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  1. Article ; Online: Peripheral blood CD4+CCR6+ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals

    Sara Svensson Akusjärvi / Shuba Krishnan / Bianca B. Jütte / Anoop T. Ambikan / Soham Gupta / Jimmy Esneider Rodriguez / Ákos Végvári / Maike Sperk / Piotr Nowak / Jan Vesterbacka / J. Peter Svensson / Anders Sönnerborg / Ujjwal Neogi

    Communications Biology, Vol 5, Iss 1, Pp 1-

    2022  Volume 13

    Abstract: The expression profiles dynamics of several chemokine receptors are lower for people living with HIV-1 who naturally control the virus compared to those on suppressive antiretroviral therapy and HIV-negative controls, shedding light on the mechanisms of ... ...

    Abstract The expression profiles dynamics of several chemokine receptors are lower for people living with HIV-1 who naturally control the virus compared to those on suppressive antiretroviral therapy and HIV-negative controls, shedding light on the mechanisms of natural control of HIV-1 infection.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Integrative proteo-transcriptomic and immunophenotyping signatures of HIV-1 elite control phenotype

    Sara Svensson Akusjärvi / Anoop T. Ambikan / Shuba Krishnan / Soham Gupta / Maike Sperk / Ákos Végvári / Flora Mikaeloff / Katie Healy / Jan Vesterbacka / Piotr Nowak / Anders Sönnerborg / Ujjwal Neogi

    iScience, Vol 25, Iss 1, Pp 103607- (2022)

    A cross-talk between glycolysis and HIF signaling

    2022  

    Abstract: Summary: Natural control of HIV-1 is a characteristic of <1% of HIV-1-infected individuals, so called elite controllers (EC). In this study, we sought to identify signaling pathways associated with the EC phenotype using integrative proteo-transcriptomic ...

    Abstract Summary: Natural control of HIV-1 is a characteristic of <1% of HIV-1-infected individuals, so called elite controllers (EC). In this study, we sought to identify signaling pathways associated with the EC phenotype using integrative proteo-transcriptomic analysis and immunophenotyping. We found HIF signaling and glycolysis as specific traits of the EC phenotype together with dysregulation of HIF target gene transcription. A higher proportion of HIF-1α and HIF-1β in the nuclei of CD4+ and CD8+ T cells in the male EC were observed, indicating a potential increased activation of the HIF signaling pathway. Furthermore, intracellular glucose levels were elevated in EC even as the surface expression of the metabolite transporters Glut1 and MCT-1 were decreased on lymphocytes indicative of unique metabolic uptake and flux profile. Combined, our data show that glycolytic modulation and altered HIF signaling is a unique feature of the male EC phenotype that may contribute to natural control of HIV-1.
    Keywords Glycobiology ; Molecular biology ; Immunology ; Virology ; Omics ; Science ; Q
    Subject code 570
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status

    Maike Sperk / Flora Mikaeloff / Sara Svensson-Akusjärvi / Shuba Krishnan / Sivasankaran Munusamy Ponnan / Anoop T. Ambikan / Piotr Nowak / Anders Sönnerborg / Ujjwal Neogi

    iScience, Vol 24, Iss 2, Pp 102111- (2021)

    2021  

    Abstract: Summary: HIV-1 elite controllers (EC) are a rare but heterogeneous group of HIV-1-infected individuals who can suppress viral replication in the absence of antiretroviral therapy. The mechanisms of how EC achieve undetectable viral loads remain unclear. ... ...

