Compartmentalization and discrimination of dsRNA in the nucleus

The long-term goal of our lab is to understand the fundamental mechanisms by which RNA structures and RNA modifications can help cells distinguish between "self" and "non-self" molecules. One of these potent non-self molecules is double-stranded RNA (dsRNA), a particular structure of RNA that is not present at high levels in unstressed cells, but can be seen as a hallmark of viral infection. Unfortunately, transcription of endogenous repetitive elements within our own genomes can lead to the formation of dsRNA and activation of RNA sensors and inappropriate destructive cell signaling pathways even in the absence of infection. As such, the balance between sensing pathogenic dsRNA and tolerating self dsRNA must be finely tuned by negative regulators of RNA sensing. In addition, RNA sensing is also compartmentalized, with sensors in the cytoplasm kept away from the nucleus where RNA transcription takes place. Important for human health, loss of this balance in either direction is harmful, with negative regulator loss-of-function leading to inflammatory disease or autoimmunity while gain-of-function has been associated with cancer. Our research has shown that human viruses can actively prevent the formation of dsRNA by regulation of RNA splicing and removal of complementary introns. However, perturbation of viral splicing efficiency leads to production of nuclear dsRNA that is sensed by cytoplasmic sensors that subsequently move to the nucleus. This tool provides a unique opportunity to assess how cells respond to dsRNA derived from the nuclear compartment, and how tolerance of this non-self molecule can be broken. This proposal will explore the basic biological principles governing the interactions between nuclear dsRNA, RNA processing, and cytoplasmic RNA sensors. We will ask fundamental questions about how RNA structures, including intramolecular hairpins and intermolecular two-stranded helices, influence RNA sensor activation and the interplay between redundant sensing pathways. Additionally, we will investigate whether nuclear dsRNA carries specific chemical modifications that modulate its structure, recognition by sensors, or sensor activity. Finally, we will determine RNA binding proteins that specifically bind or regulate nuclear dsRNA using quantitative proteomics. The results will shed light on how healthy cells prevent inappropriate activation of RNA sensing responses to self-derived RNA. We will also learn how stressful situations, such as viral infection, can rewire existing signaling pathways to allow nucleic acid surveillance of the nucleus. The completion of this project will ultimately lead to a greater mechanistic understanding of nucleic acid sensing in cellular health and homeostasis. Project Number: 1R35GM162712-01 | Fiscal Year: 2026 | NIH Institute/Center: National Institute of General Medical Sciences (NIGMS) | Principal Investigator: Alexander Price | Institution: WISTAR INSTITUTE, PHILADELPHIA, PA | Award Amount: $506,550 | Activity Code: R35 | Study Section: Special Emphasis Panel[ZRG1 MGG-F (55)] View on NIH RePORTER: https://reporter.nih.gov/project-details/11268867