A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination.

Abstract

The human immune defense mechanisms and factors associated with good versus poor health outcomes following viral respiratory tract infections (VRTI), as well as correlates of protection following vaccination against respiratory viruses, remain incompletely understood. To shed further light into these mechanisms, a number of systems-scale studies have been conducted to measure transcriptional changes in blood leukocytes of either naturally or experimentally infected individuals, or in individual’s post-vaccination. Here we are making available a public repository, for research investigators for interpretation, a collection of transcriptome datasets obtained from human whole blood and peripheral blood mononuclear cells (PBMC) to investigate the transcriptional responses following viral respiratory tract infection or vaccination against respiratory viruses. In total, Thirty one31 datasets, associated to viral respiratory tract infections and their related vaccination studies, were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application designed for interactive query and visualization of integrated large-scale data. Quality control checks, using relevant biological markers, were performed. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation. Via this interface, users can generate web links to customized graphical views, which may be subsequently inserted into manuscripts to report novel findings. The GXB tool enables browsing of a single gene across projects, providing new perspectives on the role of a given molecule across biological systems in the diagnostic and prognostic following VRTI but also in identifying new correlates of protection. This dataset collection is available at: http://vri1.gxbsidra.org/dm3/geneBrowser/list.

Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers

“…We aim to further develop an illustrative case that would lead to the publication of a review of the ISG15 literature employing the literature profiling and visualization approaches described herein. We also plan in the future to develop and make available guides and supporting material for the implementation of hands-on training workshops focusing on other topics covered by our Collective Omics Data (COD) training curriculum, which includes three modules: COD 1 focuses on retrieving, visualizing and interpretating gene-specific transcriptional profiles [24][25][26] ; COD2 focuses on constituting and curating of themed public dataset collections [27][28][29][30][31][32][33][34][35] ; COD3 focuses on global analysis of large-scale omics data. [36][37][38] These hands-on training activities would build in part on the skills developed through the implementation of the literature profiling workshop that we have presented here.…”

A modular framework for the development of targeted Covid-19 blood transcript profiling panels

“…Themed curated dataset collections have been created. GXB sepsis collection In house/open Makes 93 curated datasets relevant to sepsis http://sepsis.gxbsidra.org/dm3/geneBrowser/list https://youtu.be/D1rGYfVSAoM Toufiq et al (in preparation), and Speake et al [ 48 ] A reference dataset presenting transcript abundance profiles across purified leukocyte populations http://sepsis.gxbsidra.org/dm3/geneBrowser/show/4000098 Linsley et al [ 49 ] Reference dataset presenting the response to in vitro blood stimulations http://sepsis.gxbsidra.org/dm3/geneBrowser/show/4000152 Obermoser et al [ 22 ] GXB Acute Respiratory Infection In house/open 34 curated datasets relevant to acute respiratory infections http://vri1.gxbsidra.org/dm3/geneBrowser/list Bougarn et al [ 50 ] Reference dataset presenting changes in blood transcript abundance in patients with pneumonia http://vri1.gxbsidra.org/dm3/miniURL/view/Mh Parnell et al [ 51 ] Gene Set Annotation tool. GSAN Third party/open https://gsan.labri.fr/ Allion-Benitez et al [ 52 ] Pathway Analysis tool Ingenuity Pathway Analysis Third party/commercial Pathway enrichment.…”

In vitro model for the assessment of human immune responses to subunit RSV vaccines

“…In vitro model of human immune response to RSV vaccines A number of recent in vitro studies have looked at various human immune responses to RSV in PBMC [58][59][60][61][62][63][64][65][66][67][68] but only one, Jackson et al, compared human responses to live RSV and FI-RSV [61]. In that study, however, they assessed memory T cell associated responses in RSVprimed adult PBMCs.…”