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Objectives: The Covid-19 pandemic highlighted the importance of considering Social Determinants of Health (SDoH) in healthcare research. Administrative claims databases are widely used for research, but often lack SDoH data or sufficient transparency in how these data were obtained. This study describes innovative methods for integrating SDoH data with administrative claims to facilitate health equity research. Method(s): The HealthCore Integrated Research Database (HIRD) contains medical and pharmacy claims from a large, national US payer starting in 2006 and includes commercial (Comm), Medicare Advantage (MCare), and Medicaid (MCaid) populations. The HIRD includes individually identifiable information, which was used for linking with SDoH data from the following sources: national neighborhood-level data from the American Community Survey, the Food Access Research Atlas, and the National Center for Health Statistics' urbanicity classification;and member-level data on race/ethnicity from enrollment files, medical records, self-attestation, and imputation algorithms. We examined SDoH metrics for members enrolled as of 05-July-2022 and compared them to the respective US national data using descriptive statistics. We also examined telehealth utilization in 2022. Result(s): SDoH data were available for ~95% of currently active members in the HIRD (Comm/MCare/MCaid 12.5m/1m/7.6m). Socioeconomic characteristics at the neighborhood-level differed by membership type and vs. national data: % of members with at least a high-school education (90/88/84 vs. 87);median family income ($98k/$76k/$70k vs. $82k);% of members living in low-income low-food-access tracts (9/14/18 vs. 13);urban (57/52/47 vs. 61). At the member-level, the % of White Non-Hispanics, Black Non-Hispanics, Asian Non-Hispanics, and Hispanics were 61/6/5/6 (Comm), 76/12/2/2 (MCare), and 45/26/5/19 (MCaid). Imputation contributed 15-60% of race/ethnicity values across membership types. Telehealth utilization increased with socioeconomic status. Conclusion(s): We successfully integrated SDoH data from a variety of sources with administrative claims. SDoH characteristics differed by type of insurance coverage and were associated with differences in telehealth utilization.Copyright © 2023
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Background/Objectives: Li-Fraumeni Syndrome (LFS) is a rare hereditary cancer predisposition syndrome characterized by high lifetime risks for multiple primary malignancies. Although most individuals with LFS inherit a pathogenic TP53 variant from a parent, approximately 20% have de novo variants with no suggestive family cancer history. This may result in an LFS experience distinct from individuals with affected relatives. This multi-case study report examines the unique psychosocial experiences of three young adults with de novo TP53 variants. Method(s): The National Cancer Institute's LFS study (NCT01443468) recruited adolescents and young adults (AYAs;aged 15-39 years) with LFS for qualitative interviews. Three participants had a de novo TP53 variant and a personal cancer history. An interprofessional team analyzed interview data using extended case study and narrative methods. Result(s): De novo participants lacked familiarity with LFS to situate a cancer diagnosis, interpret genetic test results, or adjust to chronic cancer risk. Communicating with and receiving support from family was challenged by their lack of common experience. De novo participants experienced socioemotional isolation, which was amplified during the COVID-19 pandemic. To cope, they sought support in online rare disease communities or through mental health providers. Conclusion(s): Individuals with de novo variants may lack familial guides and familiar providers to address disease management and uncertainty. Specialty health and mental health providers may support de novo patients across hereditary cancer syndromes by validating their uncertainties and connecting them with diseasespecific patient advocacy groups that support adjustment to chronic cancer risk.
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Introduction: Cancer patients have a high risk of severe COVID-19 and complications from it. Although the COVID-19 pandemic has led to an increase in the conduction of clinical trials (CTs), there is a scarcity of data on CT participation among cancer patients. We aimed to describe the level of participation in a COVID-19 CT, willingness to participate, as well as trust in sources of information for CTs among persons with and without a previous cancer diagnosis in Puerto Rico. Method(s): Data collected from November 2021 to March 2022 from two cross-sectional studies were merged and used for analysis. Informed consent, telephone, face-to-face, and online interviews were conducted among participants >=18 years old living in Puerto Rico (n=987). Descriptive statistics and bivariate analysis (Fisher's exact text and chi-squared test) was done to describe the outcomes of interest, overall and by cancer status. Result(s): Mean age of participants was 41+/-15.5 years. Most participants were women (71.3%), with an educational level greater than high school (89.5%) and with an annual family income below $20,000 (75.1%). Overall, 4.4% of participants (n=43) reported history of cancer diagnosis. Only 1.8% of the population reported to have participated in a COVID-19 CT to receive either a treatment or vaccine;stratifying by cancer, none of the cancer patients had participated in a COVID-19 CT, and only 1.9% of non-cancer patients participated. While 37.0% of the participants indicated being very willing to sign up for a CT assessing COVID-19 treatment, willingness was higher in cancer patients (55.8%) than among participants without cancer (36.1%). Regarding trust in sources of information for CTs, the level of trust ("a great deal/a fair amount") was higher for their physicians (87.6%), researchers (87.0%), the National Institute of Health (86.7%), their local clinics (82.9%), and a university hospital (82.7%), while it was lower for a pharmaceutical company (64.0%), and for friend, relative, or community leader (37.6%);no differences were observed by cancer status. Conclusion(s): While participation in COVID-19 CTs was extremely low in the study population, the willingness to participate was higher among cancer patients. Education on CTs and their availability are necessary to increase participation in this understudied group. Such efforts will enhance the representation of Hispanic and vulnerable populations, such as cancer patients, on COVID-19 CTs, and thus proper generalizability of study findings in the future.
