105 results on '"Arumugaswami V"'
Search Results
2. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery
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Mulay, A., primary, Konda, B., additional, Garcia, G., additional, Yao, C., additional, Beil, S., additional, Sen, C., additional, Purkayastha, A., additional, Kolls, J. K., additional, Pociask, D. A., additional, Pessina, P., additional, Sainz de Aja, J., additional, Garcia-de-Alba, C., additional, Kim, C. F., additional, Gomperts, B., additional, Arumugaswami, V., additional, and Stripp, B.R., additional
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- 2020
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3. Marek's disease virus reactivation from latency: changes in gene expression at the origin of replication
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Parcells, MS, primary, Arumugaswami, V, additional, Prigge, JT, additional, Pandya, K, additional, and Dienglewicz, RL, additional
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- 2003
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4. Mpox Virus and its ocular surface manifestations.
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Chakravarty N, Hemani D, Paravastu R, Ahmad Z, Palani SN, Arumugaswami V, and Kumar A
- Abstract
The Mpox virus (MPXV) is the causative agent of human Mpox disease - a debilitating rash illness similar to smallpox. Although Clade I MPXV has remained endemic to West and Central Africa, Clade II MPXV has been responsible for many outbreaks worldwide. The most recent outbreak in 2022 resulted from the rapid spread of a new clade of MPXV, classified into Clade IIb - a distinct lineage from the previously circulating viral strains. The rapid spread and increased severity of Mpox disease by the Clade IIb strain have raised the serious public health imperative of better understanding the host and viral determinants during MPXV infection. In addition to typical skin rashes, including in the periorbital area, MPXV causes moderate to severe ophthalmic manifestations - most commonly, ocular surface complications (e.g., keratitis, conjunctivitis, blepharitis). While ocular manifestations of Clade I Mpox within the Congo basin have been well-reported, global incidence trends of ocular Mpox cases by Clade IIb are still emerging. Given the demonstrated ability of all MPXV strains to auto-inoculate ocular tissue, alongside the enhanced transmissibility of the Clade IIb virus, there is an urgent need to elucidate the mechanisms by which MPXV causes ocular anomalies. In this review, we discuss the viral and genomic structures of MPXV, the epidemiology, and pathology of systemic and ocular Mpox, as well as potential prophylactic and therapeutic interventions., Competing Interests: Declaration of competing interest The authors have no conflicts of interest to disclose., (Copyright © 2024 Elsevier Inc. All rights reserved.)
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- 2024
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5. Envelope protein-specific B cell receptors direct lentiviral vector tropism in vivo.
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Takano KA, Wong AAL, Brown R, Situ K, Chua BA, Abu AE, Pham TT, Reyes GC, Ramachandran S, Kamata M, Li MMH, Wu TT, Rao DS, Arumugaswami V, Dorshkind K, Cole S, and Morizono K
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- Animals, Mice, Viral Tropism, Humans, Virus Internalization, Lentivirus genetics, Receptors, Antigen, B-Cell metabolism, Receptors, Antigen, B-Cell genetics, Genetic Vectors genetics, Genetic Vectors administration & dosage, Transduction, Genetic, B-Lymphocytes metabolism, B-Lymphocytes immunology, Viral Envelope Proteins genetics, Viral Envelope Proteins metabolism, Transgenes
- Abstract
While studying transgene expression after systemic administration of lentiviral vectors, we found that splenic B cells are robustly transduced, regardless of the types of pseudotyped envelope proteins. However, the administration of two different pseudotypes resulted in transduction of two distinct B cell populations, suggesting that each pseudotype uses unique and specific receptors for its attachment and entry into splenic B cells. Single-cell RNA sequencing analysis of the transduced cells demonstrated that different pseudotypes transduce distinct B cell subpopulations characterized by specific B cell receptor (BCR) genotypes. Functional analysis of the BCRs of the transduced cells demonstrated that BCRs specific to the pseudotyping envelope proteins mediate viral entry, enabling the vectors to selectively transduce the B cell populations that are capable of producing antibodies specific to their envelope proteins. Lentiviral vector entry via the BCR activated the transduced B cells and induced proliferation and differentiation into mature effectors, such as memory B and plasma cells. BCR-mediated viral entry into clonally specific B cell subpopulations raises new concepts for understanding the biodistribution of transgene expression after systemic administration of lentiviral vectors and offers new opportunities for BCR-targeted gene delivery by pseudotyped lentiviral vectors., Competing Interests: Declaration of interests K.M. holds 2 US patents (US patent numbers 8449875 and 9163248) related to this work., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2024
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6. Harnessing Biomaterials to Amplify Immunity in Aged Mice through T Memory Stem Cells.
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Hasani-Sadrabadi MM, Majedi FS, Zarubova J, Thauland TJ, Arumugaswami V, Hsiai TK, Bouchard LS, Butte MJ, and Li S
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- Mice, Humans, Animals, Immunologic Memory, Biocompatible Materials, Stem Cells, CD8-Positive T-Lymphocytes, Vaccines
- Abstract
The durability of a protective immune response generated by a vaccine depends on its ability to induce long-term T cell immunity, which tends to decline in aging populations. The longest protection appears to arise from T memory stem cells (TMSCs) that confer high expandability and effector functions when challenged. Here we engineered artificial antigen presenting cells (aAPC) with optimized size, stiffness and activation signals to induce human and mouse CD8
+ TMSCs in vitro . This platform was optimized as a vaccine booster of TMSCs (Vax-T) with prolonged release of small-molecule blockade of the glycogen synthase kinase-3β together with target antigens. By using SARS-CoV-2 antigen as a model, we show that a single injection of Vax-T induces durable antigen-specific CD8+ TMSCs in young and aged mice, and generates humoral responses at a level stronger than or similar to soluble vaccines. This Vax-T approach can boost long-term immunity to fight infectious diseases, cancer, and other diseases.- Published
- 2024
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7. Targeting ABCG1 and SREBP-2 mediated cholesterol homeostasis ameliorates Zika virus-induced ocular pathology.
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Singh S, Wright RE 3rd, Giri S, Arumugaswami V, and Kumar A
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Zika virus (ZIKV) infection during pregnancy causes severe neurological and ocular abnormalities in infants, yet no vaccine or antivirals are available. Our transcriptomic analysis of ZIKV-infected retinal pigment epithelial (RPE) cells revealed alterations in the cholesterol pathway. Thus, we investigated the functional roles of ATP binding cassette transporter G1 (ABCG1) and sterol response element binding protein 2 (SREPB-2), two key players in cholesterol metabolism, during ocular ZIKV infection. Our in vitro data showed that increased ABCG1 activity via liver X receptors (LXRs), reduced ZIKV replication, while ABCG1 knockdown increased replication with elevated intracellular cholesterol. Conversely, inhibiting SREBP-2 or its knockdown reduced ZIKV replication by lowering cholesterol levels. In vivo , LXR agonist or SREBP-2 inhibitor treatment mitigated ZIKV-induced chorioretinal lesions in mice, concomitant with decreased expression of inflammatory mediators and increased activation of antiviral response genes. In summary, our study identifies ABCG1's antiviral role and SREBP-2's proviral effects in ocular ZIKV infection, offering cholesterol metabolism as a potential target to develop antiviral therapies., Competing Interests: The authors declare no competing interests., (© 2024 The Author(s).)
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- 2024
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8. A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation.
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Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, and Deb A
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- Mice, Animals, SARS-CoV-2, Inflammation, Cytokines, Diet, Ketogenic, COVID-19
- Abstract
The ketogenic diet (KD) has demonstrated benefits in numerous clinical studies and animal models of disease in modulating the immune response and promoting a systemic anti-inflammatory state. Here we investigate the effects of a KD on systemic toxicity in mice following SARS-CoV-2 infection. Our data indicate that under KD, SARS-CoV-2 reduces weight loss with overall improved animal survival. Muted multi-organ transcriptional reprogramming and metabolism rewiring suggest that a KD initiates and mitigates systemic changes induced by the virus. We observed reduced metalloproteases and increased inflammatory homeostatic protein transcription in the heart, with decreased serum pro-inflammatory cytokines (i.e., TNF-α, IL-15, IL-22, G-CSF, M-CSF, MCP-1), metabolic markers of inflammation (i.e., kynurenine/tryptophane ratio), and inflammatory prostaglandins, indicative of reduced systemic inflammation in animals infected under a KD. Taken together, these data suggest that a KD can alter the transcriptional and metabolic response in animals following SARS-CoV-2 infection with improved mice health, reduced inflammation, and restored amino acid, nucleotide, lipid, and energy currency metabolism., (© 2023. The Author(s).)
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- 2023
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9. The Apolipoprotein E neutralizing antibody inhibits SARS-CoV-2 infection by blocking cellular entry of lipoviral particles.
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Cui Q, Jeyachandran AV, Garcia G, Qin C, Zhou Y, Zhang M, Wang C, Sun G, Liu W, Zhou T, Feng L, Palmer C, Li Z, Aziz A, Gomperts BN, Feng P, Arumugaswami V, and Shi Y
- Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal agent for coronavirus disease 2019 (COVID-19). Although vaccines have helped to prevent uncontrolled viral spreading, our understanding of the fundamental biology of SARS-CoV-2 infection remains insufficient, which hinders effective therapeutic development. Here, we found that Apolipoprotein E (ApoE), a lipid binding protein, is hijacked by SARS-CoV-2 for infection. Preincubation of SARS-CoV-2 with a neutralizing antibody specific to ApoE led to inhibition of SARS-CoV-2 infection. The ApoE neutralizing antibody efficiently blocked SARS-CoV-2 infection of human iPSC-derived astrocytes and air-liquid interface organoid models in addition to human ACE2-expressing HEK293T cells and Calu-3 lung cells. ApoE mediates SARS-CoV-2 entry through binding to its cellular receptors such as the low density lipoprotein receptor (LDLR). LDLR knockout or ApoE mutations at the receptor binding domain or an ApoE mimetic peptide reduced SARS-CoV-2 infection. Furthermore, we detected strong membrane LDLR expression on SARS-CoV-2 Spike-positive cells in human lung tissues, whereas no or low ACE2 expression was detected. This study provides a new paradigm for SARS-CoV-2 cellular entry through binding of ApoE on the lipoviral particles to host cell receptor(s). Moreover, this study suggests that ApoE neutralizing antibodies are promising antiviral therapies for COVID-19 by blocking entry of both parental virus and variants of concern., Competing Interests: City of Hope has filed a U.S. Provisional Patent with Application No. 63/506,983 covering aspects of the technologies disclosed in this manuscript. The authors declare no other competing interests., (© 2023 The Authors. MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.)
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- 2023
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10. Differential Susceptibility of Ex Vivo Primary Glioblastoma Tumors to Oncolytic Effect of Modified Zika Virus.
