approach, which defines both positive and detrimental impacts of inactivating 40 genes across candidate pathways on SCLC development. This analysis and subsequent validation in human SCLC cells establish TSC1 in the PI3K-AKT-mTOR pathway as a robust tumor suppressor in SCLC. This approach should illuminate drivers of SCLC, facilitate the development of precision therapies for defined SCLC genotypes, and identify therapeutic targets.
