Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: Study Design Under BSL-4 containment, we collected blood samples from a total of 21 rhesus monkeys at multiple days post-EBOV inoculation, extracted peripheral blood mononuclear cells (PBMCs), and profiled single-cell transcriptomes and 42 protein markers using Seq-Well and CyTOF. Seq-Well quantifies both host (black) and viral (red) RNA expression, allowing comparisons between infected and bystander cells. Daily clinical parameters (body temperature, clinical signs, and body weight) were also collected for each animal, and complete blood counts were obtained for each blood draw. See also Figure S1 A and .

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: RNA Expression, Infection

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: Quantification of Cytokine Expression and Enrichment of Response Signatures, Related to and ( A ) Average expression values (log e TP10K) of literature-annotated cytokines (columns) across cell types and stages of acute EVD (rows). Values are plotted as a ratio relative to the maximum across cell types and stages. Values that are statistically different from baseline (p < 0.05) are indicated with a blue star. ( B ) Heatmap of rank-sum test statistics for comparison of differential expression log fold-changes of genes in a gene set (rows) compared to genes not in the set. The log fold-changes were defined from differential expression profiles of each cell type at each EVD stage (columns) relative to baseline. Five gene sets were tested — three from the Hallmark database (IFN ALPHA, IFN GAMMA, and TNF ALPHA VIA NFKB) ( Liberzon et al., 2015 ) and 2 constructed from the hallmark sets, as uniquely IFNα-regulated genes in “IFN ALPHA” but not “IFN GAMMA” (“IFN ALPHA - GAMMA”), and vice versa for uniquely IFNγ-regulated (“IFN GAMMA - ALPHA”). See also . ( C ) Fold change (log 2 scale) in average HLA-DR CyTOF intensity on B cells at each DPI relative to baseline for each PBMC sample. Colored lines connect serial samples from the same NHP.

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Expressing, Comparison, Quantitative Proteomics, Construct

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: ISG Suppression, Co-expression of CD14 and CD16, and Expression of Macrophage Genes Are Associated with Monocyte Infectivity (A) Differential expression between infected and bystander monocytes from DPI 5–8. Genes are colored by membership in sets of genes (Mac. Up/Down = up- or downregulated during in vitro differentiation of monocytes into macrophages). See also . (B) UMAP embedding of monocyte gene expression data, colored by (left-to-right) DPI, CD16 expression (log e TP10K), CD14 expression (log e TP10K), and percentage of cellular transcripts mapping to EBOV. (C) Smoothed expression (log e TP10K) of CD14 and CD16 for monocytes during EVD. Boxes: CD14 + , CD16 + , DN, and DP subsets described in the text; numbers: percentage of cells in each subset at that EVD stage. See also A and S5B. (D) CD14 and CD16 protein expression (CyTOF intensity) on monocytes at each DPI. Bivariate kernel density plot with 200 randomly sampled cells is overlaid as a scatterplot. See also Figure S5 C. (E) CD14 and CD16 protein expression (CyTOF intensity) on monocytes in a case of human EVD, colored by Ki67 protein expression for multiple days after symptom onset. See also Figure S5 D. (F) Percentage of assignment of NHP CD14/CD16 subsets at each EVD stage to human myeloid reference populations (BM-MP: bone marrow monocyte progenitors, PBMC-CD16 + : circulating CD16 + monocytes, PBMC-CD14 + : circulating CD14 + monocytes). See also E–S5K. (G) Percentage of infected monocytes in each CD14/CD16 subset in late EVD. Error bars: 95% CI on the mean based on 1,000 bootstraps. (H) Association between macrophage score (x axis) and percentage of infected cells (left y axis, red) and expression of the differentiation marker NR1H3 (right y axis, blue, log e TP10K). We ordered monocytes from late EVD by macrophage score, and averaged percentage of infected cells and NR1H3 expression within 400-cell sliding windows. See also A–S6C. (I) MX1 expression (log e TP10K) in monocytes at baseline, and uninfected bystanders or infected cells in late infection. Boxes: median and interquartile range; whiskers: 2.5 th and 97.5 th percentiles. Statistical significance was assessed by rank-sum test. See also Figure S6 D. (J) Scatterplot of ISG score (y axis) versus percentage of cellular transcripts mapping to EBOV (x axis) for infected monocytes in late EVD (DPI 6–8). Statistical significance was assessed by Spearman ρ.

