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Safdar B, Wang M, Guo X, Cha C, Chun HJ, Deng Y, Dziura J, El-Khoury JM, Gorelick F, Ko AI, Lee AI, Safirstein R, Simonov M, Zhou B, Desir GV. Association of renalase with clinical outcomes in hospitalized patients with COVID-19. PLoS One 2022; 17:e0264178. [PMID: 35259186 PMCID: PMC8903289 DOI: 10.1371/journal.pone.0264178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/04/2022] [Indexed: 12/27/2022] Open
Abstract
Renalase is a secreted flavoprotein with anti-inflammatory and pro-cell survival properties. COVID-19 is associated with disordered inflammation and apoptosis. We hypothesized that blood renalase levels would correspond to severe COVID-19 and survival. In this retrospective cohort study, clinicopathologic data and blood samples were collected from hospitalized COVID-19 subjects (March—June 2020) at a single institution tertiary hospital. Plasma renalase and cytokine levels were measured and clinical data abstracted from health records. Of 3,450 COVID-19 patients, 458 patients were enrolled. Patients were excluded if <18 years, or opted out of research. The primary composite outcome was intubation or death within 180 days. Secondary outcomes included mortality alone, intensive care unit admission, use of vasopressors, and CPR. Enrolled patients had mean age 64 years (SD±17), were 53% males, and 48% non-whites. Mean renalase levels was 14,108·4 ng/ml (SD±8,137 ng/ml). Compared to patients with high renalase, those with low renalase (< 8,922 ng/ml) were more likely to present with hypoxia, increased ICU admission (54% vs. 33%, p < 0.001), and cardiopulmonary resuscitation (10% vs. 4%, p = 0·023). In Cox proportional hazard model, every 1000 ng/ml increase in renalase decreased the risk of death or intubation by 5% (HR 0·95; 95% CI 0·91–0·98) and increased survival alone by 6% (HR 0·95; CI 0·90–0·98), after adjusting for socio-demographics, initial disease severity, comorbidities and inflammation. Patients with high renalase-low IL-6 levels had the best survival compared to other groups (p = 0·04). Renalase was independently associated with reduced intubation and mortality in hospitalized COVID-19 patients. Future studies should assess the pathophysiological relevance of renalase in COVID-19 disease.
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Affiliation(s)
- Basmah Safdar
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
| | - Melinda Wang
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Xiaojia Guo
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA CT HealthCare, West Haven, Connecticut, United States of America
| | - Charles Cha
- Department of Surgery, Hartford HealthCare, Hartford, Connecticut, United States of America
| | - Hyung J. Chun
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Yanhong Deng
- Yale Center of Analytics Sciences, New Haven, Connecticut, United States of America
| | - James Dziura
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Center of Analytics Sciences, New Haven, Connecticut, United States of America
| | - Joe M. El-Khoury
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Fred Gorelick
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Center of Analytics Sciences, New Haven, Connecticut, United States of America
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Alfred I. Lee
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Safirstein
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA CT HealthCare, West Haven, Connecticut, United States of America
| | - Michael Simonov
- Yale Center of Analytics Sciences, New Haven, Connecticut, United States of America
| | - Bin Zhou
- Yale Center of Analytics Sciences, New Haven, Connecticut, United States of America
| | - Gary V. Desir
- Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- VA CT HealthCare, West Haven, Connecticut, United States of America
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2
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Li B, Spronk D, Luo Y, Puett C, Inscoe CR, Tyndall DA, Lee YZ, Lu J, Zhou O. Feasibility of dual-energy CBCT by spectral filtration of a dual-focus CNT x-ray source. PLoS One 2022; 17:e0262713. [PMID: 35113908 PMCID: PMC8812859 DOI: 10.1371/journal.pone.0262713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 01/01/2022] [Indexed: 11/19/2022] Open
Abstract
Cone beam computed tomography (CBCT) is now widely used in dentistry and growing areas of medical imaging. The presence of strong metal artifacts is however a major concern of using CBCT especially in dentistry due to the presence of highly attenuating dental restorations, fixed appliances, and implants. Virtual monoenergetic images (VMIs) synthesized from dual energy CT (DECT) datasets are known to reduce metal artifacts. Although several techniques exist for DECT imaging, they in general come with significantly increased equipment cost and not available in dental clinics. The objectives of this study were to investigate the feasibility of developing a low-cost dual energy CBCT (DE-CBCT) by retrofitting a regular CBCT scanner with a carbon nanotube (CNT) x-ray source with dual focal spots and corresponding