Limiting of the Innate Immune Response by SF3A-Dependent Control of MyD88 Alternative mRNA Splicing

Abstract

Controlling infectious disease without inducing unwanted inflammatory disease requires proper regulation of the innate immune response. Thus, innate immunity needs to be activated when needed during an infection, but must be limited to prevent damage. To accomplish this, negative regulators of innate immunity limit the response. Here we investigate one such negative regulator encoded by an alternative splice form of MyD88. MyD88 mRNA exists in two alternative splice forms: MyD88L, a long form that encodes a protein that activates innate immunity by transducing Toll-like receptor (TLR) signals; and a short form that encodes a different protein, MyD88S, that inhibits the response. We find that MyD88S levels regulate the extent of inflammatory cytokine production in murine macrophages. MyD88S mRNA levels are regulated by the SF3A and SF3B mRNA splicing complexes, and these mRNA splicing complexes function with TLR signaling to regulate MyD88S production. Thus, the SF3A mRNA splicing complex controls production of a negative regulator of TLR signaling that limits the extent of innate immune activation.

METTL3 regulates alternative splicing of MyD88 upon the lipopolysaccharide‐induced inflammatory response in human dental pulp cells

“…In our RNA sequencing data, exon skipping accounted for 39.13% of the total alternative splicing events in HDPCs. A previous study reported that the alternative splicing of MyD88 affects the inflammatory response 23. The splicing analysis herein revealed that MyD88 produced two isoforms, namely MyD88L and MyD88S, and that the expression of MyD88S, which lacks the second exon, was significantly increased by 1.3‐fold in the siMETTL3 group compared with that in the control group in LPS‐treated HDPCs (Table 2).…”

“…For the MyD88S‐specific primers, we used a reverse primer that spanned exons 3 to 1 and a forward primer that annealed to exon 1. For the primers that amplify both MyD88L and MyD88S, we used primers that annealed to exons 1 and 3 23. Using two sets of primers, we found that METTL3 inhibition did not significantly alter MyD88L mRNA levels but did significantly increase MyD88S mRNA levels (Fig.…”

“…Alternative splicing can regulate intracellular signalling and intercellular communication through the expression of diverse isoforms of cytokines, cytokine receptors, kinases, phosphatases and adaptor proteins 58. Myd88s, a splice variant of MyD88 lacking the second exon, can function as a negative regulator of TLR signalling and limit the extent of innate immune activation 23. METTL3 localizes predominantly in nuclear speckles, which are sites of mRNA splicing and storage 38.…”

“…MyD88 is encoded by an mRNA with five exons (MyD88L) and produces different splice variants through alternative splicing 21. A shorter MyD88 mRNA (MyD88S), lacking the second exon, exerts a dominant‐negative effect on LPS‐induced, TLR4‐mediated signalling pathways and inhibits inflammatory cytokine production 22, 23.…”

Alternatively Spliced Myeloid Differentiation Protein-2 Inhibits TLR4-Mediated Lung Inflammation

“…Several negative regulatory pathways have been reported, including proteins that bind an inactivate TLR signaling (19–24); microRNAs that regulate expression of TLR signaling genes (25); and of innate immune genes such as IRAK2, TLR4 and MyD88 that inhibit TLR signaling Another method of down regulating TLR4 signaling is to produce an inhibitory isoform by alternatively splicing specific genes encoding essential signaling components such as IRAK2, TLR3, MD2, and MyD88 (26–30). For instance, an alternatively spliced short form of MyD88 acts as a negative regulator of IL-1R/TLR/MyD88-triggered signals, leading to transcriptionally controlled negative regulation of innate immune responses (31, 32). …”