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1.
Hum Mol Genet ; 29(6): 955-966, 2020 04 15.
Article in English | MEDLINE | ID: covidwho-1455300

ABSTRACT

γ-secretase is a macromolecular complex that catalyzes intramembranous hydrolysis of more than 100 membrane-bound substrates. The complex is composed of presenilin (PS1 or PS2), anterior pharynx defect-1 (APH-1), nicastrin (NCT) and PEN-2 and early-onset; autosomal dominant forms of Alzheimer's disease (AD) are caused by inheritance of mutations of PS. No mutations in genes encoding NCT, or PEN-2 have been identified to date that cause AD. In this regard, a large genetic meta-analysis of four cohorts consisting of more than 600 000 individuals identified a common missense variant, rs117618017 in the APH1B gene that results in a T27I mutation, as a novel genome-wide significant locus. In order to confirm the findings that rs117618017 is associated with risk of AD, we performed a genetic screen from deep whole genome sequencing of the large NIMH family-based Alzheimer's Disease (AD) dataset. In parallel, we sought to uncover potential molecular mechanism(s) by which APH-1B T27I might be associated with AD by generating stable HEK293 cell lines, wherein endogenous APH-1A and APH-1B expression was silenced and into which either the wild type APH-1B or the APH-1B T27I variant was stably expressed. We then tested the impact of expressing either the wild type APH-1B or the APH-1B T27I variant on γ-secretase processing of human APP, the murine Notch derivative mNΔE and human neuregulin-1. We now report that we fail to confirm the association of rs1047552 with AD in our cohort and that cells expressing the APH-1B T27I variant show no discernable impact on the γ-secretase processing of established substrates compared with cells expressing wild-type APH-1B.


Subject(s)
Alzheimer Disease/pathology , Amyloid Precursor Protein Secretases/metabolism , Endopeptidases/genetics , Membrane Proteins/genetics , Polymorphism, Single Nucleotide , Alzheimer Disease/genetics , HEK293 Cells , Humans , Mutation , Protein Binding
2.
Genet Epidemiol ; 45(7): 685-693, 2021 10.
Article in English | MEDLINE | ID: covidwho-1279364

ABSTRACT

SARS-CoV-2 mortality has been extensively studied in relation to host susceptibility. How sequence variations in the SARS-CoV-2 genome affect pathogenicity is poorly understood. Starting in October 2020, using the methodology of genome-wide association studies (GWAS), we looked at the association between whole-genome sequencing (WGS) data of the virus and COVID-19 mortality as a potential method of early identification of highly pathogenic strains to target for containment. Although continuously updating our analysis, in December 2020, we analyzed 7548 single-stranded SARS-CoV-2 genomes of COVID-19 patients in the GISAID database and associated variants with mortality using a logistic regression. In total, evaluating 29,891 sequenced loci of the viral genome for association with patient/host mortality, two loci, at 12,053 and 25,088 bp, achieved genome-wide significance (p values of 4.09e-09 and 4.41e-23, respectively), though only 25,088 bp remained significant in follow-up analyses. Our association findings were exclusively driven by the samples that were submitted from Brazil (p value of 4.90e-13 for 25,088 bp). The mutation frequency of 25,088 bp in the Brazilian samples on GISAID has rapidly increased from about 0.4 in October/December 2020 to 0.77 in March 2021. Although GWAS methodology is suitable for samples in which mutation frequencies varies between geographical regions, it cannot account for mutation frequencies that change rapidly overtime, rendering a GWAS follow-up analysis of the GISAID samples that have been submitted after December 2020 as invalid. The locus at 25,088 bp is located in the P.1 strain, which later (April 2021) became one of the distinguishing loci (precisely, substitution V1176F) of the Brazilian strain as defined by the Centers for Disease Control. Specifically, the mutations at 25,088 bp occur in the S2 subunit of the SARS-CoV-2 spike protein, which plays a key role in viral entry of target host cells. Since the mutations alter amino acid coding sequences, they potentially imposing structural changes that could enhance viral infectivity and symptom severity. Our analysis suggests that GWAS methodology can provide suitable analysis tools for the real-time detection of new more transmissible and pathogenic viral strains in databases such as GISAID, though new approaches are needed to accommodate rapidly changing mutation frequencies over time, in the presence of simultaneously changing case/control ratios. Improvements of the associated metadata/patient information in terms of quality and availability will also be important to fully utilize the potential of GWAS methodology in this field.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Brazil , Genome-Wide Association Study , Humans , Mutation , Phylogeny , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/genetics
3.
J Neurotrauma ; 38(1): 1-43, 2021 01 01.
Article in English | MEDLINE | ID: covidwho-1066221

