Journal: Virus research

Article Title: Paracrinal regulation of neutrophil functions by coronaviral infection in iPSC-derived alveolar type II epithelial cells.

doi: 10.1016/j.virusres.2024.199391

Figure Lengend Snippet: Fig. 5. Identification of cytokines secreted by infected iAECIIs and their effect on HL-60 cells. (A) Cytokine array analysis showing the levels of the indicated cy tokines in the medium conditioned by iAECIIs infected with HCoV-229E for 24 or 48 h (24 hpi and 48 hpi). Ctrl – uninfected control. Right panel: cytokine label legend. (B) Western blot analysis of the expression of IL-8 and ICAM-1 in HCoV-229E-infected iAECIIs. (C) Transwell migration assay showing the migration capacity of HL-60 neutrophils in response to a medium conditioned by iAECIIs infected with HCoV-229E for 48 h (48 hpi) in the absence or presence of an IL-8-neutralizing antibody (IL-8 nAb). Ctrl – uninfected control conditioned medium. Data shown as means with SD error bars, n = 3, *p < 0.005, (ANOVA). (D) Representative fluorescence microscopy images of adherent HL-60 neutrophils after incubation with infected iAECIIs in the absence or presence of an ICAM-1-neutralizing antibody (ICAM-1 nAb). Ctrl – uninfected control. (E) Cell count of adherent HL-60 neutrophils. Mean values are shown with SD error bars, n = 3, *p < 0.005.

Article Snippet: Cytokines in the conditioned medium were detected using the Human Cytokine Array Kit (#ARY005B; R&D Systems), and the test strips were moistened and activated according to the manufacturer’s user manual.

Techniques: Infection, Control, Western Blot, Expressing, Transwell Migration Assay, Migration, Fluorescence, Microscopy, Incubation, Cell Counting

Journal: Virus research

Article Title: Paracrinal regulation of neutrophil functions by coronaviral infection in iPSC-derived alveolar type II epithelial cells.

doi: 10.1016/j.virusres.2024.199391

Figure Lengend Snippet: Fig. 6. RNA-seq analysis identifies upstream cytokine pathways in the immune responses by neutrophils. (A and B) Cytoscape ClueGO networks of upregulated genes by infection of iAECIIs with HCoV-229E (A) or triggered by infected HCoV-229 conditioned medium in HL-60 cells (B). (C and D) Bubble plots showing the most enriched GO-BP terms among the genes upregulated by the infection of iAECIIs with HCoV-229E (C) or the genes upregulated in HL-60 cells by cultivation in the infected HCoV-229-conditioned medium (D). (E and F) Hierarchical clustering heatmaps showing the signatures of genes differentially regulated in infected iAECIIs (E) and conditioned medium-stimulated HL-60 cells (F). (G and H) X2K network analysis showing the kinases and transcription factors predicted to regulate differentially expressed genes in infected iAECIIs (G) and conditioned medium-stimulated HL-60 cells (H).

Article Snippet: Cytokines in the conditioned medium were detected using the Human Cytokine Array Kit (#ARY005B; R&D Systems), and the test strips were moistened and activated according to the manufacturer’s user manual.

Techniques: RNA Sequencing, Infection

Journal: Cell Death & Disease

Article Title: Zebularine regulates early stages of mESC differentiation: effect on cardiac commitment

doi: 10.1038/cddis.2013.88

Figure Lengend Snippet: Characterization of HS-181 cell line after treatment with zebularine. ( a ) RT-PCR of cardiac markers after treatment with zebularine. Myh7, Myh6, Actc, cTnI and Serca2 present more expression after treatment. ( b ) Immunostaining of treated cells to detect cardiac-specific proteins. Scale bars; 50 μ m. ( c ) Blots of Proteome Profiler Array and the resulting quantification histograms demonstrating inhibition of pluripotency marker expression and ( d ) increased levels of mesodermic proteins after zebularine treatment (black arrows)

Article Snippet: Protein expression profiles were assayed using the specific human pluripotent Stem Cell array kit ‘Proteome Profiler Array' (R&D Systems Europe, Abingdon, UK; ARY010) following the manufacturer's instructions.

