Modifications in SARS-CoV-2 N Linker Region Regulate RNA Interactions and Phase Separation

The N protein of the SARS-CoV-2 virion is critical for viral genome packaging via RNA binding and regulation of viral transcription at the replication-transcription complex (RTC). The N protein can be divided into five main domains, and the central region is the linker, which is predicted to be primarily disordered and has not been heavily studied. The linker is Serine-Arginine Rich, which is phosphorylated at multiple sites by host kinases during infection, thereby promoting the N protein's role in viral transcription. Phosphorylation is a critical process for the regulation of many cellular processes and can provide recognition sites for binding complexes. In a study that examined the recognition of the SARS-CoV-2 N protein by the human 14-3-3 protein, the linker was found to contain critical phosphosites for 14-3-3 binding. The goals of this project are to determine the structure, dynamics, and RNA interactions of the Serine-Arginine Rich linker region. To accomplish this, we performed Nuclear Magnetic Resonance spectroscopy (NMR) experiments to analyze the structure of the linker region of the N protein and its ability to bind viral RNA. NMR confirms predictions that the linker is not entirely unstructured and it is able to bind RNA. The linker region of the N protein with phosphoserine incorporated at S188 was also examined via an NMR titration experiment with 1-1000 RNA. Compared to wild type, the incorporation of phosphorylation decreases binding. Other biophysical techniques such as Analytical Ultracentrifugation (AUC) and Multi-Angle Light Scattering (MALS) are used to identify the association state of the linker and the size of the resulting protein-RNA complex. We are currently working to biophysically characterize the structure, dynamics, and viral RNA binding ability of a mutation found in the Delta and Omicron variants: the R203M linker, which have been shown to enhance viral infectivity. This work was supported by the NSF EAGER grant NSF/ MCB 2034446 and URSA Engage. Support to facilities includes the Oregon State University NMR Facility funded in part by NIH, HEI Grant 1S10OD018518, and by the M. J. Murdock Charitable Trust grant # 2014162.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

OA Biology

Purpose: The field of osteoarthritis (OA) biology is rapidly evolving and brilliant progress has been made this year as well. Methods: Landmark studies of OA biology published in 2021 and early 2022 were selected through PubMed searches and classified by their molecular mechanisms, and it was largely divided into the intra-cellular mechanisms and the inter-compartment or inter-cellular interaction in OA progression. Results: The intra-cellular mechanisms involving OA progression included 1) Piezo1/TRPV4-mediated calcium signaling, 2) low grade inflammation by TLR-CD14-LBP complex and IKKβ-NFkB signaling, 3) PGRN/TNFR2/14-3-3ε/Elk-1 anabolic cascade, 4) G protein-coupled receptor (GPCR) signaling, 5) mechanical loading-cilia/Ift88-hedgehog signaling, 6) mitochondrial fission by ERK1/2-DRP1 pathway, and 7) hypoxia-DOT1L-H3K79 methylation pathway. The studies on inter-compartment or inter-cellular interaction in OA progression included the following subjects: 1) the anabolic role of Lubricin, a proteoglycan from superficial zone cells, 2) osteoclast-chondrocyte interaction via exosomal miRNA and sphingosine 1-phosphate (S1P), 3) αV integrin-mediated TGFβ activation by mechanical loading, 4) TGFβ-mediated suppression of sclerostin in osteocytes, 5) catabolic role of Flightless I as a DAMPs-triggering molecule, and 6) catabolic role of paracrine signaling from fat. Conclusions: Despite the disastrous Covid-19 pandemic situation, many outstanding studies have expanded the boundary of OA biology. They give us not only critical insight on pathophysiology, but also clue for the treatment of OA.

A CLASSIC CASE OF CREUTZFELDT-JAKOB DISEASE (CJD)

