Genome-wide CRISPR Screen to Identify Genes that Suppress Transformation in the Presence of Endogenous KrasG12D.


Cooperating gene mutations are typically required to transform normal cells enabling growth in soft agar or in immunodeficient mice. For example, mutations in Kras and transformation-related protein 53 (Trp53) are known to transform a variety of mesenchymal and epithelial cells in vitro and in vivo. Identifying other genes that can cooperate with oncogenic Kras and substitute for Trp53 mutation has the potential to lead to new insights into mechanisms of carcinogenesis. Here, we applied a genome-wide CRISPR/Cas9 knockout screen in KrasG12D immortalized mouse embryonic fibroblasts (MEFs) to search for genes that when mutated cooperate with oncogenic Kras to induce transformation. We also tested if mutation of the identified candidate genes could cooperate with KrasG12D to generate primary sarcomas in mice. In addition to identifying the well-known tumor suppressor cyclin dependent kinase inhibitor 2A (Cdkn2a), whose alternative reading frame product p19 activates Trp53, we also identified other putative tumor suppressors, such as F-box/WD repeat-containing protein 7 (Fbxw7) and solute carrier family 9 member 3 (Slc9a3). Remarkably, the TCGA database indicates that both FBXW7 and SLC9A3 are commonly co-mutated with KRAS in human cancers. However, we found that only mutation of Trp53 or Cdkn2a, but not Fbxw7 or Slc9a3 can cooperate with KrasG12D to generate primary sarcomas in mice. These results show that mutations in oncogenic Kras and either Fbxw7 or Slc9a3 are sufficient for transformation in vitro, but not for in vivo sarcomagenesis.





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Publication Info

Huang, Jianguo, Mark Chen, Eric S Xu, Lixia Luo, Yan Ma, Wesley Huang, Warren Floyd, Tyler S Klann, et al. (2019). Genome-wide CRISPR Screen to Identify Genes that Suppress Transformation in the Presence of Endogenous KrasG12D. Scientific reports, 9(1). p. 17220. 10.1038/s41598-019-53572-w Retrieved from

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Mark Chen

House Staff

So Young Kim

Associate Research Professor in Molecular Genetics and Microbiology

I serve as Director of the Duke Functional Genomics Core Facility, where our central mission is to provide resources for high-throughput analysis of gene function and small molecule screens for drug discovery. Our core works with Duke investigators to provide the expertise, infrastructure and libraries necessary for these screens and can collaborate on all stages of the screening project, including study design, assay optimization and data analysis. The facility also provides services for custom cell line engineering using techniques including CRISPR knockouts/knockins, RNAi gene suppression and ORF expression. Our lab is also interested in collaborating with investigators to develop and improve existing methodologies to enhance the utility of functional genomics tools within the lab. 

I am also the Director of the Duke Microbiome Core Facility, which supports the research of investigators seeking to uncover the roles that microbiomes play in human health and the environment. The core provides assistance with study design, sample management, DNA extractions, NGS library prep and data analysis. The lab is also interested in developing new techniques and analysis tools to better assess microbiome composition across a range of sample types.


Charles Gersbach

John W. Strohbehn Distinguished Professor of Biomedical Engineering

Diana Marcella Cardona

Associate Professor of Pathology

I am active in translational research involving gastrointestinal/hepatobiliary pathology [specifically transplant related pathology (GVHD and rejection) and carcinogenesis of the pancreas] and bone and soft tissue malignancies [imaging techniques for intraoperative margin assessment].

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