low-energy (LE) and high-energy (HE) spectral filters. A testbed with a CNT field emission x-ray source (NuRay Technology, Chang Zhou, China), a flat panel detector (Teledyne, Waterloo, Canada), and a rotating object stage was used for this feasibility study. Two distinct polychromatic x-ray spectra with the mean photon energies of 66.7keV and 86.3keV were produced at a fixed 120kVp x-ray tube voltage by using Al+Au and Al+Sn foils as the respective LE and HE filters attached to the exist window of the x-ray source. The HE filter attenuated the x-ray photons more than the LE filter. The calculated post-object air kerma rate of the HE beam was 31.7% of the LE beam. An anthropomorphic head phantom (RANDO, Nuclear Associates, Hicksville, NY) with metal beads was imaged using the testbed and the images were reconstructed using an iterative volumetric CT reconstruction algorithm. The VMIs were synthesized using an image-domain basis materials decomposition method with energy ranging from 30 to 150keV. The results were compared to the reconstructed images from a single energy clinical dental CBCT scanner (CS9300, Carestream Dental, Atlanta, GA). A significant reduction of the metal artifacts was observed in the VMI images synthesized at high energies compared to those from the same object imaged by the clinical dental CBCT scanner. The ability of the CNT x-ray source to generate the output needed to compensate the reduction of photon flux due to attenuation from the spectral filters and to maintain the CT imaging time was evaluated. The results demonstrated the feasibility of DE-CBCT imaging using the proposed approach. Metal artifact reduction was achieved in VMIs synthesized. The x-ray output needed for the proposed DE-CBCT can be generated by a fixed-anode CNT x-ray source.
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Affiliation(s)
- Boyuan Li
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Derrek Spronk
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yueting Luo
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Connor Puett
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Christina R. Inscoe
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Donald A. Tyndall
- Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Yueh Z. Lee
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Jianping Lu
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Otto Zhou
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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Celone M, Okech B, Han BA, Forshey BM, Anyamba A, Dunford J, Rutherford G, Mita-Mendoza NK, Estallo EL, Khouri R, de Siqueira IC, Pollett S. A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus. PLoS Negl Trop Dis 2021; 15:e0010016. [PMID: 34898602 PMCID: PMC8699665 DOI: 10.1371/journal.pntd.0010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/23/2021] [Accepted: 11/22/2021] [Indexed: 12/14/2022] Open
Abstract
Improving our understanding of Mayaro virus (MAYV) ecology is critical to guide surveillance and risk assessment. We conducted a PRISMA-adherent systematic review of the published and grey literature to identify potential arthropod vectors and non-human animal reservoirs of MAYV. We searched PubMed/MEDLINE, Embase, Web of Science, SciELO and grey-literature sources including PAHO databases and dissertation repositories. Studies were included if they assessed MAYV virological/immunological measured occurrence in field-caught, domestic, or sentinel animals or in field-caught arthropods. We conducted an animal seroprevalence meta-analysis using a random effects model. We compiled granular georeferenced maps of non-human MAYV occurrence and graded the quality of the studies using a customized framework. Overall, 57 studies were eligible out of 1523 screened, published between the years 1961 and 2020. Seventeen studies reported MAYV positivity in wild mammals, birds, or reptiles and five studies reported MAYV positivity in domestic animals. MAYV positivity was reported in 12 orders of wild-caught vertebrates, most frequently in the orders Charadriiformes and Primate. Sixteen studies detected MAYV in wild-caught mosquito genera including Haemagogus, Aedes, Culex, Psorophora, Coquillettidia, and Sabethes. Vertebrate animals or arthropods with MAYV were detected in Brazil, Panama, Peru, French Guiana, Colombia, Trinidad, Venezuela, Argentina, and Paraguay. Among non-human vertebrates, the Primate order had the highest pooled seroprevalence at 13.1% (95% CI: 4.3-25.1%). From the three most studied primate genera we found the highest seroprevalence was in Alouatta (32.2%, 95% CI: 0.0-79.2%), followed by Callithrix (17.8%, 95% CI: 8.6-28.5%), and Cebus/Sapajus (3.7%, 95% CI: 0.0-11.1%). We further found that MAYV occurs in a wide range of vectors beyond Haemagogus spp. The quality of evidence behind these findings was variable and prompts calls for standardization of reporting of arbovirus occurrence. These findings support further risk emergence prediction, guide field surveillance efforts, and prompt further in-vivo studies to better define the ecological drivers of MAYV maintenance and potential for emergence.