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Garcia G Jr, Chakravarty N, Paiola S, Urena E, Gyani P, Tse C, French SW, Danielpour M, Breunig JJ, Nathanson DA, and Arumugaswami V
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- Animals, Mice, Humans, Phosphatidylinositol 3-Kinases, Glioblastoma metabolism, Zika Virus physiology, Oncolytic Virotherapy methods, Zika Virus Infection
- Abstract
Glioblastoma (GBM), the most common primary malignant brain tumor, is a highly lethal form of cancer with a very limited set of treatment options. High heterogeneity in the tumor cell population and the invasive nature of these cells decrease the likely efficacy of traditional cancer treatments, thus requiring research into novel treatment options. The use of oncolytic viruses as potential therapeutics has been researched for some time. Zika virus (ZIKV) has demonstrated oncotropism and oncolytic effects on GBM stem cells (GSCs). To address the need for safe and effective GBM treatments, we designed an attenuated ZIKV strain (ZOL-1) that does not cause paralytic or neurological diseases in mouse models compared with unmodified ZIKV. Importantly, we found that patient-derived GBM tumors exhibited susceptibility (responders) and non-susceptibility (non-responders) to ZOL-1-mediated tumor cell killing, as evidenced by differential apoptotic cell death and cell viability upon ZOL-1 treatment. The oncolytic effect observed in responder cells was seen both in vitro in neurosphere models and in vivo upon xenograft. Finally, we observed that the use of ZOL-1 as combination therapy with multiple PI3K-AKT inhibitors in non-responder GBM resulted in enhanced chemotherapeutic efficacy. Altogether, this study establishes ZOL-1 as a safe and effective treatment against GBM and provides a foundation to conduct further studies evaluating its potential as an effective adjuvant with other chemotherapies and kinase inhibitors.
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- 2023
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11. Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses.
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Jeyachandran AV, Irudayam JI, Dubey S, Chakravarty N, Konda B, Shah A, Su B, Wang C, Cui Q, Williams KJ, Srikanth S, Shi Y, Deb A, Damoiseaux R, Stripp BR, Ramaiah A, and Arumugaswami V
- Abstract
Background: Hantaviruses - dichotomized into New World (i.e. Andes virus, ANDV; Sin Nombre virus, SNV) and Old-World viruses (i.e. Hantaan virus, HTNV) - are zoonotic viruses transmitted from rodents to humans. Currently, no FDA-approved vaccines against hantaviruses exist. Given the recent breakthrough to human-human transmission by the ANDV, an essential step is to establish an effective pandemic preparedness infrastructure to rapidly identify cell tropism, infective potential, and effective therapeutic agents through systematic investigation., Methods: We established human cell model systems in lung (airway and distal lung epithelial cells), heart (pluripotent stem cell-derived (PSC-) cardiomyocytes), and brain (PSC-astrocytes) cell types and subsequently evaluated ANDV, HTNV and SNV tropisms. Transcriptomic, lipidomic and bioinformatic data analyses were performed to identify the molecular pathogenic mechanisms of viruses in different cell types. This cell-based infection system was utilized to establish a drug testing platform and pharmacogenomic comparisons., Results: ANDV showed broad tropism for all cell types assessed. HTNV replication was predominantly observed in heart and brain cells. ANDV efficiently replicated in human and mouse 3D distal lung organoids. Transcriptomic analysis showed that ANDV infection resulted in pronounced inflammatory response and downregulation of cholesterol biosynthesis pathway in lung cells. Lipidomic profiling revealed that ANDV-infected cells showed reduced level of cholesterol esters and triglycerides. Further analysis of pathway-based molecular signatures showed that, compared to SNV and HTNV, ANDV infection caused drastic lung cell injury responses. A selective drug screening identified STING agonists, nucleoside analogues and plant-derived compounds that inhibited ANDV viral infection and rescued cellular metabolism. In line with experimental results, transcriptome data shows that the least number of total and unique differentially expressed genes were identified in urolithin B- and favipiravir-treated cells, confirming the higher efficiency of these two drugs in inhibiting ANDV, resulting in host cell ability to balance gene expression to establish proper cell functioning., Conclusions: Overall, our study describes advanced human PSC-derived model systems and systems-level transcriptomics and lipidomic data to better understand Old and New World hantaviral tropism, as well as drug candidates that can be further assessed for potential rapid deployment in the event of a pandemic., Competing Interests: Competing interests. The authors declare no competing interests.
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- 2023
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12. Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses.
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Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Castillo Cario S, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells MS, Ramaiah A, and Arumugaswami V
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- Animals, Mice, SARS-CoV-2, Antiviral Agents pharmacology, Antiviral Agents therapeutic use, Immunity, Innate, COVID-19, Chikungunya virus physiology, RNA Viruses, Zika Virus, Zika Virus Infection
- Abstract
RNA viruses continue to remain a threat for potential pandemics due to their rapid evolution. Potentiating host antiviral pathways to prevent or limit viral infections is a promising strategy. Thus, by testing a library of innate immune agonists targeting pathogen recognition receptors, we observe that Toll-like receptor 3 (TLR3), stimulator of interferon genes (STING), TLR8, and Dectin-1 ligands inhibit arboviruses, Chikungunya virus (CHIKV), West Nile virus, and Zika virus to varying degrees. STING agonists (cAIMP, diABZI, and 2',3'-cGAMP) and Dectin-1 agonist scleroglucan demonstrate the most potent, broad-spectrum antiviral function. Furthermore, STING agonists inhibit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and enterovirus-D68 (EV-D68) infection in cardiomyocytes. Transcriptome analysis reveals that cAIMP treatment rescue cells from CHIKV-induced dysregulation of cell repair, immune, and metabolic pathways. In addition, cAIMP provides protection against CHIKV in a chronic CHIKV-arthritis mouse model. Our study describes innate immune signaling circuits crucial for RNA virus replication and identifies broad-spectrum antivirals effective against multiple families of pandemic potential RNA viruses., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)
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- 2023
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13. Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils.
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Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G Jr, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, and Eisenberg DS
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- Humans, Amyloidogenic Proteins, Nucleocapsid Proteins, Peptides chemistry, Protein Domains, SARS-CoV-2 metabolism, Amyloid metabolism, COVID-19, Coronavirus Nucleocapsid Proteins
- Abstract
The self-assembly of the Nucleocapsid protein (NCAP) of SARS-CoV-2 is crucial for its function. Computational analysis of the amino acid sequence of NCAP reveals low-complexity domains (LCDs) akin to LCDs in other proteins known to self-assemble as phase separation droplets and amyloid fibrils. Previous reports have described NCAP's propensity to phase-separate. Here we show that the central LCD of NCAP is capable of both, phase separation and amyloid formation. Within this central LCD we identified three adhesive segments and determined the atomic structure of the fibrils formed by each. Those structures guided the design of G12, a peptide that interferes with the self-assembly of NCAP and demonstrates antiviral activity in SARS-CoV-2 infected cells. Our work, therefore, demonstrates the amyloid form of the central LCD of NCAP and suggests that amyloidogenic segments of NCAP could be targeted for drug development., (© 2023. The Author(s).)
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- 2023
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14. Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses.
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Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Cario SC, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells M, Ramaiah A, and Arumugaswami V
- Abstract
RNA viruses continue to remain a clear and present threat for potential pandemics due to their rapid evolution. To mitigate their impact, we urgently require antiviral agents that can inhibit multiple families of disease-causing viruses, such as arthropod-borne and respiratory pathogens. Potentiating host antiviral pathways can prevent or limit viral infections before escalating into a major outbreak. Therefore, it is critical to identify broad-spectrum antiviral agents. We have tested a small library of innate immune agonists targeting pathogen recognition receptors, including TLRs, STING, NOD, Dectin and cytosolic DNA or RNA sensors. We observed that TLR3, STING, TLR8 and Dectin-1 ligands inhibited arboviruses, Chikungunya virus (CHIKV), West Nile virus (WNV) and Zika virus, to varying degrees. Cyclic dinucleotide (CDN) STING agonists, such as cAIMP, diABZI, and 2',3'-cGAMP, and Dectin-1 agonist scleroglucan, demonstrated the most potent, broad-spectrum antiviral function. Comparative transcriptome analysis revealed that CHIKV-infected cells had larger number of differentially expressed genes than of WNV and ZIKV. Furthermore, gene expression analysis showed that cAIMP treatment rescued cells from CHIKV-induced dysregulation of cell repair, immune, and metabolic pathways. In addition, cAIMP provided protection against CHIKV in a CHIKV-arthritis mouse model. Cardioprotective effects of synthetic STING ligands against CHIKV, WNV, SARS-CoV-2 and enterovirus D68 (EV-D68) infections were demonstrated using human cardiomyocytes. Interestingly, the direct-acting antiviral drug remdesivir, a nucleoside analogue, was not effective against CHIKV and WNV, but exhibited potent antiviral effects against SARS-CoV-2, RSV (respiratory syncytial virus), and EV-D68. Our study identifies broad-spectrum antivirals effective against multiple families of pandemic potential RNA viruses, which can be rapidly deployed to prevent or mitigate future pandemics.
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- 2023
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15. Longitudinal Evaluation of Antibody Persistence in Mother-Infant Dyads After Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Pregnancy.
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Cambou MC, Liu CM, Mok T, Fajardo-Martinez V, Paiola SG, Ibarrondo FJ, Kerin T, Fuller T, Tobin NH, Garcia G, Bhattacharya D, Aldrovandi GM, Arumugaswami V, Foo SS, Jung JU, Vasconcelos Z, Brasil P, Brendolin M, Yang OO, Rao R, and Nielsen-Saines K
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- Pregnancy, Infant, Newborn, Female, Infant, Humans, SARS-CoV-2, Immunoglobulin A, Immunoglobulin G, Immunoglobulin M, Antibodies, Viral, Mothers, COVID-19
- Abstract
Background: There are limited data on how coronavirus disease 2019 (COVID-19) severity, timing of infection, and subsequent vaccination impact transplacental transfer and persistence of maternal and infant antibodies., Methods: In a longitudinal cohort of pregnant women with polymerase chain reaction-confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, maternal/infant sera were collected at enrollment, delivery/birth, and 6 months. Anti-SARS-CoV-2 spike immunoglobulin (Ig)G, IgM, and IgA were measured by enzyme-linked immunosorbent assay., Results: Two-hundred fifty-six pregnant women and 135 infants were enrolled; 148 maternal and 122 neonatal specimens were collected at delivery/birth; 45 maternal and 48 infant specimens were collected at 6 months. Sixty-eight percent of women produced all anti-SARS-CoV-2 isotypes at delivery (IgG, IgM, IgA); 96% had at least 1 isotype. Symptomatic disease and vaccination before delivery were associated with higher maternal IgG at labor and delivery. Detectable IgG in infants dropped from 78% at birth to 52% at 6 months. In the multivariate analysis evaluating factors associated with detectable IgG in infants at delivery, significant predictors were 3rd trimester infection (odds ratio [OR] = 4.0), mild/moderate disease (OR = 4.8), severe/critical disease (OR = 6.3), and maternal vaccination before delivery (OR = 18.8). No factors were significant in the multivariate analysis at 6 months postpartum., Conclusions: Vaccination in pregnancy post-COVID-19 recovery is a strategy for boosting antibodies in mother-infant dyads., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts of interest. All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
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- 2023
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16. Differential Susceptibility of Fetal Retinal Pigment Epithelial Cells, hiPSC- Retinal Stem Cells, and Retinal Organoids to Zika Virus Infection.
