DataSheet_1_Blood gene expression predicts intensive care unit admission in hospitalised patients with COVID-19.docx

BackgroundThe COVID-19 pandemic has created pressure on healthcare systems worldwide. Tools that can stratify individuals according to prognosis could allow for more efficient allocation of healthcare resources and thus improved patient outcomes. It is currently unclear if blood gene expression signatures derived from patients at the point of admission to hospital could provide useful prognostic information.MethodsGene expression of whole blood obtained at the point of admission from a cohort of 78 patients hospitalised with COVID-19 during the first wave was measured by high resolution RNA sequencing. Gene signatures predictive of admission to Intensive Care Unit were identified and tested using machine learning and topological data analysis, TopMD.ResultsThe best gene expression signature predictive of ICU admission was defined using topological data analysis with an accuracy: 0.72 and ROC AUC: 0.76. The gene signature was primarily based on differentially activated pathways controlling epidermal growth factor receptor (EGFR) presentation, Peroxisome proliferator-activated receptor alpha (PPAR-α) signalling and Transforming growth factor beta (TGF-β) signalling.ConclusionsGene expression signatures from blood taken at the point of admission to hospital predicted ICU admission of treatment naïve patients with COVID-19.</p

Serum HI titres against H1N1pdm virus.

<p>Serum was collected from all animals at necropsy, and from all remaining animals at 7 days post-challenge. Bars show Geometric Mean Titre (T+7), or titres from individual sera (all other days). Groups as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157887#pone.0157887.t001" target="_blank">Table 1</a>.</p

Network pathway analysis of proteins identified in the BAL fluids of samples from i.a. challenged NHP 7 days post-infection, compared to samples from i.a. challenged NHP 5 days post-infection.

<p>The network highlights proteins involved in immune response. Proteins in green highlight a 2-fold or more decrease in abundance in the NHP 7 days post-infection compared to samples from NHP 5 days post-infection. Proteins in red highlight a 2-fold or more increase in abundance. The shapes separate the different molecular classes. The solid lines represent a direct molecular interaction and the dashed lines an indirect molecular interaction.</p

Viral challenge activates BAL macrophages.

<p>BAL cells from groups C (i.t.) and D (i.a.) were resuspended in FACS buffer and analysed for HLA-DR and CD80 expression by flow cytometry. Macrophages were defined as HLA-DR+ events and CD80 expression is presented as mean fluorescence intensity (MFI).</p

Interferon-γ secreting cells following stimulation of PBMCs with H1N1pdm virus.

<p>Each panel represents one of the challenge groups. For each NHP, the frequency of virus-specific cells measured by ELISPOT at day of cull (pale grey) and 4–6 weeks prior to challenge (black) are compared. Groups as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0157887#pone.0157887.t001" target="_blank">Table 1</a>.</p

Lymphopaenia in i.t. and i.a. challenge groups.

<p>Whole blood was taken from animals and lymphocytes were counted using an IDEXX analyser. Results are expressed as cells/l. Group mean counts and standard deviation are shown.</p

Viral RNA load in BALF, as M gene RNA copies /μl fluid.

<p>Viral RNA load in BALF, as M gene RNA copies /μl fluid.</p

Viral RNA loads in lymph nodes.

<p>Viral RNA loads in lymph nodes.</p

Viral RNA in nasal wash and throat swab fluid.

<p>RNA was extracted from fluids and viral load assessed by qRT-PCR for the M gene. Viral load is expressed as M gene copies per μl fluid. Panels A and B, nasal wash; panels C and D, throat swab. No throat swab samples were available for one of the NHPs in Group D. Panels A and C, i.n. challenge groups, high dose in black and low dose in red. Panels B and D, i.t. group in green and i.a. group in blue. In each panel, symbols represent loads for individual animals, solid lines show group means, and dashed horizontal line shows limit of detection.</p

Challenge groups.

<p>Challenge groups.</p