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  1. Article ; Online: Temporal cytokine storm dynamics in dengue infection predicts severity.

    Bhatt, Puneet / Varma, Muralidhar / Sood, Vikas / Ambikan, Anoop / Jayaram, Anup / Babu, Naren / Gupta, Soham / Mukhopadhyay, Chiranjay / Neogi, Ujjwal

    Virus research

    2024  Volume 341, Page(s) 199306

    Abstract: The immunopathogenesis of dengue severity is convoluted. The primary objective of the research was to examine the dynamics of cytokine storm and its correlation with disease development in individuals affected by DENV infection. Additionally, the study ... ...

    Abstract The immunopathogenesis of dengue severity is convoluted. The primary objective of the research was to examine the dynamics of cytokine storm and its correlation with disease development in individuals affected by DENV infection. Additionally, the study aimed to discover potential biomarkers that could indicate severe dengue infection and determine the most suitable timeframe for predicting the severity of these biomarkers during the acute stage of dengue infections. We conducted a temporal analysis of the daily viral load and cytokine levels in 60 hospitalized dengue patients until discharge. Our findings reveal a distinct cytokine profile (elevated IL-8, IL-10, IL-6, GM-CSF, MCP-1, IL-13, and IL-4 and decreased IL-12, MIP-1β) on the third day after symptom onset is predictive of severe dengue in secondary dengue infection. The imbalanced cytokine signature may inform clinical decision-making in treating severe dengue infections.
    MeSH term(s) Humans ; Severe Dengue ; Dengue ; Dengue Virus ; Cytokine Release Syndrome ; Cytokines ; Biomarkers
    Chemical Substances Cytokines ; Biomarkers
    Language English
    Publishing date 2024-01-06
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 605780-9
    ISSN 1872-7492 ; 0168-1702
    ISSN (online) 1872-7492
    ISSN 0168-1702
    DOI 10.1016/j.virusres.2023.199306
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Proteomic landscape of astrocytes and pericytes infected with HIV/SARS-CoV-2 mono/co-infection, impacting on neurological complications.

    Acharya, Arpan / Ambikan, Anoop T / Thurman, Michellie / Malik, Mohid Reza / Dyavar, Shetty Ravi / Végvári, Ákos / Neogi, Ujjwal / Byrareddy, Siddappa N

    Research square

    2023  

    Abstract: Background: Although most individuals recover from coronavirus disease 2019 (COVID-19) within a few weeks, some people continue to experience a wide range of symptoms known as post-acute sequelae of SARS-CoV-2 (PASC) or long COVID. Majority of patients ... ...

    Abstract Background: Although most individuals recover from coronavirus disease 2019 (COVID-19) within a few weeks, some people continue to experience a wide range of symptoms known as post-acute sequelae of SARS-CoV-2 (PASC) or long COVID. Majority of patients with PASC develop neurological disorders like brain fog, fatigue, mood swings, sleep disorders, loss of smell and test among others collectively called neuro-PASC. While the people living with HIV (PWH) do not have a higher risk of developing severe disease and mortality/morbidity due to COVID-19. As a large section of PWH suffered from HIV-associated neurocognitive disorders (HAND), it is essential to understand the impact of neuro-PASC on people with HAND. In pursuit of this, we infected HIV/SARS-CoV-2 alone or together in primary human astrocytes and pericytes and performed proteomics to understand the impact of co-infection in the central nervous system.
    Methods: Primary human astrocytes and pericytes were infected with SARS-CoV-2 or HIV or HIV + SARS-CoV-2. The concentration of HIV and SARS-CoV-2 genomic RNA in the culture supernatant was quantified using reverse transcriptase quantitative real time polymerase chain reaction (RT-qPCR). This was followed by a quantitative proteomics analysis of mock, HIV, SARS-CoV-2, and HIV + SARS-CoV-2 infected astrocytes and pericytes to understand the impact of the virus in CNS cell types.
    Results: Both healthy and HIV-infected astrocytes and pericytes support abortive/low level of SARS-CoV-2 replication. In both mono-infected and co-infected cells, we observe a modest increase in the expression of SARS-CoV-2 host cell entry factors (ACE2, TMPRSS2, NRP1, and TRIM28) and inflammatory mediators (IL-6, TNF-α, IL-1β and IL-18). Quantitative proteomic analysis has identified uniquely regulated pathways in mock vs SARS-CoV-2, mock vs HIV + SARS-CoV-2, and HIV vs HIV + SARS-CoV-2 infected astrocytes and pericytes. The gene set enrichment analysis revealed that the top ten enriched pathways are linked to several neurodegenerative disorders, including Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis.
    Conclusions: Our study emphasizes the significance of long-term monitoring of patients co-infected with HIV and SARS-CoV-2 to detect and understand the development of neurological abnormalities. By unraveling the molecular mechanisms involved, we can identify potential targets for future therapeutic interventions.
    Language English
    Publishing date 2023-06-12
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3031591/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: TISSUE-SPECIFIC METABOLOMIC REPROGRAMMING DETERMINES THE DISEASE PATHOPHYSIOLOGY OF SARS-COV-2 VARIANTS IN HAMSTER MODEL