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Contreras D, Garcia G Jr, Jones MK, Martinez LE, Jayakarunakaran A, Gangalapudi V, Tang J, Wu Y, Zhao JJ, Chen Z, Ramaiah A, Tsui I, Kumar A, Nielsen-Saines K, Wang S, and Arumugaswami V
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- Humans, Retina pathology, Virus Replication, Organoids, Epithelial Cells pathology, Retinal Pigments metabolism, Zika Virus Infection, Zika Virus physiology, Induced Pluripotent Stem Cells, Eye Diseases
- Abstract
Zika virus (ZIKV) causes microcephaly and congenital eye disease. The cellular and molecular basis of congenital ZIKV infection are not well understood. Here, we utilized a biologically relevant cell-based system of human fetal retinal pigment epithelial cells (FRPEs), hiPSC-derived retinal stem cells (iRSCs), and retinal organoids to investigate ZIKV-mediated ocular cell injury processes. Our data show that FRPEs were highly susceptible to ZIKV infection exhibiting increased apoptosis, whereas iRSCs showed reduced susceptibility. Detailed transcriptomics and proteomics analyses of infected FRPEs were performed. Nucleoside analogue drug treatment inhibited ZIKV replication. Retinal organoids were susceptible to ZIKV infection. The Asian genotype ZIKV exhibited higher infectivity, induced profound inflammatory response, and dysregulated transcription factors involved in retinal organoid differentiation. Collectively, our study shows that ZIKV affects ocular cells at different developmental stages resulting in cellular injury and death, further providing molecular insight into the pathogenesis of congenital eye disease.
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- 2023
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17. Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response.
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Garcia G Jr, Jeyachandran AV, Wang Y, Irudayam JI, Cario SC, Sen C, Li S, Li Y, Kumar A, Nielsen-Saines K, French SW, Shah PS, Morizono K, Gomperts BN, Deb A, Ramaiah A, and Arumugaswami V
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- Humans, SARS-CoV-2, Hippo Signaling Pathway, Antiviral Agents pharmacology, COVID-19
- Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), responsible for the Coronavirus Disease 2019 (COVID-19) pandemic, causes respiratory failure and damage to multiple organ systems. The emergence of viral variants poses a risk of vaccine failures and prolongation of the pandemic. However, our understanding of the molecular basis of SARS-CoV-2 infection and subsequent COVID-19 pathophysiology is limited. In this study, we have uncovered a critical role for the evolutionarily conserved Hippo signaling pathway in COVID-19 pathogenesis. Given the complexity of COVID-19-associated cell injury and immunopathogenesis processes, we investigated Hippo pathway dynamics in SARS-CoV-2 infection by utilizing COVID-19 lung samples and human cell models based on pluripotent stem cell-derived cardiomyocytes (PSC-CMs) and human primary lung air-liquid interface (ALI) cultures. SARS-CoV-2 infection caused activation of the Hippo signaling pathway in COVID-19 lung and in vitro cultures. Both parental and Delta variant of concern (VOC) strains induced Hippo pathway. The chemical inhibition and gene knockdown of upstream kinases MST1/2 and LATS1 resulted in significantly enhanced SARS-CoV-2 replication, indicating antiviral roles. Verteporfin, a pharmacological inhibitor of the Hippo pathway downstream transactivator, YAP, significantly reduced virus replication. These results delineate a direct antiviral role for Hippo signaling in SARS-CoV-2 infection and the potential for this pathway to be pharmacologically targeted to treat COVID-19., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Garcia et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
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- 2022
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18. In Silico Genome Analysis Reveals the Evolution and Potential Impact of SARS-CoV-2 Omicron Structural Changes on Host Immune Evasion and Antiviral Therapeutics.
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Chauhan D, Chakravarty N, Jeyachandran AV, Jayakarunakaran A, Sinha S, Mishra R, Arumugaswami V, and Ramaiah A
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- Humans, Mutation, Phylogeny, Spike Glycoprotein, Coronavirus genetics, Viral Envelope Proteins genetics, Antiviral Agents pharmacology, Antiviral Agents therapeutic use, COVID-19 immunology, COVID-19 virology, Immune Evasion, SARS-CoV-2 drug effects, SARS-CoV-2 genetics
- Abstract
New variants of SARS-CoV-2 continue to evolve. The novel SARS-CoV-2 variant of concern (VOC) B.1.1.529 (Omicron) was particularly menacing due to the presence of numerous consequential mutations. In this study, we reviewed about 12 million SARS-CoV-2 genomic and associated metadata using extensive bioinformatic approaches to understand how evolutionary and mutational changes affect Omicron variant properties. Subsampled global data based analysis of molecular clock in the phylogenetic tree showed 29.56 substitutions per year as the evolutionary rate of five VOCs. We observed extensive mutational changes in the spike structural protein of the Omicron variant. A total of 20% of 7230 amino acid and structural changes exclusive to Omicron's spike protein were detected in the receptor binding domain (RBD), suggesting differential selection pressures exerted during evolution. Analyzing key drug targets revealed mutation-derived differential binding affinities between Delta and Omicron variants. Nine single-RBD substitutions were detected within the binding site of approved therapeutic monoclonal antibodies. T-cell epitope prediction revealed eight immunologically important functional hotspots in three conserved non-structural proteins. A universal vaccine based on these regions may likely protect against all these SARS-CoV-2 variants. We observed key structural changes in the spike protein, which decreased binding affinities, indicating that these changes may help the virus escape host cellular immunity. These findings emphasize the need for continuous genomic surveillance of SARS-CoV-2 to better understand how novel mutations may impact viral spread and disease outcome.
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- 2022
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19. Replication-Deficient Zika Vector-Based Vaccine Provides Maternal and Fetal Protection in Mouse Model.
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Garcia G Jr, Chakravarty N, Abu AE, Jeyachandran AV, Takano KA, Brown R, Morizono K, and Arumugaswami V
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- Pregnancy, Female, Child, Mice, Humans, Animals, CD8-Positive T-Lymphocytes, 3' Untranslated Regions, Antibodies, Viral, Viral Envelope Proteins genetics, Mosquito Vectors, Antibodies, Neutralizing, Disease Models, Animal, Zika Virus genetics, Zika Virus Infection prevention & control, Viral Vaccines genetics
- Abstract
Zika virus (ZIKV), a mosquito-borne human pathogen, causes dire congenital brain developmental abnormalities in children of infected mothers. The global health crisis precipitated by this virus has led to a concerted effort to develop effective therapies and prophylactic measures although, unfortunately, not very successfully. The error-prone nature of RNA viral genome replication tends to promote evolution of novel viral strains, which could cause epidemics and pandemics. As such, our objective was to develop a safe and effective replication-deficient ZIKV vector-based vaccine candidate. We approached this by generating a ZIKV vector containing only the nonstructural (NS) 5'-untranslated (UTR)-NS-3' UTR sequences, with the structural proteins capsid (C), precursor membrane (prM), and envelope (E) (CprME) used as a packaging system. We efficiently packaged replication-deficient Zika vaccine particles in human producer cells and verified antigen expression in vitro . In vivo studies showed that, after inoculation in neonatal mice, the Zika vaccine candidate (ZVAX) was safe and did not produce any replication-competent revertant viruses. Immunization of adult, nonpregnant mice showed that ZVAX protected mice from lethal challenge by limiting viral replication. We then evaluated the safety and efficacy of ZVAX in pregnant mice, where it was shown to provide efficient maternal and fetal protection against Zika disease. Mass cytometry analysis showed that vaccinated pregnant animals had high levels of splenic CD8
+ T cells and effector memory T cell responses with reduced proinflammatory cell responses, suggesting that endogenous expression of NS proteins by ZVAX induced cellular immunity against ZIKV NS proteins. We also investigated humoral immunity against ZIKV, which is potentially induced by viral proteins present in ZVAX virions. We found no significant difference in neutralizing antibody titer in vaccinated or unvaccinated challenged animals; therefore, it is likely that cellular immunity plays a major role in ZVAX-mediated protection against ZIKV infection. In conclusion, we demonstrated ZVAX as an effective inducer of protective immunity against ZIKV, which can be further evaluated for potential prophylactic application in humans. IMPORTANCE This research is important as it strives to address the critical need for effective prophylactic measures against the outbreak of Zika virus (ZIKV) and outlines an important vaccine technology that could potentially be used to induce immune responses against other pandemic-potential viruses.- Published
- 2022
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20. Importance of clitellar tissue in the regeneration ability of earthworm Eudrilus eugeniae.
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Paul S, Balakrishnan S, Arumugaperumal A, Lathakumari S, Syamala SS, Vijayan V, Durairaj SCJ, Arumugaswami V, and Sivasubramaniam S
- Subjects
- Animals, Gene Expression Profiling, Oligochaeta genetics, Oligochaeta metabolism
- Abstract
Among the annelids, earthworms are renowned for their phenomenal ability to regenerate the lost segments. The adult earthworm Eudrilus eugeniae contains 120 segments and the body segments of the earthworm are divided into pre-clitellar, clitellar and post-clitellar segments. The present study denoted that clitellum plays vital role in the successful regeneration of the species. We have performed histological studies to identify among the three skin layers of the earthworm, which cellular layer supports the blastema formation and regeneration of the species. The histological evidences denoted that the proliferation of the longitudinal cell layer at the amputation site is crucial for the successful regeneration of the earthworm and it takes place only in the presence of an intact clitellum. Besides we have performed clitellar transcriptome analysis of the earthworm Eudrilus eugeniae to monitor the key differentially expressed genes and their associated functions and pathways controlling the clitellar tissue changes during both anterior and posterior regeneration of the earthworm. A total of 4707 differentially expressed genes (DEGs) were identified between the control clitellum and clitellum of anterior regenerated earthworms and 4343 DEGs were detected between the control clitellum and clitellum of posterior regenerated earthworms. The functional enrichment analysis confirmed the genes regulating the muscle mass shape and structure were significantly downregulated and the genes associated with response to starvation and anterior-posterior axis specification were significantly upregulated in the clitellar tissue during both anterior and posterior regeneration of the earthworm. The RNA sequencing data of clitellum and the comparative transcriptomic analysis were helpful to understand the complex regeneration process of the earthworm., (© 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)
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- 2022
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21. Mitoquinone mesylate targets SARS-CoV-2 infection in preclinical models.
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Petcherski A, Sharma M, Satta S, Daskou M, Vasilopoulos H, Hugo C, Ritou E, Dillon BJ, Fung E, Garcia G, Scafoglio C, Purkayastha A, Gomperts BN, Fishbein GA, Arumugaswami V, Liesa M, Shirihai OS, and Kelesidis T
- Abstract
To date, there is no effective oral antiviral against SARS-CoV-2 that is also anti-inflammatory. Herein, we show that the mitochondrial antioxidant mitoquinone/mitoquinol mesylate (Mito-MES), a dietary supplement, has potent antiviral activity against SARS-CoV-2 and its variants of concern in vitro and in vivo . Mito-MES had nanomolar in vitro antiviral potency against the Beta and Delta SARS-CoV-2 variants as well as the murine hepatitis virus (MHV-A59). Mito-MES given in SARS-CoV-2 infected K18-hACE2 mice through oral gavage reduced viral titer by nearly 4 log units relative to the vehicle group. We found in vitro that the antiviral effect of Mito-MES is attributable to its hydrophobic dTPP+ moiety and its combined effects scavenging reactive oxygen species (ROS), activating Nrf2 and increasing the host defense proteins TOM70 and MX1. Mito-MES was efficacious reducing increase in cleaved caspase-3 and inflammation induced by SARS-CoV2 infection both in lung epithelial cells and a transgenic mouse model of COVID-19. Mito-MES reduced production of IL-6 by SARS-CoV-2 infected epithelial cells through its antioxidant properties (Nrf2 agonist, coenzyme Q10 moiety) and the dTPP moiety. Given established safety of Mito-MES in humans, our results suggest that Mito-MES may represent a rapidly applicable therapeutic strategy that can be added in the therapeutic arsenal against COVID-19. Its potential long-term use by humans as diet supplement could help control the SARS-CoV-2 pandemic, especially in the setting of rapidly emerging SARS-CoV-2 variants that may compromise vaccine efficacy., One-Sentence Summary: Mitoquinone/mitoquinol mesylate has potent antiviral and anti-inflammatory activity in preclinical models of SARS-CoV-2 infection.
