Nucleic Acid Sensing and Systemic Lupus Erythematosus: The Danger of Self

Pathogens carry conserved features, distinct from those of mammals, which alert the mammalian immune system to emerging infection. Receptors for these features include sensors for microbial nucleic acids that display modifications rarely found in the healthy host (1). Not all such modifications, however, are exclusive to microbes. For example, unmethylated CpG motifs typical of bacterial DNA also exist in promoter regions of the mammalian genome (2). Other motifs, such as oxidized mitochondrial DNA or DNA sequestered in neutrophil extracellular traps, are generated during tissue injury and are potent stimulators of innate immunity (3–5). Furthermore, whereas some nucleic acid sensors, such as retinoic acid–inducible gene-I (RIG-I)-like receptors, preferentially bind to nucleic acids with microbial features (6, 7), others such as the DNA sensor cyclic GMP-AMP synthase (cGAS) bind to dsDNA regardless of its sequence (8). This promiscuity imposes a risk for breaching tolerance and eliciting disease, particularly systemic lupus erythematosus (SLE), a multisystem autoimmune disease characterized by the production of autoantibodies to nucleic acids.

In this Pillars of Immunology article, Leadbetter et al. (9) introduced a paradigm shift in our understanding of SLE by showing that dual engagement of the BCR and endosomal TLRs by nucleic acid–containing immune complexes activates autoreactive B cells. Based on the observation that immune complexes containing DNA are more potent B cell activators than those containing hapten Ags, Leadbetter et al. searched for a DNA sensing coreceptor. Deletion of MyD88, a TLR adapter that is essential for recognition of bacterial CpG DNA (10), confirmed that the coreceptor is a TLR. It was discovered that recognition of bacterial DNA by TLR9 requires endocytosis and endosomal maturation, suggesting that the DNA is transported into TLR9-containing intracellular vesicles (11). Leadbetter et al. found that inhibition of endosomal acidification blocked B cell activation by DNA-containing immune complexes, thereby implicating an endosomal TLR, most likely TLR9, as the culprit in recognizing self-DNA and promoting autoimmunity. In subsequent work, they showed that hypomethylated mammalian DNA is enriched in apoptotic cells and strongly stimulates TLR9 (12). They were also prescient in suggesting that other autoantigens might signal through different TLRs, although they could not anticipate the vast array of nucleic acid disposal mechanisms and sensing receptors that were yet to be discovered.

Within a few years, the same group reported that coengagement of the BCR and the RNA sensor TLR7 enhanced B cell activation by RNA-containing autoantigens (13) and that deletion of MyD88 in B cells abrogated autoantibody production and clinical lupus in a mouse model (14). This finding was followed shortly thereafter by the discovery that the Y-linked autoimmune accelerating (Yaa) locus encompasses a segment of the X chromosome containing Tlr7 and that introduction of four to eight copies of Tlr7 into B cells of wild-type mice induces a robust lupus-like disease (15, 16). Discovery of BAFF, a B cell survival cytokine, provided further understanding of this process: induction of BAFF receptors by TLR activation enhances survival of autoreactive B cells that endocytose nucleic acid–containing material through their BCR (17).

Meanwhile, parallel work identified multiple cytoplasmic sensors for RNA and DNA. Signaling pathways triggered by these sensors induce inflammatory cytokines and type 1 IFNs and can prime the inflammasome pathway or even cause cell death (18, 19). Gain-of-function mutations of nucleic acid sensing pathways were identified in humans and the term “interferonopathy” was coined to describe the severe syndromes, some with lupus-like features, caused by these mutations (20). Concurrently, several groups identified an “interferon signature” in PBMCs of most SLE patients, and genome-wide association studies suggested that polymorphisms of genes in the type1 IFN pathway are associated with SLE (21, 22). These studies, in sum, have led to a current view of lupus as a disease in which excess endogenous nucleic acids trick the host into sensing that there is a persistent infection or injury. Regardless of the initiating cause, amplification of the autoreactive response ensues as endogenous nucleic acids are delivered in the form of nucleic acid–containing immune complexes or debris to intracellular compartments, including the endosomes, where they encounter TLRs in the manner first demonstrated by Leadbetter et al. (9).

These findings inform us that engagement of the same nucleic acid sensing system that grants host defense against microbes may breach immune tolerance when we are exposed to infections and cellular debris during tissue damage and remodeling. Homeostatic control is exercised by the presence of nucleases that process nucleic acids, thereby limiting their access to nucleic acid sensors (23) as well as by the preferential stimulatory activity of pathogen-specific chemical modifications (1). However, perturbations, whether genetic or induced, that cause excess production, atypical chemical modifications, cytosolic entry, or decreased disposal of self-nucleic acids, or that interfere with processing and subcellular translocation of their receptors, can tip the balance toward autoimmunity.

Although a simplistic view of therapeutic intervention for SLE would then be to decrease nucleic acid access to sensing receptors, block receptor activation and downstream signaling pathways, or inhibit the cytokine-driven inflammatory response, the hurdles have been substantial. Neutralization of type 1 IFN has some benefits in patients with SLE, but it is only moderately effective (24), indicating that other pathways contribute to active disease. BAFF inhibition, although a welcome addition to the SLE armamentarium, has similar moderate efficacy (25). Other approaches that are currently in development include targeting of sensors, adapter proteins, and downstream transcription factors. The main challenge inherent in these approaches is that of immunosuppression: the dangers associated with loss of function in components of the nucleic sensing pathway, or low levels of type 1 IFN, were only too obvious during the recent SARS-CoV-2 pandemic (26). Recognition of endogenous retroviral RNA by cytosolic receptors is also likely to be beneficial in protection against cancer. An alternative and potentially less toxic approach is to deliver nucleases to decrease the inciting load (27, 28) or to prevent mitochondrial escape from cells (29). Here the challenge lies in the redundancy of this system, the cytoplasmic location of some nucleases, and the multiple sources of potentially pathogenic nucleic acids, some of which are degraded only by specific nucleases or are resistant to degradation (3–5, 30).

As therapeutic development continues along these lines, important conundrums must be solved to fully harness the therapeutic possibilities offered by the nucleic acid sensing system. Although deficiency of the TLR adapter MyD88 in B cells abrogates lupus in mice (14), further studies have uncovered unexpected protective functions of the nucleic acid sensing machinery, as exemplified by the exacerbation of lupus in mice deficient in TLR9, nucleotide-binding oligomerization domain (NOD)-leucine–rich repeat, and pyrin domain-containing protein 3 (NLRP3), cGAS, and stimulator of IFN genes (STING) (31–34). Thus, it is clear that under some circumstances, nucleic acid recognition is anti-inflammatory and imposes tolerance in a noninfected host. How the various receptors modulate tolerance versus inflammation during different disease stages, and in particular organs, remains to be fully explained.

Despite the lag in translation, the fundamental observations made in this Pillars of Immunology article heralded 20 y of remarkable progress in a new field. The relevance of nucleic acid sensing pathways has extended far beyond their contribution to infection control and autoreactivity, now reaching into the realms of cancer biology, “inflammaging,” and human longevity (9, 35). Thus, the considerations related to therapeutics are far reaching and will require better understanding of the level of specificity needed to modulate these pathways safely.