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus attacks multiple organs of coronavirus disease 2019 (COVID-19) patients, including the brain. There are worldwide descriptions of neurological deficits in COVID-19 patients. Central nervous system (CNS) symptoms can be present early in the course of the disease. As many as 55% of hospitalized COVID-19 patients have been reported to have neurological disturbances three months after infection by SARS-CoV-2. The mutability of the SARS-COV-2 virus and its potential to directly affect the CNS highlight the urgency of developing technology to diagnose, manage, and treat brain injury in COVID-19 patients. The pathobiology of CNS infection by SARS-CoV-2 and the associated neurological sequelae of this infection remain poorly understood. In this review, we outline the rationale for the use of blood biomarkers (BBs) for diagnosis of brain injury in COVID-19 patients, the research needed to incorporate their use into clinical practice, and the improvements in patient management and outcomes that can result. BBs of brain injury could potentially provide tools for detection of brain injury in COVID-19 patients. Elevations of BBs have been reported in cerebrospinal fluid (CSF) and blood of COVID-19 patients. BB proteins have been analyzed in CSF to detect CNS involvement in patients with infectious diseases, including human immunodeficiency virus and tuberculous meningitis. BBs are approved by the U.S. Food and Drug Administration for diagnosis of mild versus moderate traumatic brain injury and have identified brain injury after stroke, cardiac arrest, hypoxia, and epilepsy. BBs, integrated with other diagnostic tools, could enhance understanding of viral mechanisms of brain injury, predict severity of neurological deficits, guide triage of patients and assignment to appropriate medical pathways, and assess efficacy of therapeutic interventions in COVID-19 patients.


Subject(s)
Brain Injuries/blood , Brain Injuries/diagnosis , Brain/metabolism , COVID-19/blood , COVID-19/diagnosis , Biomarkers/blood , Brain/pathology , Brain Injuries/etiology , COVID-19/complications , Humans , Nervous System Diseases/blood , Nervous System Diseases/diagnosis , Nervous System Diseases/etiology , Prospective Studies , Retrospective Studies
4.
J Altern Complement Med ; 26(7): 547-556, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-612822

ABSTRACT

Editor's Note: As an acute condition quickly associated with multiple chronic susceptibilities, COVID-19 has rekindled interest in, and controversy about, the potential role of the host in disease processes. While hundreds of millions of research dollars have been funneled into drug and vaccine solutions that target the external agent, integrative practitioners tuned to enhancing immunity faced a familiar mostly unfunded task. First, go to school on the virus. Then draw from the global array of natural therapies and practices with host-enhancing or anti-viral capabilities to suggest integrative treatment strategies. The near null-set of conventional treatment options propels this investigation. In this paper, researchers from the Massachusetts Institute of Technology, University of California-San Diego, Chopra Library for Integrative Studies, and Harvard University share one such exploration. Their conclusion, that "certain meditation, yoga asana (postures), and pranayama (breathing) practices may possibly be effective adjunctive means of treating and/or preventing SARS-CoV-2 infection" underscores the importance of this rekindling. At JACM, we are pleased to have the opportunity to publish this work. We hope that it might help diminish in medicine and health the polarization that, like so much in the broader culture, seems to be an obstacle to healing. -John Weeks, Editor-in-Chief, JACM.


Subject(s)
Coronavirus Infections/therapy , Infection Control/methods , Meditation , Pneumonia, Viral/therapy , Yoga , Betacoronavirus , COVID-19 , Coronavirus Infections/prevention & control , Humans , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , SARS-CoV-2
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