    Sardarni, Urvinder Kaur / Ambikan, Anoop / Acharya, Arpan / Johnson, Samuel D / Avedissian, Sean N / Vegvari, Akos / Neogi, Ujjwal / Byrareddy, Siddappa

    bioRxiv

    Abstract: Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To ... ...

    Abstract Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between organs and specific SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed increased viremia in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection.
    Keywords covid19
    Language English
    Publishing date 2024-02-27
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.25.581989
    Database COVID19

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  4. Article ; Online: Tissue-Specific Metabolomic Reprogramming Determines the Disease Pathophysiology of Sars-Cov-2 Variants in Hamster Model

    Sardarni, Urvinder Kaur / Ambikan, Anoop T / Acharya, Arpan / Johnson, Samuel D / Avedissian, Sean N. / Vegvan, Akos / Neogi, Ujjwal / Byrareddy, Siddappa N.

    bioRxiv

    Abstract: Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To ... ...

    Abstract Despite significant effort, a clear understanding of host tissue-specific responses and their implications for immunopathogenicity against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant infection has remained poorly defined. To shed light on the interaction between organs and specific SARS-CoV-2 variants, we sought to characterize the complex relationship among acute multisystem manifestations, dysbiosis of the gut microbiota, and the resulting implications for SARS-CoV-2 variant-specific immunopathogenesis in the Golden Syrian Hamster (GSH) model using multi-omics approaches. Our investigation revealed increased viremia in diverse tissues of delta-infected GSH compared to the omicron variant. Multi-omics analyses uncovered distinctive metabolic responses between the delta and omicron variants, with the former demonstrating dysregulation in synaptic transmission proteins associated with neurocognitive disorders. Additionally, delta-infected GSH exhibited an altered fecal microbiota composition, marked by increased inflammation-associated taxa and reduced commensal bacteria compared to the omicron variant. These findings underscore the SARS-CoV-2-mediated tissue insult, characterized by modified host metabolites, neurological protein dysregulation, and gut dysbiosis, highlighting the compromised gut-lung-brain axis during acute infection.
    Keywords covid19
    Language English
    Publishing date 2024-02-27
    Publisher Cold Spring Harbor Laboratory
    Document type Article ; Online
    DOI 10.1101/2024.02.25.581989
    Database COVID19

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  5. Article ; Online: Rural and urban exposures shape early life immune development in South African children with atopic dermatitis and nonallergic children

    Lunjani, Nonhlanhla / Ambikan, Anoop T. / Hlela, Carol / Levin, Michael / Mankahla, Avumile / Heldstab‐Kast, Jeannette I. / Boonpiyathad, Tadech / Tan, Ge / Altunbulakli, Can / Gray, Clive / Nadeau, Kari C. / Neogi, Ujjwal / Akdis, Cezmi A. / O'Mahony, Liam

    Allergy. 2024 Jan., v. 79, no. 1, p. 65-79

    2024  , Page(s) 65–79

    Abstract: BACKGROUND: Immunological traits and functions have been consistently associated with environmental exposures and are thought to shape allergic disease susceptibility and protection. In particular, specific exposures in early life may have more ... ...