Techniques: Reverse Transcription Polymerase Chain Reaction, Expressing, Immunostaining, Inhibition, Marker

Journal: Oncotarget

Article Title: CCL20 mediates RANK/RANKL-induced epithelial-mesenchymal transition in endometrial cancer cells

doi: 10.18632/oncotarget.8291

Figure Lengend Snippet: ( A ) The Human XL Oncology Array detected multiple analytes in cell culture lysates. The lysates were gained from HEC-1A Control and HEC-1A RANK cells under the treatment of RANKL for 48 h. ( B ) The graph summarized the relative signal intensity of indicated molecules. Among them, CCL20 varied most significantly. ( C , D ) The cell supernatant was collected from HEC-1A/Ishikawa Control cells and HEC-1A/Ishikawa RANK cells treated by RANKL for 48 h. The serum concentration of CCL20 was measured with ELISA kit. *** P < 0.001, n = 3. ( E ) Immunofluorescence staining showed the expression of CCL20 in HEC-1A Control and HEC-1A RANK cells after 48 h stimulation of RANKL. The images were obtained by fluorescence microscopy. Bar = 100 μm.

Article Snippet: Then, 200 μg of cell lysate was run on each array of the Human XL Oncology Array Kit from RandD Systems (Cat. ARY026, USA).

Techniques: Cell Culture, Control, Concentration Assay, Enzyme-linked Immunosorbent Assay, Immunofluorescence, Staining, Expressing, Fluorescence, Microscopy

Journal: International Journal of Molecular Sciences

Article Title: The Effect of Neddylation Inhibition on Inflammation-Induced MMP9 Gene Expression in Esophageal Squamous Cell Carcinoma

doi: 10.3390/ijms22041716

Figure Lengend Snippet: Effect of tumor necrosis factor-alpha (TNF-α) and MLN4924 on the signaling pathways mediating matrix metalloproteinase 9 (MMP9) gene expression in esophageal squamous cell carcinoma (ESCC) cells. ( A ) Proteome profiling of the nuclear factor kappa B (NFκB) pathway by antibody array analyses in the KYSE150 cells treated with MLN4924 and TNF-α. Protein lysates from the untreated controls and cells treated with MLN4924 or TNF-α alone or in combination were analyzed using a human NFκB array (R&D). ( B ) Bar graphs showing the phosphorylation ratio (upper) and the protein level ratio (bottom) calculated after the semi-quantitative analysis of selected proteins. Results are presented as means ± SEM from duplicates. * p < 0.001, ** p < 0.05 vs. controls. The complete array is shown in . ( C ) Western blot analysis showing time-dependent activation of inhibitor of nuclear factor kappa B-alpha (IκB-α), NFκB/p65 and c-Jun in the KYSE150 cells treated with TNF-α (30 ng/mL). ( D ) MLN4924-dependent changes in the activation of IκB-α, NFκB/p65 and c-Jun as well as increasing levels of cyclin dependent kinase inhibitor 1A (CDKN1a/p21) protein in the KYSE150 cells within 24 h. ( E ) A dose-dependent effect of MLN4924 on activation of NFκB/p65 and c-Jun signaling pathways in the KYSE150 cells treated with TNF-α (30 g/mL) for 24 h. The effect of the KYSE70 cells treatment with different concentrations (0.25, 0.5, 1.0, 2.5 and 5.0 µM) of MLN4924 for 24 and 48 h is shown in .

Article Snippet: To determine the relative levels of 41 total and 4 serine/tyrosine phosphorylated proteins involved in NFκB signal transduction, the Proteome Profiler Human NF-κB Pathway Array (R&D Systems, ARY029) was used.

Techniques: Protein-Protein interactions, Gene Expression, Ab Array, Phospho-proteomics, Western Blot, Activation Assay

Journal: Frontiers in Bioengineering and Biotechnology

Article Title: A novel method for the establishment of autologous skin cell suspensions: characterisation of cellular sub-populations, epidermal stem cell content and wound response-enhancing biological properties

doi: 10.3389/fbioe.2024.1386896

Figure Lengend Snippet: Proteomic analysis of the ACS secretome. Semiquantitative analysis using proteome arrays and quantitative detection by ELISA assays of soluble mediators secreted by ACS-derived cell populations cultured in serum-free medium at the indicated time points. Supernatants from cultures established from ACS were collected and analysed as detailed in the Methods. (A) Relative intensity values of densitometric analysis of ACS-secreted soluble factors using an angiogenesis array on days 1, 3 and 6 after isolation. (B) Relative intensity values of similar analysis using a cytokine proteome array on the same time-points post-isolation. (C) Detection of Interleukin-1 alpha, HMGB1 and Hsp90α in the ACS secretome by analyte-specific ELISA. *, p < 0.05; **, p < 0.01; ***, p < 0.001; ****, p < 0.0001; ns, non-significance.

