ZBP1-dependent inflammatory cell death, PANoptosis, and cytokine storm disrupt IFN therapeutic efficacy during coronavirus infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), continues to cause substantial morbidity and mortality in the ongoing global pandemic. Understanding the fundamental mechanisms that govern innate immune and inflammatory responses during SARS-CoV-2 infection is critical for developing effective therapeutic strategies. Whereas interferon (IFN)-based therapies are generally expected to be beneficial during viral infection, clinical trials in COVID-19 have shown limited efficacy and potential detrimental effects of IFN treatment during SARS-CoV-2 infection. However, the underlying mechanisms responsible for this failure remain unknown. In this study, we found that IFN induced Z-DNA-binding protein 1 (ZBP1)-mediated inflammatory cell death, PANoptosis, in human and murine macrophages and in the lungs of mice infected with β-coronaviruses, including SARS-CoV-2 and mouse hepatitis virus (MHV). In patients with COVID-19, expression of the innate immune sensor ZBP1 was increased in immune cells from those who succumbed to the disease compared with those who recovered, further suggesting a link between ZBP1 and pathology. In mice, IFN-β treatment after β-coronavirus infection increased lethality, and genetic deletion of Zbp1 or its Zα domain suppressed cell death and protected the mice from IFN-mediated lethality during β-coronavirus infection. Overall, our results identify that ZBP1 induced during coronavirus infection limits the efficacy of IFN therapy by driving inflammatory cell death and lethality. Therefore, inhibiting ZBP1 activity may improve the efficacy of IFN therapy, paving the way for the development of new and critically needed therapeutics for COVID-19 as well as other infections and inflammatory conditions where IFN-mediated cell death and pathology occur.

Z-DNA binding protein 1 (ZBP1) is an innate sensor of Influenza vRNPs and activates programmed cell death and assembly of NLRP3 inflammasome

Influenza A virus (IAV) infection triggers pulmonary epithelial cell death and inflammation which promote bronchioalveolar tissue damage and failure of lung function. However, the mechanism of IAV induced cell death and inflammation remains unclear. RIP homotypic interaction motif (RHIM) has evolved to play critical role in cell death and inflammation. Z-DNA binding protein 1 (ZBP1/DAI) is unique among RHIM-containing proteins since it has additional Za nucleic acid binding domains. Although ZBP1 domain architecture suggests its function as nucleic acid sensor, its precise physiological role is not established.

We discovered that ZBP1 is a central activator of IAV induced programmed cell death and NLRP3 inflammasome activation in both immune and non-immune cells. Mechanistically, ZBP1 senses ribonucleoprotein complexes (vRNPs) of IAV and engage RIPK3-caspase-8 dependent apoptosis, necroptosis and NLRP3 inflammasome assembly. ZBP1 also drives RIPK1 dependent secretion of TNF and IL-6 cytokines after IAV infection. We also discovered that apical activation of RIG-I/MAVS/IFNAR signaling licenses ZBP1 upregulation and activation. In contrast to other RNA viruses, IAV replicates inside the nucleus. Accordingly, we observed localization of ZBP1 in the nucleus suggesting its role in sensing IAV inside the nucleus. Strikingly, we also found that ZBP1 undergoes ubiquitination in response to IAV infection to assemble cell death signaling complexes. In IAV infected mice, ZBP1 induces cell death in lung epithelial cells and its absence conferred better survival advantage, despite high viral titers in the lung. Overall, our work demonstrates the central role of ZBP1 in sensing IAV infection to trigger cell death and inflammation.

Molecular characterization of LC3-associated phagocytosis reveals distinct roles for Rubicon, NOX2 and autophagy proteins

LC3-associated phagocytosis (LAP) is a process wherein elements of autophagy conjugate LC3 to phagosomal membranes. We characterize the molecular requirements for LAP, and identify Rubicon as being required for LAP but not autophagy. Rubicon is recruited to LAPosomes and is required for the activity of a Class III PI(3)K complex containing UVRAG but lacking ATG14 and Ambra1. This allows for the sustained localization of PtdIns(3)P, which is critical for recruitment of downstream autophagic proteins and stabilization of the NOX2 complex to produce reactive oxygen species. Both PtdIns(3)P and reactive oxygen species are required for conjugation of LC3 to LAPosomes and subsequent association with LAMP1(+) lysosomes. LAP is induced by engulfment of Aspergillus fumigatus, a fungal pathogen that commonly afflicts immunocompromised hosts, and is required for its optimal clearance in vivo. Therefore, we have identified molecules that distinguish LAP from canonical autophagy, thereby elucidating the importance of LAP in response to A. fumigatus infection.

PARP-1 regulates pro-inflammatory cell death (34.13)

PARP-1(poly (ADP-ribose) polymerase 1), an enzyme involved in DNA repair, is a nuclear chromatin associated multifunctional protein and belongs to a large family of enzymes that can synthesize long branched polymers of ADP-ribose units by using NAD+( Nicotinamide adenine dinucleotide) as the substrate. DNA strand nicks and breaks activate PARP-1 and the activated enzyme makes branched chains of up to 200 ADP-ribose units and adds covalently to various nuclear proteins such as histones and especially PARP-1 itself. PARP-1 has been shown to play a major role in a number of pathophysiological situations. In this study, we show that cytokine and chemokine profiles from PARP-WT and -KO BMDM showed no significant differences. However, IL1-β secretion is reduced in PARP-1 deficient macrophages, suggesting a role for PARP-1 in pro-inflammatory signaling. PARP-1 deficient macrophages had displayed prominent protection from pro-inflammatory cell death in response to LPS+ATP stimuli. Together, these results demonstrate that PARP-1 contribute to the pathophysiology by regulating the pro-inflammatory cytokine profiles.