    Abstract BACKGROUND: Immunological traits and functions have been consistently associated with environmental exposures and are thought to shape allergic disease susceptibility and protection. In particular, specific exposures in early life may have more significant effects on the developing immune system, with potentially long‐term impacts. METHODS: We performed RNA‐Seq on peripheral blood mononuclear cells (PBMCs) from 150 children with atopic dermatitis and healthy nonallergic children in rural and urban settings from the same ethnolinguistic AmaXhosa background in South Africa. We measured environmental exposures using questionnaires. RESULTS: A distinct PBMC gene expression pattern was observed in those children with atopic dermatitis (132 differentially expressed genes [DEGs]). However, the predominant influences on the immune cell transcriptome were related to early life exposures including animals, time outdoors, and types of cooking and heating fuels. Sample clustering revealed two rural groups (Rural_1 and Rural_2) that separated from the urban group (3413 and 2647 DEGs, respectively). The most significantly regulated pathways in Rural_1 children were related to innate activation of the immune system (e.g., TLR and cytokine signaling), changes in lymphocyte polarization (e.g., TH17 cells), and immune cell metabolism (i.e., oxidative phosphorylation). The Rural_2 group displayed evidence for ongoing lymphocyte activation (e.g., T cell receptor signaling), with changes in immune cell survival and proliferation (e.g., mTOR signaling, insulin signaling). CONCLUSIONS: This study highlights the importance of the exposome on immune development in early life and identifies potentially protective (e.g., animal) exposures and potentially detrimental (e.g., pollutant) exposures that impact key immunological pathways.
    Keywords T-lymphocytes ; animals ; atopic dermatitis ; cell viability ; cytokines ; disease susceptibility ; exposome ; gene expression regulation ; insulin ; lymphocyte proliferation ; oxidative phosphorylation ; pollutants ; sequence analysis ; transcriptome ; South Africa
    Language English
    Dates of publication 2024-01
    Size p. 65-79
    Publishing place John Wiley & Sons, Ltd
    Document type Article ; Online
    Note JOURNAL ARTICLE
    ZDB-ID 391933-x
    ISSN 1398-9995 ; 0105-4538
    ISSN (online) 1398-9995
    ISSN 0105-4538
    DOI 10.1111/all.15832
    Database NAL-Catalogue (AGRICOLA)

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  6. Article ; Online: Inflammatory, metabolic, and sex-dependent gene-regulatory dynamics of microglia and macrophages in neonatal hippocampus after hypoxia-ischemia.

    Di Martino, Elena / Ambikan, Anoop / Ramsköld, Daniel / Umekawa, Takashi / Giatrellis, Sarantis / Vacondio, Davide / Romero, Alejandro Lastra / Galán, Marta Gómez / Sandberg, Rickard / Ådén, Ulrika / Lauschke, Volker M / Neogi, Ujjwal / Blomgren, Klas / Kele, Julianna

    iScience

    2024  Volume 27, Issue 4, Page(s) 109346

    Abstract: Neonatal hypoxia-ischemia (HI) is a major cause of perinatal death and long-term disabilities worldwide. Post-ischemic neuroinflammation plays a pivotal role in HI pathophysiology. In the present study, we investigated the temporal dynamics of microglia ( ...

    Abstract Neonatal hypoxia-ischemia (HI) is a major cause of perinatal death and long-term disabilities worldwide. Post-ischemic neuroinflammation plays a pivotal role in HI pathophysiology. In the present study, we investigated the temporal dynamics of microglia (CX3CR1
    Language English
    Publishing date 2024-02-28
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.109346
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa.

    Obasa, Adetayo Emmanuel / Ambikan, Anoop T / Gupta, Soham / Neogi, Ujjwal / Jacobs, Graeme Brendon

    BMC infectious diseases

    2021  Volume 21, Issue 1, Page(s) 214

    Abstract: Background: HIV-1C has been shown to have a greater risk of virological failure and reduced susceptibility towards boosted protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study ... ...

