Journal: medRxiv

Article Title: Anomalous epithelial variations and ectopic inflammatory response in chronic obstructive pulmonary disease

doi: 10.1101/2020.12.03.20242412

Figure Lengend Snippet: A. Representative images immunostained with CCL2, TNC, and CXCL8 with AT2 cell markers (SFTPC or ABCA3) in COPD and never-smoker lung sections. B . Violin plots for COL4A1, COL4A2, and COL4A3 in AT1 clusters. C. Violin plots for FKBP5 in selected cell types. a) present dataset; b) combined publicly-available datasets.

Article Snippet: Antibodies and reagents were as follows: anti-PD-L1 (rabbit, 1:1000, #ab205921, Abcam, Cambridge, UK); anti-TNC (rabbit, 1:100, #HPA004823, Sigma-Aldrich); anti-CCL2 (rabbit, 1:100, #HPA019163, Sigma-Aldrich); anti-RAGE (rabbit, 1:1000, #ab216329, Abcam); anti-SFTPC (rabbit, 1:1000, #HPA010928, Sigma-Aldrich); anti-ABCA3 (mouse, 1:1000, #WMAB-ABCA3-17, Seven Hills Bioreagents, OH, USA); anti- macrophage inflammatory protein 3 alpha (rabbit, 1:1000, #ab224188, Abcam); anti- CXCL1 (mouse, 1:100, #MAB275, R&D Systems, MN, USA); anti-CXCL8 (mouse, 1:100, #MAB208, R&D Systems); and Hoechst 33242 (1:1000, #H342, Sigma-Aldrich).

Techniques:

Journal: medRxiv

Article Title: Anomalous epithelial variations and ectopic inflammatory response in chronic obstructive pulmonary disease

doi: 10.1101/2020.12.03.20242412

Figure Lengend Snippet: A. 100% stacked bar charts of the percentage of cell populations for AT1 subtype clusters, AT2 subtype clusters, and basal lineage clusters. B. Bar charts displaying the percentages of subpopulations such as AT1-B, AT2-A, AT2-B, club, goblet, and basal clusters across patient states. C. a UMAP plot of epithelial cells focusing on the AT2-C cluster (left). The cell population of the AT2-C cluster (right). The y-axis represents the ratio of cells in the AT2-C cluster across patient states. Brackets () represent the percentage of cells of the AT2-C cluster based on epithelial cells in each of the patient states. D. Violin plots of representative inflammatory-related genes displaying the AT2-C (iAT2) cluster. E. Violin plots for CXCL1 and CXCL8 in AT2 cells in combined publicly-available datasets. F. Representative images immunostained with CD274 (PD-L1), CXCL1 and CXCL20 with AT2 cell markers (SFTPC or ABCA3) in COPD and never-smoker lung sections. Scale bars, 25 μm (left), 12.5 μm (right).

Article Snippet: Antibodies and reagents were as follows: anti-PD-L1 (rabbit, 1:1000, #ab205921, Abcam, Cambridge, UK); anti-TNC (rabbit, 1:100, #HPA004823, Sigma-Aldrich); anti-CCL2 (rabbit, 1:100, #HPA019163, Sigma-Aldrich); anti-RAGE (rabbit, 1:1000, #ab216329, Abcam); anti-SFTPC (rabbit, 1:1000, #HPA010928, Sigma-Aldrich); anti-ABCA3 (mouse, 1:1000, #WMAB-ABCA3-17, Seven Hills Bioreagents, OH, USA); anti- macrophage inflammatory protein 3 alpha (rabbit, 1:1000, #ab224188, Abcam); anti- CXCL1 (mouse, 1:100, #MAB275, R&D Systems, MN, USA); anti-CXCL8 (mouse, 1:100, #MAB208, R&D Systems); and Hoechst 33242 (1:1000, #H342, Sigma-Aldrich).

Techniques:

Journal: Frontiers in Microbiology

Article Title: Probing Clostridium difficile Infection in Complex Human Gut Cellular Models

doi: 10.3389/fmicb.2019.00879

Figure Lengend Snippet: Production of C. difficile spores, toxins, and host responses to infection. (A) Colony counts of spores recovered after heat treatment, and total cells in the cell-associated C. difficile fraction (infected cell lysates) in the 2D epithelial model. Data shown are the mean of three independent experiments and error bars indicate SD, * p < 0.05 as determined by two-way ANOVA. (B) ELISA for C. difficile toxins A and B shows increased toxin production after extended infection. Toxins were measured from medium obtained from the apical compartment containing uninfected cell layers incubated for 24 or 48 h (Control) or cells infected with C. difficile for 3, 6, 24, or 48 h. Data shown are the mean of three independent experiments and error bars indicate SD, * p < 0.05 as determined by two-way ANOVA. Gray line represents the sensitivity of the test at 0.5 ng/ml. (C) ELISA for human IL-8 indicates increased IL-8 production at 24 and 48 h p.i. IL-8 was measured in medium obtained from the basolateral compartment containing uninfected cell layers incubated for 3, 6, 24, or 48 h (Control) or cells infected with C. difficile for 3–48 h. Gray line represents the limit of detection at 32 pg/ml. Data shown are the mean of three independent experiments and error bars indicate SD, * p < 0.05, ** p < 0.01, and *** p < 0.001, **** p < 0.0001 as determined by one-way ANOVA with Tukey’s test for multiple comparison.

