Recognition of Endogenous Nucleic Acids by the Innate Immune System

The Sixth Sense: Self-nucleic acid sensing in the brain.

A synthetic double-stranded RNA, poly I:C, induces a rapid apoptosis of human CD34+ cells

A successful antimicrobial immune response involves the coordinate action of cells and soluble factors, with the cytokine family of type I interferons (IFNs) having a central role. Type I IFNs are not only crucial in conferring immediate antimicrobial, most importantly antiviral effects, but they also have an essential role in bridging the innate with the adaptive immune response. Therefore, production of these key cytokines must be tightly controlled. To this effect the host has evolved a set of pattern recognition receptors (PRRs) that reliably and specifically detect the presence of microbial pathogens before mounting an IFN response. Most PRR pathways that are known to induce type I IFNs are triggered upon recognition of nucleic acids. This mode of sensing is not straightforward, as large amounts of RNA and DNA are also present within the host. Nevertheless, in some cases distinct molecular features that are present within foreign nucleic acids but absent in endogenous nucleic acids, allow the host to reliably discriminate between 'self' and 'non-self'. At the same time, compartmentalization of PRRs within subcellular organelles that are usually devoid of host nucleic acids, but are sites of pathogen localization, is another principle that enables the host to distinguish self from non-self. The latter mode of sensing applies to the detection of microbial DNA within the cytoplasm, a compartment in which host DNAs are usually not present. Despite the past years' tremendous progress in the field of innate immunity, our understanding of cytoplasmic DNA sensing mechanisms is only beginning to form/take form. In this review, we outline the recent advancements in the elucidation of intracellular DNA-sensing pathways and discuss the future directions of this emerging field.

Interface dermatitis is a histopathological pattern mirroring a distinct cytotoxic immune response shared by a number of clinically diverse inflammatory skin diseases amongst which lichen planus and cutaneous lupus erythematosus are considered prototypic. Interface dermatitis is characterized by pronounced cytotoxic immune cell infiltration and necroptotic keratinocytes at the dermoepidermal junction. The initial inflammatory reaction is established by cytotoxic immune cells that express CXC chemokine receptor 3 and lesional keratinocytes that produce corresponding ligands, CXC motif ligands 9/10/11, recruiting the effector cells to the site of inflammation. During the resulting anti-epithelial attack, endogenous immune complexes and nucleic acids are released from perishing keratinocytes, which are then perceived by the innate immune system as danger signals. Keratinocytes express a distinct signature of pattern recognition receptors and binding of endogenous nucleic acid motifs to these receptors results in interferon-mediated immune responses and further enhancement of CXC chemokine receptor 3 ligand production. In this perspective article, we will discuss the role of innate nucleic acid sensing as a common mechanism in the perpetuation of clinically heterogeneous diseases featuring interface dermatitis based on own data and a review of the literature. Furthermore, we will introduce a keratinocyte-specific in vitro model of interface dermatitis as follows: Stimulation of human keratinocytes with endogenous nucleic acids alone and in combination with interferon gamma leads to pronounced production of distinct cytokines, which are essential in the pathogenesis of interface dermatitis. This experimental approach bears the capability to investigate potential therapeutics in this group of diseases with unmet medical need.

Nucleic acids (NAs) represent one of the most important classes of molecules recognized by the innate immune system. However, NAs are not limited to pathogens, but are also present within the host. As such, the immune system has evolved an elaborate set of pathogen recognition receptors (PRRs) that employ various strategies to recognize distinct types of NAs, while reliably distinguishing between self and nonself. The here-employed strategies encompass the positioning of NA-sensing PRRs in certain subcellular compartments that potentially come in contact with pathogens but not host NAs, the existence of counterregulatory measures that keep endogenous NAs below a certain threshold, and also the specific identification of certain nonself patterns. Here, we review recent advances in the molecular mechanisms of NA recognition by TLRs, RLRs, and the cGAS-STING axis. We highlight the differences in NA-PRR interfaces that confer specificity and selectivity toward an NA ligand, as well as the NA-dependent induced conformational changes required for signal transduction.