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- 2022
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22. Draft Genome Sequence of the Earthworm Eudrilus eugeniae .
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Arumugaperumal A, Sudalaimani DK, Arumugaswami V, and Sivasubramaniam S
- Abstract
Background : Earthworms are annelids. They play a major role in agriculture and soil fertility. Vermicompost is the best organic manure for plant crops. Eudrilus eugeniae is an earthworm well suited for efficient vermicompost production. The worm is also used to study the cell and molecular biology of regeneration, molecular toxicology, developmental biology, etc ., because of its abilities like high growth rate, rapid reproduction, tolerability toward wide temperature range, and less cost of maintenance. Objective : The whole genome has been revealed only for Eisenia andrei and Eisenia fetida. Methods : In the present work, we sequenced the genome of E. eugeniae using the Illumina platform and generated 160,684,383 paired-end reads. Results : The reads were assembled into a draft genome of size 488 Mb with 743,870 contigs and successfully annotated 24,599 genes. Further, 208 stem cell-specific genes and 3,432 non-coding genes were identified. Conclusion : The sequence and annotation details were hosted in a web application available at https://sudhakar-sivasubramaniam-labs.shinyapps.io/eudrilus_genome/., (© 2022 Bentham Science Publishers.)
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- 2022
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23. Identification, tissue specific expression analysis and functional characterization of arrestin gene (ARRDC) in the earthworm Eudrilus eugeniae: a molecular hypothesis behind worm photoreception.
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Paul S, Dinesh Kumar SM, Syamala SS, Balakrishnan S, Vijayan V, Arumugaswami V, and Sudhakar S
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- Animals, Arrestin genetics, Arrestin metabolism, In Situ Hybridization, Mammals metabolism, Proteins genetics, RNA, Small Interfering metabolism, Oligochaeta genetics, Oligochaeta metabolism
- Abstract
Background: The arrestin domain containing proteins (ARRDCs) are crucial adaptor proteins assist in signal transduction and regulation of sensory physiology. The molecular localization of the ARRDC gene has been confined mainly to the mammalian system while in invertebrates the expression pattern was not addressed significantly. The present study reports the identification, tissue specific expression and functional characterization of an ARRDC transcript in earthworm, Eudrilus eugeniae., Methods and Results: The coding region of earthworm ARRDC transcript was 1146 bp in length and encoded a protein of 381 amino acid residues. The worm ARRDC protein consists of conserved N-terminal and C-terminal regions and showed significant homology with the ARRDC3 sequence of other species. The tissue specific expression analysis through whole mount in-situ hybridization denoted the expression of ARRDC transcript in the central nervous system of the worm which includes cerebral ganglion and ventral nerve cord. Besides, the expression of ARRDC gene was observed in the epidermal region of earthworm skin. The functional characterization of ARRDC gene was assessed through siRNA silencing and the gene was found to play key role in the light sensing ability and photophobic movement of the worm., Conclusions: The neuronal and dermal expression patterns of ARRDC gene and its functional characterization hypothesized the role of the gene in assisting the photosensory cells to regulate the process of photoreception and phototransduction in the worm., (© 2022. The Author(s), under exclusive licence to Springer Nature B.V.)
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- 2022
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24. Development of off-the-shelf hematopoietic stem cell-engineered invariant natural killer T cells for COVID-19 therapeutic intervention.
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Li YR, Dunn ZS, Garcia G Jr, Carmona C, Zhou Y, Lee D, Yu J, Huang J, Kim JT, Arumugaswami V, Wang P, and Yang L
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- Animals, Hematopoietic Stem Cells, Humans, Mice, SARS-CoV-2, COVID-19 therapy, Natural Killer T-Cells
- Abstract
Background: New COVID-19 treatments are desperately needed as case numbers continue to rise and emergent strains threaten vaccine efficacy. Cell therapy has revolutionized cancer treatment and holds much promise in combatting infectious disease, including COVID-19. Invariant natural killer T (iNKT) cells are a rare subset of T cells with potent antiviral and immunoregulatory functions and an excellent safety profile. Current iNKT cell strategies are hindered by the extremely low presence of iNKT cells, and we have developed a platform to overcome this critical limitation., Methods: We produced allogeneic HSC-engineered iNKT (
Allo HSC-iNKT) cells through TCR engineering of human cord blood CD34+ hematopoietic stem cells (HSCs) and differentiation of these HSCs into iNKT cells in an Ex Vivo HSC-Derived iNKT Cell Culture. We then established in vitro SARS-CoV-2 infection assays to assessAllo HSC-iNKT cell antiviral and anti-hyperinflammation functions. Lastly, using in vitro and in vivo preclinical models, we evaluatedAllo HSC-iNKT cell safety and immunogenicity for off-the-shelf application., Results: We reliably generatedAllo HSC-iNKT cells at high-yield and of high-purity; these resulting cells closely resembled endogenous human iNKT cells in phenotypes and functionalities. In cell culture,Allo HSC-iNKT cells directly killed SARS-CoV-2 infected cells and also selectively eliminated SARS-CoV-2 infection-stimulated inflammatory monocytes. In an in vitro mixed lymphocyte reaction (MLR) assay and an NSG mouse xenograft model,Allo HSC-iNKT cells were resistant to T cell-mediated alloreaction and did not cause GvHD., Conclusions: Here, we report a method to robustly produce therapeutic levels ofAllo HSC-iNKT cells. Preclinical studies showed that theseAllo HSC-iNKT cells closely resembled endogenous human iNKT cells, could reduce SARS-CoV-2 virus infection load and mitigate virus infection-induced hyperinflammation, and meanwhile were free of GvHD-risk and resistant to T cell-mediated allorejection. These results support the development ofAllo HSC-iNKT cells as a promising off-the-shelf cell product for treating COVID-19; such a cell product has the potential to target the new emerging SARS-CoV-2 variants as well as the future new emerging viruses., (© 2022. The Author(s).)- Published
- 2022
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25. Compound screen identifies the small molecule Q34 as an inhibitor of SARS-CoV-2 infection.
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Cui Q, Garcia G Jr, Zhang M, Wang C, Li H, Zhou T, Sun G, Arumugaswami V, and Shi Y
- Abstract
The COVID-19 outbreak poses a serious threat to global public health. Effective countermeasures and approved therapeutics are desperately needed. In this study, we screened a small molecule library containing the NCI-DTP compounds to identify molecules that can prevent SARS-CoV-2 cellular entry. By applying a luciferase assay-based screening using a pseudotyped SARS-CoV-2-mediated cell entry assay, we identified a small molecule compound Q34 that can efficiently block cellular entry of the pseudotyped SARS-CoV-2 into human ACE2-expressing HEK293T cells, and inhibit the infection of the authentic SARS-CoV-2 in human ACE2-expressing HEK293T cells, human iPSC-derived neurons and astrocytes, and human lung Calu-3 cells. Importantly, the safety profile of the compound is favorable. There is no obvious toxicity observed in uninfected cells treated with the compound. Thus, this compound holds great potential as both prophylactics and therapeutics for COVID-19 and future pandemics by blocking the entry of SARS-CoV-2 and related viruses into human cells., Competing Interests: A patent application related to this work has been filed. The authors declare no other competing interests., (© 2021 The Authors.)
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- 2022
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26. ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling.
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Wu B, Ramaiah A, Garcia G Jr, Hasiakos S, Arumugaswami V, and Srikanth S
- Subjects
- A549 Cells, Angiotensin-Converting Enzyme 2 genetics, Angiotensin-Converting Enzyme 2 metabolism, COVID-19 immunology, Calcium Signaling, Clustered Regularly Interspaced Short Palindromic Repeats, Disease Resistance, Disease Susceptibility, Gene Expression Profiling, HEK293 Cells, Humans, Lung virology, MEF2 Transcription Factors genetics, Neoplasm Proteins genetics, ORAI1 Protein genetics, Stromal Interaction Molecule 1 genetics, Transcription Factor AP-1 genetics, COVID-19 metabolism, Interferon Type I metabolism, Lung immunology, Neoplasm Proteins metabolism, ORAI1 Protein metabolism, Respiratory Mucosa metabolism, SARS-CoV-2 physiology, Stromal Interaction Molecule 1 metabolism
- Abstract
ORAI1 and stromal interaction molecule 1 (STIM1) are the critical mediators of store-operated Ca
2+ entry by acting as the pore subunit and an endoplasmic reticulum-resident signaling molecule, respectively. In addition to Ca2+ signaling, STIM1 is also involved in regulation of the type I IFN (IFN-I) response. To examine their potential role in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, we generated ORAI1 and STIM1 knockout human HEK293-angiotensin-converting enzyme 2 cells and checked their responses. STIM1 knockout cells showed strong resistance to SARS-CoV-2 infection as a result of enhanced IFN-I response. On the contrary, ORAI1 deletion induced high susceptibility to SARS-CoV-2 infection. Mechanistically, ORAI1 knockout cells showed reduced homeostatic cytoplasmic Ca2+ concentration and severe impairment in tonic IFN-I signaling. Transcriptome analysis showed downregulation of multiple antiviral signaling pathways in ORAI1 knockout cells, likely because of reduced expression of the Ca2+ -dependent transcription factors of the AP-1 family and MEF2C Accordingly, modulation of homeostatic Ca2+ concentration by pretreatment with ORAI1 blocker or agonist could influence baseline IFNB expression and resistance to SARS-CoV-2 infection in a human lung epithelial cell line. Our results identify a novel role of ORAI1-mediated Ca2+ signaling in regulating the tonic IFN-I levels, which determine host resistance to SARS-CoV-2 infection., (Copyright © 2021 by The American Association of Immunologists, Inc.)- Published
- 2022
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27. SARS-CoV-2 and its beta variant of concern infect human conjunctival epithelial cells and induce differential antiviral innate immune response.