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Affiliation(s)
- Michael Celone
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - Bernard Okech
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - Barbara A. Han
- Cary Institute of Ecosystem Studies, Millbrook, New York, United States of America
| | - Brett M. Forshey
- Armed Forces Health Surveillance Division, Silver Spring, Maryland, United States of America
| | - Assaf Anyamba
- University Space Research Association & NASA/Goddard Space Flight Center, Biospheric Sciences Laboratory, Greenbelt, Maryland, United States of America
| | - James Dunford
- Uniformed Services University of the Health Sciences, F. Edward Hébert School of Medicine, Department of Preventive Medicine & Biostatistics, Bethesda, Maryland, United States of America
| | - George Rutherford
- Institute for Global Health Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | | | - Elizabet Lilia Estallo
- Instituto de Investigaciones Biológicas y Tecnológicas (IIByT) CONICET-Universidad Nacional de Córdoba, Centro de Investigaciones Entomológicas de Córdoba, Córdoba, Argentina
| | - Ricardo Khouri
- Instituto Gonçalo Moniz-Fiocruz, R. Waldemar Falcão, Salvador, Bahia, Brazil
| | | | - Simon Pollett
- Infectious Disease Clinical Research Program, Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
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De La Rosa-Reyes V, Duprey-Díaz MV, Blagburn JM, Blanco RE. Retinoic acid treatment recruits macrophages and increases axonal regeneration after optic nerve injury in the frog Rana pipiens. PLoS One 2021; 16:e0255196. [PMID: 34739478 PMCID: PMC8570512 DOI: 10.1371/journal.pone.0255196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/21/2021] [Indexed: 11/18/2022] Open
Abstract
Retinoic acid (RA) plays major roles during nervous system development, and during regeneration of the adult nervous system. We have previously shown that components of the RA signaling pathway are upregulated after optic nerve injury, and that exogenous application of all-trans retinoic acid (ATRA) greatly increases the survival of axotomized retinal ganglion cells (RGCs). The objective of the present study is to investigate the effects of ATRA application on the macrophages in the optic nerve after injury, and to determine whether this affects axonal regeneration. The optic nerve was crushed and treated with PBS, ATRA and/or clodronate-loaded liposomes. Nerves were examined at one and two weeks after axotomy with light microscopy, immunocytochemistry and electron microscopy. ATRA application to the optic nerve caused transient increases in the number of macrophages and microglia one week after injury. The macrophages are consistently labeled with M2-type markers, and have considerable phagocytic activity. ATRA increased ultrastructural features of ongoing phagocytic activity in macrophages at one and two weeks. ATRA treatment also significantly increased the numbers of regenerating GAP-43-labeled axons. Clodronate liposome treatment depleted macrophage numbers by 80%, completely eliminated the ATRA-mediated increase in axonal regeneration, and clodronate treatment alone decreased axonal numbers by 30%. These results suggest that the success of axon regeneration is partially dependent on the presence of debris-phagocytosing macrophages, and that the increases in regeneration caused by ATRA are in part due to their increased numbers. Further studies will examine whether macrophage depletion affects RGC survival.