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OnTrackNY is a nationally recognized Coordinated Specialty Care model disseminated across New York state for young people experiencing early non-affective psychosis. OnTrackNY is a network of 22 teams located in licensed outpatient clinics, serving over 2500 individuals. OnTrackNY offers medication management, case management, individual and group cognitive behaviourally oriented therapy, family support and psychoeducation, supported employment and education, and peer support services. Teams receive training for implementation through an intermediary organization called OnTrack Central. OnTrackNY was selected as a regional hub of the National Institute of Mental Health Early Psychosis Intervention Network (EPINET), a national learning healthcare system (LHS) for young adults with early psychosis. This symposium will present the different ways in which EPINET OnTrackNY implemented systematic communitybased participatory processes to ensure robust stakeholder involvement to improve the quality of OnTrackNY care. Florence will present results of an assessment of stakeholder feedback experiences used to develop strategies for assertive outreach and engagement of program participants, families and providers. Bello will present on mechanisms for integrating of co-creation principles to design, develop and execute quality improvement projects in EPINET OnTrackNY. Stefancic will present on quality improvement projects that used rapid cycle qualitative methods, tools, and strategies to build team capacity and flexibility to respond to an LHS. Montague will present adaptations to OnTrackNY services during the COVID-19 pandemic using an implementation science framework. Finally, Patel will lead a discussion on the implications of involving individuals with lived experiences in all phases of the process to maximize learning in an LHS.
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BACKGROUND: The core of the healthcare system is healthcare workers (HCWs). A skilled and healthy workforce is essential during a health emergency like the coronavirus disease 2019 (COVID-19) epidemic. AIM: This study evaluated knowledge of COVID-19, its preventive measures, and factors affecting it among HCWs at the National Cancer Institute (NCI), Cairo University to determine their desire to obtain the available COVID-19 vaccines in addition to the factors that may affect it. METHOD(S): This descriptive cross-sectional study included 151 HCWs in Egypt using a self-administered questionnaire created by the researchers after examining the information supplied by the Egyptian Ministry of Health and Population, World Health Organization, and the relevant research regarding knowledge assessment. Initially, demographic data were collected. Participants were asked their source of knowledge about COVID-19 and their intent to receive the available vaccines. Knowledge about COVID-19 and preventive measures was compared between different HCWs in NCI. In addition, knowledge score was compared according to different factors to determine factors affecting knowledge. RESULT(S): Physicians represented about 40% of the total number of participants. HCWs' knowledge of COVID-19 was higher among physicians, with a higher percentage of correct answers than the other two groups (nurses and pharmacists and employees and technicians). Younger age groups had a significantly higher median knowledge score than the older groups. Physicians had significantly higher median scores than employee and technician groups. CONCLUSION(S): The overall knowledge about COVID-19 and its preventive measures among HCWs was generally good, especially among physicians more than allied health professionals. However, some of the virus-related knowledge was less advanced than expected for the HCWs position.Copyright © 2023 Nora Atef, Mohamed Bendary, Amira Khater.
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Background: Iatrogenic coronary artery dissection during diagnostic or therapeutic catheterization is a rare and mortal complication that may result in a newly developed myocardial infarction. In this study, we aimed to share the results of CABG treatment of patients with iatrogenic coronary artery dissection after coronary angiography (CAG) in our clinic. Method(s): All patients who underwent CAG or percutaneous coronary intervention (PCI) in our hospital between January 2014 and December 2021 were analyzed retrospectively and patients who underwent CABG after iatrogenic coronary artery dissection were included in the study. The dissection classification was achived according to the National Heart, Lung and Blood Institute (NHLBI) classification. Result(s): During the eight years, CAG was applied to 20,398 patients and PCI to 9583 patients. Needed to treat CABG in iatrogenic coronary artery dissection developed in 17 of the patients (0.06%). LMCA was dissected in 6 (35.3%) patients and LAD in 6 (35.3%), CX in 2 (11.8%) and RCA dissection in 3 (17.6%). 3 patients (17.6%) had an intubation time longer than 48 hours. One of them has recently had a COVID infection. Another was suffering from pulmonary edema. The other patient died on the 4th postoperative day due to low cardiac output. The length of stay in the intensive care unit was 2 (min: 1 - max: 13) days. The hospital stay was 6 (min: 4 - max: 20) days. Conclusion(s): The development of a critical clinical condition prior to surgery is strongly associated with a higher probability of early and late postoperative death. For this reason, it is clear that the treatments applied at every stage of the pre-, per-, and postoperative period are the most important determinants of the results.Copyright © 2023, CKS.