Besides their well known functions in storage and translation of information nucleic acids have emerged as a target of pattern recognition receptors that drive activation of innate immunity. Due to the paucity of building block monomers used in nucleic acids, discrimination of host and microbial nucleic acids as a means of self/foreign discrimination is a complicated task. Pattern recognition receptors rely on discrimination by sequence, structural features and spatial compartmentalization to differentiate microbial derived nucleic acids from host ones. Microbial nucleic acid detection is important for the sensing of infectious danger and initiating an immune response to microbial attack. Failures in the underlying recognitions systems can have severe consequences: thus, inefficient recognition of microbial nucleic acids may increase susceptibility to infectious diseases. On the other hand, excessive immune responses as a result of failed self/foreign discrimination are associated with autoimmune diseases. This review gives a general overview over the underlying concepts of nucleic acid sensing by Toll-like receptors. Within this general framework, we focus on bacterial RNA and synthetic RNA oligomers.

Microbial as well as endogenous nucleic acids are recognized by a group of endosomal Toll-like receptors TLR3, TLR7, TLR8 and TLR9. Recent discoveries significantly improved our understanding of molecular mechanism of their activation and their physiological role. Those include recognition of dsRNA through two nucleic acid binding sites of TLR3 ectodomain, activation of TLR9 by phosphodiester backbone of ssDNA, independent of the nucleotide sequence and phosphorothioate modified bonds, and the role of proteolysis in activation of TLR9. In addition, proteins that chaperone nucleic acids, such as HMGB1 or LL-37, have been described to mediate TLR activation. There is growing evidence that supports involvement of endosomal TLRs in a number of autoimmune diseases, suggesting a therapeutic potential of immunomodulatory endosomal TLR ligands. So far, inhibitory nucleic acids against TLR7, TLR8 and TLR9 as well as small compounds targeting downstream signal transduction of single or several endosomal TLRs have been reported. TLR-targeting drugs have been included in clinical trials as vaccine adjuvants or as therapeutic agents for the treatment of diseases, ranging from cancer, infections, asthma and allergy to autoimmune diseases.

SAM domain and HD domain-containing protein 1 (SAMHD1) is a dGTP-dependent triphosphohydrolase that degrades deoxyribonucleoside triphosphates (dNTPs) thereby limiting the intracellular dNTP pool. Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), an inflammatory encephalopathy that mimics congenital viral infection and that phenotypically overlaps with the autoimmune disease systemic lupus erythematosus. Both disorders are characterized by activation of the antiviral cytokine interferon-α initiated by immune recognition of self nucleic acids. Here we provide first direct evidence that SAMHD1 associates with endogenous nucleic acids in situ. Using fluorescence cross-correlation spectroscopy, we demonstrate that SAMHD1 specifically interacts with ssRNA and ssDNA and establish that nucleic acid-binding and formation of SAMHD1 complexes are mutually dependent. Interaction with nucleic acids and complex formation do not require the SAM domain, but are dependent on the HD domain and the C-terminal region of SAMHD1. We finally demonstrate that mutations associated with AGS exhibit both impaired nucleic acid-binding and complex formation implicating that interaction with nucleic acids is an integral aspect of SAMHD1 function.

Autoimmunity--promoting and stabilizing innate immunity 'UNWUCHT'.

