IFN-γ induced transcriptional profile of A549 cells in absence of key transcriptional regulators IRF1 and NF2

Type-II interferon or IFN-gamma is a critical cytokine in innate immunity that control multitude of intracellular infections. IFN-gamma binds to interferon gamma receptors to phosphorylate and activate STAT1 mediated transcription of interferon stimulated genes (ISGs). We executed a genome-wide CRISPR-Cas9 screen against ~20,000 human genes to identify IRF-1 and NF2 as significant regulators of Toxoplasma infection in A549 lung epithelial cells. IRF-1 is a key transcription factor immediately downstream of STAT1 induced transcription that amplifies ISG expression in different cell types. NF2 or MERLIN is a tumor suppressor that is known to regulate expression of genes involved with cellular growth and metabolism. Transcriptomic signature of A549 cells lacking IRF-1 and NF2 were measured upon activation with IFN-gamma to find set of genes that may be regulating Toxoplasma infection. A total of 1,046,709,676 reads from 3 independent biological replicates were mapped to human hg38 reference genome. Expression of a ISGs that failed to induced in cells lacking IRF1 were found to be dysregulated in absence of NF2 as well. Wild type, IRF1 KO and NF2 KO A549 cells were left untreated or treated with IFN-gamma treatment (100 U/ml) for 24 h. Total RNA was extracted from 3 independent biological replicates and submitted for next generation sequencing to analyze the role of IRF-1 and NF2 in IFN-gamma induced transcriptional profile of A549 cells.