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Affiliation(s)
- Valeria De La Rosa-Reyes
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Mildred V. Duprey-Díaz
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
| | - Jonathan M. Blagburn
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Rosa E. Blanco
- Department of Anatomy and Neurobiology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
- Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico, United States of America
- * E-mail:
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Yates PL, Patil A, Sun X, Niceforo A, Gill R, Callahan P, Beck W, Piermarini E, Terry AV, Sullivan KA, Baas PW, Qiang L. A cellular approach to understanding and treating Gulf War Illness. Cell Mol Life Sci 2021; 78:6941-6961. [PMID: 34580742 PMCID: PMC9669894 DOI: 10.1007/s00018-021-03942-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023]
Abstract
Gulf War Illness (GWI), a disorder suffered by approximately 200,000 veterans of the first Gulf War, was caused by exposure to low-level organophosphate pesticides and nerve agents in combination with battlefield stress. To elucidate the mechanistic basis of the brain-related symptoms of GWI, human-induced pluripotent stem cells (hiPSCs) derived from veterans with or without GWI were differentiated into forebrain glutamatergic neurons and then exposed to a Gulf War (GW) relevant toxicant regimen consisting of a sarin analog and cortisol, a human stress hormone. Elevated levels of total and phosphorylated tau, reduced microtubule acetylation, altered mitochondrial dynamics/transport, and decreased neuronal activity were observed in neurons exposed to the toxicant regimen. Some of the data are consistent with the possibility that some veterans may have been predisposed to acquire GWI. Wistar rats exposed to a similar toxicant regimen showed a mild learning and memory deficit, as well as cell loss and tau pathology selectively in the CA3 region of the hippocampus. These cellular responses offer a mechanistic explanation for the memory loss suffered by veterans with GWI and provide a cell-based model for screening drugs and developing personalized therapies for these veterans.
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Affiliation(s)
- Philip L Yates
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Ankita Patil
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Xiaohuan Sun
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Alessia Niceforo
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Ramnik Gill
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Patrick Callahan
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Wayne Beck
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Emanuela Piermarini
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Alvin V Terry
- Department of Pharmacology and Toxicology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Kimberly A Sullivan
- Department of Environmental Health, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Peter W Baas
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA
| | - Liang Qiang
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, 2900 Queen Lane, Philadelphia, PA, 19129, USA.
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Zhang J, Liang Y, Bradford WH, Sheikh F. Desmosomes: emerging pathways and non-canonical functions in cardiac arrhythmias and disease. Biophys Rev 2021; 13:697-706. [PMID: 34765046 PMCID: PMC8555023 DOI: 10.1007/s12551-021-00829-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/12/2021] [Indexed: 12/14/2022] Open
Abstract
Desmosomes are critical adhesion structures in cardiomyocytes, with mutation/loss linked to the heritable cardiac disease, arrhythmogenic right ventricular cardiomyopathy (ARVC). Early studies revealed the ability of desmosomal protein loss to trigger ARVC disease features including structural remodeling, arrhythmias, and inflammation; however, the precise mechanisms contributing to diverse disease presentations are not fully understood. Recent mechanistic studies demonstrated the protein degradation component CSN6 is a resident cardiac desmosomal protein which selectively restricts cardiomyocyte desmosomal degradation and disease. This suggests defects in protein degradation can trigger the structural remodeling underlying ARVC. Additionally, a subset of ARVC-related mutations show enhanced vulnerability to calpain-mediated degradation, further supporting the relevance of these mechanisms in disease. Desmosomal gene mutations/loss has been shown to impact arrhythmogenic pathways in the absence of structural disease within ARVC patients and model systems. Studies have shown the involvement of connexins, calcium handling machinery, and sodium channels as early drivers of arrhythmias, suggesting these may be distinct pathways regulating electrical function from the desmosome. Emerging evidence has suggested inflammation may be an early mechanism in disease pathogenesis, as clinical reports have shown an overlap between myocarditis and ARVC. Recent studies focus on the association between desmosomal mutations/loss and inflammatory processes including autoantibodies and signaling pathways as a way to understand the involvement of inflammation in ARVC pathogenesis. A specific focus will be to dissect ongoing fields of investigation to highlight diverse pathogenic pathways associated with desmosomal mutations/loss.