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Singh S, Garcia G Jr, Shah R, Kramerov AA, Wright RE 3rd, Spektor TM, Ljubimov AV, Arumugaswami V, and Kumar A
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- Antiviral Agents, Epithelial Cells, Humans, Immunity, Innate, RNA, Viral, COVID-19, SARS-CoV-2
- Abstract
Purpose: SARS-CoV-2 RNA has been detected in ocular tissues, but their susceptibility to SARS-CoV-2 infection is unclear. Here, we tested whether SARS-CoV-2 can infect human conjunctival epithelial cells (hCECs) and induce innate immune response., Methods: Conjunctival tissue from COVID-19 donors was used to detect SARS-CoV-2 spike and envelope proteins. Primary hCECs isolated from cadaver eyes were infected with the parental SARS-CoV-2 and its beta variant of concern (VOC). Viral genome copy number, and expression of viral entry receptors, TLRs, interferons, and innate immune response genes were determined by qPCR. Viral entry receptors were examined in hCECs and tissue sections by immunostaining. Spike protein was detected in the cell culture supernatant by dot blot., Results: Spike and envelope proteins were found in conjunctiva from COVID-19 patients. SARS-CoV-2 infected hCECs showed high viral copy numbers at 24-72h post-infection; spike protein levels were the highest at 24hpi. Viral entry receptors ACE2, TMPRSS2, CD147, Axl, and NRP1 were detected in conjunctival tissue and hCECs. SARS-CoV-2 infection-induced receptor gene expression peaked at early time points post-infection, but gene expression of most TLRs peaked at 48 or 72hpi. SARS-CoV-2 infected hCECs showed higher expression of genes regulating antiviral response, RIG-I, interferons (α, β, & λ), ISG15 & OAS2, cytokines (IL6, IL1β, TNFα), and chemokines (CXCL10, CCL5). Compared to the parental strain, beta VOC induced increased viral copy number and innate response in hCECs., Conclusions: Conjunctival epithelial cells are susceptible to SARS-CoV-2 infection. Beta VOC is more infectious than the parental strain and evokes a higher antiviral and inflammatory response., (Copyright © 2021 Elsevier Inc. All rights reserved.)
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- 2022
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28. Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: a comparative analysis.
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Chakravarty N, Senthilnathan T, Paiola S, Gyani P, Castillo Cario S, Urena E, Jeysankar A, Jeysankar P, Ignatius Irudayam J, Natesan Subramanian S, Lavretsky H, Joshi S, Garcia G Jr, Ramaiah A, and Arumugaswami V
- Subjects
- COVID-19 epidemiology, COVID-19 genetics, COVID-19 metabolism, COVID-19 physiopathology, Humans, Mutation, Blood-Brain Barrier metabolism, Blood-Brain Barrier physiopathology, Blood-Brain Barrier virology, Henipavirus Infections epidemiology, Henipavirus Infections genetics, Henipavirus Infections metabolism, Henipavirus Infections physiopathology, Nipah Virus genetics, Nipah Virus metabolism, SARS-CoV-2 genetics, SARS-CoV-2 metabolism, Zika Virus genetics, Zika Virus metabolism, Zika Virus Infection epidemiology, Zika Virus Infection genetics, Zika Virus Infection metabolism, Zika Virus Infection physiopathology
- Abstract
SARS-CoV-2 has infected hundreds of millions of people with over four million dead, resulting in one of the worst global pandemics in recent history. Neurological symptoms associated with COVID-19 include anosmia, ageusia, headaches, confusion, delirium, and strokes. These may manifest due to viral entry into the central nervous system (CNS) through the blood-brain barrier (BBB) by means of ill-defined mechanisms. Here, we summarize the abilities of SARS-CoV-2 and other neurotropic RNA viruses, including Zika virus and Nipah virus, to cross the BBB into the CNS, highlighting the role of magnetic resonance imaging (MRI) in assessing presence and severity of brain structural changes in COVID-19 patients. We present new insight into key mutations in SARS-CoV-2 variants B.1.1.7 (P681H) and B.1.617.2 (P681R), which may impact on neuropilin 1 (NRP1) binding and CNS invasion. We postulate that SARS-CoV-2 may infect both peripheral cells capable of crossing the BBB and brain endothelial cells to traverse the BBB and spread into the brain. COVID-19 patients can be followed up with MRI modalities to better understand the long-term effects of COVID-19 on the brain., (© 2021 Federation of European Biochemical Societies.)
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- 2021
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29. The systemic inflammatory landscape of COVID-19 in pregnancy: Extensive serum proteomic profiling of mother-infant dyads with in utero SARS-CoV-2.
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Foo SS, Cambou MC, Mok T, Fajardo VM, Jung KL, Fuller T, Chen W, Kerin T, Mei J, Bhattacharya D, Choi Y, Wu X, Xia T, Shin WJ, Cranston J, Aldrovandi G, Tobin N, Contreras D, Ibarrondo FJ, Yang O, Yang S, Garner O, Cortado R, Bryson Y, Janzen C, Ghosh S, Devaskar S, Asilnejad B, Moreira ME, Vasconcelos Z, Soni PR, Gibson LC, Brasil P, Comhair SAA, Arumugaswami V, Erzurum SC, Rao R, Jung JU, and Nielsen-Saines K
- Subjects
- Adolescent, Adult, COVID-19 blood, COVID-19 metabolism, Female, Humans, Infant, Newborn, Mothers, Pregnancy, Serum metabolism, Young Adult, COVID-19 immunology, Cytokines blood, Inflammation, Proteomics
- Abstract
While pregnancy increases the risk for severe COVID-19, the clinical and immunological implications of COVID-19 on maternal-fetal health remain unknown. Here, we present the clinical and immunological landscapes of 93 COVID-19 mothers and 45 of their SARS-CoV-2-exposed infants through comprehensive serum proteomics profiling for >1,400 cytokines of their peripheral and cord blood specimens. Prenatal SARS-CoV-2 infection triggers NF-κB-dependent proinflammatory immune activation. Pregnant women with severe COVID-19 show increased inflammation and unique IFN-λ antiviral signaling, with elevated levels of IFNL1 and IFNLR1. Furthermore, SARS-CoV-2 infection re-shapes maternal immunity at delivery, altering the expression of pregnancy complication-associated cytokines, inducing MMP7, MDK, and ESM1 and reducing BGN and CD209. Finally, COVID-19-exposed infants exhibit induction of T cell-associated cytokines (IL33, NFATC3, and CCL21), while some undergo IL-1β/IL-18/CASP1 axis-driven neonatal respiratory distress despite birth at term. Our findings demonstrate COVID-19-induced immune rewiring in both mothers and neonates, warranting long-term clinical follow-up to mitigate potential health risks., Competing Interests: J.U.J. is a scientific adviser to Vaccine Stabilization, a California corporation., (© 2021 The Author(s).)
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- 2021
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30. A CRISPR Activation Screen Identifies an Atypical Rho GTPase That Enhances Zika Viral Entry.
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Luu AP, Yao Z, Ramachandran S, Azzopardi SA, Miles LA, Schneider WM, Hoffmann HH, Bozzacco L, Garcia G Jr, Gong D, Damoiseaux R, Tang H, Morizono K, Rudin CM, Sun R, Arumugaswami V, Poirier JT, MacDonald MR, Rice CM, and Li MMH
- Subjects
- A549 Cells, CRISPR-Cas Systems, GTP-Binding Proteins genetics, Humans, Neoplasm Proteins genetics, Transcriptional Coactivator with PDZ-Binding Motif Proteins genetics, Transcriptional Coactivator with PDZ-Binding Motif Proteins metabolism, Virus Internalization, Virus Replication, Zika Virus genetics, Zika Virus Infection genetics, Zika Virus Infection virology, p21-Activated Kinases genetics, p21-Activated Kinases metabolism, rhoB GTP-Binding Protein genetics, GTP-Binding Proteins metabolism, Neoplasm Proteins metabolism, Zika Virus physiology, Zika Virus Infection enzymology, rhoB GTP-Binding Protein metabolism
- Abstract
Zika virus (ZIKV) is a re-emerging flavivirus that has caused large-scale epidemics. Infection during pregnancy can lead to neurologic developmental abnormalities in children. There is no approved vaccine or therapy for ZIKV. To uncover cellular pathways required for ZIKV that can be therapeutically targeted, we transcriptionally upregulated all known human coding genes with an engineered CRISPR-Cas9 activation complex in human fibroblasts deficient in interferon (IFN) signaling. We identified Ras homolog family member V ( RhoV ) and WW domain-containing transcription regulator 1 ( WWTR1 ) as proviral factors, and found them to play important roles during early ZIKV infection in A549 cells. We then focused on RhoV, a Rho GTPase with atypical terminal sequences and membrane association, and validated its proviral effects on ZIKV infection and virion production in SNB-19 cells. We found that RhoV promotes infection of some flaviviruses and acts at the step of viral entry. Furthermore, RhoV proviral effects depend on the complete GTPase cycle. By depleting Rho GTPases and related proteins, we identified RhoB and Pak1 as additional proviral factors. Taken together, these results highlight the positive role of RhoV in ZIKV infection and confirm CRISPR activation as a relevant method to identify novel host-pathogen interactions.
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- 2021
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31. Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition.
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Liu X, Verma A, Garcia G Jr, Ramage H, Lucas A, Myers RL, Michaelson JJ, Coryell W, Kumar A, Charney AW, Kazanietz MG, Rader DJ, Ritchie MD, Berrettini WH, Schultz DC, Cherry S, Damoiseaux R, Arumugaswami V, and Klein PS
- Subjects
- Adult, Aged, Female, Glycogen Synthase Kinase 3 metabolism, HEK293 Cells, Humans, Lithium Compounds pharmacology, Male, Middle Aged, Molecular Targeted Therapy, Phosphoproteins metabolism, Phosphorylation drug effects, Retrospective Studies, COVID-19 prevention & control, Coronavirus Nucleocapsid Proteins metabolism, Glycogen Synthase Kinase 3 antagonists & inhibitors, Lithium Compounds therapeutic use
- Abstract
The coronaviruses responsible for severe acute respiratory syndrome (SARS-CoV), COVID-19 (SARS-CoV-2), Middle East respiratory syndrome-CoV, and other coronavirus infections express a nucleocapsid protein (N) that is essential for viral replication, transcription, and virion assembly. Phosphorylation of N from SARS-CoV by glycogen synthase kinase 3 (GSK-3) is required for its function and inhibition of GSK-3 with lithium impairs N phosphorylation, viral transcription, and replication. Here we report that the SARS-CoV-2 N protein contains GSK-3 consensus sequences and that this motif is conserved in diverse coronaviruses, raising the possibility that SARS-CoV-2 may be sensitive to GSK-3 inhibitors, including lithium. We conducted a retrospective analysis of lithium use in patients from three major health systems who were PCR-tested for SARS-CoV-2. We found that patients taking lithium have a significantly reduced risk of COVID-19 (odds ratio = 0.51 [0.35-0.74], P = 0.005). We also show that the SARS-CoV-2 N protein is phosphorylated by GSK-3. Knockout of GSK3A and GSK3B demonstrates that GSK-3 is essential for N phosphorylation. Alternative GSK-3 inhibitors block N phosphorylation and impair replication in SARS-CoV-2 infected lung epithelial cells in a cell-type-dependent manner. Targeting GSK-3 may therefore provide an approach to treat COVID-19 and future coronavirus outbreaks., Competing Interests: Competing interest statement: M.D.R. is on the Scientific Advisory Board for Goldfinch Bio and Cipherome., (Copyright © 2021 the Author(s). Published by PNAS.)
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- 2021
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32. A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro.
