IRF1 Knockout Cell Line (A549)

Interferon-γ (IFN-γ)-mediated adaptive resistance is one major barrier to improving immunotherapy in solid tumors. However, the mechanisms are not completely understood. Here, we report that IFN-γ promotes nuclear translocation and phase separation of YAP after anti-PD-1 therapy in tumor cells. Hydrophobic interactions of the YAP coiled-coil domain mediate droplet initiation, and weak interactions of the intrinsically disordered region in the C terminus promote droplet formation. YAP partitions with the transcription factor TEAD4, the histone acetyltransferase EP300, and Mediator1 and forms transcriptional hubs for maximizing target gene transcriptions, independent of the canonical STAT1-IRF1 transcription program. Disruption of YAP phase separation reduced tumor growth, enhanced immune response, and sensitized tumor cells to anti-PD-1 therapy. YAP activity is negatively correlated with patient outcome. Our study indicates that YAP mediates the IFN-γ pro-tumor effect through its nuclear phase separation and suggests that YAP can be used as a predictive biomarker and target of anti-PD-1 combination therapy.

Host cell-intrinsic antiviral responses are largely mediated by pattern-recognition receptor (PRR) signaling and the interferon (IFN) system. The IFN regulatory factor (IRF) family of transcription factors takes up a central role in transcriptional regulation of antiviral innate immunity. IRF3 and IRF7 are known to be key players downstream of PRRs mediating the induction of type I and III IFNs. IFN signaling then requires IRF9 for the expression of the full array of interferon stimulated genes (ISGs) ultimately defining the antiviral state of the cell. Other members of the IRF family clearly play a role in mediating or modulating IFN responses, such as IRF1, IRF2 or IRF5, however their relative contribution to mounting a functional antiviral response is much less understood. In this study, we systematically and comparatively assessed the impact of six members of the IRF family on antiviral signaling in alveolar epithelial cells. We generated functional knockouts of IRF1, -2, -3, -5, -7, and -9 in A549 cells, and measured their impact on the expression of IFNs and further cytokines, ISGs and other IRFs, as well as on viral replication. Our results confirmed the vital importance of IRF3 and IRF9 in establishing an antiviral state, whereas IRF1, 5 and 7 were largely dispensable. The previously described inhibitory activity of IRF2 could not be observed in our experimental system.

Interferon-γ (IFNγ), a key inflammatory cytokine that orchestrates immune responses, also emerges as a regulator of cellular metabolism; however, in alveolar epithelial cells its impact on amino acid homeostasis remains poorly defined. Here, we investigated the effects of IFNγ on intracellular amino acid content and transmembrane transport in human alveolar epithelial A549 cells, focusing on the contribution of the JAK/STAT/IRF1 signaling axis. To this end, A549 WT and IRF1 knockout (IRF1 KO) cells were used to investigate IRF1 contribution, and baricitinib to evaluate the role of the JAK/STAT pathway. HPLC analysis reveals that in WT, but not in IRF1 KO cells, IFNγ markedly increases the intracellular concentration of many amino acids, including glutamine, glutamate, and several neutral and cationic amino acids, without affecting the cell volume, thus indicating true metabolic accumulation. The measurement of the transmembrane uptake of specific radiolabeled amino acids demonstrates a concomitant increase in transport Systems ASC, A, L, and y activity; an upregulation of the related transporters ASCT2, SNAT2, LAT1, and CAT1 has also been observed by means of qPCR analysis. Moreover, conditioned medium from SARS-CoV-2 spike-activated macrophages recapitulates IFNγ-driven amino acid remodeling in a JAK/STAT/IRF1-dependent manner. Overall, our findings identify IFNγ as a potent regulator of intracellular amino acid availability in alveolar epithelial cells through the modulation of the activity of membrane transporters. The observed IFNγ-reprogramming is IRF1 dependent, ascribing a crucial role to this transcription factor in linking inflammation and amino acid metabolism.