Set Of Interferon-stimulated Genes Research Articles

Cell-type-specific expression analysis of liver transcriptomics with clinical parameters to decipher the cause of intrahepatic inflammation in chronic hepatitis B.

Functional cure for chronic hepatitis B (CHB) remains challenging due to the lack of direct intervention methods for hepatic inflammation. Multi-omics research offers a promising approach to understand hepatic inflammation mechanisms in CHB. A Bayesian linear model linked gene expression with clinical parameters, and population-specific expression analysis (PSEA) refined bulk gene expression into specific cell types across different clinical phases. These models were integrated into our analysis of key factors like inflammatory cells, immune activation, T cell exhaustion, chemokines, receptors, and interferon-stimulated genes (ISGs). Validation through multi-immune staining in liver specimens from CHB patients bolstered our findings. In CHB patients, increased gene expression related to immune cell activation and migration was noted. Marker genes of macrophages, T cells, immune-negative regulators, chemokines, and ISGs showed a positive correlation with serum alanine aminotransferase (ALT) levels but not hepatitis B virus DNA levels. The PSEA model confirmed T cells as the source of exhausted regulators, while macrophages primarily contributed to chemokine expression. Upregulated ISGs (ISG20, IFI16, TAP2, GBP1, PSMB9) in the hepatitis phase were associated with T cell and macrophage infiltration and positively correlated with ALT levels. Conversely, another set of ISGs (IFI44, ISG15, IFI44L, IFI6, MX1) mainly expressed by hepatocytes and B cells showed no correlation with ALT levels. Our study presents a multi-omics analysis integrating bulk transcriptomic, single-cell sequencing data, and clinical data from CHB patients to decipher the cause of intrahepatic inflammation in CHB. The findings confirm that macrophages secrete chemokines like CCL20, recruiting exhausted T cells into liver tissue; concurrently, hepatocyte innate immunity is suppressed, hindering the antiviral effects of ISGs.

Human basonuclin 2 up-regulates a cascade set of interferon-stimulated genes with anti-cancerous properties in a lung cancer model

BackgroundHuman basonuclin 2 (BNC2) acts as a tumor suppressor in multiple cancers in an as yet unidentified manner. The role and expression of the BNC2 gene in lung cancer has not yet been investigated.MethodsBNC2 expression was studied in the A549 and BEAS-2B cell lines, as well as in lung cancer tissue. Illumina array analysis and a viability assay were used to study the effects of transient transfection of BNC2 in A549 cells. Ingenuity pathway analysis and g:Profiler were applied to identify affected pathways and networks. RT-qPCR was used to validate the array results.ResultsWe showed the reduced mRNA expression of BNC2 in non-small cell lung cancer tissue and lung cancer cell line A549 compared to non-cancerous lung tissue and BEAS-2B cells, respectively. Further array analysis demonstrated that the transfection of BNC2 into A549 cells resulted in the increased expression of 139 genes and the down-regulation of 13 genes. Pathway analysis revealed that half of the up-regulated genes were from the interferon/signal transducer and activator of transcription signaling pathways. The differential expression of selected sets of genes, including interferon-stimulated and tumor suppressor genes of the XAF1 and OAS families, was confirmed by RT-qPCR. In addition, we showed that the over-expression of BNC2 inhibited the proliferation of A549 cells.ConclusionOur data suggest that human BNC2 is an activator of a subset of IFN-regulated genes and might thereby act as a tumor suppressor.

Abstract 485: Chronic exposure to a low dose of interferon-β increases levels of DNA damage resistance signature genes through unphosphorylated ISGF3