- Author
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Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G Jr, Arumugaswami V, Fries BC, Arditi M, and Bahar I
- Subjects
- Antibodies, Monoclonal, Enterotoxins, Humans, Spike Glycoprotein, Coronavirus, Superantigens, Systemic Inflammatory Response Syndrome, COVID-19, SARS-CoV-2
- Abstract
We recently discovered a superantigen-like motif sequentially and structurally similar to a staphylococcal enterotoxin B (SEB) segment, near the S1/S2 cleavage site of the SARS-CoV-2 spike protein, which might explain the multisystem inflammatory syndrome (MIS-C) observed in children and the cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif at its polybasic (PRRA) insert to inhibit infection in live virus assays. The overlap between the superantigenic site of the spike and its proteolytic cleavage site suggests that the mAb prevents viral entry by interfering with the proteolytic activity of cell proteases (furin and TMPRSS2). The high affinity of 6D3 for this site originates from a polyacidic segment at its heavy chain CDR2. The study points to the potential utility of 6D3 for possibly treating COVID-19, MIS-C, or common colds caused by human coronaviruses that also possess a furin-like cleavage site., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
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- 2021
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33. Comparative transcriptomic analysis of SARS-CoV-2 infected cell model systems reveals differential innate immune responses.
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Sun G, Cui Q, Garcia G Jr, Wang C, Zhang M, Arumugaswami V, Riggs AD, and Shi Y
- Subjects
- Humans, HEK293 Cells, Gene Expression Profiling, Endoplasmic Reticulum Stress immunology, Endoplasmic Reticulum Stress genetics, Unfolded Protein Response genetics, Unfolded Protein Response immunology, SARS-CoV-2 immunology, SARS-CoV-2 genetics, SARS-CoV-2 physiology, Angiotensin-Converting Enzyme 2 genetics, Angiotensin-Converting Enzyme 2 metabolism, COVID-19 immunology, COVID-19 virology, COVID-19 genetics, Immunity, Innate genetics, Transcriptome, Viral Load
- Abstract
The transcriptome of SARS-CoV-2-infected cells that reflects the interplay between host and virus has provided valuable insights into mechanisms underlying SARS-CoV-2 infection and COVID-19 disease progression. In this study, we show that SARS-CoV-2 can establish a robust infection in HEK293T cells that overexpress human angiotensin-converting enzyme 2 (hACE2) without triggering significant host immune response. Instead, endoplasmic reticulum stress and unfolded protein response-related pathways are predominantly activated. By comparing our data with published transcriptome of SARS-CoV-2 infection in other cell lines, we found that the expression level of hACE2 directly correlates with the viral load in infected cells but not with the scale of immune responses. Only cells that express high level of endogenous hACE2 exhibit an extensive immune attack even with a low viral load. Therefore, the infection route may be critical for the extent of the immune response, thus the severity of COVID-19 disease status., (© 2021. The Author(s).)
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- 2021
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34. Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication.
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Li Y, Garcia G Jr, Arumugaswami V, and Guo F
- Abstract
Antisense oligonucleotides (ASOs) are an emerging class of drugs that target RNAs. Current ASO designs strictly follow the rule of Watson-Crick base pairing along target sequences. However, RNAs often fold into structures that interfere with ASO hybridization. Here we developed a structure-based ASO design method and applied it to target severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our method makes sure that ASO binding is compatible with target structures in three-dimensional (3D) space by employing structural design templates. These 3D-ASOs recognize the shapes and hydrogen bonding patterns of targets via tertiary interactions, achieving enhanced affinity and specificity. We designed 3D-ASOs that bind to the frameshift stimulation element and transcription regulatory sequence of SARS-CoV-2 and identified lead ASOs that strongly inhibit viral replication in human cells. We further optimized the lead sequences and characterized structure-activity relationship. The 3D-ASO technology helps fight coronavirus disease-2019 and is broadly applicable to ASO drug development., Competing Interests: Competing interests: A provisional patent (application # 63226617) has been filed by UCLA and is currently pending. F.G. and V.A. are the inventors. The authors have no other competing interests.
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- 2021
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35. Development of a blocker of the universal phosphatidylserine- and phosphatidylethanolamine-dependent viral entry pathways.
- Author
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Song DH, Garcia G Jr, Situ K, Chua BA, Hong MLO, Do EA, Ramirez CM, Harui A, Arumugaswami V, and Morizono K
- Subjects
- A549 Cells, Animals, Cell Line, Chlorocebus aethiops, Culicidae virology, Female, HEK293 Cells, Humans, Intercellular Signaling Peptides and Proteins metabolism, Male, Mice, Mice, Inbred C57BL, Mice, Knockout, Proto-Oncogene Proteins metabolism, Receptor Protein-Tyrosine Kinases metabolism, Receptor, Interferon alpha-beta genetics, Vero Cells, Viral Envelope metabolism, Viral Load drug effects, Zika Virus growth & development, Zika Virus Infection drug therapy, Zika Virus Infection pathology, Zika Virus Infection transmission, Axl Receptor Tyrosine Kinase, Antiviral Agents pharmacology, Phosphatidylethanolamines antagonists & inhibitors, Phosphatidylserines antagonists & inhibitors, Virus Attachment drug effects, Virus Internalization drug effects, Zika Virus drug effects
- Abstract
Envelope phosphatidylserine (PtdSer) and phosphatidylethanolamine (PtdEtr) have been shown to mediate binding of enveloped viruses. However, commonly used PtdSer binding molecules such as Annexin V cannot block PtdSer-mediated viral infection. Lack of reagents that can conceal envelope PtdSer and PtdEtr and subsequently inhibit infection hinders elucidation of the roles of the envelope phospholipids in viral infection. Here, we developed sTIM1dMLDR801, a reagent capable of blocking PtdSer- and PtdEtr-dependent infection of enveloped viruses. Using sTIM1dMLDR801, we found that envelope PtdSer and/or PtdEtr can support ZIKV infection of not only human but also mosquito cells. In a mouse model for ZIKV infection, sTIM1dMLDR801 reduced ZIKV load in serum and the spleen, indicating envelope PtdSer and/or PtdEtr support in viral infection in vivo. sTIM1dMLDR801 will enable elucidation of the roles of envelope PtdSer and PtdEtr in infection of various virus species, thereby facilitating identification of their receptors and transmission mechanisms., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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36. A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection.
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Chen F, Shi Q, Pei F, Vogt A, Porritt RA, Garcia G Jr, Gomez AC, Cheng MH, Schurdak ME, Liu B, Chan SY, Arumugaswami V, Stern AM, Taylor DL, Arditi M, and Bahar I
- Subjects
- Angiotensin-Converting Enzyme 2 genetics, Angiotensin-Converting Enzyme 2 metabolism, Animals, Anti-Inflammatory Agents, Non-Steroidal pharmacology, COVID-19 genetics, COVID-19 virology, Chlorocebus aethiops, Drug Repositioning, HEK293 Cells, Host-Pathogen Interactions drug effects, Host-Pathogen Interactions physiology, Humans, Imidazoles pharmacology, Pyrazines pharmacology, SARS-CoV-2 drug effects, SARS-CoV-2 pathogenicity, Salmeterol Xinafoate pharmacology, Vero Cells, Antiviral Agents pharmacology, Drug Evaluation, Preclinical methods, Virus Internalization drug effects, COVID-19 Drug Treatment
- Abstract
Understanding the mechanism of SARS-CoV-2 infection and identifying potential therapeutics are global imperatives. Using a quantitative systems pharmacology approach, we identified a set of repurposable and investigational drugs as potential therapeutics against COVID-19. These were deduced from the gene expression signature of SARS-CoV-2-infected A549 cells screened against Connectivity Map and prioritized by network proximity analysis with respect to disease modules in the viral-host interactome. We also identified immuno-modulating compounds aiming at suppressing hyperinflammatory responses in severe COVID-19 patients, based on the transcriptome of ACE2-overexpressing A549 cells. Experiments with Vero-E6 cells infected by SARS-CoV-2, as well as independent syncytia formation assays for probing ACE2/SARS-CoV-2 spike protein-mediated cell fusion using HEK293T and Calu-3 cells, showed that several predicted compounds had inhibitory activities. Among them, salmeterol, rottlerin, and mTOR inhibitors exhibited antiviral activities in Vero-E6 cells; imipramine, linsitinib, hexylresorcinol, ezetimibe, and brompheniramine impaired viral entry. These novel findings provide new paths for broadening the repertoire of compounds pursued as therapeutics against COVID-19., (© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)
- Published
- 2021
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37. Deleterious Effects of SARS-CoV-2 Infection on Human Pancreatic Cells.
- Author
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Shaharuddin SH, Wang V, Santos RS, Gross A, Wang Y, Jawanda H, Zhang Y, Hasan W, Garcia G Jr, Arumugaswami V, and Sareen D
- Subjects
- Acute Disease, Humans, Pancreas, Pandemics, SARS-CoV-2, COVID-19, Pancreatitis
- Abstract
COVID-19 pandemic has infected more than 154 million people worldwide and caused more than 3.2 million deaths. It is transmitted by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and affects the respiratory tract as well as extra-pulmonary systems, including the pancreas, that express the virus entry receptor, Angiotensin-Converting Enzyme 2 (ACE2) receptor. Importantly, the endocrine and exocrine pancreas, the latter composed of ductal and acinar cells, express high levels of ACE2, which correlates to impaired functionality characterized as acute pancreatitis observed in some cases presenting with COVID-19. Since acute pancreatitis is already one of the most frequent gastrointestinal causes of hospitalization in the U.S. and the majority of studies investigating the effects of SARS-CoV-2 on the pancreas are clinical and observational, we utilized human iPSC technology to investigate the potential deleterious effects of SARS-CoV-2 infection on iPSC-derived pancreatic cultures containing endocrine and exocrine cells. Interestingly, iPSC-derived pancreatic cultures allow SARS-CoV-2 entry and establish infection, thus perturbing their normal molecular and cellular phenotypes. The infection increased a key cytokine, CXCL12, known to be involved in inflammatory responses in the pancreas. Transcriptome analysis of infected pancreatic cultures confirmed that SARS-CoV-2 hijacks the ribosomal machinery in these cells. Notably, the SARS-CoV-2 infectivity of the pancreas was confirmed in post-mortem tissues from COVID-19 patients, which showed co-localization of SARS-CoV-2 in pancreatic endocrine and exocrine cells and increased the expression of some pancreatic ductal stress response genes. Thus, we demonstrate that SARS-CoV-2 can directly infect human iPSC-derived pancreatic cells with strong supporting evidence of presence of the virus in post-mortem pancreatic tissue of confirmed COVID-19 human cases. This novel model of iPSC-derived pancreatic cultures will open new avenues for the comprehension of the SARS-CoV-2 infection and potentially establish a platform for endocrine and exocrine pancreas-specific antiviral drug screening., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Shaharuddin, Wang, Santos, Gross, Wang, Jawanda, Zhang, Hasan, Garcia, Arumugaswami and Sareen.)
- Published
- 2021
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38. ORAI1 establishes resistance to SARS-CoV-2 infection by regulating tonic type I interferon signaling.
