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Tonic ISG expression promotes efficient induction of IFNL in response to influenza infection

ABSTRACT: Tonic ISG expression promotes efficient induction of IFNL in response to influenza infection

PROVIDER: PRJNA1210996 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32005403.fastq.gz	Fastqsanger.gz
	SRR32005404.fastq.gz	Fastqsanger.gz
	SRR32005405.fastq.gz	Fastqsanger.gz
	SRR32005406.fastq.gz	Fastqsanger.gz
	SRR32005407.fastq.gz	Fastqsanger.gz

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Tonic ISG expression promotes efficient induction of IFNL in response to influenza infection

Project description:The innate immune response, especially the interferon (IFN) response, plays a critical role in limiting initial dissemination of viruses from the site of infection. While the pathogen-associated molecular patterns (PAMPs) and pattern recognition receptors (PRRs) involved in sensing and inducing the innate immune response during influenza A virus (IAV) infections are well-characterized, the factors that regulate IFNL production in infected cells remain poorly understood. Previous studies have highlighted that most infected cells fail to express either type I or III IFNs in response to stimulus, suggesting a regulatory mechanism that controls the activation of IFNs during infection. To investigate the factors influencing IFNL induction during IAV infection, we performed single-cell RNA sequencing (scRNA-seq) of A549 cells infected with A/Perth/16/2009 and sampled at multiple time points post-infection. Using a novel pseudotime analysis approach tailored for temporal scRNA-seq data, we aim to identify host genes whose tonic expression modulates IFNL production in response to IAV infection.

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Dependency of ISG expression on IFNAR1 and Tyk2

Project description:We analyze the expression profile of ISGs in the context of IFNAR1-KO primary murine B cells and macrophages. These analses were used to define ISG gene sets that are under tonic control. Furthermore, these analyses enabled the definition of ISGs that are dependent on Tyk2 signaling. Male C57BL/6 IFNAR1-KO mice were injected subcutaneously with 10,000U IFNa for 2hrs. Splenic B cells and peritoneal macrophages were sorted by FACS directly into TriZol and gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

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Project description:Role of PML in ISG induction in primary postnatal sympathetic neurons

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Role of PML in ISG induction in primary postnatal sympathetic neurons

Project description:A previous study has shown that PML-dependent recruitment of HIRA to ISG promoters contributes to the up-regulation of gene expression as a result of cytokine release in response to HSV infection (McFarlane et al., 2019). Although carried out in non-neuronal cells, this study and others (Ulbricht et al., 2012, Kim and Ahn, 2015, Scherer et al., 2016, Chen et al., 2015) suggest that PML itself may contribute to ISG upregulation, so to determine whether PML was indeed required for ISG stimulation in SCG neurons, we carried out RNA sequence analysis in IFNα-treated neurons depleted of PML.

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Project description:The circulation of seasonal influenza A viruses (IAVs) in humans relies on effective evasion and subversion of the host immune response. While the evolution of seasonal H1N1 and H3N2 viruses to avoid humoral immunity is well characterized, relatively little is known about the evolution of innate immune antagonism phenotypes in these viruses. Numerous studies have established that only a small subset of infected cells are responsible for initiating the type I and type III interferon (IFN) response during IAV infection, emphasizing the importance of single cell studies to accurately characterize the IFN response during infection. We developed a flow cytometry-based method to examine transcriptional changes in IFN and interferon stimulated gene (ISG) expression at the single cell level. We observed that NS segments derived from seasonal H3N2 viruses are more efficient at antagonizing IFN signaling but less effective at suppressing IFN induction, compared to the pdm2009 H1N1 lineage. We compared a collection of NS segments spanning the natural history of the current seasonal IAV lineages, and demonstrate long periods of stability in IFN antagonism potential, punctuated by occasional phenotypic shifts. Altogether, our data reveal significant differences in how seasonal and pandemic H1N1 and H3N2 viruses antagonize the human IFN response at the single cell level.

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