Xuetao Cao’s team discovered a new molecule lncRNA-ISIR that enhances the effect of interferon

Editor’s note iNature is China’s largest academic official account.
It is jointly created by the doctoral team of Tsinghua University, Harvard University, Chinese Academy of Sciences and other units.
The iNature Talent Official Account is now launched, focusing on talent recruitment, academic progress, scientific research information, interested parties can Long press or scan the QR code below to follow us
.

iNature Interferon Regulatory Factor 3 (IRF3) is an important transduction factor that initiates many immune responses
.

At present, there is no research report showing that IRF3 molecules can directly bind to lncRNA and be regulated
.

Therefore, whether there is a lncRNA that directly binds to IRF3 to more effectively regulate the natural immune response pattern needs further research
.

On November 2, 2021, Cao Xuetao’s team, an academician of the Chinese Academy of Engineering (Institute of Basic Medicine, Chinese Academy of Medical Sciences as the first unit), published an online report entitled "IRF3-binding lncRNA-ISIR strengthens interferon production in viral infection and autoinflammation" in Cell Reports.
A research article reported on the new lncRNA discovered by the team and called it Interferon StimulatedIRF3-associating RNA (lncRNA-ISIR), and found that the lncRNA-ISIR induced by type I IFN can block The inhibitory effect of Fli-1 enhances the type I IFN response mediated by IRF3, and the positive feedback regulation mechanism of lncRNA-mediated transcription factors is proposed
.

Virus infection has always been one of the most common infectious diseases in humans, seriously endangering human health and public health safety
.

Innate immunity is the host’s first line of defense against pathogen infections.
It can resist viral infections by inducing the production of interferon (IFN).
Interferon regulatory factor 3 (IRF3) is the core of the innate immune response and IFN production.
One of the transcription factors
.

The immune response not only needs to eliminate infections by viruses and other pathogens, but also to avoid excessive damage leading to tissue damage, so it is finely regulated in many aspects
.

In recent years, the role of lncRNA has received widespread attention.
Previous studies have found that multiple lncRNA molecules are involved in regulating the activation of IRF3 molecules and the regulation of natural immune response, but they all indirectly regulate the activation of IRF3
.

At present, there is no research report showing that IRF3 molecules can directly bind to lncRNA and be regulated
.

Therefore, whether there is a lncRNA that directly binds to IRF3 to more effectively regulate the natural immune response pattern needs further research
.

This study used formaldehyde-crosslink IP technology to enrich IRF3-RNA complexes from virus-infected macrophages, and screened by RNA sequencing and UV-crosslink IP technology.
Fluorescence co-localization verification confirmed that IRF3 specifically binds to lncRNA XR_386561.
1 (lncRNA-ISIR) in the early stage of virus infection of macrophages
.

The author determined that lncRNAXR_386561.
1 is an Interferon stimulated gene (ISG) through a variety of different experimental methods, and transcription is mediated by the JAK1/STAT1 signaling pathway
.

It is named Interferon Stimulated IRF3-associating RNA (lncRNA-ISIR)
.

Then, using macrophages derived from lncRNA-ISIR-/- mice and littermate WT mice for functional experiments, the authors found that lncRNA-ISIR gene defects significantly inhibited the phosphorylation and dimerization of IRF3 protein stimulated by the VSV virus.
When it enters the nucleus, the secretion of type I interferons-IFNα and IFNβ is inhibited, and virus replication is significantly increased
.

In vivo experiments in mice also proved that lncRNA-ISIR enhanced IRF3-mediated type I interferon and other natural immune responses, inhibited virus replication in different organs of mice, reduced lung inflammation damage, and assisted the host in resisting viral infections
.

Article pattern diagram (picture from Cell Reports) Next, the author explored the molecular mechanism of lncRNA-ISIR to promote IRF3-mediated innate immune response
.

Stimulate lncRNA-ISIR+/+PM or lncRNA-ISIR-/- PM with VSV virus, and perform IP experiment with anti-IRF3 antibody.
It was found that lncRNA-ISIR-/- PM specifically enriched a protein strip near 170 kD.
Band, identified by mass spectrometry as Fli-1 protein (Gene: Flii, Gene ID: 14248), that is, in virus-infected lncRNA-ISIR-/-PM, but not wild-type PM, IRF3 protein specifically binds to Fli-1
.

co-IP further verified this result
.

Unexpectedly, in the resting state, both lncRNA-ISIR-/- macrophages or lncRNA-ISIR+/+ macrophages have IRF3-Fli-1 complexes
.

The above results indicate that IRF3 binds to Fli-1 when cells are in an unstimulated state.
After virus infection, the interferon-induced expression of lncRNA-ISIR promotes the dissociation of IRF3 from Fli-1, and then IRF3 enters the nucleus
.

As an IRF3 binding protein, what function does Fli-1 play in the antiviral immune response? To answer this question, the author silenced the expression of the Flii gene, and WB detection found that after interfering with the Flii gene in WT macrophages, the virus-induced phosphorylation of IRF3 did not change significantly.
On the contrary, in lncRNA-ISIR-/-macrophages In cells, after the Flii gene was silenced, the phosphorylation level of IRF3 increased significantly
.

Consistent with this, silencing Flii gene expression does not affect the stress expression of type I IFN and viral replication in WT macrophages, but the down-regulated type I IFN response and increased viral replication of lncRNA-ISIR-/- macrophages are to a certain extent Cover
.

The above experimental results show that lncRNA-ISIR blocks the inhibition of IRF3 activation by Fli-1, thereby promoting IRF3-mediated antiviral natural immunity
.

In summary, this study found a new lncRNA-lncRNA-ISIR stimulated by IFN expression and proved that it can block the inhibitory effect of Fli-1 on IRF3 by binding to IRF3, thereby enhancing the IRF3-mediated IFN immune response
.

In addition, in clinically relevant autoimmune injury disease samples, the authors found that lncRNA-ISIR in systemic lupus erythematosus SLE samples increased significantly, while lncRNA-ISIR decreased to the level of healthy controls after effective treatment
.

This shows that the IFN/lncRNA-ISIR/IRF3 regulatory axis plays an important role in the regulation of the immune response of clinical autoimmune diseases, and provides new potential intervention targets for autoimmune diseases and antiviral immune responses
.

This research work reveals the function and molecular mechanism of lncRNA regulating the immune response by directly combining with the key molecule IRF3 of innate immunity, opening a new perspective for the regulation of innate immune response
.

Academician Cao Xuetao and Professor Wang Pin from the Institute of Immunology of Naval Military Medical University are the co-corresponding authors of the paper.
Xu Junfang, Wang Pin and Li Zemeng are the co-first authors of the paper
.

This work was supported by the Medical and Health Innovation Project of the Chinese Academy of Medical Sciences, the National Natural Science Foundation of China and the National Postdoctoral Fund
.

Reference message: https://doi.
org/10.
1016/j.
celrep.
2021.
109926