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Wu B, Ramaiah A, Garcia G Jr, Gwack Y, Arumugaswami V, and Srikanth S
- Abstract
ORAI1 and STIM1 are the critical mediators of store-operated Ca
2+ entry by acting as the pore subunit and an endoplasmic reticulum-resident signaling molecule, respectively. In addition to Ca2+ signaling, STIM1 is also involved in regulation of a cytosolic nucleic acid sensing pathway. Using ORAI1 and STIM1 knockout cells, we examined their contribution to the host response to SARS-CoV-2 infection. STIM1 knockout cells showed strong resistance to SARS-CoV-2 infection due to enhanced type I interferon response. On the contrary, ORAI1 knockout cells showed high susceptibility to SARS-CoV-2 infection as judged by increased expression of viral proteins and a high viral load. Mechanistically, ORAI1 knockout cells showed reduced homeostatic cytoplasmic Ca2+ concentration and severe impairment in tonic interferon signaling. Transcriptome analysis showed downregulation of multiple cellular defense mechanisms, including antiviral signaling pathways in ORAI1 knockout cells, which are likely due to reduced expression of the Ca2+ -dependent transcription factors of the activator protein 1 (AP-1) family and MEF2C . Our results identify a novel role of ORAI1-mediated Ca2+ signaling in regulating the baseline type I interferon level, which is a determinant of host resistance to SARS-CoV-2 infection.- Published
- 2021
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39. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery.
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Mulay A, Konda B, Garcia G Jr, Yao C, Beil S, Villalba JM, Koziol C, Sen C, Purkayastha A, Kolls JK, Pociask DA, Pessina P, de Aja JS, Garcia-de-Alba C, Kim CF, Gomperts B, Arumugaswami V, and Stripp BR
- Subjects
- Adenosine Monophosphate analogs & derivatives, Adenosine Monophosphate pharmacology, Adult, Aged, Alanine analogs & derivatives, Alanine pharmacology, Alveolar Epithelial Cells metabolism, COVID-19 metabolism, COVID-19 virology, Child, Preschool, Drug Discovery methods, Epithelial Cells virology, Epithelium metabolism, Epithelium virology, Female, Fibroblasts cytology, Fibroblasts metabolism, Humans, Lung pathology, Male, Middle Aged, Models, Biological, Primary Cell Culture, Respiratory Mucosa virology, SARS-CoV-2 physiology, Virus Replication drug effects, Alveolar Epithelial Cells virology, COVID-19 pathology, Lung virology, SARS-CoV-2 drug effects, COVID-19 Drug Treatment
- Abstract
Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic caused by severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Although infection initiates in the proximal airways, severe and sometimes fatal symptoms of the disease are caused by infection of the alveolar type 2 (AT2) cells of the distal lung and associated inflammation. In this study, we develop primary human lung epithelial infection models to understand initial responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface (ALI) cultures of proximal airway epithelium and alveosphere cultures of distal lung AT2 cells are readily infected by SARS-CoV-2, leading to an epithelial cell-autonomous proinflammatory response with increased expression of interferon signaling genes. Studies to validate the efficacy of selected candidate COVID-19 drugs confirm that remdesivir strongly suppresses viral infection/replication. We provide a relevant platform for study of COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and emergent respiratory pathogens., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021. Published by Elsevier Inc.)
- Published
- 2021
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40. Antiviral drug screen identifies DNA-damage response inhibitor as potent blocker of SARS-CoV-2 replication.
- Author
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Garcia G Jr, Sharma A, Ramaiah A, Sen C, Purkayastha A, Kohn DB, Parcells MS, Beck S, Kim H, Bakowski MA, Kirkpatrick MG, Riva L, Wolff KC, Han B, Yuen C, Ulmert D, Purbey PK, Scumpia P, Beutler N, Rogers TF, Chatterjee AK, Gabriel G, Bartenschlager R, Gomperts B, Svendsen CN, Betz UAK, Damoiseaux RD, and Arumugaswami V
- Subjects
- A549 Cells, Animals, COVID-19 metabolism, COVID-19 pathology, Chlorocebus aethiops, Drug Evaluation, Preclinical, HEK293 Cells, HeLa Cells, Humans, MAP Kinase Signaling System drug effects, Middle East Respiratory Syndrome Coronavirus metabolism, Vero Cells, Antiviral Agents pharmacology, DNA Damage, Isoxazoles pharmacology, Pyrazines pharmacology, SARS-CoV-2 physiology, Virus Replication drug effects, COVID-19 Drug Treatment
- Abstract
SARS-CoV-2 has currently precipitated the COVID-19 global health crisis. We developed a medium-throughput drug-screening system and identified a small-molecule library of 34 of 430 protein kinase inhibitors that were capable of inhibiting the SARS-CoV-2 cytopathic effect in human epithelial cells. These drug inhibitors are in various stages of clinical trials. We detected key proteins involved in cellular signaling pathways mTOR-PI3K-AKT, ABL-BCR/MAPK, and DNA-damage response that are critical for SARS-CoV-2 infection. A drug-protein interaction-based secondary screen confirmed compounds, such as the ATR kinase inhibitor berzosertib and torin2 with anti-SARS-CoV-2 activity. Berzosertib exhibited potent antiviral activity against SARS-CoV-2 in multiple cell types and blocked replication at the post-entry step. Berzosertib inhibited replication of SARS-CoV-1 and the Middle East respiratory syndrome coronavirus (MERS-CoV) as well. Our study highlights key promising kinase inhibitors to constrain coronavirus replication as a host-directed therapy in the treatment of COVID-19 and beyond as well as provides an important mechanism of host-pathogen interactions., Competing Interests: Declaration of interests U.A.K.B. is an employee of Merck KGaA, Darmstadt, Germany. Berzosertib compound is licensed by Merck KGaA, Darmstadt, Germany. The other authors declare no competing financial interests., (Copyright © 2021 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2021
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41. SARS-CoV-2 infection rewires host cell metabolism and is potentially susceptible to mTORC1 inhibition.
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Mullen PJ, Garcia G Jr, Purkayastha A, Matulionis N, Schmid EW, Momcilovic M, Sen C, Langerman J, Ramaiah A, Shackelford DB, Damoiseaux R, French SW, Plath K, Gomperts BN, Arumugaswami V, and Christofk HR
- Subjects
- Animals, Benzamides pharmacology, Cell Line, Chlorocebus aethiops, Glucose metabolism, Glutamine metabolism, HEK293 Cells, Humans, Lung metabolism, Lung virology, Morpholines pharmacology, Naphthyridines pharmacology, Pyrimidines pharmacology, Pyruvate Carboxylase biosynthesis, SARS-CoV-2 metabolism, Vero Cells, Virus Replication drug effects, COVID-19 pathology, Citric Acid Cycle physiology, Mechanistic Target of Rapamycin Complex 1 antagonists & inhibitors, Mechanistic Target of Rapamycin Complex 1 metabolism, Protein Kinase Inhibitors pharmacology
- Abstract
Viruses hijack host cell metabolism to acquire the building blocks required for replication. Understanding how SARS-CoV-2 alters host cell metabolism may lead to potential treatments for COVID-19. Here we profile metabolic changes conferred by SARS-CoV-2 infection in kidney epithelial cells and lung air-liquid interface (ALI) cultures, and show that SARS-CoV-2 infection increases glucose carbon entry into the TCA cycle via increased pyruvate carboxylase expression. SARS-CoV-2 also reduces oxidative glutamine metabolism while maintaining reductive carboxylation. Consistent with these changes, SARS-CoV-2 infection increases the activity of mTORC1 in cell lines and lung ALI cultures. Lastly, we show evidence of mTORC1 activation in COVID-19 patient lung tissue, and that mTORC1 inhibitors reduce viral replication in kidney epithelial cells and lung ALI cultures. Our results suggest that targeting mTORC1 may be a feasible treatment strategy for COVID-19 patients, although further studies are required to determine the mechanism of inhibition and potential efficacy in patients.
- Published
- 2021
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42. Systemic diseases and the cornea.
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Shah R, Amador C, Tormanen K, Ghiam S, Saghizadeh M, Arumugaswami V, Kumar A, Kramerov AA, and Ljubimov AV
- Subjects
- Autoimmune Diseases diagnosis, Comorbidity, Humans, SARS-CoV-2, Autoimmune Diseases epidemiology, COVID-19 epidemiology, Cornea pathology
- Abstract
There is a number of systemic diseases affecting the cornea. These include endocrine disorders (diabetes, Graves' disease, Addison's disease, hyperparathyroidism), infections with viruses (SARS-CoV-2, herpes simplex, varicella zoster, HTLV-1, Epstein-Barr virus) and bacteria (tuberculosis, syphilis and Pseudomonas aeruginosa), autoimmune and inflammatory diseases (rheumatoid arthritis, Sjögren's syndrome, lupus erythematosus, gout, atopic and vernal keratoconjunctivitis, multiple sclerosis, granulomatosis with polyangiitis, sarcoidosis, Cogan's syndrome, immunobullous diseases), corneal deposit disorders (Wilson's disease, cystinosis, Fabry disease, Meretoja's syndrome, mucopolysaccharidosis, hyperlipoproteinemia), and genetic disorders (aniridia, Ehlers-Danlos syndromes, Marfan syndrome). Corneal manifestations often provide an insight to underlying systemic diseases and can act as the first indicator of an undiagnosed systemic condition. Routine eye exams can bring attention to potentially life-threatening illnesses. In this review, we provide a fairly detailed overview of the pathologic changes in the cornea described in various systemic diseases and also discuss underlying molecular mechanisms, as well as current and emerging treatments., (Copyright © 2021 Elsevier Ltd. All rights reserved.)
- Published
- 2021
- Full Text
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43. ApoE-Isoform-Dependent SARS-CoV-2 Neurotropism and Cellular Response.
- Author
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Wang C, Zhang M, Garcia G Jr, Tian E, Cui Q, Chen X, Sun G, Wang J, Arumugaswami V, and Shi Y
- Subjects
- Adenosine Monophosphate analogs & derivatives, Adenosine Monophosphate pharmacology, Alanine analogs & derivatives, Alanine pharmacology, Animals, Antiviral Agents pharmacology, Astrocytes drug effects, Astrocytes pathology, Astrocytes virology, Cell Differentiation, Chlorocebus aethiops, Humans, Nerve Degeneration pathology, Neurites pathology, Neurons drug effects, Neurons pathology, Neurons virology, Organoids drug effects, Organoids pathology, Organoids virology, Protein Isoforms metabolism, Synapses pathology, Vero Cells, Apolipoproteins E metabolism, Brain pathology, Brain virology, COVID-19 virology, Induced Pluripotent Stem Cells virology, SARS-CoV-2 physiology, Tropism physiology
- Abstract
ApoE4, a strong genetic risk factor for Alzheimer disease, has been associated with increased risk for severe COVID-19. However, it is unclear whether ApoE4 alters COVID-19 susceptibility or severity, and the role of direct viral infection in brain cells remains obscure. We tested the neurotropism of SARS-CoV2 in human-induced pluripotent stem cell (hiPSC) models and observed low-grade infection of neurons and astrocytes that is boosted in neuron-astrocyte co-cultures and organoids. We then generated isogenic ApoE3/3 and ApoE4/4 hiPSCs and found an increased rate of SARS-CoV-2 infection in ApoE4/4 neurons and astrocytes. ApoE4 astrocytes exhibited enlarged size and elevated nuclear fragmentation upon SARS-CoV-2 infection. Finally, we show that remdesivir treatment inhibits SARS-CoV2 infection of hiPSC neurons and astrocytes. These findings suggest that ApoE4 may play a causal role in COVID-19 severity. Understanding how risk factors impact COVID-19 susceptibility and severity will help us understand the potential long-term effects in different patient populations., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