Abstract Ionizing radiation and DNA damaging chemotherapeutic agents are used widely to treat many cancers, but the presence of cells that resist DNA damage often leads to failure to cure. One of the specific features of therapy-resistance is high expression of Interferon-Related DNA damage resistance Signature (IRDS) genes. The IRDS genes are a subset of (about 30 genes) Interferon Stimulated Genes (ISGs) including IFI27, OAS2, Mx1, and IFIT1. However, pro-apoptotic and anti-proliferative ISGs, such as IRF1, caspases, and FASL, are not included in this signature. In this study, we elucidated the molecular mechanism of how the expression of IRDS genes are increased, with no increase of other ISGs, in therapy-resistant cancer cells. When cells expressed high levels of IRF9 and STATs 1 and 2 in the absence of phosphorylation of Tyr-701-STAT1 and Tyr-690-STAT2, the expression of IRDS genes was increased, but that of other ISGs was not. The un-phosphorylated STAT1, STAT2, and IRF9 proteins formed a complex resembling Interferon Stimulated Gene Factor 3 (ISGF3), a major transcription factor in type I interferon signaling. While ISGF3, consisting of phosphorylated STATs 1 and 2 and IRF9, mediates the expression of whole set of ISGs, the unphosphorylated ISGF3 (U-ISGF3) induces only IRDS genes. ChIP assay revealed that U-ISGF3 selectively bound to the promoters of IRDS genes (IFI27, OAS2, and Mx1), but not to those of other ISGs (MyD88, IFI16, and IRF1). Continuous exposure of cells to a low level of interferonβ, which might be produced by cancer cells or surrounding immune cells, lead to steady-state increases in the expression of only U-ISGF3 and IRDS genes with no increase of phosphorylated ISGF3 and non-IRDS ISGs. We examined the correlation between the U-ISGF3 levels and DNA damage resistance in various small cell lung carcinoma (SCLC) cell lines. The expression of IRF9 and STATs 1 and 2 proteins varied in different SCLC cell lines, and high levels of U-ISGF3 correlated with resistance to DNA damage. H82, H1048, and H146 cells, which express low levels of U-ISGF3, were sensitive to DNA damage induced by radiation, etoposide, and doxorubicin, while H196, H1688, and H2195 cells expressing high levels of U-ISGF3 were resistant to DNA damage. In response to radiation, γH2A.X levels were significantly increased and remained high up to 48 hrs in H1048 cells, but the increased γH2A.X levels returned to lower levels in H196 cells, suggesting that U-ISGF3-induced gene products may increase DNA damage repair. When STAT1 was knocked down to reduce U-ISGF3 levels in H196 cells, γH2A.X levels increased by radiation remained high. Knocking IRF9 down also decreased the resistance to DNA damage. In conclusion, U-ISGF3, which is increased by a low dose of interferons, plays an important role in inducing DNA damage resistance, and its targeting sensitizes cancer cells to DNA damage induced by various cancer therapies. Citation Format: HyeonJoo Cheon, Elise G. Holvey-Bates, George R. Stark. Chronic exposure to a low dose of interferon-β increases levels of DNA damage resistance signature genes through unphosphorylated ISGF3. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 485. doi:10.1158/1538-7445.AM2014-485

Increased expression of 2′5′oligoadenylate synthetase and double-stranded RNA dependent protein kinase messenger RNAs on affected skin of systemic sclerosis patients

Scleroderma or systemic sclerosis (SSc) is an autoimmune disorder of unknown aetiology characterized by excessive collagen synthesis and subsequent deposition on the skin and various internal organs. Interferons (IFNs) are well-known immunomodulators and inhibitors of collagen production. However, IFN therapy has been implicated in the development or exacerbation of several autoimmune diseases, including SSc. We analyzed the expression of several interferon-stimulated genes (ISGs) in affected skin of SSc patients (skin tissue and cultured skin fibroblasts). A set of ISGs (PKR, 2'5'OAS, MxA, and 6-16) was analyzed by real-time PCR using RNA extracted from cultured skin fibroblasts and skin tissue of normal individuals and SSc patients. Both normal and SSc affected skin cultured fibroblasts were sensitive to the IFN treatment and presented similar levels of all ISGs tested. However, PKR and 2'5'OAS mRNA expression levels were significantly higher in the affected skin tissue of SSc patients when compared to normal controls. These data suggest that the IFN system plays a role in the pathogenesis of SSc.

Interfering with Interferon

The early host response to viral infection is regulated by the type I interferons (IFNα/β), which are induced after detection of virus-specific products. The subsequent transcriptional response is mediated via the Janus kinase-signal transducers and activators of transcription (JAK-STAT) pathway, which controls transcription of a range of interferon-stimulated genes (ISGs). The IKK-related kinases TBK and IKKε (an inhibitor of nuclear factor κB kinase) are also integral components of the IFNβ pathway. However, tenOever et al . reveal that, although mice deficient in IKKε are susceptible to viral infection, this susceptibility is not because of a loss of IFNβ expression. Rather, the deficiency resulted from an unanticipated downstream effect in which IKKε prevents homodimerization of STAT-1 by its phosphorylation. Instead, STAT-1 was incorporated into a heterotrimeric complex transcribing a distinct set of ISGs. B. R. tenOever, S.-L. Ng, M. A. Chua, S. M. McWhirter, A. García-Sastre, T. Maniatis, Multiple functions of the IKK-related kinase IKKε in interferon-mediated antiviral immunity. Science 315 , 1274-1278 (2007). [Abstract] [Full Text]

Immediate/Early Response to Trypanosoma cruzi Infection Involves Minimal Modulation of Host Cell Transcription

Host cell infection by the intracellular pathogen, Trypanosoma cruzi, involves activation of signaling pathways, cytoskeletal reorganization, and targeted recruitment of host cell lysosomes. To determine the consequences of T. cruzi invasion on host cell gene expression, high density microarrays consisting of approximately 27,000 human cDNAs were hybridized with fluorescent probes generated from T. cruzi-infected human fibroblasts (HFF) at early time points following infection (2-24 h). Surprisingly, no genes were induced > or =2-fold in HFF between 2 and 6 h post-infection (hpi) in repeated experiments while immediate repression of six host cell transcripts was observed. A significant increase in transcript abundance for 106 host cell genes was observed at 24 hpi. Among the most highly induced is a set of interferon-stimulated genes, indicative of a type I interferon (IFN) response to T. cruzi. In support of this, T. cruzi-infected fibroblasts begin to secrete IFNbeta at 18 hpi following the induction of IFNbeta transcripts. As compared with global transcriptional responses evoked by other intracellular pathogens, T. cruzi is a stealth parasite that elicits few changes in host cell transcription during the initiation of infection.