CASE: A 64-year-old woman was brought in by husband for inability to care for patient. Previously active, she developed gait instability, slurred speech, and memory lapse to the point of selective mutism and being bed-bound within three months. Her medical history was notable for hypertension and Covid four months prior. She had had mild upper respiratory symptoms and recovered in ten days. Examination revealed general encephalopathy, dysarthria, limited ability to follow commands. She had decreased strength but increased tone and rigidity in all extremities. She had rhythmic jaw movement and bradykinesia with scatter myoclonic movements. Cerebellar exam was notable for ataxia, but she had normal cranial nerve and sensory exams and normal reflexes. MRI of the brain revealed restricted diffusion and T2/Flair signal abnormality involving bilateral basal ganglia, ventral medial thalami, hippocampi, and cerebral cortices. Toxic metabolic workup was unrevealing. CSF was positive for 14-3-3 protein and elevated total tau protein, confirming Creutzfeldt-Jakob disease. IMPACT/DISCUSSION: Creutzfeldt-Jakob Disease (CJD) is a prion disease with one in a million prevalence. Patients present with rapidly progressing dementia, myoclonus, and signs of cerebellar, corticospinal and extrapyramidal involvement including nystagmus, ataxia, hyperreflexia, spasticity, hypokinesia, bradykinesia, dystonia, and rigidity. CJD is fatal within months to two years. Patients with end stage disease may have akinetic mutism. Magnetic resonance imaging (MRI), electroencephalogram (EEG), and cerebrospinal fluid (CSF) analysis are important for evaluation of CJD. Most sensitive in early stages, MRI Brain commonly shows hyperintense signal involving the cerebral cortex, corpus striatum, caudate, and putamen. EEG may capture pattern of periodic bi-or triphasic period sharp wave complexes. CSF might detect 14-3-3 protein with elevation of tau protein but real-time quaking-induced conversion (RT-QuIC) has the highest specificity for diagnosis for CJD. Though brain biopsy is the sole method of definitive diagnosis, results of MRI, EEG, and CSF analysis along with presenting signs and symptoms are sufficient for clinical diagnosis of CJD. Our patient's dementia, myoclonus, ataxia, hypokinesia, bradykinesia, dystonia, and rigidity all progressing to akinetic mutism within three months are classic presentation of CJD. EEG was normal, but MRI with hyperintensity of basal ganglia and cerebral cortices and CSF analysis with positive 14-3-3 and elevated tau proteins are all lead to diagnosis of CJD. CONCLUSION: This case illustrates a classic case of a Creutzfeldt-Jakob Disease, a rare prion disease marked by rapidly progressive dementia with neuropsychiatric features.

A Novel Host-Targeted Viral Assembly Inhibitor Blocks SARS-CoV-2 in Airway Epithelial Cells

Introduction: The rapid emergence of the SARS-CoV-2 Omicron variant that evades many monoclonal antibody therapies illustrates the need for anti-viral treatments with low susceptibility to evolutionary escape. The small molecule PAV-104, identified through a moderate-throughput screen involving cell-free protein synthesis, was recently shown to target a subset of host protein assembly machinery in a manner specific to viral assembly. This compound has minimal host toxicity, including once daily oral dosing in rats that achieves >200-fold of the 90% effective concentration (EC90) in blood. The chemotype shows broad activity against respiratory viral pathogens, including Orthomyxoviridae, Paramyxoviridae, Adenoviridae, Herpesviridae, and Picornaviridae, with low suceptability to evolutionary escape. We hypothesized that PAV-104 would be active against SARSCoV- 2 variants in human airway epithelial cells. Methods: Airway epithelial cells were differentiated from lung transplant tissue at air-liquid interface (ALI) for four weeks prior to challenge with Alpha (Pango lineage designation B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) SARS-CoV-2 variants. Viral replication was determined by quantitative PCR measurement of the SARS-CoV-2 nucleocapsid (N) gene. Dose-dependent virus inhibition and cytotoxicity of PAV-104 in the Calu-3 airway epithelial cell line was determined by PCR and MTT assay. Student's t-tests were used to evaluate statistical significance. Results: Alpha, Beta, Gamma, and Delta variants of SARS-CoV-2 showed comparable infectivity in human primary airway epithelial cells at ALI (N=3 donors), 47- to 550-fold higher than the parent (USA-WA1/2020) strain. PAV-104 reached 50% cytotoxicity in Calu-3 cells at 240 nM (Fig. 1A). Dose-response studies in Calu-3 cells demonstrated PAV-104 has a 6 nM 50% inhibitory concentration (IC50) for blocking replication of SARS-CoV-2 (USA-WA1/2020) (Fig.1B). In primary cells at ALI from 3 donors tested, there was >99% inhibition of infection by SARS-CoV-2 Gamma variant (N=3, MOI 0.1, P <0.01) with 100 nM PAV-104 (Fig. 1C). Addition of 100 nM PAV-104 2-hours post-infection, but not pre-infection, resulted in >99% suppression of viral replication, indicating a post-entry drug mechanism. PAV-104 bound a small subset of the known allosteric modulator 14-3-3, itself implicated in the interactome of SARS-CoV-2. Conclusion: PAV-104 is a host-targeted, orally bioavailable, pan-viral small molecule inhibitor with promising activity against SARS-CoV-2 variants in human primary airway epithelial cells. (Figure Presented).