    Abstract Background: HIV-1C has been shown to have a greater risk of virological failure and reduced susceptibility towards boosted protease inhibitors (bPIs), a component of second-line combination antiretroviral therapy (cART) in South Africa. This study entailed an evaluation of HIV-1 drug resistance-associated mutations (RAMs) among minor viral populations through high-throughput sequencing genotypic resistance testing (HTS-GRT) in patients on the South African national second-line cART regimen receiving bPIs.
    Methods: During 2017 and 2018, 67 patient samples were sequenced using high-throughput sequencing (HTS), of which 56 samples were included in the final analysis because the patient's treatment regimen was available at the time of sampling. All patients were receiving bPIs as part of their cART. Viral RNA was extracted, and complete pol genes were amplified and sequenced using Illumina HiSeq2500, followed by bioinformatics analysis to quantify the RAMs according to the Stanford HIV Drug Resistance Database.
    Results: Statistically significantly higher PI RAMs were observed in minor viral quasispecies (25%; 14/56) compared to non-nucleoside reverse transcriptase inhibitors (9%; 5/56; p = 0.042) and integrase inhibitor RAM (4%; 2/56; p = 0.002). The majority of the drug resistance mutations in the minor viral quasispecies were observed in the V82A mutation (n = 13) in protease and K65R (n = 5), K103N (n = 7) and M184V (n = 5) in reverse transcriptase.
    Conclusions: HTS-GRT improved the identification of PI and reverse transcriptase inhibitor (RTI) RAMs in second-line cART patients from South Africa compared to the conventional GRT with ≥20% used in Sanger-based sequencing. Several RTI RAMs, such as K65R, M184V or K103N and PI RAM V82A, were identified in < 20% of the population. Deep sequencing could be of greater value in detecting acquired resistance mutations early.
    MeSH term(s) Anti-Retroviral Agents/therapeutic use ; Drug Resistance, Viral/drug effects ; Drug Resistance, Viral/genetics ; Genes, pol/genetics ; Genotype ; HIV Infections/drug therapy ; HIV Infections/virology ; HIV Protease Inhibitors/therapeutic use ; HIV-1/drug effects ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Mutation ; Quasispecies/drug effects ; Quasispecies/genetics ; RNA, Viral/genetics ; South Africa/epidemiology
    Chemical Substances Anti-Retroviral Agents ; HIV Protease Inhibitors ; RNA, Viral
    Language English
    Publishing date 2021-02-25
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041550-3
    ISSN 1471-2334 ; 1471-2334
    ISSN (online) 1471-2334
    ISSN 1471-2334
    DOI 10.1186/s12879-021-05905-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection.

    Ambikan, Anoop T / Svensson-Akusjärvi, Sara / Krishnan, Shuba / Sperk, Maike / Nowak, Piotr / Vesterbacka, Jan / Sönnerborg, Anders / Benfeitas, Rui / Neogi, Ujjwal

    Life science alliance

    2022  Volume 5, Issue 9

    Abstract: Genome-scale metabolic models (GSMMs) can provide novel insights into metabolic reprogramming during disease progression and therapeutic interventions. We developed a context-specific system-level GSMM of people living with HIV (PLWH) using global RNA ... ...

    Abstract Genome-scale metabolic models (GSMMs) can provide novel insights into metabolic reprogramming during disease progression and therapeutic interventions. We developed a context-specific system-level GSMM of people living with HIV (PLWH) using global RNA sequencing data from PBMCs with suppressive viremia either by natural (elite controllers, PLWH
    MeSH term(s) Genome ; HIV Infections/genetics ; HIV-1 ; Humans ; Oxidative Phosphorylation
    Language English
    Publishing date 2022-05-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2575-1077
    ISSN (online) 2575-1077
    DOI 10.26508/lsa.202201405
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease.

