Y-RNAs Lead an Endogenous Program of RIG-I Agonism Mobilized upon RNA Virus Infection and Targeted by HIV

Abstract

34Pattern recognition receptors (PRRs) protect against host invasion by detecting specific 35 molecular patterns found in pathogens and initiating an immune response. While 36 microbial-derived PRR ligands have been extensively characterized, the contribution and 37 relevance of endogenous ligands to PRR activation during viral infection remain 38 overlooked. In this work, we characterize the landscape of endogenous ligands that 39 engage RIG-I-like receptors (RLRs) upon infection by a positive-sense RNA virus, a 40 negative-sense RNA virus or a retrovirus. We found that several endogenous RNAs 41 transcribed by RNA polymerase 3 (Pol3) specifically engage RLRs, and in particular the 42 family of small non-coding repeats Y-RNAs, which presents the highest affinity as RIG-I 43 ligands. We show that this recognition is dependent on Y-RNA mimicking viral secondary 44 structure and its 5'-triphosphate extremity. Further, we found that HIV-1 infection triggers 45 a VPR-dependent downregulation of RNA triphosphatase DUSP11 in vitro and in vivo, 46 leading to an increase of Y-RNA 5'-triphosphorylation that enables their immunogenicity. 47Pattern Recognition Receptors (PRRs) were initially described as innate immune sensors 53 of molecular patterns commonly found in pathogens but rarely, if ever, found in their hosts. 54In recent years, this view has been challenged by evidence that ligands originating from 55 self can engage these same PRRs. Notably, sensing of self-RNA by innate receptors has 56 been observed in various settings such as autoimmune disorders (1-3), tumorigenesis 57 and cancer therapies (4-9) or infection by DNA viruses (10, 11). While the importance of 58 endogenous ligands in priming immune responses is progressively uncovered, little is 59 known about the breadth of biological processes in which they happen, nor about their 60 functional and evolutionary interplay with immune sensors. Furthermore, we lack 61 understanding of what features confers self-RNAs the ability to activate sensors and 62 whether this is a general response to aberrant transcription or is dominated by specific 63 RNA species. 64Further confounding matters, we previously determined that conventional RNA 65 sequencing approaches fail to capture the full spectrum of RNA expression in tumors (12). 66In particular, repetitive RNA, which can harbor immunostimulatory features (13), require 67 further computational analysis for unbiased screening of their transcription. Here, we 68 apply these approaches to identify novel RNA agonists of RIG-I-like receptors (RLRs). 69RLRs are a family of cytosolic RNA sensors composed of three members: RIG-I, LGP2 70 and MDA5 (14). Their intracellular localization and proximity with host RNA species 71 implies a delicate balance between a need to develop high affinity for microbial features 72 and the possibility to encounter self-RNAs that display similar structures. However, 73 despite a growing knowledge of the role of RLRs during RNA virus infection and the 74 microbial-derived ligands they recognize...

RIG-I-like receptors: their regulation and roles in RNA sensing

“…Given that RIG-I activation prevents lytic KSHV infection 53 , it is possible that a pathway involving DUSP11, vtRNAs, RIG-I and type I interferons determines the balance between lytic and latent infection. It is noteworthy that HIV-1 may also downregulate DUSP11 by means of the viral Vpr protein 59 . Concomitantly, non-coding cellular Y-rNAs were found to accumulate in their 5′-PPP-containing form and to bind to RIG-I in HIV-1-infected cells 59 .…”

“…It is noteworthy that HIV-1 may also downregulate DUSP11 by means of the viral Vpr protein 59 . Concomitantly, non-coding cellular Y-rNAs were found to accumulate in their 5′-PPP-containing form and to bind to RIG-I in HIV-1-infected cells 59 . Moreover, endogenous RNAs lacking the canonical features of RIG-I agonists, including RNAs cleaved by RNase L 60 and microrNAs (miRNAs) 61 , have been suggested to activate RIG-I in virus-infected cells.…”

DUSP11-mediated control of 5′-triphosphate RNA regulates RIG-I sensitivity

“…DUSP11 is an RNA triphosphatase that we and others have previously demonstrated to be active on the 5 ′ ends of structured host and viral transcripts (Deshpande et al 1999;Burke et al 2016;Burke and Sullivan 2017;Kincaid et al 2018;Vabret et al 2019). The 5 ′ -triphosphates of hepatitis C virus (HCV) RNAs are converted to monophosphates rendering them susceptible to exonuclease XRNmediated attack (Amador-Cañizares et al 2018;Kincaid et al 2018).…”

“…These viral miRNAs require DUSP11 for full silencing activity via stable loading of 5 ′ -monophosphate miRNAs into the RNA-induced silencing complex (RISC) (Burke et al 2016). Additionally, the 5 ′ -triphosphate status of several host RNAP III noncoding RNA transcripts including vault RNAs (vtRNAs), Alu SINE RNAs, Y RNAs, and RMRP RNA are also modulated by DUSP11 (Burke et al 2016;Zhao et al 2018;Vabret et al 2019). The ability of DUSP11 to convert the 5 ′ end of diverse structured and partially double-stranded host and viral transcripts into monophosphates opens up the possibility that DUSP11 can alter the immunostimulatory activity of endogenous and exogenous triphosphorylated transcripts (Burke and Sullivan 2017).…”

“…Although DUSP11 can convert structured triphosphate RNAs into monophosphates (Burke and Sullivan 2017), and DUSP11 has been implicated as being reduced during infection by some viruses (Zhao et al 2018;Vabret et al 2019), the physiological role of DUSP11 in the innate immune response is poorly understood. Here we test the hypothesis that DUSP11 is a modulator of the RNA-induced innate immune response.…”