Journal: The Lancet. Digital Health

Article Title: Development of a multiomics model for identification of predictive biomarkers for COVID-19 severity: a retrospective cohort study

doi: 10.1016/S2589-7500(22)00112-1

Figure Lengend Snippet: Significantly upregulated genes in patients with severe COVID-19 compared with patients with mild COVID-19 and control participants in both a single-cell RNA sequencing study and the current study The pink boxes denote genes that are upregulated in the severe cohort as compared with the mild cohort in both stem-cell RNA sequencing and plasma proteomics analysis. T cell 1, T cell 2, plasma cells, macrophages, epithelial cells, and club cells represent the various clusters of cells described in the single-cell RNA sequencing study. TNF=tumour necrosis factor. PFDN2=prefoldin subunit 2. PSME2=proteasome activator complex subunit 2. BTN3A2=butyrophilin subfamily 3 member A2. CAPG=macrophage-capping protein. FLT1=vascular endothelial growth factor receptor 1. CASP1=caspase-1. DDX58=antiviral innate immune response receptor RIG-I. CCL2=C-C motif chemokine 2. IL1B=antiviral innate immune response receptor RIG-I. HMOX1=heme oxygenase 1. MMP7=matrilysin.

Article Snippet: Publicly available single-cell RNA sequencing data were analysed from three COVID-19 studies using the in-house platform at nference (Cambridge, MA, USA; ).

Techniques: Control, RNA Sequencing, Clinical Proteomics

Journal: The Journal of Infectious Diseases

Article Title: Measles Virus Infects and Programs MAIT Cells for Apoptosis

doi: 10.1093/infdis/jiaa407

Figure Lengend Snippet: MAIT cells express the highest levels of SLAMF1/CD150 among PBMC subsets. A, Publicly available scRNA-Seq data from 11 769 PBMCs were analyzed. The 9432 cells that passed quality control filters are visualized on a t-SNE projection (left panel) demonstrating clusters corresponding to CD14+ monocytes (n = 2992), CD16+ monocytes (n = 328), cDCs (n = 74), pDCs (n = 68), NK cells (n = 544), B cells (n = 1419), CD4+ T cells (n = 2643), CD8+ T cells (n = 720), MAIT cells (n = 592), and platelets (n = 52). Each dot represents a single cell. The expression of SLAMF1 across indicated clusters, quantified as normalized and scaled count data, is shown in a violin plot (right panel), in which dots represent single cells and widths denote cell densities. B and C, MAIT cells and other peripheral blood T cell subsets were examined for CD150 expression. MAIT and iNKT cells were identified by MR1 tetramer staining (PubMed IDs 24101382 and 24695216) and CD1d tetramer staining (PubMed IDs 10839805 and 10974039), respectively. Open and filled histograms correspond to the staining of PBMCs with anti-CD150 and isotype control, respectively, after gating on CD3+MR1 tetramer+ MAIT cells (B). The frequencies of CD150+ cells and the gMFI of CD150 staining (C) in indicated T cell subsets are summarized using Box-and-Whisker plots, with each symbol representing an individual donor. *, *** and **** denote differences with P < .05, P < .001, and P < .0001, respectively, using matched one-way ANOVA with Dunnett post-hoc analysis. D, PBMCs (n = 4) were left untreated or stimulated with rhIL-12 plus rhIL-18. The frequencies of MAIT cells expressing CD150, CD69, or CD46 were determined 24 hours later by flow cytometry. ** denotes a difference with P < .05 by paired Student t test. Abbreviations: 5-OP-RU, 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil; APC, allophycocyanin; cDC, classic dendritic cell; FITC, fluorescein isothiocyanate; gMFI, geometric mean fluorescence intensity; iNKT, invariant natural killer T cell; MAIT, mucosa-associated invariant T cell; MR1, MHC-related protein 1; NK cell, natural killer cell; NS, not significant; PBMC, peripheral blood mononuclear cell; pDC, plasmacytoid pre-dendritic cell; PE, phycoerythrin; rhIL, recombinant human interleukin; scRNA-Seq, single-cell RNA sequencing; TCM, central memory T cell; TEM, effector memory T cell; TN, naive T cell; t-SNE, t-distributed stochastic neighbor embedding.

Article Snippet: Transcriptomic Analysis of Peripheral Blood Mononuclear Cells The pbmc_10k_v3 dataset, consisting of single-cell RNA sequencing (scRNA-Seq) data from 11 769 peripheral blood mononuclear cells (PBMCs), was created by 10x Genomics ( https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.0/pbmc_10k_v3 ).

Techniques: Control, Expressing, Staining, Whisker Assay, Flow Cytometry, Fluorescence, Recombinant, RNA Sequencing