PIKfyve, a Class III Lipid Kinase, Is Required for TLR-Induced Type I IFN Production via Modulation of ATF3

Abstract

Type I IFN plays a key role in antiviral responses. It also has been shown that deregulation of type I IFN expression following abnormal activation of TLRs contributes to the pathogenesis of systemic lupus erythematosus. In this study, we find that PIKfyve, a class III lipid kinase, is required for endolysosomal TLR-induced expression of type I IFN in mouse and human cells. PIKfyve binds to phosphatidylinositol 3-phosphate and synthesizes phosphatidylinositol 3,5-bisphosphate, and plays a critical role in endolysosomal trafficking. However, PIKfyve modulates type I IFN production via mechanisms independent of receptor and ligand trafficking in endolysosomes. Instead, pharmacological or genetic inactivation of PIKfyve rapidly induces expression of the transcription repressor ATF3, which is necessary and sufficient for suppression of type I IFN expression by binding to its promoter and blocking its transcription. Thus, we have uncovered a novel phosphoinositide-mediated regulatory mechanism that controls TLR-mediated induction of type I IFN, which may provide a new therapeutic indication for the PIKfyve inhibitor.

ATF3 Is a Key Regulator of Macrophage IFN Responses

“…These findings are consistent with a recent study showing that TLR-induced type I IFN levels were reduced by a PIKfyve inhibitor in RAW264.7 murine macrophage cells via induction of ATF3 (21). Immune cells can rapidly respond to low systemic concentrations of type I IFNs, which are constitutively maintained under homeostatic conditions by the commensal microflora (48,49).…”

“…Additionally, virus infection induces nucleosome remodeling of the Ifnb1 promoter (via histone acetyl transferases, as well as the SWI/SNF chromatin remodeling complex), allowing for increased transcription (56). Consistent with the role of ATF3 as a transcriptional repressor, two recent studies suggested that ATF3 has binding sites within the Ifnb1 promoter (21,30). Our ChIP-seq dataset (26) has identified an ATF3 binding site at a regulatory element 15 kbp upstream of the Ifnb1 TSS, which showed significant and specific enrichment of ATF3 under basal conditions (Fig.…”

“…ATF3 is induced during TLR-dependent immune responses and negatively regulates numerous proinflammatory cytokines (e.g., IL-6, IL-12p40) and chemokines (e.g., MIP-1b), and, as such, mice deficient in ATF3 are more susceptible to endotoxin shock owing to excessive cytokine production (16)(17)(18)(19). ATF3 can also modulate the expression of IFN-g in NK cells during the antiviral response to murine CMV infection (20), and it has recently been shown to directly regulate TLR-induced IFN-b expression following its induction by an inhibitor of the class III lipid kinase, PIKfyve (21). Whereas the ability of ATF3 to repress proinflammatory cytokine expression is firmly established, its role in regulating type I IFN responses requires further investigation.…”

The Fab1/PIKfyve Phosphoinositide Phosphate Kinase Is Not Necessary to Maintain the pH of Lysosomes and of the Yeast Vacuole

“…Second, drug-treated mammalian cells retain small levels of PtdIns(3,5)P 2 that may suffice to maintain acidic lysosomes. Yet, at these low levels of PtdIns(3,5)P 2 , many other defects are observed including lysosome swelling, phagosome maturation arrest, cytokine production impairment, and trafficking inhibition (38,39,51). Third, we do not exclude the possibility that extremely enlarged lysosomes may be more prone to alkalinization, as suggested elsewhere (31).…”

REPA: Applying Pathway Analysis to Genome-Wide Transcription Factor Binding Data

“…Out of those 37 TFs predicted to regulate genes in the SLE pathway, we found literature support for 13 (or 35%). The TFs associated by REPA with SLE are the following (supporting literature is referred to after the corresponding TF): ATF2, ATF3 [46], BCLAF1, CBX3, CEBPB, CEBPD, ETS1 [47], FOS [45], FOXM1, GR [48], HEY1, INI1, JUND [49], MBD4 [50], MTA3, MYBL2, NFATC1 [49], NFIC, P300 [51], PAX5 [52], PML, POL2, POU2F2, RUNX3 [53], RXRA, SIN3AK20, SP1 [54], SP4, STAT5A, TAF1, TAF7, TBP [55], TCF12, TCF3, TEAD4, YY1 [56], and ZBTB33.…”