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Phosphoserine (pSer) sites are primarily located within disordered protein regions, making it difficult to experimentally ascertain their effects on protein structure and function. Therefore, the production of 15N- (and 13C)-labeled proteins with site-specifically encoded pSer for NMR studies is essential to uncover molecular mechanisms of protein regulation by phosphorylation. While genetic code expansion technologies for the translational installation of pSer in Escherichia coli are well established and offer a powerful strategy to produce site-specifically phosphorylated proteins, methodologies to adapt them to minimal or isotope-enriched media have not been described. This shortcoming exists because pSer genetic code expansion expression hosts require the genomic DELTAserB mutation, which increases pSer bioavailability but also imposes serine auxotrophy, preventing growth in minimal media used for isotopic labeling of recombinant proteins. Here, by testing different media supplements, we restored normal BL21(DE3) DELTAserB growth in labeling media but subsequently observed an increase of phosphatase activity and mis-incorporation not typically seen in standard rich media. After rounds of optimization and adaption of a high-density culture protocol, we were able to obtain >=10 mg/L homogenously labeled, phosphorylated superfolder GFP. To demonstrate the utility of this method, we also produced the intrinsically disordered serine/arginine-rich region of the SARS-CoV-2 Nucleocapsid protein labeled with 15N and pSer at the key site S188 and observed the resulting peak shift due to phosphorylation by 2D and 3D heteronuclear single quantum correlation analyses. We propose this cost-effective methodology will pave the way for more routine access to pSer-enriched proteins for 2D and 3D NMR analyses. GCE4All Biomedical Technology Development and Dissemination Center was supported by National Institute of General Medical Science, OSU NMR Facility funded in part by the National Institutes of Health, the Medical Research Foundation at OHSU and the Collins Medical Trust, National Science Foundation EAGER, and by the M. J. Murdock Charitable Trust.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
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Background: Modulator therapy has improved nutritional status in individuals with cystic fibrosis (CF), which is associated with favorable outcomes. Because of the high metabolic demands of CF, nutritional recommendations include energy intake of 110% to 200% of daily estimated needs for healthy individuals. With changes in energy balance after initiation of modulator therapy, these recommendations may no longer be appropriate for some people with CFand may lead to excessiveweight gain. Overweight and obesity are being reported, and nutrition concerns now include dietary quality. Dietary quality in relation to growth in young children starting lumacaftor/ivacaftor therapy has not been examined over a 24-week period and may provide new data for future nutrition guidance for individuals with CF. Method(s): The purpose of this observational study was to determine the effect of lumacaftor/ivacaftor treatment on growth and diet in medicationnaive children. Subjects aged 2 to 5 with D508/D508 mutations were recruited from the United States and Canada. Length/height, weight, and body mass index (BMI) were measured in triplicate and averaged. Z-scores were calculated using Centers for Disease Control and Prevention reference data. Dietary data were captured using 3-day weighted food records after study visits. The Healthy Eating Index (HEI) was generated using the U.S. Department of Agriculture scoring system for each recorded day and averaged. Outcomes were assessed before treatment (baseline) and 12 and 24 weeks after beginning medication. Mixed longitudinal models were used for analysis over time. Result(s): Participants (mean age 2.9 +/- 1.4, 50% female) who completed food records for at least their baseline visit plus one other visit (n = 14) had significant increases inweight-for-age z-score (WAZ) 12 (0.6 +/- 1.7, p = 0.02) and 24 (0.21 +/- 1.8, p = 0.001) weeks after therapy. There was no significant change in height-for-age (HAZ), BMI-for-age (BMIZ), or head circumference- for-age (HCZ) z-score at 12 or 24 weeks. Although not statistically significant, percentage estimated energy requirement (%EER) decreased at 12 (-7 +/- 90%, p = 0.54) and 24 (-27 +/- 90%, p = 0.08) weeks. HEI total score did not change over the 24 weeks, although vegetables and greens and beans HEI subgroup scores decreased significantly from baseline to 24 weeks (-0.73 +/- 2.2, p = 0.02;-0.68 +/- 2.1, p = 0.02, respectively). Pooled visit correlation between total vegetables and WAZ indicated a positive association (r = 0.35, p = 0.04). Conclusion(s): WAZ increased significantly over 24 weeks of lumacaftor/ ivacaftor therapy and was positively correlated with total vegetable intake, suggesting that participants with greater WAZ scores consumed more vegetables, although over the course of the study, total vegetable intake and intake of greens and beans decreased, and WAZ increased. %EER decreased over the course of the study, but not statistically significantly so, probably because of variability in energy intake within this small study sample with some COVID-19 interruptions. In summary, WAZ of children aged 2 to 5 with D508/D508 mutations increased, with no significant changes in HAZ, BMIZ, or HCZ, and they consumed fewer total vegetables and greens and beans after 24 weeks of lumacaftor/ivacaftor therapy. Acknowledgements: Supported by Vertex Pharmaceutics Inc. and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant UL1TR001878.Copyright © 2022, European Cystic Fibrosis Society. All rights reserved
ABSTRACT
