Research Article

Human NLRP1 is a sensor for double-stranded RNA

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Science  29 Jan 2021:
Vol. 371, Issue 6528, eabd0811
DOI: 10.1126/science.abd0811

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A dsRNA detector in the immune toolkit

Nod-like receptor (NLR) proteins recognize pathogen-associated molecular patterns within cells, which triggers the formation of signaling complexes called inflammasomes. These complexes then initiate pyroptosis, a highly inflammatory form of cell death. Recent work has shown that a rhinovirus protease can activate the human NLRP1 inflammasome, but it was unclear whether this is the only pathogen-derived trigger for NLRP1. Bauernfried et al. report that long, double-stranded RNA (dsRNA) generated in the course of Semliki Forest virus infection binds and activates NLRP1 in epithelial cells. dsRNA binding triggered NLRP1 to acquire adenosine triphosphatase (ATPase) activity, a common feature of activated NLR proteins. Thus, in addition to its ability to recognize viral protease activity, human NLRP1 can act as a genuine sensor of virus-associated nucleic acids.

Science, this issue p. eabd0811

Structured Abstract

INTRODUCTION

The innate immune system constitutes the first line of host defense. To detect pathogens, it uses a set of germline-encoded pattern recognition receptors (PRRs) that have evolved to sense the presence of non-self. PRRs can either directly sense pathogens or they can indirectly respond to the perturbation of cellular homeostasis during the course of pathogen infection. One group of cytosolic PRRs are inflammasome-forming nucleotide-binding domain leucine-rich repeat (NLR) proteins. After activation, they form high-molecular-weight signaling complexes that result in the direct or ASC-dependent engagement and activation of caspase-1. Active caspase-1, in turn, cleaves and thereby activates the highly proinflammatory cytokine interleukin-1β (IL-1β). In addition, caspase-1 cleaves gasdermin D (GSDMD), which results in the activation of a lytic cell death pathway known as pyroptosis. NLRP1 was one of the first inflammasome-forming PRRs to be identified, yet its role in pathogen defense in the human system remains poorly defined.

RATIONALE

NLRP1 is highly expressed and functional in epithelial barrier tissues, e.g., in keratinocytes. Unlike myeloid immune cells, keratinocytes appear to express only a limited set of inflammasome sensors, which makes them an interesting model system in which to study the role of NLRP1. To identify a potential NLRP1 stimulus, we used an immortalized keratinocyte cell line to screen a panel of viral pathogens for their potential inflammasome activation.

RESULTS

Screening different types of viruses, we found that Semliki Forest virus (SFV) triggered inflammasome activation in keratinocytes in an NLRP1-dependent fashion. As a positive-strand RNA virus, SFV generates ample amounts of double-stranded (ds) RNA during its life cycle, and the production of dsRNA coincided with the activation of NLRP1. We therefore tested poly(I:C), a synthetic dsRNA analog, and in vitro transcribed dsRNA molecules for inflammasome activation. These experiments revealed that NLRP1 was indeed stimulated by dsRNA, yet long dsRNA was required to trigger activation. These findings could be recapitulated in primary keratinocytes and immortalized bronchial epithelial cells. To determine whether this phenotype was specific for human NLRP1, we reconstituted NLRP1-deficient keratinocytes with transgenes for either human NLRP1 or murine Nlrp1b. Indeed, only keratinocytes expressing human NLRP1 were responsive to dsRNA. dsRNA-induced inflammasome activation was independent of other known dsRNA sensors, because their depletion did not decrease NLRP1 activation after dsRNA delivery. Because of these findings, we then investigated whether NLRP1 directly interacted with dsRNA. Pull-down studies revealed that human NLRP1, but not murine NLRP1B, could be immunoprecipitated by dsRNA. Using recombinant proteins, we found that NLRP1 bound nucleic acids with high affinity, predominantly through its leucine-rich repeat (LRR) domain. To ascertain whether dsRNA binding activated NLRP1 in vitro, we subsequently studied ATP hydrolysis of NLRP1 as a proxy for its activation. These studies revealed that dsRNA, but not dsDNA, triggered ATPase activity.

CONCLUSION

In 2002, human NLRP1 became the first inflammasome-forming sensor to be characterized. However, no direct ligand had been identified so far. Our work demonstrates that human NLRP1 is a bona fide nucleic acid sensor. NLRP1 directly interacts with dsRNA, a typical intermediate of viral replication, which subsequently results in the activation of the inflammasome pathway.

The pathogen-associated molecular pattern dsRNA interacts with human NLRP1 and leads to inflammasome activation.

Infection with a positive-strand RNA virus leads to the formation of dsRNA, and the generated dsRNA recruits human NLRP1. This results in the activation of NLRP1, which leads to the formation of an inflammasome complex. Inflammasome activation results in IL-1β maturation and the induction of pyroptosis.

Abstract

Inflammasomes function as intracellular sensors of pathogen infection or cellular perturbation and thereby play a central role in numerous diseases. Given the high abundance of NLRP1 in epithelial barrier tissues, we screened a diverse panel of viruses for inflammasome activation in keratinocytes. We identified Semliki Forest virus (SFV), a positive-strand RNA virus, as a potent activator of human but not murine NLRP1B. SFV replication and the associated formation of double-stranded (ds) RNA was required to engage the NLRP1 inflammasome. Moreover, delivery of long dsRNA was sufficient to trigger activation. Biochemical studies revealed that NLRP1 binds dsRNA through its leucine-rich repeat domain, resulting in its NACHT domain gaining adenosine triphosphatase activity. Altogether, these results establish human NLRP1 as a direct sensor for dsRNA and thus RNA virus infection.

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