GSE132707
mRNA-Seq of BC-3 IRF4 KO, BATF KO, and vIRF3 KD
The Kaposi's sarcoma-associated herpesviruses causes several cancers including Kaposi's sarcoma and primary effusion lymphoma (PEL). Our work reveals that the cellular transcription factors interferon regulatory factor 4 (IRF4) and basic leucine zipper ATF-like transcription factor (BATF), as well as the viral interferon regulatory factor 3 (vIRF3) are critical oncogenic dependencies specific to PEL cell lines. To understand the functions of these transcription factors, we performed mRNA-Seq on the PEL BC-3 cell lines that have been targeted for CRISPR/Cas9 IRF4 KO, BATF KO and MDM4 KO (as unrelated negative control) and CRISPRi-mediated vIRF3 KD. Our results reveal that these oncogenic factors may cooperate to regulate the expression of the same mRNAs. Overall design: BC-3 Cas9 cells were infected with lentiviruses expressing sgRNAs against AAVS1, IRF4, BATF or MDM4. Cells were harvested after d3, d8 or d16 when gene KO affected cumulative live cell counts. BC-3 dCas9-KRAB cells were infected with lentiviruses expressing sgRNAs against AAVS1 and vIRF3 (guides i7 and i8). Cells were harvested after d4 when gene KO affected cumulative live cell counts.