Two Probable Creutzfeldt-Jakob Disease Cases Within One Month in a Single Hospital inGrand Rapids, Michigan

Objective: NA Background: Creutzfeldt-Jakob disease (CJD) is an extremely rare but fatal neurodegenerative disease with incidence of one in a million worldwide, and few than 1000 cases per year in the United States per year. Design/Methods: NA Case Summary: We present two probable CJD cases seen in the same hospital within one month. Case one was a 67-year-old white female, former psychology practice manager, presenting with worsening cognition, vertigo, behavioral changes and 15 lb weight loss over 6 months. Exam findings significant for MoCA of 17/30 (decreased to 15/30 after one week), constant right eye shut, mild dysmetria in both lower extremities, a wide based gait with small strides. Blood work and initial Spinal fluid studies were negative. Continuous EEG showing occasional right temporal slow, frequent generalized rhythmic theta and delta slowing. MRI brain findings were suggestive of CJD with hyperintensities in bilateral caudate nucleus and putamen. Patient did not respond to high dose steroid. Case two was a 78-year-old white male, admitted for deterioration in cognition, gait, speech, fatigue and intermittent body jerking. Progression of his symptoms was so rapid, from a highly functional retired funeral director, he became minimal speech, loss of ADL within 3 months. Exam was significant for orientation to self only, global aphasia, muscle weakness and startle myoclonus. Blood work and initial spinal fluid studies were negative. MRI brain showed asymmetric cortically based diffuse restriction within cingulate, caudate nucleus also left temporoparietal. EEG showed generalized rhythmic delta activity. CSF from both cases eventually showed positive RT-QuIC, 14-3-3 protein and highly elevated T-Tau protein. Conclusions: CJD is a transmittable, reportable disease. Two cases seen in the same hospital within one month skews from the previously known CJD prevalence. Surveillance and investigation on the reason of regional CJD arise during COVID-19 pandemic may prove to be important and urgent.

CREUTZFELDT-JAKOB DISEASE: ACCELERATED BY COVID?

TYPE: Late Breaking TOPIC: Chest Infections INTRODUCTION: Creutzfeld Jakob Disease (CJD) is a collective group of rare neurodegenerative diseases characterized by rapidly progressing cognitive decline, deficits in cortical function (aphasia, apraxia, agnosia), myoclonic jerks and extrapyramidal symptoms with a mortality of 100%. CASE PRESENTATION: We present a 72-year-old female who initially presented with aphasia, dyscalculia, right hemiparesis and dysgraphia.Upon arrival, she was hemodynamically stable and labs were remarkable for a positive COVID PCR test. CT head and CT angiogram was within normal limits. MRI was nonspecific. EEG showed left temporal lateralized periodic discharges (PLDs) at 1 Hz with a triphasic morphology and Lumbar puncture disclosed a protein of 79 mg/dL, glucose 65 mg/dL, WBC 1, HSV 1 and 2 PCR, cryptococcus, gram stain/culture AFB, and cytology were all negative. With concern for autoimmune encephalitis she was empirically started on IVIG without improvement. Paraneoplastic and autoimmune evaluation resulted pan negative. 14-3-3 CSF protein assay reported positive and diagnosis CJD was made. After goals of care discussion with the family, she was discharged home with hospice. DISCUSSION: Sporadic type (sCJD) accounts for about 85% of cases and occurs after somatic mutation in the gene for PrP protein. Rapid neurocognitive decline and cortical function deficits with negative infectious, autoimmune, and paraneoplastic workups should prompt further evaluation for CJD. CSF protein 14-3-3 has a sensitivity of 92%–96% for sCJD. EEG showing of a 1/second periodic triphasic sharp wave complex is present in 1/3 cases. CONCLUSIONS: Most recently, there have been some case reports indicating that the systemic immune response in COVID-19 could accelerate the clinical course of sCJD, however, a potential causal link remains unclear. DISCLOSURE: No significant relationships. KEYWORD: CJD

Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein and structure model of sequestration by protein 14-3-3.

SARS-CoV-2 is the etiologic agent of COVID-19. There is currently no effective means of preventing infections by SARS-CoV-2, except through restriction of population movement and contact. An understanding of the origin, evolution and biochemistry (molecular biology) of SARS-CoV-2 is a prerequisite to its control. Mutations in the phosphorylation sites of SARS-CoV-2 encoded nucleocapsid protein isolated from various populations and locations, are described. Mutations occurred in the phosphorylation sites, all located within a stretch which forms a phosphorylation dependent interaction site, including C-TAK1 phosphorylation sites for 14-3-3. The consequences of these mutations are discussed and a structure-based model for the role of protein 14-3-3 in the sequestration and inhibition of SARS-CoV-2 nucleocapsid protein's function is presented. It is proposed that the phosphorylation of SARS-CoV-2 nucleocapsid protein and its sequestration by Protein 14-3-3 is a cellular response mechanism for the control and inhibition of the replication, transcription and packaging of the SARS-CoV-2 genome.