    Abstract Summary: HIV-1 elite controllers (EC) are a rare but heterogeneous group of HIV-1-infected individuals who can suppress viral replication in the absence of antiretroviral therapy. The mechanisms of how EC achieve undetectable viral loads remain unclear. This study aimed to investigate host plasma metabolomics and targeted plasma proteomics in a Swedish HIV-1 cohort including EC and treatment-naïve viremic progressors (VP) as well as HIV-negative individuals (HC) to get insights into EC phenotype. Metabolites belonging to antioxidant defense had higher levels in EC relative to VP, whereas inflammation markers were increased in VP compared with EC. Only four plasma proteins (CCL4, CCL7, CCL20, and NOS3) were increased in EC compared with HC, and CCL20/CCR6 axis can play an essential role in EC status. Our study suggests that low-level inflammation and oxidative stress at physiological levels could be important factors contributing to elite control phenotype.
    Keywords Immunology ; Proteomics ; Metabolomics ; Science ; Q
    Language English
    Publishing date 2021-02-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers

    Wang Zhang / Anoop T. Ambikan / Maike Sperk / Robert van Domselaar / Piotr Nowak / Kajsa Noyan / Aman Russom / Anders Sönnerborg / Ujjwal Neogi

    EBioMedicine, Vol 27, Iss C, Pp 40-

    2018  Volume 50

    Abstract: A small subset of HIV-1 infected individuals, the “Elite Controllers” (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted ... ...

    Abstract A small subset of HIV-1 infected individuals, the “Elite Controllers” (EC), can control viral replication and restrain progression to immunodeficiency without antiretroviral therapy (ART). In this study, a cross-sectional transcriptomics and targeted proteomics analysis were performed in a well-defined Swedish cohort of untreated EC (n = 19), treatment naïve patients with viremia (VP, n = 32) and HIV-1-negative healthy controls (HC, n = 23). The blood transcriptome identified 151 protein-coding genes that were differentially expressed (DE) in VP compared to EC. Genes like CXCR6 and SIGLEC1 were downregulated in EC compared to VP. A definite distinction in gene expression between males and females among all patient-groups were observed. The gene expression profile between female EC and the healthy females was similar but did differ between male EC and healthy males. At targeted proteomics analysis, 90% (29/32) of VPs clustered together while EC and HC clustered separately from VP. Among the soluble factors, 33 were distinctive to be statistically significant (False discovery rate = 0.02). Cell surface receptor signaling pathway, programmed cell death, response to cytokine and cytokine-mediated signaling seem to synergistically play an essential role in HIV-1 control in EC.
    Keywords HIV-1 Elite Controllers ; Transcriptome ; Proteome ; Medicine ; R ; Medicine (General) ; R5-920
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Book ; Online: Dysregulation in mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS- CoV-2 infected cells - Proteomic data obtained with Huh-7 cells

    Sofia Appelberg / Soham Gupta / Anoop T Ambikan / Flora Mikealoff / Akos Vegvari / Sara Svensson Akusjärvi / Rui Benfeitas / Maike Sperk / Marie Ståhlberg / Shuba Krishnan / Kamalendra Singh / Josef M Penninger / Ali Mirazimi / Ujjwal Neogi

    2020  

    Abstract: Cultured human Huh-7 cells were infected with SARS-CoV-2 and harvested after 24, 48 and 72 h. The extracted proteins were processed in triplicates preparing for mass spectrometric analysis. Data acquisition was completed, including control samples of non- ...

    Abstract Cultured human Huh-7 cells were infected with SARS-CoV-2 and harvested after 24, 48 and 72 h. The extracted proteins were processed in triplicates preparing for mass spectrometric analysis. Data acquisition was completed, including control samples of non-infected cells, following isobaric tandem mass tag (TMT) chemical labeling and on-line fractionation of the 12 combined biological replicates. The resulted vendor specific raw files (Thermo Scientific) of 12 fractions are provided. The data is further analyzed in order to identify regulated proteins upon SARS-CoV-2 infection to understand the underlying biological processes through pathway analysis. Additional details about the study is going to be completed in the manuscript already submitted for publication.
    Keywords mass spectrometry ; proteomics ; SARS-CoV-2 ; Huh-7 ; TMT-Pro labeling ; covid19
    Language English
    Publishing date 2020-04-28
    Publishing country eu
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs

    Ujjwal Neogi / Kyle J. Hill / Anoop T Ambikan / Xiao Heng / Thomas P. Quinn / Siddappa N. Byrareddy / Anders Sönnerborg / Stefan G. Sarafianos / Kamal Singh

    Pathogens, Vol 9, Iss 320, p

    2020  Volume 320

    Abstract: Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as ... ...

