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  1. Article ; Online: Transcriptome profiling of PBMCs and formalin-fixed autopsy tissues from COVID-19 patients

    Marta Vuerich / Na Wang / Ahmadreza Kalbasi / Jonathon J. Graham / Maria Serena Longhi

    STAR Protocols, Vol 3, Iss 1, Pp 101156- (2022)

    2022  

    Abstract: Summary: Here we present an optimized protocol for transcriptome profiling of COVID-19 patient samples, including peripheral blood mononuclear cells (PBMCs) and formalin-fixed paraffin-embedded tissue samples obtained from the lung, liver, heart, kidney, ...

    Abstract Summary: Here we present an optimized protocol for transcriptome profiling of COVID-19 patient samples, including peripheral blood mononuclear cells (PBMCs) and formalin-fixed paraffin-embedded tissue samples obtained from the lung, liver, heart, kidney, and spleen, with the matched controls. We describe RNA extraction and subsequent transcriptome analysis using NanoString technology of the patient samples. The protocol provides information about sample preparation, RNA extraction, and NanoString profiling and analysis. It can be also applied to differentiated Th17 and Treg subsets or formalin-fixed colon tissue samples.For complete details on the use and execution of this protocol, please refer to Wang et al. (2021).
    Keywords Cell Biology ; Cell isolation ; Cell-based Assays ; Clinical Protocol ; Gene Expression ; Health Sciences ; Science (General) ; Q1-390
    Language English
    Publishing date 2022-03-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Limited TCR repertoire and ENTPD1 dysregulation mark late-stage COVID-19

    Na Wang / Marta Vuerich / Ahmadreza Kalbasi / Jonathon J. Graham / Eva Csizmadia / Zachary James Manickas-Hill / Ann Woolley / Clement David / Eric M. Miller / Kara Gorman / Jonathan L. Hecht / Shahzad Shaefi / Simon C. Robson / Maria Serena Longhi

    iScience, Vol 24, Iss 10, Pp 103205- (2021)

    2021  

    Abstract: Summary: T cell exhaustion and dysfunction are hallmarks of severe COVID-19. To gain insights into the pathways underlying these alterations, we performed a comprehensive transcriptome analysis of peripheral-blood-mononuclear-cells (PBMCs), spleen, lung, ...

    Abstract Summary: T cell exhaustion and dysfunction are hallmarks of severe COVID-19. To gain insights into the pathways underlying these alterations, we performed a comprehensive transcriptome analysis of peripheral-blood-mononuclear-cells (PBMCs), spleen, lung, kidney, liver, and heart obtained at autopsy from COVID-19 patients and matched controls, using the nCounter CAR-T-Characterization panel. We found substantial gene alterations in COVID-19-impacted organs, especially the lung where altered TCR repertoires are noted. Reduced TCR repertoires are also observed in PBMCs of severe COVID-19 patients. ENTPD1/CD39, an ectoenzyme defining exhausted T-cells, is upregulated in the lung, liver, spleen, and PBMCs of severe COVID-19 patients where expression positively correlates with markers of vasculopathy. Heightened ENTPD1/CD39 is paralleled by elevations in STAT-3 and HIF-1α transcription factors; and by markedly reduced CD39-antisense-RNA, a long-noncoding-RNA negatively regulating ENTPD1/CD39 at the post-transcriptional level. Limited TCR repertoire and aberrant regulation of ENTPD1/CD39 could have permissive roles in COVID-19 progression and indicate potential therapeutic targets to reverse disease.
    Keywords Immunology ; Virology ; Science ; Q
    Subject code 610
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

    More links

    Kategorien

    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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