Pulmonary aspergillosis (PA) is a category of respiratory illnesses that significantly impacts the lives of immunocompromised individuals. However, new classifications of secondary infections like influenza associated aspergillosis (IAA) and COVID-19 associated pulmonary aspergillosis (CAPA) only exacerbate matters by expanding the demographic beyond the immunocompromised. Meanwhile anti-fungal resistant strains of Aspergillus are causing current treatments to act less effectively. Symptoms can range from mild (difficulty breathing, and expectoration of blood) to severe (multi organ failure, and neurological disease). Millions are affected yearly, and mortality rates range from 20-90% making it imperative to develop novel medicines to curtail this evolving group of diseases. Chalcones and imidazoles are current antifungal pharmacophores used to treat PA. Chalcones are a group of plant-derived flavonoids that have a variety of pharmacological effects, such as, antibacterial, anticancer, antimicrobial, and anti-inflammatory activities. Imidazoles are another class of drug that possess antibacterial, antiprotozoal, and anthelmintic activities. The increase in antifungal resistant Aspergillus and Candida species make it imperative for us to synthesize novel pharmacophores for therapeutic use. Our objective was to synthesize a chalcone and imidazole into a single pharmacophore and to evaluate its effectiveness against three different fungi from the Aspergillus or Candida species. The chalcones were synthesized via the Claisen-Schmidt aldol condensation of 4-(1H-Imizadol-1-yl) benzaldehyde with various substituted acetophenones using aqueous sodium hydroxide in methanol. The anti-fungal activity of the synthesized chalcones were evaluated via a welldiffusion assay against Aspergillus fumigatus, Aspergillus niger, and Candida albicans. The data obtained suggests that chalcone derivatives with electron-withdrawing substituents are moderately effective against Aspergillus and has the potential for further optimization as a treatment for pulmonary aspergillosis. This project was supported by grants from the National Institutes of Health (NIH), National Institute of General Medicine Sciences (NIGMS), IDeA Networks of Biomedical Research Excellence (INBRE), Award number: P20GM103466. The content is solely the responsibility of the authors and do not necessarily represent the official views of the NIH.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Lipid enveloped viruses replicate and bud from the host cell where they acquire their lipid coat. Lipid-enveloped viruses include dangerous pathogens such as coronaviruses (SARSCoV-2, etc.), filoviruses (Ebola virus and Marburg virus) and paramyxoviruses (Nipah virus, Hendra virus, etc.). Despite understanding some of the basics of how these viruses cause disease and enter host cells, not much is known on how these dangerous pathogens interact with host cell lipids to achieve new virion formation. The viral matrix or membrane protein regulates assembly and budding from the host cell membrane, connecting the viral lipid envelope to the viral nucleocapsid. Depending on the virus family, this assembly and budding may occur at the plasma membrane or the ER-Golgi intermediate compartment. This presentation will detail the biophysical and biochemical basis of how these emerging pathogens hijack host lipid membrane and metabolic networks to form new virus particles that undergo release from the host cell. These studies were funded in part by the National Institute of Allergy and Infectious Diseases (R01AI081077, AI158220, AI169896).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
SARS-like coronaviruses, including SARS-CoV and SARS-CoV-2, encode spike proteins that bind human ACE2 protein on the cell surface to enter target cells and cause infection. The efficiency of virus entry depends on ACE2 sequence and expression levels in target cells. A small fraction of humans encodes variants of ACE2, thus altering the biochemical properties at the protein interaction interface. All humans possess cells with vastly differing amounts of ACE2 on the cell surface, ranging from cell types with high expression in the gut and lungs to lower expression in the liver and pancreas. Mastering our understanding of spike-ACE2 interaction and infection requires experiments precisely perturbing both variables. Thus, we developed a synthetic cell engineering approach compatible with high throughput assays for pseudo-typed virus infection. Our assay system is capable of assessing both variables individually and in combination. We adapted an engineered HEK293T DNA recombinase landing pad cell line capable of expressing transgenic ACE2 sequences at highly precise levels. Infection with lentiviruses pseudotyped with the spikes of SARS-like coronaviruses revealed that high ACE2 abundance could mask the effects of impaired binding thereby making it challenging to know the role of affinity altering mutations during infection. We limited the ACE2 abundance on the cell surface by expressing transgenic ACE2 behind a suboptimal Kozak sequence, thereby altering its protein translation rate. This allowed us to understand how ACE2 sequence could impact its interaction with coronavirus spike proteins as two human ACE2 variants at the binding interface, K31D and D355N, exhibited reduced infection. Our experiments suggested that we need to better understand how ACE2 expression determines the susceptibility of cells for SARS-like coronavirus binding and infection. We thus created an ACE2 Kozak library consisting of ~4,096 Kozak variants, each conferring a different ACE2 protein translation rate thus resulting in a range of ACE2 steady-state abundances. Combining fluorescence-activated cell sorting and high-throughput DNA sequencing (FACS-seq) revealed the library to span two orders of magnitude of ACE2 abundance. Challenging this library of cells with spike pseudotyped lentiviruses revealed how ACE2 abundance correlated with infection rate. The library-based experiments yielded a dynamic range wider than traditional single sample infection assay, likely more representative of infection dynamics in vivo. Now that we have characterized the impacts of ACE2 abundance on infectivity in engineered cells, our next goal is to expand the comparison to physiologically relevant cells with endogenously expressed proteins. Modulating protein abundance levels will be key to creating maximally informative functional assays for any protein in cell-based assays, and we have laid the groundwork for being able to simultaneously test the impacts of protein abundance and sequence in combination for proteins involved in diverse cellular processes. This research was supported by a National Institute of Health (NIH) grant GM142886 (KAM).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