    Abstract Coronaviruses (CoVs) are positive-stranded RNA viruses that infect humans and animals. Infection by CoVs such as HCoV-229E, -NL63, -OC43 and -HKU1 leads to the common cold, short lasting rhinitis, cough, sore throat and fever. However, CoVs such as Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), Middle East Respiratory Syndrome Coronavirus (MERS-CoV), and the newest SARS-CoV-2 (the causative agent of COVID-19) lead to severe and deadly diseases with mortality rates ranging between ~1 to 35% depending on factors such as age and pre-existing conditions. Despite continuous global health threats to humans, there are no approved vaccines or drugs targeting human CoVs, and the recent outbreak of COVID-19 emphasizes an urgent need for therapeutic interventions. Using computational and bioinformatics tools, here we present the feasibility of reported broad-spectrum RNA polymerase inhibitors as anti- SARS-CoV-2 drugs targeting its main RNA polymerase, suggesting that investigational and approved nucleoside RNA polymerase inhibitors have potential as anti-SARS-CoV-2 drugs. However, we note that it is also possible for SARS-CoV-2 to evolve and acquire drug resistance mutations against these nucleoside inhibitors.
    Keywords coronavirus ; SARS-CoV ; MERS-CoV ; SARS-CoV-2 ; COVID-19 ; RNA polymerase ; Medicine ; R ; covid19
    Subject code 572
    Language English
    Publishing date 2020-04-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus

    Aralaguppe, Shambhu G / Abu Bakar Siddik / Ashokkumar Manickam / Anoop T. Ambikan / Milner M. Kumar / Sunjay Jude Fernandes / Wondwossen Amogne / Dhinoth K. Bangaruswamy / Luke Elizabeth Hanna / Anders Sonnerborg / Ujjwal Neogi

    Journal of virological methods. 2016 Oct., v. 236

    2016  

    Abstract: Analysing the HIV-1 near full-length genome (HIV-NFLG) facilitates new understanding into the diversity of virus population dynamics at individual or population level. In this study we developed a simple but high-throughput next generation sequencing ( ... ...

    Abstract Analysing the HIV-1 near full-length genome (HIV-NFLG) facilitates new understanding into the diversity of virus population dynamics at individual or population level. In this study we developed a simple but high-throughput next generation sequencing (NGS) protocol for HIV-NFLG using clinical specimens and validated the method against an external quality control (EQC) panel. Clinical specimens (n=105) were obtained from three cohorts from two highly conserved HIV-1C epidemics (India and Ethiopia) and one diverse epidemic (Sweden). Additionally an EQC panel (n=10) was used to validate the protocol. HIV-NFLG was performed amplifying the HIV-genome (Gag-to-nef) in two fragments. NGS was performed using the Illumina HiSeq2500 after multiplexing 24 samples, followed by de novo assembly in Iterative Virus Assembler or VICUNA. Subtyping was carried out using several bioinformatics tools. Amplification of HIV-NFLG has 90% (95/105) success-rate in clinical specimens. NGS was successful in all clinical specimens (n=45) and EQA samples (n=10) attempted. The mean error for mutations for the EQC panel viruses were <1%. Subtyping identified two as A1C recombinant. Our results demonstrate the feasibility of a simple NGS-based HIV-NFLG that can potentially be used in the molecular surveillance for effective identification of subtypes and transmission clusters for operational public health intervention.
    Keywords Human immunodeficiency virus 1 ; bioinformatics ; disease outbreaks ; genome ; high-throughput nucleotide sequencing ; monitoring ; mutation ; population dynamics ; public health ; quality control ; viruses ; Ethiopia ; India ; Sweden
    Language English
    Dates of publication 2016-10
    Size p. 98-104.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 8013-5
    ISSN 1879-0984 ; 0166-0934
    ISSN (online) 1879-0984
    ISSN 0166-0934
    DOI 10.1016/j.jviromet.2016.07.010
    Database NAL-Catalogue (AGRICOLA)

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