The following interview was conducted by Signals+ Editor Maialen Sebastian-delaCruz, Ph.D. Connect with her on LinkedIn.
A recent study by Pasquesi et al from the Chuong lab published in Cell, “Regulation of human interferon signaling by transposon exonization” showed that transposable element exonization can yield functional protein isoforms as seen for primate-specific IFNAR2. Their study focuses on the functional characterization of a short transposon-derived isoform of IFNAR2, one of the Type I IFNs receptors. They demonstrated IFNAR2-S is a primate-specific isoform of IFNAR2 that functions as a decoy receptor. Besides, the dysregulation of IFNAR2 splicing is associated with some human disease, such as severe COVID. Thus, they pointed out the importance of taking into account also the non-canonical isoforms and highlight that uncovering these transposon exonization events and understanding their regulation will be important for gaining a complete understanding of immune regulation and dysregulation in disease.
Summary
Innate immune signaling is essential for clearing pathogens and damaged cells and must be tightly regulated to avoid excessive inflammation or autoimmunity. Here, we found that the alternative splicing of exons derived from transposable elements is a key mechanism controlling immune signaling in human cells. By analyzing long-read transcriptome datasets, we identified numerous transposon exonization events predicted to generate functional protein variants of immune genes, including the type I interferon receptor IFNAR2. We demonstrated that the transposon-derived isoform of IFNAR2 is more highly expressed than the canonical isoform in almost all tissues and functions as a decoy receptor that potently inhibits interferon signaling, including in cells infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our findings uncover a primate-specific axis controlling interferon signaling and show how a transposon exonization event can be co-opted for immune regulation.
Conversation with Edward Chuong, Ph.D.
Dr. Chuong is an Assistant Professor at Biofrontiers Institute, at the University of Colorado Boulder, and his lab studies the interplay between transposons and immune evolution. In 2023 he won an ICIS-Regeneron New Investigator Award, presented in Athens, Greece. In January 2025, Signals+ Editor Maialen Sebastian-delaCruz, Ph.D. spoke with him about the latest article from his lab.
What was the key question you addressed with this paper, and what led you to ask it?
Transposons are genetic parasites that make up over 50% of the human genome, and my lab is broadly interested in how they have shaped our evolution, particularly by controlling immune gene regulation. In this study, we asked about the importance of a process known as transposon exonization, which is when a transposon contains cryptic splice sites and becomes spliced into a cellular transcript. This can generate “chimeric” transcript isoforms partly derived from transposons, but the prevailing view has been that they are nonfunctional and largely suppressed. This makes sense because otherwise the cell would be wasting energy making many partial/incomplete gene transcripts instead of making the “correct” one.
But are all chimeric transcripts just mistakes? The lead author, Giulia Pasquesi, wanted to revisit this issue when she joined my lab as a postdoc. While most are likely nonfunctional, she asked if there were exceptions to the rule—ones that were biologically important for immunity. The key to answering this question was the advent of long-read RNA-seq. She found that short-read RNA-seq did a very poor job at detecting alternative isoforms, but long-read data was ideally suited for the job, making it the perfect time to ask this question.
Which of your findings was the most unexpected and/or exciting to you?
Giulia focused her genomic screen on immune genes, given the importance of fine-tune regulation in immunity. The main surprise was finding that there were dozens of these chimeric transcripts that were expressed at high levels—many even higher than the canonical isoform. One such example was for type I IFN receptor IFNAR2. By looking at long-read data, she could clearly see that a “chimeric” short isoform of IFNAR2 was expressed at much higher levels than the “canonical” full-length isoform. We also saw that this isoform was conserved and expressed in other primate species, which suggested this could be a functional isoform. This made it a potentially ideal example of a transposon-derived splice variant that could be important but was previously ignored due to conceptual and technical limitations.
Could you tell us how the initial idea and/or observation led to the major discovery?
For the IFNAR2 example, this was more of a “rediscovery”. The IFNAR2 short isoform was first noticed in the initial cloning of IFNAR2 (Novick et al Cell 1994) and shown to have a dominant negative effect in mouse cells (Pfeffer et al, JBC 1997). But despite thousands of papers on type I IFN signaling in the past 30 years, the isoform has otherwise been completely forgotten. This is presumably because alternative splice variants, particularly those derived from transposons, remain neglected by most studies.
Giulia’s transposon-focused approach was key to rediscovering this isoform because it showed up as a very robustly expressed transcript in her genome-wide screen. Importantly, Giulia didn’t stop at the bioinformatic analysis, but conducted a tour de force of experiments to show that the IFNAR2 short isoform was important in human cells. While many studies have dissected canonical IFNAR2 function, she was the first to dissect the functions of each isoform, using CRISPR and siRNA to selectively delete the transposon exon or the canonical exon or both. These experiments revealed that the transposon isoform functioned as a potent decoy receptor that fine-tunes type I IFN signaling. This is particularly relevant because this isoform is broadly expressed and dysregulated in many diseases. Consistent with a role in disease, we found that many genetic risk variants associated with severe COVID are also associated with splicing dysregulation at IFNAR2.
If people take away only three things from this paper, what do you want them to be?
- Immune genes undergo frequent alternative splicing, often mediated by transposons, but studying these elements is challenging unless using long-read technology.
- A transposon-derived isoform of IFNAR2 encodes a primate-specific decoy receptor that fine-tunes IFN signaling in virtually all cells.
- Mis-regulation of transposon splicing could be an underappreciated mechanism of immune regulation and immune-mediated diseases like severe COVID.
Why is this discovery of particular significance to the Cytokines community?
Decoy receptors are a common paradigm in cytokine signaling, with natural and engineered examples showing potent activity. However, while some viruses encode IFN decoy receptors (like vaccinia virus B18), our study revealed that humans express a highly potent IFN decoy receptor in virtually all cells. Beyond IFNAR2, our screen revealed multiple signaling pathways in human that are potentially regulated by these cryptic isoforms. Uncovering these events and understanding their regulation will be important for gaining a complete understanding of immune regulation and dysregulation in disease.
Citation of the article: Pasquesi et al., 2024, Cell 187, 7621–7636
Link (open access): https://www.cell.com/cell/fulltext/S0092-8674(24)01333-3