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Type I Interferon Regulates the Expression of Long Non-Coding RNAs.

Carnero E, Barriocanal M, Segura V, Guruceaga E, Prior C, Börner K, Grimm D, Fortes P - Front Immunol (2014)

Bottom Line: Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV.This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response.Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.

View Article: PubMed Central - PubMed

Affiliation: Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain.

ABSTRACT
Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). To address whether IFN can also regulate the expression of lncRNAs, we analyzed the transcriptome of HuH7 cells treated or not with IFNα2 by expression arrays. Analysis of the arrays showed increased levels of several well-characterized coding genes that respond to IFN both at early or late times. Furthermore, we identified several IFN-stimulated or -downregulated lncRNAs (ISRs and IDRs). Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response. These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. IFNβ also induced the expression of these lncRNAs. ISR2 and 8 were also induced by an influenza virus unable to block the IFN response but not by other wild-type lytic viruses tested. Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV. Increased levels of ISR2 were also detected in patients chronically infected with HIV. This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response. Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.

No MeSH data available.


Related in: MedlinePlus

ISR2, 8, and 12 respond to low doses of IFN. HuH7 cells were treated for 6, 24, 48, or 72 h with 0, 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 and the expression levels of ISR2 and 8 and ISR12 were evaluated by qRT-PCR. GAPDH expression was also evaluated and used as a reference to calculate the relative levels of each transcript. The experiment was performed three times and each value shows the average of three replicas from a representative experiment. Error bars indicate standard deviations. The fold-change of treated versus non-treated cells is indicated at the top of each bar when higher than two.
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Figure 5: ISR2, 8, and 12 respond to low doses of IFN. HuH7 cells were treated for 6, 24, 48, or 72 h with 0, 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 and the expression levels of ISR2 and 8 and ISR12 were evaluated by qRT-PCR. GAPDH expression was also evaluated and used as a reference to calculate the relative levels of each transcript. The experiment was performed three times and each value shows the average of three replicas from a representative experiment. Error bars indicate standard deviations. The fold-change of treated versus non-treated cells is indicated at the top of each bar when higher than two.

Mentions: All the experiments performed so far with these lncRNAs have studied the response to high doses of IFN. To determine whether ISR2, 8, and 12 also respond to lower doses, their expression level was evaluated in HuH7 cells treated for 6, 24, 48, or 72 h with 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 (Figure 5). The results show that induction of these lncRNAs is similar to that observed for their corresponding neighboring coding genes (compare Figure 5 with Figure 1). Similar results were observed when IFNβ was used instead of IFNα2 (data not shown). Further, we evaluated whether expression of these transcripts was induced after treatment with TNFα. TNFα, similarly to some pathogen-associated molecular patterns, induces NFκβ signaling and expression of pro-inflammatory genes. However, the NFκβ pathway is a poor inducer of ISGs. A treatment of HuH7 cells with 20 ng/ml of TNFα for 6 h, induced the expression of CXCL10, used as a positive control, more than 100-fold. A significant increase in expression of only 2–3-fold was observed after TNFα treatment for GBP1, IRF1, IL6, and ISR12, but not for ISR2. Similar results were obtained in HuH7 cells treated with LPS or polyI:C (data not shown).


Type I Interferon Regulates the Expression of Long Non-Coding RNAs.

Carnero E, Barriocanal M, Segura V, Guruceaga E, Prior C, Börner K, Grimm D, Fortes P - Front Immunol (2014)

ISR2, 8, and 12 respond to low doses of IFN. HuH7 cells were treated for 6, 24, 48, or 72 h with 0, 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 and the expression levels of ISR2 and 8 and ISR12 were evaluated by qRT-PCR. GAPDH expression was also evaluated and used as a reference to calculate the relative levels of each transcript. The experiment was performed three times and each value shows the average of three replicas from a representative experiment. Error bars indicate standard deviations. The fold-change of treated versus non-treated cells is indicated at the top of each bar when higher than two.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222131&req=5

Figure 5: ISR2, 8, and 12 respond to low doses of IFN. HuH7 cells were treated for 6, 24, 48, or 72 h with 0, 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 and the expression levels of ISR2 and 8 and ISR12 were evaluated by qRT-PCR. GAPDH expression was also evaluated and used as a reference to calculate the relative levels of each transcript. The experiment was performed three times and each value shows the average of three replicas from a representative experiment. Error bars indicate standard deviations. The fold-change of treated versus non-treated cells is indicated at the top of each bar when higher than two.
Mentions: All the experiments performed so far with these lncRNAs have studied the response to high doses of IFN. To determine whether ISR2, 8, and 12 also respond to lower doses, their expression level was evaluated in HuH7 cells treated for 6, 24, 48, or 72 h with 5, 50, 250, 1000, or 10,000 units/ml of IFNα2 (Figure 5). The results show that induction of these lncRNAs is similar to that observed for their corresponding neighboring coding genes (compare Figure 5 with Figure 1). Similar results were observed when IFNβ was used instead of IFNα2 (data not shown). Further, we evaluated whether expression of these transcripts was induced after treatment with TNFα. TNFα, similarly to some pathogen-associated molecular patterns, induces NFκβ signaling and expression of pro-inflammatory genes. However, the NFκβ pathway is a poor inducer of ISGs. A treatment of HuH7 cells with 20 ng/ml of TNFα for 6 h, induced the expression of CXCL10, used as a positive control, more than 100-fold. A significant increase in expression of only 2–3-fold was observed after TNFα treatment for GBP1, IRF1, IL6, and ISR12, but not for ISR2. Similar results were obtained in HuH7 cells treated with LPS or polyI:C (data not shown).

Bottom Line: Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV.This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response.Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.

View Article: PubMed Central - PubMed

Affiliation: Department of Gene therapy and Hepatology, Center for Applied Medical Research (CIMA), University of Navarra , Pamplona , Spain.

ABSTRACT
Interferons (IFNs) are key players in the antiviral response. IFN sensing by the cell activates transcription of IFN-stimulated genes (ISGs) able to induce an antiviral state by affecting viral replication and release. IFN also induces the expression of ISGs that function as negative regulators to limit the strength and duration of IFN response. The ISGs identified so far belong to coding genes. However, only a small proportion of the transcriptome corresponds to coding transcripts and it has been estimated that there could be as many coding as long non-coding RNAs (lncRNAs). To address whether IFN can also regulate the expression of lncRNAs, we analyzed the transcriptome of HuH7 cells treated or not with IFNα2 by expression arrays. Analysis of the arrays showed increased levels of several well-characterized coding genes that respond to IFN both at early or late times. Furthermore, we identified several IFN-stimulated or -downregulated lncRNAs (ISRs and IDRs). Further validation showed that ISR2, 8, and 12 expression mimics that of their neighboring genes GBP1, IRF1, and IL6, respectively, all related to the IFN response. These genes are induced in response to different doses of IFNα2 in different cell lines at early (ISR2 or 8) or later (ISR12) time points. IFNβ also induced the expression of these lncRNAs. ISR2 and 8 were also induced by an influenza virus unable to block the IFN response but not by other wild-type lytic viruses tested. Surprisingly, both ISR2 and 8 were significantly upregulated in cultured cells and livers from patients infected with HCV. Increased levels of ISR2 were also detected in patients chronically infected with HIV. This is relevant as genome-wide guilt-by-association studies predict that ISR2, 8, and 12 may function in viral processes, in the IFN pathway and the antiviral response. Therefore, we propose that these lncRNAs could be induced by IFN to function as positive or negative regulators of the antiviral response.

No MeSH data available.


Related in: MedlinePlus