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Mycobacterium tuberculosis is the second leading infectious killer after COVID-19. The bacteria utilizes several metal transport systems to help it survive in the host.With an increase in the number of multiresistant, extensively resistant and totally drug-resistant strains, the development of new therapeutic strategies that target other essential pathways in the bacteria is critical. The bacteria contain several metal transport systems which are necessary for its survival. Additionally, the bacteria has two metalloregulators that are associated with nickel and cobalt export, NmtR and KmtR. The focus of this research is on KmtR, which represses the expression of the genes, cdf (which encodes the export protein) and kmtR. The goal of our research is to identify the residues that are responsible for binding the cognate metals, nickel and cobalt, as well as the noncognate metal, zinc, to KmtR. Mutagenesis studies coupled with metal binding experiments will be used to determine how KmtR binds these metals. The E101Q, H102Q, and H111Q mutants, among others, have been made, expressed, and purified in our lab. Data obtained from Isothermal Titration Calorimetry determined that all three mutant proteins bind cobalt with nanomolar affinities and the H111Q mutant KmtR proteins binds cobalt an order of magnitude weaker than the other two mutant proteins. Research reported as supported fully by the RI Institutional Development Award (IDeA) Network for Biomedical Research Excellence (RI-INBRE) from the National Institute of General Medical Sciences of the National Institutes of Health under grant #P20GM103430.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Mammals, bacteria, and archaea have domesticated transposases (e.g., RAG1 and Cas1) to form adaptive immune systems. Bacteria and archaea acquire resistance to viruses and plasmids by preferentially integrating fragments of foreign DNA at one end of a CRISPR locus. DNA motifs upstream of the CRISPR (i.e., leader) facilitate integration at the first CRISPR repeat. But how do these upstream DNA motifs act over large distances of 130 bp, or roughly 440 A, to regulate integration allosterically? Here, we determine the structure of a 560 KDa integration complex that explains how the CRISPR leader DNA recruits Cas (i.e., Cas1-2/3) and non-Cas proteins (i.e., IHF). Cas1-2/3 and IHF cooperate to fold the genome into a successive U-shaped bend and a loop. The genomic U-bend traps foreign DNA against the integrase, whereas the genomic loop positions the leader-repeat junction at the Cas1 active site. The foreign DNA and the CRISPR repeat wrap around opposite faces of Cas2, poised for a Cas1-catalyzed strand-transfer reaction. The post-integration structure suggests that strand-transfer releases tension in the DNA loop. Therefore Cas1-2/3 may harness protein-induced DNA tension to favor the completion of the isoenergetic integration reaction. Cas1-2/3 interacts extensively with the leader and repeat without making sequence-specific contacts, and we demonstrate that protein-mediated folding of DNA drives integration into diverse sequences. These results reveal Cas1-2/3 and IHF strain DNA to enhance integration allosterically and suggest a mechanism for the de novo generation of new CRISPRs. Further, to address an urgent need for inexpensive and rapid detection of viruses, we recently repurposed a CRISPR immune signaling pathway to detect SARS-CoV-2 in patient samples. A.S-F. is a postdoctoral fellow of the Life Science Research Foundation, supported by the Simons Foundation. A.S-F. is supported by the PDEP award from the Burroughs Wellcome Fund, and by the National Institutes of Health, United States grant 1K99GM147842. This work was also supported by NSF (1828765), NIH (U24 GM129539, R35GM134867).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Background: The rapid development of SARS-CoV-2 mRNA vaccines has been a remarkable success of the COVID-19 pandemic, but vaccine-induced immunity is heterogeneous in immunocompromised populations. We sought to determine the immunogenicity of SARS-CoV-2 mRNA vaccines in a cohort of people with idiopathic CD4 lymphopenia (ICL). Method(s): 25-patients with ICL followed at the National Institutes of Health on a natural history protocol were evaluated between 2020-2022. Blood and serum was collected within 4-12 weeks after their second and/or third SARS-CoV-2 mRNA vaccine dose. Twenty-three matched healthy volunteers (HVs) provided blood samples at similar timepoints post-mRNA vaccination on a separate clinical protocol. Pre-vaccine blood samples were also used when available. Anti-spike and anti-receptor binding domain antibodies were measured. T-cell stimulation assays were performed to quantify SARS-CoV-2 specific T-cell responses. Comparisons were made with Wilcoxon test. Result(s): Twenty-participants with ICL had samples collected after their second mRNA vaccine and 7-individuals after the third dose. Median age at vaccination was 51-years (IQR: 44-62) and 12 were women (48%). Median CD4 T-cell count was 150 cells/muL (IQR: 85-188) at the time of vaccination, and 11-individuals (44%) had a baseline CD4 count <=100 cells/muL. HVs had a median age of 54-years (IQR: 43-60) with 13-women (56.5%). Anti-spike IgG antibody levels were significantly greater in HVs than those with ICL after 2-doses. Lower SARS-CoV-2 IgG antibody production was primarily observed in those with baseline CD4 T-cells <=100 cells/mul (Figure-1A). The decreased production in ICL remained after a third vaccine dose (Figure-1B). There was a significant correlation between anti-spike IgG and baseline CD4 count. Spike-specific CD4 T-cell responses in volunteers compared to those with ICL demonstrated similar levels of activation induced markers (CD154+CD69+) and cytokine production (IFNgamma+, TNFalpha+, IL2+) after two or three mRNA vaccine doses. Quantitatively the smallest responses were observed in those with lower baseline CD4 T-cells (Figure 1C-D). Minimal SARS-CoV-2 CD8 T-cell responses were detected in both groups. Conclusion(s): Patients with ICL and baseline CD4 T-cells >100 mount similar humoral and cellular immune responses to SARS-CoV-2 vaccination as healthy volunteers. Those with baseline CD4 T-cells <=100 have impaired vaccine- induced immunity and should be prioritized to additional boosters and continue other risk mitigation strategies. (Figure Presented).