    Capendale, Pamela E / García-Rodríguez, Inés / Ambikan, Anoop T / Mulder, Lance A / Depla, Josse A / Freeze, Eline / Koen, Gerrit / Calitz, Carlemi / Sood, Vikas / Vieira de Sá, Renata / Neogi, Ujjwal / Pajkrt, Dasja / Sridhar, Adithya / Wolthers, Katja C

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2532

    Abstract: Picornaviruses are a leading cause of central nervous system (CNS) infections. While genotypes such as parechovirus A3 (PeV-A3) and echovirus 11 (E11) can elicit severe neurological disease, the highly prevalent PeV-A1 is not associated with CNS disease. ...

    Abstract Picornaviruses are a leading cause of central nervous system (CNS) infections. While genotypes such as parechovirus A3 (PeV-A3) and echovirus 11 (E11) can elicit severe neurological disease, the highly prevalent PeV-A1 is not associated with CNS disease. Here, we expand our current understanding of these differences in PeV-A CNS disease using human brain organoids and clinical isolates of the two PeV-A genotypes. Our data indicate that PeV-A1 and A3 specific differences in neurological disease are not due to infectivity of CNS cells as both viruses productively infect brain organoids with a similar cell tropism. Proteomic analysis shows that PeV-A infection significantly alters the host cell metabolism. The inflammatory response following PeV-A3 (and E11 infection) is significantly more potent than that upon PeV-A1 infection. Collectively, our findings align with clinical observations and suggest a role for neuroinflammation, rather than viral replication, in PeV-A3 (and E11) infection.
    MeSH term(s) Humans ; Parechovirus/genetics ; Proteomics ; Picornaviridae Infections ; Inflammation ; Brain ; Enterovirus B, Human ; Central Nervous System Diseases
    Language English
    Publishing date 2024-03-21
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-46634-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment.

    Svensson Akusjärvi, Sara / Krishnan, Shuba / Ambikan, Anoop T / Mikaeloff, Flora / Munusamy Ponnan, Sivasankaran / Vesterbacka, Jan / Lourda, Magda / Nowak, Piotr / Sönnerborg, Anders / Neogi, Ujjwal

    AIDS (London, England)

    2023  Volume 37, Issue 7, Page(s) 1023–1033

    Abstract: Objective: Why people with HIV-1 on ART (PWH ART ) display convoluted metabolism and immune cell functions during prolonged suppressive therapy is not well evaluated. In this study, we aimed to address this question using multiomics methodologies to ... ...

    Abstract Objective: Why people with HIV-1 on ART (PWH ART ) display convoluted metabolism and immune cell functions during prolonged suppressive therapy is not well evaluated. In this study, we aimed to address this question using multiomics methodologies to investigate immunological and metabolic differences between PWH ART and HIV-1 negative individuals (HC).
    Design: Cross-sectional study.
    Methods: Untargeted and targeted metabolomics was performed using gas and liquid chromatography/mass spectrometry, and targeted proteomics using Olink inflammation panel on plasma samples. The cellular metabolic state was further investigated using flow cytometry and intracellular metabolic measurement in single-cell populations isolated by EasySep cell isolation. Finally, flow cytometry was performed for deep-immunophenotyping of mononuclear phagocytes.
    Results: We detected increased levels of glutamate, lactate, and pyruvate by plasma metabolomics and increased inflammatory markers (e.g. CCL20 and CCL7) in PWH ART compared to HC. The metabolite transporter detection by flow cytometry in T cells and monocytes indicated an increased expression of glucose transporter 1 (Glut1) and monocarboxylate transporter 1 (MCT-1) in PWH ART . Single cell-type metabolite measurement identified decreased glucose, glutamate, and lactate in monocytic cell populations in PWH ART . Deep-immunophenotyping of myeloid cell lineages subpopulations showed no difference in cell frequency, but expression levels of CCR5 were increased on classical monocytes and some dendritic cells.
    Conclusions: Our data thus suggest that the myeloid cell populations potentially contribute significantly to the modulated metabolic environment during suppressive HIV-1 infection.
    MeSH term(s) Humans ; HIV Infections ; HIV-1 ; Cross-Sectional Studies ; HIV Seropositivity ; Myeloid Cells ; Glutamates ; Lactates
    Chemical Substances Glutamates ; Lactates
    Language English
    Publishing date 2023-03-21
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000003512
    Database MEDical Literature Analysis and Retrieval System OnLINE

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