Stress-induced endogenous-dsRNAs drive beta-cells to IFN-I state
Authors: Chi Kevin K. , Senapati Parijat , Leung Amy , Schones Dustin E. 
Published: November 2023

Aims/hypothesis

Endogenous dsRNAs originating from retrotransposons within the human genome have the potential to trigger autoimmunogenic recognition via RIG-like receptors such as MDA5. This phenomenon, known as “viral mimicry”, induces potent interferon-beta expression, resulting in cell death and potential collateral death to surrounding cells. Viral mimicry has been mostly studied in relation to epigenetic therapeutics, although there are indications the phenomenon is relevant in other physiological contexts. Here, we demonstrate that proinflammatory cytokine stress leads to the dysregulation of retrotransposons in human beta-cells, resulting in beta-cell death via viral mimicry.

Methods

Human islets from donors were treated with/without proinflammatory cytokines (IFN-γ, TNF-α, IL-1β) and immunostained for dsRNA. Publicly available transcriptome and chromatin accessibility data from proinflammatory cytokine treated EndoC-βH1 cells were analyzed to examine changes in transcriptional regulatory activity at retrotransposon loci. Transcriptome profiling experiments in 1.1B4 and MIN6 cells were performed to examine the generality of the results. Adenosine to inosine (A-to-I) editing was compared between sample groups to gauge the extent of RNA editing on dsRNAs. Additional transcriptome data from normal vs. type 1 diabetic human islets was also assessed for differences in A-to-I editing activity between sample groups.

Results

Proinflammatory cytokine stress increases the amount of dsRNA in human islets, co-incident with cells that express insulin. In the EndoC-βH1 human beta-cell line, proinflammatory cytokine stress leads to a substantial increase in transcription at RTE loci, including SINE/Aluelements and LINE elements, along with increased expression of RLRs (including MDA5), inflammatory transcription factors (e.g. IRF3, STAT1), and most critically, IFNB1, a potent instigator of type 1 interferon responses. Similar trends were observed in 1.1B4 and MIN6 cells. Gene ontology analysis revealed an enrichment of genes related to interferon signaling and inflammation. Inflammatory stress furthermore leads to an increase in chromatin accessibility at many RTE loci, with enrichment in a variety of RTE subfamilies (including L1,AluY,AluSp,AluSq2, andAluSc elements). Binding sites for inflammatory transcription factors, such as IRFs, are also enriched at these loci. While inflammatory stress increased the overall A-to-I editing events atAluelements, the pool of total uneditedAlus was increased upon inflammatory stress. Examination of A-to-I editing in RNA-seq data from type 1 diabetic human islets and normal controls revealed that editing in diabetic islets is dramatically lower (∼1%) than islets from normal controls (∼15%).

Conclusions/interpretation

Transcription and chromatin accessibility are both increased at RTEs (notablyAlus) upon proinflammatory cytokine stress, accompanied by an increase in RLR expression and a shift to a type I interferon state, as indicated by increased IFNB1 and other interferon-stimulated genes, including MDA5, an RLR gene which is also a type 1 diabetes risk gene. The overall increase in A-to-I editing upon inflammatory stress is associated with increases in ADAR1 expression, yet the increase in overall uneditedAlus shows that cytokine stress leads to a higher dsRNA burden in the beta-cell. This increase in dsRNA burden is further compounded by increased MDA5 expression, exacerbating the inflammatory state of the beta-cell. Comparisons of A-to-I editing between normal vs. type 1 diabetic human islets suggest that type 1 diabetics have more unedited dsRNAs, hindering their ability to prevent autoimmunogenic recognition.

Research in context

What is already known about this subject?

Cytokine stress during insulitis is a feature of autoimmune diabetes.

Stress-induced dysregulation of retrotransposons can lead to a dsRNA-based type-I interferon response in a variety of cells (‘viral mimicry’)

Endogenous dsRNAs are subject to adenine to inosine (A-to-I) editing by ADAR1 to prevent self-recognition.

What is the key question?

Can cytokine stress drive beta-cells into an IFN-I state via recognition of endogenous dsRNAs derived from retrotransposons that lose silencing under cytokine stress?

What are the new findings?

Cytokine stress causes an increase in dsRNAs derived from retrotransposons in beta-cells from human islets.

The SINE/Alu subset of these endogenous dsRNAs are less edited in stressed beta-cells, making them more self-recognizable.

Type 1 diabetic human islets exhibit more uneditedAlus.

How might this impact on clinical practice in the foreseeable future?

Innate autoimmunity via endogenous dsRNAs can cause damage to beta-cells; therapies to target this pathway may help treat autoimmune diabetes.