ABSTRACT
RNA viruses are the major class of human pathogens responsible for many global health crises, including the COVID-19 pandemic. However, the current repertoire of U.S. Food and Drug Administration (FDA)-approved antivirals is limited to only nine out of the known 214 human-infecting RNAviruses, and almost all these antivirals target viral proteins. Traditional antiviral development generally proceeds in a virus-centric fashion, and successful therapies tend to be only marginally effective as monotherapies, due to dose-limiting toxicity and the rapid emergence of drug resistance. Host-based antivirals have potential to alleviate these shortcomings, but do not typically discriminate between infected and uninfected cells, thus eliciting unintended effects. In infected cells where host proteins are repurposed by a virus, normal host protein functions are compromised;a situation analogous to a loss-of-function mutation, and cells harboring the hypomorph have unique vulnerabilities. As well-established in model systems and in cancer therapeutics, these uniquely vulnerable cells can be selectively killed by a drug that inhibits a functionally redundant protein. This is the foundation of synthetic lethality (SL). To test if viral induced vulnerabilities can be exploited for viral therapeutics, we selectively targeted synthetic lethal partners of GBF1, a Golgi membrane protein and a critical host factor for many RNA viruses including poliovirus, Coxsackievirus, Dengue, Hepatitis C and E virus, and Ebola virus. GBF1 becomes a hypomorph upon interaction with the poliovirus protein 3A. A genome-wide chemogenomic CRISPR screen identified synthetic lethal partners of GBF1 and revealed ARF1 as the top hit. Disruption of ARF1, selectively killed cells that synthesize poliovirus 3A alone or in the context of a poliovirus replicon. Combining 3A expression with sub-lethal amounts of GCA - a specific inhibitor of GBF1 further exacerbated the GBF1-ARF1 SL effect. Together our data demonstrate proof of concept for host-based SL targeting of viral infection. We are currently testing all druggable synthetic lethal partners of GBF1 from our chemogenomic CRISPR-screen, in the context of dengue virus infection for their abilities to selectively kill infected cells and inhibit viral replication and infection. Importantly, these SL gene partners of viral-induced hypomorphs only become essential in infected cells and in principle, targeting them will have minimal effects on uninfected cells. Our strategy to target SL interactions of the viral-induced hypomorph has the potential to change the current paradigm for host-based therapeutics that can lead to broad-spectrum antivirals and can be applied to other intracellular pathogens. This work is supported by National Institutes of Health grants R01 GM112108 and P41 GM109824, R21 AI151344 and foundation grant FDN-167277 from the Canadian Institutes of Health Research.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Towards the end of 2019 a novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) caused the ongoing global pandemic. The virus surface consists of spike proteins that mediate SARS-CoV-2 entry into cells through its receptor-binding domain (RBD) that attaches to the human receptor Angiotensin- Converting Enzyme 2 (ACE2). Upon infection with foreign material, like viruses and bacteria, the human immune system responds by producing a humoral response specific to the viral antigen. Cells from the innate immune system and antibodies generated in the humoral response work to destroy and block infectious antigens from causing damage to the human cells. The S protein of SARSCoV- 2 is the key protein that stimulates the immune system to generate neutralizing antibodies. To safely test and investigate SARS-CoV-2 in BSL-2 lab setting, we propagated a surrogate pseudo typed virus to evaluate the ability of antibodies to reduce viral cell entry and replication in SARS-CoV-2 infected mice model. Quantifying the functional ability of neutralizing antibodies would help us understand how they influence reinfection in recovered individuals. We hypothesize that antibodies generated in SARS-CoV-2 infected mice models will induce a protective immune response against the SARSCoV- 2 infection. To detect and quantify the protective immune response generated in mice, we performed two different serological assays and identified antibodies endpoint titers. Mice were infected with Delta and Beta at time points Day 3 and Day 4. We performed a SARS-CoV-2 Spike pseudo virus neutralization assay and measured luminescence to determine the percentage neutralization of functional antibodies induced in mice serum samples upon infection. Utilizing indirect ELISAs,' we measured absorbance for IgA antibodies in Bronchoalveolar lavage fluid (BALF) serum and total IgG antibodies in cardiac bleeds. Our results showed we did not obtain neutralizing activity of antibodies in mice serum samples taken at early time points, 24 hrs and 4 days, after infection with the Delta variant of SARS CoV2 virus using both the pseudo viruses Omicron andWA spike.We obtained 100% neutralizing activity in mice serum samples taken at day 21 and infected with Beta variant of SARS CoV2 virus using both the pseudo viruses Omicron and WA spike demonstrating that there is cross-neutralization against various variants of concern. Antibodies (IgA, IgM, IgG) generated in mice 3 weeks post infection with SARS CoV2 (Beta) virus are capable of neutralizing and inhibiting the entry of WA spike and Omicron pseudo viruses in human HEK293 T Ace2 cells. Moving forward utilizing samples with timepoints surpassing 3 weeks could possibly yield higher concentrations of IgA and IgM antibodies that can neutralize the SARS-CoV-2 pseudo virus. Thank you to Dr. Rhea Coler, the entire Coler lab, National Institutes of Health (NIH), and Seattle Children's Research Institute.