CRISPR/Cas9 Screens Reveal Epstein-Barr Virus-Transformed B Cell Host Dependency Factors

• Published in: Cell host & microbe 2017-05, Vol.21 (5), p.580-591.e7
• Main Authors: Ma, Yijie, Walsh, Michael J., Bernhardt, Katharina, Ashbaugh, Camille W., Trudeau, Stephen J., Ashbaugh, Isabelle Y., Jiang, Sizun, Jiang, Chang, Zhao, Bo, Root, David E., Doench, John G., Gewurz, Benjamin E.
• Format: Article
• Language: English
• Subjects: apoptosis; Apoptosis - drug effects; Apoptosis Regulatory Proteins - metabolism; B-Lymphocytes - virology; Basic-Leucine Zipper Transcription Factors - metabolism; Burkitt Lymphoma - virology; Cell Line; Cell Transformation, Viral; Complement Factor B - metabolism; CRISPR; CRISPR-Cas Systems - genetics; CRISPR-Cas Systems - physiology; dependency factor; Epstein-Barr virus; gamma-herpesvirus; Gene Expression Regulation; Gene Knockdown Techniques; Herpesvirus 4, Human - genetics; Herpesvirus 4, Human - metabolism; Herpesvirus 4, Human - physiology; Humans; interferon regulatory factor; Interferon Regulatory Factor-2 - metabolism; Interferon Regulatory Factors - metabolism; Mutagenesis; NF-kappa B - metabolism; NF-kappaB; Oncogene Proteins - metabolism; oncoprotein; Phosphatidylinositol 3-Kinases - metabolism; Positive Regulatory Domain I-Binding Factor 1; synthetic lethal; Tumor Necrosis Factor-alpha - pharmacology; tumor virus
• ISSN: 1931-3128; 1934-6069
• DOI: 10.1016/j.chom.2017.04.005

Epstein-Barr virus (EBV) causes endemic Burkitt lymphoma (BL) and immunosuppression-related lymphomas. These B cell malignancies arise by distinct transformation pathways and have divergent viral and host expression programs. To identify host dependency factors resulting from these EBV+, B cell-transformed cell states, we performed parallel genome-wide CRISPR/Cas9 loss-of-function screens in BL and lymphoblastoid cell lines (LCLs). These highlighted 57 BL and 87 LCL genes uniquely important for their growth and survival. LCL hits were enriched for EBV-induced genes, including viral super-enhancer targets. Our systematic approach uncovered key mechanisms by which EBV oncoproteins activate the PI3K/AKT pathway and evade tumor suppressor responses. LMP1-induced cFLIP was found to be critical for LCL defense against TNFα-mediated programmed cell death, whereas EBV-induced BATF/IRF4 were critical for BIM suppression and MYC induction in LCLs. Finally, EBV super-enhancer-targeted IRF2 protected LCLs against Blimp1-mediated tumor suppression. Our results identify viral transformation-driven synthetic lethal targets for therapeutic intervention. [Display omitted] •CRISPR screens reveal key EBV-transformed B cell dependency factors•Lymphoblastoid B cells are addicted to multiple EBV-induced genes•LMP1-induced cFLIP protects LCLs from TNFα-mediated apoptosis and necroptosis•EBV-induced IRF4 and BATF are critical for BIM suppression and MYC induction Ma et al. perform CRISPR loss-of-function screens to systematically identify host dependency factors critical for Epstein-Barr virus (EBV)-infected lymphoblastoid and Burkitt lymphoma B cell growth and survival. They identify multiple non-redundant mechanisms by which EBV prevents apoptotic responses to oncogene stress in transformed B cells, and identify key EBV-induced synthetic lethal targets.