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Affiliation(s)
- Jing Zhang
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Yan Liang
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - William H. Bradford
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Farah Sheikh
- Department of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
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Corley MJ, Sacdalan C, Pang APS, Chomchey N, Ratnaratorn N, Valcour V, Kroon E, Cho KS, Belden AC, Colby D, Robb M, Hsu D, Spudich S, Paul R, Vasan S, Ndhlovu LC. Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART. PLoS Pathog 2021; 17:e1009785. [PMID: 34388205 PMCID: PMC8386872 DOI: 10.1371/journal.ppat.1009785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/25/2021] [Accepted: 07/06/2021] [Indexed: 02/06/2023] Open
Abstract
HIV-1 disrupts the host epigenetic landscape with consequences for disease pathogenesis, viral persistence, and HIV-associated comorbidities. Here, we examined how soon after infection HIV-associated epigenetic changes may occur in blood and whether early initiation of antiretroviral therapy (ART) impacts epigenetic modifications. We profiled longitudinal genome-wide DNA methylation in monocytes and CD4+ T lymphocytes from 22 participants in the RV254/SEARCH010 acute HIV infection (AHI) cohort that diagnoses infection within weeks after estimated exposure and immediately initiates ART. We identified monocytes harbored 22,697 differentially methylated CpGs associated with AHI compared to 294 in CD4+ T lymphocytes. ART minimally restored less than 1% of these changes in monocytes and had no effect upon T cells. Monocyte DNA methylation patterns associated with viral load, CD4 count, CD4/CD8 ratio, and longitudinal clinical phenotypes. Our findings suggest HIV-1 rapidly embeds an epigenetic memory not mitigated by ART and support determining epigenetic signatures in precision HIV medicine. Trial Registration:NCT00782808 and NCT00796146. The epigenetic marker, DNA methylation, plays a key role regulating the immune system during host-pathogen interactions. Using cell-type specific DNA methylation profiling, we explored whether epigenetic changes occurred soon after HIV infection and following early treatment with anti-HIV drugs. Acute infection was associated with early DNA methylation changes in purified monocytes and CD4+ T cells isolated from blood. In monocytes, rapid anti-HIV treatment minimally restored DNA methylation changes associated with infection and unexpectedly had no impact in CD4+ T cells. DNA methylation patterns before treatment informed long term clinical outcomes including CD4+ T cell counts and favorable clinical phenotypes. These findings identify candidates for consideration in epigenome editing approaches in HIV prevention, treatment, and cure strategies.
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Affiliation(s)
- Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Carlo Sacdalan
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Alina P. S. Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
| | - Nitiya Chomchey
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | | | - Victor Valcour
- Memory and Aging Center, University of California San Francisco; San Francisco, California, United States of America
| | - Eugene Kroon
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Kyu S. Cho
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Andrew C. Belden
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Donn Colby
- Institute of HIV Research and Innovation; Bangkok, Thailand
- SEARCH, South East Asia Research Collaboration in HIV; Bangkok, Thailand
| | - Merlin Robb
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Denise Hsu
- Armed Forces Research Institute of Medical Sciences; Bangkok, Thailand
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
| | - Serena Spudich
- Department of Neurology, Yale University; New Haven, Connecticut, United States of America
| | - Robert Paul
- Missouri Institute of Mental Health University of Missouri; St. Louis, Missouri, United States of America
| | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine; Bethesda, Maryland, United States of America
- US Military HIV Research Program; Silver Spring, Maryland, United States of America
| | - Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine; New York, New York, United States of America
- * E-mail:
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8