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Coronavirus disease 19 (COVID-19) is a highly contagious and lethal disease caused by the SARS-CoV-2 positive-strand RNA virus. Nonstructural protein 13 (Nsp13) is the highly conserved ATPase/helicase required for replication of the SARS-CoV-2 genome which allows for the infection and transmission of COVID-19. We biochemically characterized the purified recombinant SARS-CoV-2 Nsp13 helicase protein expressed using a eukaryotic cell-based system and characterized its catalytic functions, focusing on optimization of its reaction conditions and assessment of functional cooperativity among Nsp13 molecules during unwinding of duplex RNA substrates. These studies allowed us to carefully determine the optimal reaction conditions for binding and unwinding various nucleic acid substrates. Previously, ATP concentration was suggested to be an important factor for optimal helicase activity by recombinant SARS-CoV-1 Nsp13. Apart from a single study conducted using fixed concentrations of ATP, the importance of the essential divalent cation for Nsp13 helicase activity had not been examined. Given the importance of the divalent metal ion cofactor for ATP hydrolysis and helicase activity, we assessed if the molar ratio of ATP to Mg2+ was important for optimal SARS-CoV-2 Nsp13 RNA helicase activity. We determined that Nsp13 RNA helicase activity was dependent on ATP and Mg2+ concentrations with an optimum of 1 mM Mg2+ and 2 mM ATP. Next, we examined Nsp13 helicase activity as a function of equimolar ATP:Mg2+ ratio and determined that helicase activity decreased as the equimolar concentration increased, especially above 5 mM. We determined that Nsp13 catalytic functions are sensitive to Mg2+ concentration suggesting a regulatory mechanism for ATP hydrolysis, duplex unwinding, and protein remodeling, processes that are implicated in SARS-CoV-2 replication and proofreading to ensure RNA synthesis fidelity. Evidence is presented that excess Mg2+ impairs Nsp13 helicase activity by dual mechanisms involving both allostery and ionic strength. In addition, using single-turnover reaction conditions, Nsp13 unwound partial duplex RNA substrates of increasing doublestranded regions (16-30 base pairs) with similar kinetic efficiency, suggesting the enzyme unwinds processively in this range under optimal reaction conditions. Furthermore, we determined that Nsp13 displayed sigmoidal behavior for helicase activity as a function of enzyme concentration, suggesting that functional cooperativity and oligomerization are important for optimal activity. The observed functional cooperativity of Nsp13 protomers suggests the essential coronavirus RNA helicase has roles in RNA processing events beyond its currently understood involvement in the SARS-CoV-2 replication-transcription complex (RTC), in which it was suggested that only one of the two Nsp13 subunits has a catalytic function, whereas the other has only a structural role in complex stability. Altogether, the intimate regulation of Nsp13 RNA helicase by divalent cation and protein oligomerization suggests drug targets for modulation of enzymatic activity that may prove useful for the development of novel anti-coronavirus therapeutic strategies. This work was supported by the Intramural Training Program, National Institute on Aging (NIA), NIH, and a Special COVID-19 Grant from the Office of the Scientific Director, NIA, NIH.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.
ABSTRACT
Aim and Background: The coronavirus disease 2019 (Covid-19) virus pandemic is still ravaging the world with its ongoing resurgence and the continuous mutation, suggesting the need for continuous research on safe and effective novel vaccines. Presently several types of vaccines have been developed and emerged in the global market to control COVID-19 virus. Consequently, the knowledge and information on COVID-19 have been expanding at a high level. Researchers need to gain relevant knowledge regarding the different vaccines;however scattered information makes this process time-consuming and laborious. The present study aimed to evaluate the characteristics and trends in global COVID-19 vaccine high-cited literature using bibliometric and visualizations methods and offer some directions and suggestions for future research. Methodology: Studies published between December 2019 and 22 Nov 2022 on COVID-19 vaccines were retrieved from the Scopus database. From the 16026 studies retrieved, 406 were identified as high-cited papers (HCPs) having received 100 or more citations. From the 406 HCPs, information about publications outputs, countries, institutions, journals, keywords, and citation counts was identified. Data analysis and visualization were conducted using Microsoft Excel, VOSviewer and Bibliometrix R software. Result(s): The 406 global HCPs on COVID-19 vaccines research were identified in Scopus database since Dec 2019 till 30 Nov 2022 using a search strategy, which received 123614 citations, averaging 304.17 citations per publication (CPP). An external funding was received by 53.20% (216 publications), which were cited 76107 times (with an average of 352.35 CPP). The 7086 authors from 694 organizations affiliated to 76 countries and publishing in 121 journals were involved in global COVID-19 vaccine research. The most productive countries were USA (n=213), U.K (n=91), China (n=36) and Germany (n=35). The most impactful countries in terms of citations per paper (CPP) and relative citation index (RCI) were South Africa (794.68 and 2.61), Germany (507.11 and 1.67), U.K. (396.59 and 1.30) and Spain (367.5 and 1.121). The most productive organizations were University of