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

doi:10.1016/j.celrep.2023.111990

A multiplexed in vivo approach to identify driver genes in small cell lung cancer

Cell Rep. 2023 Jan 31;42(1):111990. doi: 10.1016/j.celrep.2023.111990. Epub 2023 Jan 13.

Authors

Myung Chang Lee¹, Hongchen Cai², Christopher W Murray², Chuan Li³, Yan Ting Shue¹, Laura Andrejka², Andy L He¹, Alessandra M E Holzem¹, Alexandros P Drainas¹, Julie H Ko¹, Garry L Coles¹, Christina Kong⁴, Shirley Zhu⁴, ChunFang Zhu⁴, Jason Wang⁴, Matt van de Rijn⁴, Dmitri A Petrov⁵, Monte M Winslow⁶, Julien Sage⁷

Affiliations

¹ Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA.
² Department of Genetics, Stanford University, Stanford, CA 94305, USA.
³ Department of Biology, Stanford University, Stanford, CA 94305, USA.
⁴ Department of Pathology, Stanford University, Stanford, CA 94305, USA.
⁵ Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
⁶ Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA.
⁷ Department of Pediatrics, Stanford University, 265 Campus Drive, SIM1 G2078, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: julsage@stanford.edu.

Abstract

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.

Keywords: CP: Cancer; CRISPR screening; MTOR; SCLC; TSC1; functional genomics; meta-analysis; mouse models; naphthalene; small cell lung cancer; tumor suppression.

Publication types

Meta-Analysis
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Genes, Tumor Suppressor
Genomics
Humans
Lung Neoplasms* / pathology
Mice
Phosphatidylinositol 3-Kinases / metabolism
Small Cell Lung Carcinoma* / pathology

Substances

Phosphatidylinositol 3-Kinases

Abstract

Publication types

MeSH terms

Substances

Grants and funding