Article Snippet: IL-8 production was also determined by analysis of basolateral supernatants from the VDC using a human IL-8 ELISA kit (R&D systems, Minneapolis, MN, United States) following the manufacturer’s instruction.

Techniques: Infection, Enzyme-linked Immunosorbent Assay, Incubation, Control, Comparison

Journal: Frontiers in Microbiology

Article Title: Probing Clostridium difficile Infection in Complex Human Gut Cellular Models

doi: 10.3389/fmicb.2019.00879

Figure Lengend Snippet: C. difficile spores and toxin production, and host response to infection in the 3D-VDC model. (A) Colony counts of spores and total cells in the host cell-associated C. difficile fraction (infected cell lysates). Data shown are the mean of three independent experiments and error bars indicate SD, ns, not significant as determined by two-way ANOVA. (B) Toxin A and B levels from apical compartment supernatants as determined by ELISA in the 3D model. Data shown are the mean of three independent experiments and error bars indicate SD, ns, not significant as determined by two-way ANOVA. Gray line represents the sensitivity of the test at 0.5 ng/ml. (C) Human IL-8 levels in supernatants from the basolateral compartments with uninfected cells incubated for 24 h or with cells infected with C. difficile for 3 and 24 h, as determined by ELISA. Gray line represents the limit of detection at 32 pg/ml. Data shown are the mean of three independent experiments and error bars indicate SD, ** p < 0.01, as determined by the one-way ANOVA with Tukey’s test for multiple comparison.

Article Snippet: IL-8 production was also determined by analysis of basolateral supernatants from the VDC using a human IL-8 ELISA kit (R&D systems, Minneapolis, MN, United States) following the manufacturer’s instruction.

Techniques: Infection, Enzyme-linked Immunosorbent Assay, Incubation, Comparison

Journal: Scientific reports

Article Title: Protein profiling identified key chemokines that regulate the maintenance of human pluripotent stem cells.

doi: 10.1038/s41598-017-15081-6

Figure Lengend Snippet: Figure 2. Chemokine screening strategy for hPSCs. (a–d) Immunofluorescence of pluripotency markers TRA- 1-81 and Oct4 on hPSCs. KSR medium (a,b); mTeSR1 medium (c,d); hESCs (a,c); hiPSCs (d); Feeder cells (b); Scale bars, 50 μm (a–d; arrows) and 10 μm (insets). Cells were counterstained with DAPI. (e) Chemokine screening strategy for hPSCs cultured in KSR (red) or mTeSR1 (green) media.

Article Snippet: Recombinant human chemokine proteins IL-8, SDF-1α, and IP-10 were purchased from R&D Systems (USA).

Techniques: Immunofluorescence, Cell Culture

Journal: Scientific reports

Article Title: Protein profiling identified key chemokines that regulate the maintenance of human pluripotent stem cells.

doi: 10.1038/s41598-017-15081-6

Figure Lengend Snippet: Figure 4. Chemokine signaling functionally mediates the transmigration of hPSCs. Chemoattractant effect of exogenous IP-10, IL-8, and SDF-1α on hPSCs. hESCs (a,b,e,f,i,j); hiPSCs (c,d,g,h,k,l); IL-8 (a,c) and CXCR2 antagonist SB265610 (b,d); SDF-1α (e,g) and CXCR4 antagonist AMD3100 (f,h); IP-10 (i,k) and CXCR3 antagonist NBI74330 (j,l). Values on graphs represent means ± sem, n = 3 individual experiments. *P < 0.05, **P < 0.01.

Article Snippet: Recombinant human chemokine proteins IL-8, SDF-1α, and IP-10 were purchased from R&D Systems (USA).

Techniques: Transmigration Assay

Journal: Scientific reports

Article Title: Protein profiling identified key chemokines that regulate the maintenance of human pluripotent stem cells.

doi: 10.1038/s41598-017-15081-6

Figure Lengend Snippet: Figure 5. Chemokine IL-8 facilitates the differentiation of hPSCs. Stemness of hPSCs was evaluated by the expressions of three pluripotency genes (Oct4, Nanog, and Rex-1) after treatment with IL-8 and CXCR2 antagonists reparixin/SB265610. hESCs (a–c); hiPSCs (d–f); IL-8 (a,d); Reparixin (b,e); and SB265610 (c,f). Values on graphs represent means ± sem, n = 3 individual experiments. *P < 0.05, **P < 0.01, ***P < 0. 001.

Article Snippet: Recombinant human chemokine proteins IL-8, SDF-1α, and IP-10 were purchased from R&D Systems (USA).

Techniques:

Journal: Scientific reports

Article Title: Protein profiling identified key chemokines that regulate the maintenance of human pluripotent stem cells.

doi: 10.1038/s41598-017-15081-6

Figure Lengend Snippet: Figure 7. Mobility and maintenance of hPSCs require multiple chemokine signals. Schematic representation of predominant chemokines from feeder cells or hPSCs themselves. 1) Released chemokines uniformly mediate the migration of hPSCs; 2) Both differentiating and maintaining chemokines were secreted in the culture supernatant. However, the final effect of chemokines tended to maintain the stemness of hPSCs in vitro.

Article Snippet: Recombinant human chemokine proteins IL-8, SDF-1α, and IP-10 were purchased from R&D Systems (USA).

Techniques: Migration, In Vitro