44. Metabolic reprogramming and epigenetic changes of vital organs in SARS-CoV-2-induced systemic toxicity.
- Author
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Li S, Ma F, Yokota T, Garcia G Jr, Palermo A, Wang Y, Farrell C, Wang YC, Wu R, Zhou Z, Pan C, Morselli M, Teitell MA, Ryazantsev S, Fishbein GA, Hoeve JT, Arboleda VA, Bloom J, Dillon B, Pellegrini M, Lusis AJ, Graeber TG, Arumugaswami V, and Deb A
- Subjects
- Angiotensin-Converting Enzyme 2 genetics, Angiotensin-Converting Enzyme 2 metabolism, Animals, Animals, Genetically Modified, COVID-19 metabolism, COVID-19 physiopathology, COVID-19 virology, Citric Acid Cycle physiology, DNA Methylation physiology, Disease Models, Animal, Failure to Thrive physiopathology, Humans, Immunity genetics, Male, Mice, Oxidative Phosphorylation, Renin-Angiotensin System physiology, SARS-CoV-2 metabolism, Wasting Syndrome physiopathology, COVID-19 complications, Epigenesis, Genetic immunology, Failure to Thrive etiology, SARS-CoV-2 pathogenicity, Wasting Syndrome etiology
- Abstract
Extrapulmonary manifestations of COVID-19 are associated with a much higher mortality rate than pulmonary manifestations. However, little is known about the pathogenesis of systemic complications of COVID-19. Here, we create a murine model of SARS-CoV-2-induced severe systemic toxicity and multiorgan involvement by expressing the human ACE2 transgene in multiple tissues via viral delivery, followed by systemic administration of SARS-CoV-2. The animals develop a profound phenotype within 7 days with severe weight loss, morbidity, and failure to thrive. We demonstrate that there is metabolic suppression of oxidative phosphorylation and the tricarboxylic acid (TCA) cycle in multiple organs with neutrophilia, lymphopenia, and splenic atrophy, mirroring human COVID-19 phenotypes. Animals had a significantly lower heart rate, and electron microscopy demonstrated myofibrillar disarray and myocardial edema, a common pathogenic cardiac phenotype in human COVID-19. We performed metabolomic profiling of peripheral blood and identified a panel of TCA cycle metabolites that served as biomarkers of depressed oxidative phosphorylation. Finally, we observed that SARS-CoV-2 induces epigenetic changes of DNA methylation, which affects expression of immune response genes and could, in part, contribute to COVID-19 pathogenesis. Our model suggests that SARS-CoV-2-induced metabolic reprogramming and epigenetic changes in internal organs could contribute to systemic toxicity and lethality in COVID-19.
- Published
- 2021
- Full Text
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45. The transcriptome of anterior regeneration in earthworm Eudrilus eugeniae.
- Author
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Paul S, Balakrishnan S, Arumugaperumal A, Lathakumari S, Syamala SS, Arumugaswami V, and Sivasubramaniam S
- Subjects
- Animals, Gene Expression Profiling methods, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Oligochaeta growth & development, Regeneration physiology, Exome Sequencing, Oligochaeta genetics, Regeneration genetics, Transcriptome genetics
- Abstract
The oligochaete earthworm, Eudrilus eugeniae is capable of regenerating both anterior and posterior segments. The present study focuses on the transcriptome analysis of earthworm E. eugeniae to identify and functionally annotate the key genes supporting the anterior blastema formation and regulating the anterior regeneration of the worm. The Illumina sequencing generated a total of 91,593,182 raw reads which were assembled into 105,193 contigs using CLC genomics workbench. In total, 40,946 contigs were annotated against the NCBI nr and SwissProt database and among them, 15,702 contigs were assigned to 14,575 GO terms. Besides a total of 9389 contigs were mapped to 416 KEGG biological pathways. The RNA-Seq comparison study identified 10,868 differentially expressed genes (DEGs) and of them, 3986 genes were significantly upregulated in the anterior regenerated blastema tissue samples of the worm. The GO enrichment analysis showed angiogenesis and unfolded protein binding as the top enriched functions and the pathway enrichment analysis denoted TCA cycle as the most significantly enriched pathway associated with the upregulated gene dataset of the worm. The identified DEGs and their function and pathway information can be effectively utilized further to interpret the key cellular, genetic and molecular events associated with the regeneration of the worm.
- Published
- 2021
- Full Text
- View/download PDF
46. Direct Exposure to SARS-CoV-2 and Cigarette Smoke Increases Infection Severity and Alters the Stem Cell-Derived Airway Repair Response.
- Author
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Purkayastha A, Sen C, Garcia G Jr, Langerman J, Shia DW, Meneses LK, Vijayaraj P, Durra A, Koloff CR, Freund DR, Chi J, Rickabaugh TM, Mulay A, Konda B, Sim MS, Stripp BR, Plath K, Arumugaswami V, and Gomperts BN
- Subjects
- COVID-19 genetics, COVID-19 immunology, COVID-19 therapy, Cells, Cultured, Down-Regulation, Humans, Immunity, Innate, Interferon-beta therapeutic use, Patient Acuity, Respiratory Mucosa virology, COVID-19 physiopathology, Respiratory Mucosa physiopathology, Smoking adverse effects, Stem Cells virology
- Abstract
Current smoking is associated with increased risk of severe COVID-19, but it is not clear how cigarette smoke (CS) exposure affects SARS-CoV-2 airway cell infection. We directly exposed air-liquid interface (ALI) cultures derived from primary human nonsmoker airway basal stem cells (ABSCs) to short term CS and then infected them with SARS-CoV-2. We found an increase in the number of infected airway cells after CS exposure with a lack of ABSC proliferation. Single-cell profiling of the cultures showed that the normal interferon response was reduced after CS exposure with infection. Treatment of CS-exposed ALI cultures with interferon β-1 abrogated the viral infection, suggesting one potential mechanism for more severe viral infection. Our data show that acute CS exposure allows for more severe airway epithelial disease from SARS-CoV-2 by reducing the innate immune response and ABSC proliferation and has implications for disease spread and severity in people exposed to CS., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
47. A monoclonal antibody against staphylococcal enterotoxin B superantigen inhibits SARS-CoV-2 entry in vitro .
- Author
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Cheng MH, Porritt RA, Rivas MN, Krieger JM, Ozdemir AB, Garcia G Jr, Arumugaswami V, Fries BC, Arditi M, and Bahar I
- Abstract
We recently discovered a superantigen-like motif, similar to Staphylococcal enterotoxin B (SEB), near the S1/S2 cleavage site of SARS-CoV-2 Spike protein, which might explain the multisystem-inflammatory syndrome (MIS-C) observed in children and cytokine storm in severe COVID-19 patients. We show here that an anti-SEB monoclonal antibody (mAb), 6D3, can bind this viral motif, and in particular its PRRA insert, to inhibit infection by blocking the access of host cell proteases, TMPRSS2 or furin, to the cleavage site. The high affinity of 6D3 for the furin-cleavage site originates from a poly-acidic segment at its heavy chain CDR2, a feature shared with SARS-CoV-2-neutralizing mAb 4A8. The affinity of 6D3 and 4A8 for this site points to their potential utility as therapeutics for treating COVID-19, MIS-C, or common cold caused by human coronaviruses (HCoVs) that possess a furin-like cleavage site.
- Published
- 2020
- Full Text
- View/download PDF
48. Cold atmospheric plasma for SARS-CoV-2 inactivation.
- Author
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Chen Z, Garcia G Jr, Arumugaswami V, and Wirz RE
- Abstract
Syndrome coronavirus 2 (SARS-CoV-2) infectious virions are viable on various surfaces (e.g., plastic, metals, and cardboard) for several hours. This presents a transmission cycle for human infection that can be broken by developing new inactivation approaches. We employed an efficient cold atmospheric plasma (CAP) with argon feed gas to inactivate SARS-CoV-2 on various surfaces including plastic, metal, cardboard, basketball composite leather, football leather, and baseball leather. These results demonstrate the great potential of CAP as a safe and effective means to prevent virus transmission and infections for a wide range of surfaces that experience frequent human contact. Since this is the first-ever demonstration of cold plasma inactivation of SARS-CoV-2, it is a significant milestone in the prevention and treatment of coronavirus disease 2019 (COVID-19) and presents a new opportunity for the scientific, engineering, and medical communities., (© 2020 Author(s).)
- Published
- 2020
- Full Text
- View/download PDF
49. Human iPSC-Derived Cardiomyocytes Are Susceptible to SARS-CoV-2 Infection.
- Author
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Sharma A, Garcia G Jr, Wang Y, Plummer JT, Morizono K, Arumugaswami V, and Svendsen CN
- Abstract
Coronavirus disease 2019 (COVID-19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is defined by respiratory symptoms, but cardiac complications including viral myocarditis are also prevalent. Although ischemic and inflammatory responses caused by COVID-19 can detrimentally affect cardiac function, the direct impact of SARS-CoV-2 infection on human cardiomyocytes is not well understood. Here, we utilize human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a model to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. Microscopy and RNA sequencing demonstrate that SARS-CoV-2 can enter hiPSC-CMs via ACE2. Viral replication and cytopathic effect induce hiPSC-CM apoptosis and cessation of beating after 72 h of infection. SARS-CoV-2 infection activates innate immune response and antiviral clearance gene pathways, while inhibiting metabolic pathways and suppressing ACE2 expression. These studies show that SARS-CoV-2 can infect hiPSC-CMs in vitro , establishing a model for elucidating infection mechanisms and potentially a cardiac-specific antiviral drug screening platform., Competing Interests: The authors declare no competing interests., (© 2020 The Author(s).)
- Published
- 2020
- Full Text
- View/download PDF
50. SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery.
- Author
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Mulay A, Konda B, Garcia G Jr, Yao C, Beil S, Sen C, Purkayastha A, Kolls JK, Pociask DA, Pessina P, de Aja JS, Garcia-de-Alba C, Kim CF, Gomperts B, Arumugaswami V, and Stripp BR
- Abstract
Coronavirus disease 2019 (COVID-19) is the latest respiratory pandemic resulting from zoonotic transmission of severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). Severe symptoms include viral pneumonia secondary to infection and inflammation of the lower respiratory tract, in some cases causing death. We developed primary human lung epithelial infection models to understand responses of proximal and distal lung epithelium to SARS-CoV-2 infection. Differentiated air-liquid interface cultures of proximal airway epithelium and 3D organoid cultures of alveolar epithelium were readily infected by SARS-CoV-2 leading to an epithelial cell-autonomous proinflammatory response. We validated the efficacy of selected candidate COVID-19 drugs confirming that Remdesivir strongly suppressed viral infection/replication. We provide a relevant platform for studying COVID-19 pathobiology and for rapid drug screening against SARS-CoV-2 and future emergent respiratory pathogens., One Sentence Summary: A novel infection model of the adult human lung epithelium serves as a platform for COVID-19 studies and drug discovery.
- Published
- 2020
- Full Text
- View/download PDF
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