Insights into the SARS-CoV-2-Mediated Alteration in the Stress Granule Protein Regulatory Networks in Humans

The rapidly and constantly evolving coronavirus, SARS-CoV-2, imposes a great threat to human health causing severe lung disease and significant mortality. Cytoplasmic stress granules (SGs) exert anti-viral activities due to their involvement in translation inhibition and innate immune signaling. SARS-CoV-2 sequesters important SG nucleator proteins and impairs SG formation, thus evading the host response for efficient viral replication. However, the significance of SGs in COVID-19 infection remains elusive. In this study, we utilize a protein-protein interaction network approach to systematically dissect the crosstalk of human post-translational regulatory networks governed by SG proteins due to SARS-CoV-2 infection. We uncovered that 116 human SG proteins directly interact with SARS-CoV-2 proteins and are involved in 430 different brain disorders including COVID-19. Further, we performed gene set enrichment analysis to identify the drugs against three important key SG proteins (DYNC1H1, DCTN1, and LMNA) and also looked for potential microRNAs (miRNAs) targeting these proteins. We identified bexarotene as a potential drug molecule and miRNAs, hsa-miR-615-3p, hsa-miR-221-3p, and hsa-miR-124-3p as potential candidates for the treatment of COVID-19 and associated manifestations.

Impact Of Adaptive Natural Killer Cells, KLRC2 Genotype And Cytomegalovirus Reactivation On Late Mortality In Patients With Severe Covid-19 Lung Disease

Objective: COVID-19 infection results in severe lung disease in a small but significant number of infected patients. The etiopathogenesis in a subset of such patients, who continue to have progressive pulmonary disease following virus clearance remains unexplored. Methods: We investigated the role of NKG2C+/NKG2A- adaptive natural killer (ANK) cells, KLRC2 genotype and cytomegalovirus reactivation in 22 such patients. Results: The median duration of virus positivity was 23 days and the median duration of hospitalisation was 48 days. The overall survival at 60 days in this group was 50%. Older age and comorbidities impacted survival negatively. CMV viremia was documented in 11 patients, with a survival of 25% vs 80% in those without viremia with viral load correlating with mortality. ANK cells were markedly depressed in all patients at day 15. However, persistently low ANK cells at 30 days along with an inversely high NKG2C-/NKG2A+ inhibitory NK cells significantly correlated with high CMV viremia as well as mortality, irrespective of KLRC2 genotype. Day 30 ANK cells were significantly lower in KLRC2 deletion group. IFN-gamma and Perforin release were severely compromised in all patients at day +15, with significant improvement in the survivors at day +30, but not in those with adverse outcome. Conclusion: Patients with severe lung disease even after negative SARS-CoV-2 status, with persistently reduced and functionally compromised ANK cells, are more likely to have CMV reactivation and an adverse outcome, independent of KLRC2 genotype.

Emerging Genotype-Phenotype Relationships in Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a rare inherited condition affecting motile cilia and leading to organ laterality defects, recurrent sino-pulmonary infections, bronchiectasis, and severe lung disease. Research over the past twenty years has revealed variability in clinical presentations, ranging from mild to more severe phenotypes. Genotype and phenotype relationships have emerged. The increasing availability of genetic panels for PCD continue to redefine these genotype-phenotype relationships and reveal milder forms of disease that had previously gone unrecognized.

SARS-CoV-2 nucleocapsid protein impairs stress granule formation to promote viral replication

The newly emerging coronavirus SARS-CoV-2 causes severe lung disease and substantial mortality. How the virus evades host defense for efficient replication is not fully understood. In this report, we found that the SARS-CoV-2 nucleocapsid protein (NP) impaired stress granule (SG) formation induced by viral RNA. SARS-CoV-2 NP associated with the protein kinase PKR after dsRNA stimulation. SARS-CoV-2 NP did not affect dsRNA-induced PKR oligomerization, but impaired dsRNA-induced PKR phosphorylation (a hallmark of its activation) as well as SG formation. SARS-CoV-2 NP also targeted the SG-nucleating protein G3BP1 and impaired G3BP1-mediated SG formation. Deficiency of PKR or G3BP1 impaired dsRNA-triggered SG formation and increased SARS-CoV-2 replication. The NP of SARS-CoV also targeted both PKR and G3BP1 to impair dsRNA-induced SG formation, whereas the NP of MERS-CoV targeted PKR, but not G3BP1 for the impairment. Our findings suggest that SARS-CoV-2 NP promotes viral replication by impairing formation of antiviral SGs, and reveal a conserved mechanism on evasion of host antiviral responses by highly pathogenic human betacoronaviruses.