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Expressing, Infection, Quantitative Proteomics, In Vitro, Gene Expression, Marker

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: Extended Characterization of Interferon and Double-Negative CD14 – CD16 – Monocytes, Related to Figure 5 ( A ) Clustermap of pairwise Pearson correlations between cell type clusters at baseline and late EVD. Correlations are computed on average log e TP10K expression values of overdispersed genes. DN and DP monocytes at late EVD are more similar to monocytes (including baseline CD14+s) than other cell types. ( B ) Scatterplot of MAGIC-smoothed expression values (log e TP10K) of CD14 and CD16 for monocytes in baseline, early, mid, and late disease stages. Cells are colored by smoothed expression levels of MKI67 (the gene coding for Ki67 protein). Boxes: CD14+, CD16+, DN, and DP subsets described in the text; numbers: percentage of cells falling into each subset. ( C ) Scatterplot of protein expression (CyTOF intensity) of CD14 and CD16 for 1,000 randomly sampled monocytes at each DPI. Cells are colored by Ki67 expression. Boxes: CD14+, CD16+, DN, and DP subsets described in the text; numbers: percentage of cells falling into each subset. ( D ) Scatterplot of protein expression (CyTOF intensity) of CD14 and CD16 for monocytes during human EVD. Left: monocytes from healthy human controls. Right: monocytes from 3 EVD cases (S1, S2, and S3) at various days post symptom onset. Cells are colored by Ki67 marker intensity. Boxes: CD14+, CD16+, DN, and DP subsets described in the text; numbers: percentage of cells falling into each subset. ( E ) UMAP embedding of healthy human PBMCs dataset, colored by annotated cluster assignment, based on known marker genes. (Plasma.: Plasmablast). ( F ) UMAP embedding of healthy bone marrow cells, colored by cluster assignment, based on marker genes. (HSC: hematopoietic stem cell, Plasma.: Plasmablast, Megakar.: Megakaryocyte, Mono/DC: monocyte and dendritic cell, BM-Macro: bone marrow macrophage). ( G ) UMAP embedding of sub-clustered HSC and monocyte/dendritic lineage cells. (BM: bone marrow, MP: monocyte progenitor) ( H ) Same UMAP embedding as Figure S5 G, but colored by the cluster identity of their nearest neighbor in the human PBMC dataset ( Figure S5 E). ( I ) UMAP embedding of the merged reference dataset of healthy bone marrow HSCs and monocyte lineage cells and PBMCs. Left sub-panel is colored by cluster assignment. Right sub-panels are colored by marker gene expression (log e TP10K). ( J ) Expression profiles of selected genes for human bone marrow monocyte progenitors (BM-MPs) and human circulating monocytes (PBMC-Monos). Circle area: percentage of cells in which the gene was detected; color: average expression ( Z -normalized log e TP10K). ( K ) Expression profiles of selected genes for NHP monocyte subsets at baseline or late EVD for orthologs of the genes in (J). Circle area: percentage of cells in which the gene was detected; color: average expression level ( Z -normalized log e TP10K). CD34 is grayed out because it is detected in <10 cells.

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Expressing, Marker, Clinical Proteomics, Gene Expression

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: Viral Transcriptional Dynamics of Infected Monocytes In Vivo and Ex Vivo (A) Schematic of EBOV challenge of PBMCs ex vivo . See also Figure S7 . (B and C) Percentage of cellular transcripts derived from EBOV (intracellular viral load) in monocytes from PBMCs inoculated with live virus ex vivo (B) or from PBMCs of NHPs infected in vivo (C). See also A–S8D. (D) Schematic of EBOV transcription. The viral RNA-directed RNA-polymerase transcribes each gene sequentially but occasionally releases the genomic RNA template, ending transcription. As a result, transcription frequency decreases from NP to L . (E and F) Proportion of each EBOV gene versus viral load (log 10 scale), ex vivo (E) or in vivo (F). We ordered infected monocytes by viral load and averaged the percentage of each viral gene over 50-cell sliding windows. Bands: mean ± 1 SD. See also E and S8F.

