Chimeric RNAs produce immune proteins that tune inflammation

Inflammatory stimulation can make genes on distant parts of the mammalian genome meet at the RNA level, creating chimeric transcripts that encode previously unrecognized proteins. A study in mouse immune cells found that one such molecule, a chimera joining the Gsdmd and Tmem106a genes, produces a fusion protein that accelerates the membrane pores associated with pyroptotic cell death. The protein increased the release of the inflammatory cytokine IL-1β and helped determine the balance between bacterial defense and damaging inflammation in mice. The results indicate that functional complexity can extend beyond the number of protein-coding genes: independently transcribed regions may be joined and translated into proteins with effects disproportionate to the abundance of their parent genes.

The work focused on chimeric RNAs, or chRNAs, formed when sequences from separate genomic loci are combined within one transcript. Researchers had previously linked some chimeric transcripts to cancer-associated chromosomal rearrangements, but earlier work had also shown that RNA-level trans-splicing can generate chRNAs and functional fusion proteins without corresponding changes in genomic structure. Isolated examples had been reported in normal contexts, including JAZF1-JJAZ1 in endometrial fibroblasts and PAX3-FOXO1 during muscle differentiation. The new study, described in a research highlight published in Cell Research, asks whether additional trans-spliced RNAs occur widely in mammalian tissues and whether they can make functional proteins in normal immune cells.

To map chRNAs in mouse macrophages, the researchers combined long-read Oxford Nanopore direct RNA sequencing with short-read sequencing, computational analysis, PCR and Sanger sequencing. They also used NanoString junction-specific profiling, an orthogonal hybridization-based method for testing predefined RNA junctions. More than 30,000 candidate chimeric RNAs were detected. Many joined genes on different chromosomes or separated by large genomic distances, and numerous transcripts changed after inflammatory stimulation. That regulation argues that chRNA formation is not merely random noise generated during transcription. Instead, the joining of RNA sequences appears to respond to the physiological state of the cell, although the researchers did not directly test the function of every candidate transcript.

Validating such molecules presents a central technical problem. Short-read sequencing usually involves reverse transcription, and template switching during reverse transcription or library preparation can create artificial sequence junctions that resemble genuine RNA fusions. Direct RNA sequencing avoids that particular source of error, while the independent NanoString assay and PCR-based tests provide additional ways to confirm selected junctions. Agreement among these methods strengthened the case that the identified chRNAs are endogenous. The technologies did not recover identical transcript sets, however. Abundance, isoform structure, sequencing chemistry and assay sensitivity can all affect which low-level chRNAs are detected, leaving standardized validation criteria as an important requirement for future studies.

The analysis also connected chRNA production with the three-dimensional organization of the genome. Inflammatory stimulation increased contacts between several parental genomic loci involved in forming chRNAs. Depleting CTCF, a protein that helps organize chromatin loops, reduced those contacts and decreased chRNA production without substantially altering expression of the parent genes. This supports a model in which the physical arrangement of chromosomes helps determine which independently transcribed RNAs can be connected. Proximity alone is unlikely to be sufficient, though. The study did not resolve how two transcripts are selected, aligned and joined, or which splice-site features, RNA-binding proteins, transcriptional timing or regulatory sequences guide the process. Genomic architecture may therefore facilitate RNA-level gene joining without being its sole determinant.

The strongest functional evidence came from the Gsdmd-Tmem106a chimera. Its RNA joined exons 1–2 of Gsdmd with exons 6–9 of Tmem106a without an accompanying chromosomal rearrangement. Translation produced an unannotated GSDMD-TMEM106A fusion protein containing the membrane-associated N-terminal region of GSDMD and a shifted C-terminal region derived from TMEM106A. GSDMD normally acts as an executor of pyroptosis: inflammatory caspase-mediated cleavage releases its N-terminal domain, which oligomerizes in membranes to form pores. Those pores promote membrane permeabilization and IL-1β release. The fusion protein localized to the plasma membrane and associated with activated GSDMD-NT domains, adding a regulatory layer to an established inflammatory pathway.

Experiments showed that the effect was not simply a consequence of making more GSDMD. The chimeric RNA was expressed at less than 10% of the level of parental Gsdmd. Adding an amount of GSDMD-TMEM106A-encoding messenger RNA equal to that lower level nearly doubled IL-1β release when supplied alongside GSDMD-encoding messenger RNA, whereas a comparable increase in GSDMD had little effect. Removing the TMEM106A-derived C-terminal segment abolished the enhancement. These results indicate that the fusion protein performs a specific function rather than acting merely as an additional source of GSDMD. The work also provides a concrete example of why conventional expression measurements alone can miss biologically important activity: a relatively scarce transcript can encode a protein with a large effect on cellular behavior.

Complementary mouse genetic models established relevance during infection and systemic inflammation. A GSDMD-TMEM106A-MYC knock-in allowed the fusion protein to be detected directly, while a Gsdmd-Tmem106aStop model selectively prevented translation of the fusion while preserving both parental genes. Eliminating GSDMD-TMEM106A increased bacterial burden after infection with Salmonella Typhimurium but protected mice from lethal endotoxemia. Increasing fusion activity produced the opposite pattern, improving bacterial clearance while worsening inflammatory pathology. The chimera therefore appears to help tune a trade-off: preserving an effective response against intracellular bacteria can also intensify inflammatory injury. The experiments were performed in mice, so they do not establish that the same quantitative balance operates in people.

The findings may not transfer directly from mice to humans. The researchers identified more than 900 chRNAs in human monocyte-derived macrophages and detected chRNAs involving the same parent genes in both mouse and human cells, but they did not detect GSDMD-TMEM106A itself in the human macrophages examined. Conservation of the genes from which a chimera is assembled therefore does not guarantee conservation of the assembled RNA. Species differences in exon structure, splice-site compatibility, regulatory sequences, RNA-binding factors and genome organization could all affect whether a particular chRNA is generated. More broadly, the study suggests that cellular responses may depend not only on how strongly individual genes are expressed, but also on which transcripts become connected, when they are translated and whether the resulting proteins are functional.

That implication reaches beyond immune biology. Stimulus-responsive chRNAs could contribute to regulatory networks in development, nervous-system function, tissue repair, aging and disease, but the present study does not demonstrate such roles. Its strongest conclusion is that mammalian immune cells contain a large, regulated landscape of chimeric RNAs and that at least one member can encode a functional fusion protein in vivo. By linking chromatin contacts and CTCF-dependent genome organization to RNA joining, and then to the control of pyroptosis, the work reframes the transcriptome as more than a collection of transcripts encoded one gene at a time. It also exposes a deeper question for future research: how far the three-dimensional organization of the genome determines which genes become functionally connected at the RNA level, and how often that connection creates a protein with a biological role that would be missed by measuring parent-gene expression alone.

Subject of Research: Inflammation-induced chimeric RNAs in mammalian immune cells and fusion-protein control of pyroptosis

Article Title: Functional chimeric RNAs expand the mammalian proteome

Article References: Xie, Z., & Li, H. (2026). Functional chimeric RNAs expand the mammalian proteome. Cell Research. https://doi.org/10.1038/s41422-026-01309-6

Image Credits: AI Generated

DOI: 10.1038/s41422-026-01309-6

Keywords: chimeric RNA, pyroptosis, inflammation, immune cells, fusion proteins, CTCF, genome organization, macrophages, IL-1β, RNA sequencing, Functional, chimeric