Marine Mammals and Respiration: Evidence of Poor Pulmonary Health in Bottlenose Dolphins Following the Deepwater Horizon Oil Spill

ABSTRACT The Deepwater Horizon (DWH) disaster resulted in large-scale contamination of bays, sounds, and estuaries in the northern Gulf of Mexico (GoM), home to multiple stocks of bottlenose dolphins. Inhalation, direct aspiration, ingestion with subsequent aspiration, and dermal absorption of oil and its toxic components were all considered possible routes of exposure for dolphins living within the oil spill footprint. To determine if dolphins were adversely impacted, capture-release health assessments were performed in heavily-oiled Barataria Bay (BB), Louisiana, and in Sarasota Bay (SB), Florida, a comparison site with no DWH oil contamination. Initial studies were conducted as part of a Natural Resource Damage Assessment (2011–2014), with follow-on studies supported by the Gulf of Mexico Research Initiative (2016–2018). To specifically evaluate pulmonary health, transthoracic ultrasound techniques previously developed for managed dolphins were applied to wild dolphins. Results showed that BB dolphins were ~5 times more likely to have moderate to severe lung disease than SB dolphins in 2011, the year following the spill. Concurrent pathology investigations of dead dolphins in the northern GoM reported similar pulmonary findings. In 2013 and 2014, moderate to severe lung disease persisted among BB dolphins, and remained elevated relative to the prevalence at the SB comparison site. More recent live animal health assessments (2016–2018) showed long-term persistence and potential worsening of moderate to severe lung disease in BB dolphins, specifically in animals alive during the oil spill (prevalence of 0.20, 0.35, and 0.55 in 2016, 2017, and 2018, respectively). Long-term monitoring of dolphin populations is critical to fully understand the potential for and timeline of individual and population recovery from the impacts of a large-scale oil spill event, as well as the cost-benefit trade-offs for restoration activities. In particular, BB dolphins provide valuable insight into the long-lasting effects of oil and oil-related contaminants on animal, human, and ecosystem health.

A SARS CoV-2 nucleocapsid vaccine protects against distal viral dissemination

The SARS CoV-2 pandemic has killed millions of people. This viral infection can also result in substantial morbidity, including respiratory insufficiency and neurological manifestations, such as loss of smell and psychiatric diseases. Most SARS CoV-2 vaccines are based on the spike antigen, and although they have shown extraordinary efficacy at preventing severe lung disease and death, they do not always confer sterilizing immune protection. We performed studies in K18-hACE2 mice to evaluate whether the efficacy of SARS CoV-2 vaccines could be augmented by incorporating nucleocapsid as a vaccine antigen. We vaccinated mice with adenovirus-based vaccines encoding spike antigen alone, nucleocapsid antigen alone, or combined spike and nucleocapsid antigens. Mice were then challenged intranasally with SARS CoV-2, and acute viral loads were quantified at a proximal site of infection (lung) and a distal site of infection (brain). Interestingly, the spike-based vaccine conferred acute protection in the lung, but not in the brain. The spike-based vaccine conferred acute protection in the brain only if combined with the nucleocapsid-based vaccine. These findings suggest that nucleocapsid-specific immunity is important for the distal control of SARS CoV-2, warranting the inclusion of nucleocapsid in next-generation COVID-19 vaccines.

Case Report: Novel SAVI-Causing Variants in STING1 Expand the Clinical Disease Spectrum and Suggest a Refined Model of STING Activation

Gain-of-function mutations in STING1 cause the monogenic interferonopathy, SAVI, which presents with early-onset systemic inflammation, cold-induced vasculopathy and/or interstitial lung disease. We identified 5 patients (3 kindreds) with predominantly peripheral vascular disease who harbor 3 novel STING1 variants, p.H72N, p.F153V, and p.G158A. The latter two were predicted by a previous cryo-EM structure model to cause STING autoactivation. The p.H72N variant in exon 3, however, is the first SAVI-causing variant in the transmembrane linker region. Mutations of p.H72 into either charged residues or hydrophobic residues all led to dramatic loss of cGAMP response, while amino acid changes to residues with polar side chains were able to maintain the wild type status. Structural modeling of these novel mutations suggests a reconciled model of STING activation, which indicates that STING dimers can oligomerize in both open and closed states which would obliviate a high-energy 180° rotation of the ligand-binding head for STING activation, thus refining existing models of STING activation. Quantitative comparison showed that an overall lower autoactivating potential of the disease-causing mutations was associated with less severe lung disease, more severe peripheral vascular disease and the absence of a robust interferon signature in whole blood. Our findings are important in understanding genotype-phenotype correlation, designing targeted STING inhibitors and in dissecting differentially activated pathways downstream of different STING mutations.

Intrahepatic cholangiocarcinoma in a non-cirrhotic liver in a patient with homozygous ZZ alpha-1 antitrypsin deficiency

Alpha-1 antitrypsin (AAT) deficiency, which is an under-recognised metabolic genetic disorder, is known to cause severe lung disease and liver cirrhosis in about 10%–15% of cases. Patients with AAT deficiency are at a higher risk for developing hepatocellular carcinoma, both in cirrhotic and in non-cirrhotic livers. In this case report, a 48-year-old woman with homozygous ZZ AAT deficiency presented with abdominal pain, and by imaging, an abnormal area in the liver was found. The initial differential diagnosis consisted of benign abnormalities but a malignancy could not be ruled out. Finally, this abnormality turned out to be an intrahepatic cholangiocarcinoma (iCCA) in a non-cirrhotic liver. Since this type of tumour has been very infrequently described to be associated with AAT deficiency, the question remains whether alpha-1 trypsin accumulation in the hepatocytes was responsible for the development of iCCA. However, other associated factors for developing an iCCA were ruled out.