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Infection, In Vivo, Ex Vivo, Derivative Assay, Virus

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet: EBOV Infection Downregulates Host Antiviral Genes and Upregulates Putative Pro-viral Genes (A and B) Association between host gene expression and viral load within infected monocytes from PBMCs 24 HPI treated with live virus ex vivo (A) or from PBMCs of NHPs in vivo on DPI 5–8 (B). See also . (C and D) Select negatively (C) and positively (D) associated genes in monocytes from ex vivo infections. We ordered infected cells by viral load and averaged gene expression (log e TP10K) over 100-cell sliding windows; Spearman correlation (ρ) is given in the legend. Boxplots show gene expression in uninfected cells (boxes: median and interquartile range; whiskers: 2.5 th and 97.5 th percentiles). See also G and S8H.

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Infection, Gene Expression, Virus, Ex Vivo, In Vivo

Journal: Cell

Article Title: Single-Cell Profiling of Ebola Virus Disease In Vivo Reveals Viral and Host Dynamics

doi: 10.1016/j.cell.2020.10.002

Figure Lengend Snippet:

Article Snippet: Human healthy PBMC scRNA-Seq , 10X , https://support.10xgenomics.com/single-cell-gene-expression/datasets “Aggregate of 8 Chromium Connect channels and 8 manual channels,” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor (Next GEM),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (v3 chemistry),” “5k Peripheral blood mononuclear cells (PBMCs) from a healthy donor with cell surface proteins (Next GEM),” “10k PBMCs from a Healthy Donor - Gene Expression and Cell Surface Protein,” “10k PBMCs from a Healthy Donor (v3 chemistry)”.

Techniques: Virus, Recombinant, Lysis, Electron Microscopy, Infection, Gene Expression, Sequencing, Software

Journal: International Journal of Nanomedicine

Article Title: Cathepsin B-Activatable Bioactive Peptide Nanocarrier for High-Efficiency Immunotherapy of Asthma

doi: 10.2147/IJN.S455633

Figure Lengend Snippet: Effect of PEG-Liker (PEG-IALLIPF), Trp, or MPP-Trp on the production of NO and Pro-inflammatory cytokines. ( A ) In Control-PBMCs, Asthma-PBMCs, Asthma-PBMCs + PEG-Liker, Asthma-PBMCs + Trp and Asthma-PBMCs + MPP-Trp group, NO production were examined by NO assay kit. Pro-inflammatory cytokines ( B ) TNF-α, ( C ) IL-1β, and ( D ) IL-6 contents in all groups were examined by ELISA assay. Data were presented as mean ± SD of three independent experiments. * P <0.05, ** P <0.01, *** P <0.001 vs Asthma-PBMCs group.

Article Snippet: The total peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of control group and asthma group by mouse peripheral blood mononuclear cell isolation kit (P6340; Solarbio, Beijing, China) according to the manufacturer's protocol.

Techniques: Control, Enzyme-linked Immunosorbent Assay

Journal: International Journal of Nanomedicine

Article Title: Cathepsin B-Activatable Bioactive Peptide Nanocarrier for High-Efficiency Immunotherapy of Asthma

doi: 10.2147/IJN.S455633

Figure Lengend Snippet: MPP-Trp was closely correlated with the balanced Th1/Th2 level and Th1/Th2-type cytokine production. ( A ) In Control-PBMCs, Asthma-PBMCs, Asthma-PBMCs + PEG-Liker, Asthma-PBMCs + Trp and Asthma-PBMCs + MPP-Trp group, Th1 population (CD4+IFN-γ+) and Th2 population (CD4+IL-4+) were selected by flow cytometry assay. ( B ) Relative mRNA expressions of IFN-γ, IL-4, IL-13, and IL-5 in all groups were assessed by qRT-PCR. ( C ) The IFN-γ, IL-4, IL-13, and IL-5 contents in all groups were examined by ELISA assay. Data were presented as mean ± SD of three independent experiments. * P <0.05, ** P <0.01, *** P <0.001 vs Asthma-PBMCs group.

Article Snippet: The total peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of control group and asthma group by mouse peripheral blood mononuclear cell isolation kit (P6340; Solarbio, Beijing, China) according to the manufacturer's protocol.