Oxford, U.K., Imperial College London, U.K. (n=25 each), Center for Disease Control and Prevention (CDC), USA and Tel Aviv University (n=19 each) and the most impactful organizations were University of Cambridge, U.K (783.4 and 2.57), Emory University, USA (780.1 and 2.56), John Hopkins Bloomberg School of Public Health, USA (702.67 and 2.31) and National Institute of Allergy and Infectious Diseases. USA (676.41 and 2.22). The most productive authors were A.J. Pollard (n=16) and T. Lambe (n=14) (of University of Oxford), O. Tureci and P.R. Dormitzer (n=12 each) (of BioNTechSE, Germany) and the most impactful were D. Cooper (1239.22 and 4.07), K.J. Janseu (1228.11 and 4.03) (BioNTechSE, Germany, K.A. Swanson (987.0 and 3.24) (University of Oxford, U.K.) and P.R. Dormitzer (983 and 3.23) (BioNTechSE, Germany). The most productive journals were New England Journal of Medicine (n=53), The Lancet (n=28), Nature (n=22) and JAMA (N=17). The most impactful journals (as per citations per paper) were New England Journal of Medicine (613.15), Lancet (496.39), Human Vaccines and Immunotherapeutics (369.67) and Nature (360.64). Among population age groups, the major focus was on adults (51.48%) and Middle Aged (39.16%). Among publication types, the major focus was Clinical Studies (26.85%), Epidemiology (22.66%) and Genetics (21.92%). The most significant keywords by frequency of appearances were "Covid-19" (n=388), "Covid-19 Vaccines" (n=357), "Vaccination" (n=221), "Prevention and Control" (n=181) and "Vaccine Immunogenicity" (n=133), Conclusion(s): The HCPs in COVID-19 vaccine research was done mainly by the authors and institutions of high-income Countries (HIC) and was published in high-impact medical journals. Our research has identified the leading countries, institutions, journals, hotspots and development trend in the field that could provide the foundati n for further investigations. The bibliometric analysis will help the clinicians to rapidly identify the potential collaborative partners, identify significant studies, and research topics within their domains of COVID-19 vaccines.Copyright Author (s) 2023.
ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded, positive-sense RNA virus responsible for COVID-19, requires a set of virally encoded nonstructural proteins that compose a replication-transcription complex (RTC) to replicate its 30 kilobase genome. One such nonstructural protein within the RTC is Nsp13, a highly conserved molecular motor ATPase/helicase. Upon purification of the recombinant SARS-CoV-2 Nsp13 protein expressed using a eukaryotic cell-based system, we biochemically characterized the enzyme by examining its catalytic functions, nucleic acid substrate specificity, and putative protein-nucleic acid remodeling activity. We determined that Nsp13 preferentially interacts with single-stranded (ss) DNA compared to ssRNA during loading to unwind with greater efficiency a partial duplex helicase substrate. The binding affinity of Nsp13 to nucleic acid was confirmed through electrophoretic mobility shift assays (EMSA) by determining that Nsp13 binds to DNA substrates with significantly greater efficiency than RNA. These results demonstrate strand-specific interactions of SARS-CoV-2 Nsp13 that dictate its ability to load and unwind structured nucleic acid substrates. We next determined that Nsp13 catalyzed unwinding of double-stranded (ds) RNA forked duplexes on substrates containing a backbone disruption (neutrally charged polyglycol linker (PGL)) was strongly inhibited when the PGL was positioned in the 5' ssRNA overhang, suggesting an unwinding mechanism in which Nsp13 is strictly sensitive to perturbation of the translocating strand sugar-phosphate backbone integrity. Furthermore, we demonstrated for the first time the ability of the coronavirus Nsp13 helicase to disrupt a high-affinity nucleic acid-protein interaction, i.e., a streptavidin tetramer bound to biotinylated RNA or DNA substrate, in a uni-directional manner and with a preferential displacement of the streptavidin complex from biotinylated ssDNA versus ssRNA. In contrast to the poorly hydrolysable ATP-gamma-S or non-hydrolysable AMP-PNP, ATP supports Nsp13-catalyzed disruption of the nucleic acidprotein complex, suggesting that nucleotide binding by Nsp13 is not sufficient for protein-RNA disruption and the chemical energy of nucleoside triphosphate hydrolysis is required to fuel remodeling of protein bound to RNA or DNA. Our results build upon structural studies of the SARS-CoV-2 RTC in which it was suggested that Nsp13 pushes the RNA polymerase (Nsp12) backward on the template RNA strand. Experimental evidence from our studies demonstrate that Nsp13 helicase efficiently remodels a large high affinity protein-RNA complex in a manner dependent on its intrinsic ATP hydrolysis function. We proposed that this novel biochemical activity of Nsp13 is relevant to its role in SARS-CoV-2 RNA processing functions and replication. It was proposed that Nsp13 facilitates proofreading during coronavirus replication when a mismatched base is inadvertently incorporated into the SARS-CoV-2 genome during replication to reposition the RTC so that the proofreading nuclease complex (Nsp14-Nsp10) can gain access and remove the nascently synthesized nucleotide to ensure polymerase fidelity. Our findings implicate a direct catalytic role of Nsp13 in protein-RNA remodeling during coronavirus genome replication beyond its duplex strand separation or structural stabilization of the RTC, yielding new insight into the proofreading mechanism. This work was supported by the Intramural Training Program, National Institute on Aging (NIA), NIH, and a Special COVID-19 Grant from the Office of the Scientific Director, NIA, NIH.Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.