SnapShot: Nucleic Acid Immune Sensors, Part 1

SnapShot: Nucleic Acid Immune Sensors, Part 2

Cellular noncoding RNA (ncRNA) transcription and regulation has only recently been systematically investigated. Extended transcriptomic analysis from recent studies has demonstrated abundant transcription of a set of ncRNAs preferentially within tumors, as opposed to normal tissue. Many of those ncRNA are associated with repeated regions of the genomes that in steady state are prone to regulation by epigenetic silencing. The contribution of the abnormal expression of this component of the dark matter genome to the oncogenic or antitumoral process remains unknown. In some cases, these tumor-associated ncRNAs have been associated with specific inflammatory transcriptomic regulation such as type I-IFN signatures, suggesting that the cell can sense these ncRNA and that they have potential immunostimulatory qualities. Derived from Eukaryotic cells possess a large panel of innate immune nucleic acid sensors, allowing the recognition of exogenous nucleic acids associated with microbial infections, but also of endogenous nucleic acids. Nucleic acid recognition is strongly associated with the antiviral innate immune response, autoimmune diseases development such as SLE and RA, but also inflammatory cancer development and anti-cancer immunity priming. The goal of this project was to identify novel endogenous immune modulators derived from tumor-associated ncRNAs that have immune stimulatory properties. Using mathematical methods adapted from physics statistics we previously analyzed the viral genome versus their host genomes and identified abnormal nucleotide motifs patterns. Using this novel approach to quantify transcriptome-wide motif usage in human and murine ncRNAs, we observed that, whereas most of the ncRNA are similar to the coding genome, an outlier subset of tumor-associated ncRNAs, typically of recent evolutionary origin, has motif usage more associated with pathogen derived RNA. Previous extended analysis of viral genomes highlighted that such motif patterns are strongly associated with immunogenic properties and absence of host-pathogen adaptation. We have now demonstrated that those ncRNA function directly as immunostimulatory “self-agonists” and can be classified as danger associated molecular patterns (DAMPS). A key subset of these ncRNA directly activate cells of the mononuclear phagocytic system (MPS), inducing pro-inflammatory cytokines in a MYD88 and UNC93b-dependent and possibly TLR8-dependant manner. Some of these ncRNA are also upregulated in specific tumor cell lines when they proliferate in spheroids. We have shown that the high level of ncRNA expression also correlates with immunogenic properties related to the RNA extracted from those tumor spheroids versus their 2D counterparts. We therefore propose that a part of the innate response in tumors could initiate from direct, likely extrinsic, interaction of immunogenic ncRNAs expressed in cancer cells, with innate pattern recognition receptors on APC. We are extensively characterizing the innate immune pathways involved in their sensing using forward genetic strategies, biochemistry and cellular biology techniques. We are also characterizing their intrinsic functions at the cellular level and to understand their function in the tumor microenvironment. The pattern of expression in different cancer models is under evaluation to establish their relevancy as prognostic and therapeutic strategies, or as biomarkers in addition to characterizing their relevancy as new immunotherapeutic adjuvants. In conclusion, we are characterizing an epigenome guardian function related to the newly discovered immunogenic properties of those non-coding RNA. Deeper analysis and refinement of our computational analysis will allow us to associate specific RNA features to their immunogenic properties in cancer. Citation Format: Antoine Tanne, Luciana Muniz, David Ting, Arnold Levine, Nina Bhardwaj, Benjamin Greenbaum. Unraveling predicted immunomodulatory effects of novel cancer-associated noncoding RNAs. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A077.

Microbial nucleic acids are major signatures of invading pathogens, and their recognition by various host pattern recognition receptors (PRRs) represents the first step toward an efficient innate immune response to clear the pathogens. The nucleic acid-sensing PRRs are localized at the plasma membrane, the cytosol, and/or various cellular organelles. Sensing of nucleic acids and signaling by PRRs involve recruitment of distinct signaling components, and PRRs are intensively regulated by cellular organelle trafficking. PRR-mediated innate immune responses are also heavily regulated by posttranslational modifications, including phosphorylation, polyubiquitination, sumoylation, and glutamylation. In this review, we focus on our current understanding of recognition of microbial nucleic acid by PRRs, particularly on their regulation by organelle trafficking and posttranslational modifications. We also discuss how sensing of self nucleic acids and dysregulation of PRR-mediated signaling lead to serious human diseases.

Toll-like receptors (TLRs), first identified as pattern recognition receptors, are now recognized to serve as a key interface between innate and adaptive immunity. Systemic lupus erythematosus (SLE) is characterized by both continuous and cyclic stimulation of the innate and adaptive immune system by endogenous nucleic acids released from apoptotic or necrotic cells. TLR7 and TLR9 function as innate sensors of viral infection as their ligands are ssRNA and dsDNA, respectively. Recognition of self nucleic acids by endosomal TLRs in B cells and pDCs is thought to be an important step in the pathogenesis of SLE, generating anti-nuclear antibodies and producing type I IFN. In this review, we take a specific look at how TLR7, non-coding RNA, and SSA/Ro60 can contribute to clinical autoimmunity and organ damage in the context of neonatal lupus (NL). Although 15 times less common than SLE, NL provides a unique opportunity to study two different aspects of autoimmunity: passively acquired tissue injury in a developing fetus and clinical progression of disease in an asymptomatic mother found to have anti-Ro60 autoantibodies only after identification of heart block/rash in a child. Finally, we discuss hydroxychloroquine (HCQ) use by asymptomatic subjects which may forestall the clinical expression of autoimmunity.

FRI0274 Hydroxychloroquine down-regulates interferon-alfa elevation through tlr-9 recognition of nucleotides which is irresponsive to glucocorticoid