Techniques: Control, Flow Cytometry, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

Journal: International Journal of Nanomedicine

Article Title: Cathepsin B-Activatable Bioactive Peptide Nanocarrier for High-Efficiency Immunotherapy of Asthma

doi: 10.2147/IJN.S455633

Figure Lengend Snippet: MPP-Trp altered cytokine gene expression and production in a concentration-dependent way. In Control-PBMCs, Asthma-PBMCs, and Asthma-PBMCs + MPP-Trp (10, 50, 100 and 200 μg/mL) group, ( A ) Th1/Th2 cytokine gene expressions (IFN-γ, IL-4, IL-13, and IL-5) were determined by RT-qPCR. ( B ) The cytokines (IFN-γ, IL-4, IL-13, and IL-5) levels in all groups were detected by ELISA. Data were presented as mean ± SD of three independent experiments. ** P <0.01, *** P <0.001 vs Control-PBMCs group; # P <0.05, ## P <0.01, ### P <0.001 vs Asthma-PBMCs group.

Article Snippet: The total peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of control group and asthma group by mouse peripheral blood mononuclear cell isolation kit (P6340; Solarbio, Beijing, China) according to the manufacturer's protocol.

Techniques: Gene Expression, Concentration Assay, Control, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

Journal: International Journal of Nanomedicine

Article Title: Cathepsin B-Activatable Bioactive Peptide Nanocarrier for High-Efficiency Immunotherapy of Asthma

doi: 10.2147/IJN.S455633

Figure Lengend Snippet: MPP-Trp altered cytokine gene expression and production in a time-dependent way. ( A ) In Control-PBMCs, Asthma-PBMCs, and 100 μg/mL Asthma-PBMCs + MPP-Trp (6, 12, 24, and 48 h) group, IFN-γ, IL-4, IL-13, and IL-5 mRNA levels were determined by RT-qPCR. ( B ) The Th1/Th2-type cytokines (IFN-γ, IL-4, IL-13, and IL-5) productions in all group were examined by ELISA. Data were presented as mean ± SD of three independent experiments. *** P <0.001 vs Control-PBMCs group; # P <0.05; ## P <0.01; ### P <0.001 vs Asthma-PBMCs group.

Article Snippet: The total peripheral blood mononuclear cells (PBMCs) were isolated from the whole blood samples of control group and asthma group by mouse peripheral blood mononuclear cell isolation kit (P6340; Solarbio, Beijing, China) according to the manufacturer's protocol.

Techniques: Gene Expression, Control, Quantitative RT-PCR, Enzyme-linked Immunosorbent Assay

Journal: Poultry Science

Article Title: Engineered Salmonella Enteritidis vector targeting innate immune molecules provides protection against Salmonella Enteritidis and Salmonella Typhimurium

doi: 10.1016/j.psj.2025.105724

Figure Lengend Snippet: Specific cellular immune responses induced by SIRV in chickens. (A-C) Lymphocyte proliferation. PBMCs are stimulated with SE ( C50041 )-OMPs (A), SE (CVCC3949)-OMPs (B), and ST-OMPs (C), and proliferation is measured using the CCK-8 assay. (D-F) Cytokine production upon in vitro stimulation of lymphocytes. PBMCS are stimulated with SE ( C50041 )-OMPs (D), SE (CVCC3949)-OMPs (E), and ST-OMPs (F). mRNA expression levels of IFN‐γ and IL‐4 are quantified by qRT-PCR. Data are expressed as the mean ± SD of three chickens. Ns, not significant, *, P < 0.05, **, P < 0.01, ***, P < 0.001.

Article Snippet: Peripheral blood mononuclear cells (PBMCs) were isolated 1 week post-vaccination using the chicken PBMC isolation kit (Solarbio).

Techniques: CCK-8 Assay, In Vitro, Expressing, Quantitative RT-PCR

Journal: Viruses

Article Title: The Mechanism of PEDV-Carrying CD3 + T Cells Migrate into the Intestinal Mucosa of Neonatal Piglets

doi: 10.3390/v13030469

Figure Lengend Snippet: Blood-derived CD3 + T cells could be hijacked by PEDV in vitro. Blood-derived CD3 + T cells were infected with PEDV at different times. The viral loads in blood-derived CD3 + T cells were detected by Western blotting ( a ), plaque assay ( b ), and FACS ( c ). At least three independent experiments were performed. PBMC: Peripheral blood monoculear cell; FACS: Fluorescence Activated Cell Sorte.

Article Snippet: Porcine PBMCs (Peripheral blood mononuclear cells) were isolated from the blood of neonatal piglets by density centrifugation using a porcine peripheral blood lymphocyte separation kit (Solarbio, Beijing, China).

Techniques: Derivative Assay, In Vitro, Infection, Western Blot, Plaque Assay, Fluorescence