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Coyne AN, Rothstein JD. The ESCRT-III protein VPS4, but not CHMP4B or CHMP2B, is pathologically increased in familial and sporadic ALS neuronal nuclei. Acta Neuropathol Commun 2021; 9:127. [PMID: 34281622 PMCID: PMC8287756 DOI: 10.1186/s40478-021-01228-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Nuclear pore complex injury has recently emerged as an early and significant contributor to familial and sporadic ALS disease pathogenesis. However, the molecular events leading to this pathological phenomenon characterized by the reduction of specific nucleoporins from neuronal nuclear pore complexes remain largely unknown. This is due in part to a lack of knowledge regarding the biological pathways and proteins underlying nuclear pore complex homeostasis specifically in human neurons. We have recently uncovered that aberrant nuclear accumulation of the ESCRT-III protein CHMP7 initiates nuclear pore complex in familial and sporadic ALS neurons. In yeast and non-neuronal mammalian cells, nuclear relocalization of CHMP7 has been shown to recruit the ESCRT-III proteins CHMP4B, CHMP2B, and VPS4 to facilitate nuclear pore complex and nuclear envelope repair and homeostasis. Here, using super resolution structured illumination microscopy, we find that neither CHMP4B nor CHMP2B are increased in ALS neuronal nuclei. In contrast, VPS4 expression is significantly increased in ALS neuronal nuclei prior to the emergence of nuclear pore injury in a CHMP7 dependent manner. However, unlike our prior CHMP7 knockdown studies, impaired VPS4 function does not mitigate alterations to the NPC and the integral transmembrane nucleoporin POM121. Collectively our data suggest that while alterations in VPS4 subcellular localization appear to be coincident with nuclear pore complex injury, therapeutic efforts to mitigate this pathogenic cascade should be targeted towards upstream events such as the nuclear accumulation of CHMP7 as we have previously described.
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Affiliation(s)
- Alyssa N. Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
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Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 2021; 22:190. [PMID: 34183059 PMCID: PMC8240250 DOI: 10.1186/s13059-021-02411-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
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MESH Headings
- Alternative Splicing
- Antibodies, Bispecific/pharmacology
- Antineoplastic Agents, Immunological/pharmacology
- Artifacts
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Datasets as Topic
- Exons
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Introns
- Models, Biological
- Nucleic Acid Conformation
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Reverse Transcription
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Affiliation(s)
- Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Present address: Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Rangarajan S, Richter JR, Richter RP, Bandari SK, Tripathi K, Vlodavsky I, Sanderson RD. Heparanase-enhanced Shedding of Syndecan-1 and Its Role in Driving Disease Pathogenesis and Progression. J Histochem Cytochem 2020; 68:823-840. [PMID: 32623935 PMCID: PMC7711244 DOI: 10.1369/0022155420937087] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/29/2020] [Indexed: 02/08/2023] Open
Abstract
Both heparanase and syndecan-1 are known to be present and active in disease pathobiology. An important feature of syndecan-1 related to its role in pathologies is that it can be shed from the surface of cells as an intact ectodomain composed of the extracellular core protein and attached heparan sulfate and chondroitin sulfate chains. Shed syndecan-1 remains functional and impacts cell behavior both locally and distally from its cell of origin. Shedding of syndecan-1 is initiated by a variety of stimuli and accomplished predominantly by the action of matrix metalloproteinases. The accessibility of these proteases to the core protein of syndecan-1 is enhanced, and shedding facilitated, when the heparan sulfate chains of syndecan-1 have been shortened by the enzymatic activity of heparanase. Interestingly, heparanase also enhances shedding by upregulating the expression of matrix metalloproteinases. Recent studies have revealed that heparanase-induced syndecan-1 shedding contributes to the pathogenesis and progression of cancer and viral infection, as well as other septic and non-septic inflammatory states. This review discusses the heparanase/shed syndecan-1 axis in disease pathogenesis and progression, the potential of targeting this axis therapeutically, and the possibility that this axis is widespread and of influence in many diseases.
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Affiliation(s)
| | | | | | | | | | - Israel Vlodavsky
- The University of Alabama at Birmingham, Birmingham, Alabama, and Technion Integrated Cancer Center, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
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