Article Snippet: Detection of analytes released in vitro from collected conditioned medium (at the indicated time points following culture initiation) from ACS-derived cultures was performed using an angiogenesis array kit (#ARY007) and a cytokine array kit (#ARY005B) (both from R&D Systems, supplied by Bio-Techne, Abingdon, United Kingdom).

Techniques: Enzyme-linked Immunosorbent Assay, Derivative Assay, Cell Culture, Isolation

Journal: RSC Advances

Article Title: pH-responsive niosome-based nanocarriers of antineoplastic agents †

doi: 10.1039/d4ra01334d

Figure Lengend Snippet: Changes in expression levels of apoptosis-related proteins in T-24 cells following treatment with: curcumin (B); Tw60 : Sp60 : Chol – S4 (C); Tw60 : Sp60 : Chol : HD-PAA 17 – S19 (D), as compared to untreated control (A). Cells were exposed to equieffective concentrations (IC 50 ) of free curcumin and its niosome formulations for 24 h, following which a human proteome profiler assay was performed according to manufacturer's instructions. Further densitometric analysis of the array spots was conducted using ImageJ software and the most prominent changes in the proteome were ex-pressed graphically (E). Legend: 1 – bad; 2 – TRAILR1, 3 – TRAILR2; 4 – bcl-2; 5 – bcl- x ; 6 – fas, CD95; 7 – pro-caspase 3; 8 – HIF-1α; 9 – HMOX1 (antiapoptotic); 10 – cIAP1; 11 – HSP60; 12 – survivin; 13 – claspin; 14 – HSP70; 15 – TNF RI; 16 – XIAP; 17 – HTRA/Omi.

Article Snippet: Proteome Profiler Human Apoptosis Array Kit, R&D Systems and a Proteome Profiler Human Cytokine Array Kit, R&D Systems were used for the parallel determination of multiple apoptosis- and inflammation-related protein endpoints.

Techniques: Expressing, Control, Software

Journal: RSC Advances

Article Title: pH-responsive niosome-based nanocarriers of antineoplastic agents †

doi: 10.1039/d4ra01334d

Figure Lengend Snippet: Changes in expression levels of apoptosis-related proteins in MJ cells following treatment with: curcumin (B); Tw60 : Sp60 : Chol – S4 (C); Tw60 : Sp60 : Ch : HD-PAA 17 – S19 (D), as compared to untreated control (A). Cells were exposed to equieffective concentrations (IC 50 ) of free curcumin and its niosome formulations for 24 h, following which a human proteome profiler assay was performed according to manufacturer's instructions. Further densitometric analysis of the array spots was conducted using ImageJ software and the most prominent changes in the proteome were ex-pressed graphically (E). Legend: 1 – bcl-2; 2 – bcl- x ; 3 – HIF-1α; 4 – phospho p53; 5 – cIAP1; 6 – cIAP2; 7 – survivin; 8 – claspin; 9 – HSP70; 10 – XIAP.

Article Snippet: Proteome Profiler Human Apoptosis Array Kit, R&D Systems and a Proteome Profiler Human Cytokine Array Kit, R&D Systems were used for the parallel determination of multiple apoptosis- and inflammation-related protein endpoints.

Techniques: Expressing, Control, Software

Journal: RSC Advances

Article Title: pH-responsive niosome-based nanocarriers of antineoplastic agents †

doi: 10.1039/d4ra01334d

Figure Lengend Snippet: Changes in expression levels of inflammation-related proteins in T-24 cells following treatment with: curcumin (B); Tw60 : Sp60 : Chol – S4 (C); Tw60 : Sp60 : Ch : HD-PAA 17 – S19 (D), as compared to untreated control (A). Cells were exposed to equieffective concentrations (IC 50 ) of free curcumin and its niosome formulations for 24 h, following which a human cytokine profiler assay was performed according to manufacturer instructions. Further densitometric analysis of the array spots was conducted using ImageJ software and the most prominent changes in the proteome were expressed graphically (E). Legend: 1 – MIF; 2 – PAI1; 3 – G-CSF; 4 – ICAM-1; 5 – IL-6; 6 – IL-18; 7 – IL-8; 8 – CXCL1; 9 – IL-1α; 10 – IL-1β.

Article Snippet: Proteome Profiler Human Apoptosis Array Kit, R&D Systems and a Proteome Profiler Human Cytokine Array Kit, R&D Systems were used for the parallel determination of multiple apoptosis- and inflammation-related protein endpoints.

Techniques: Expressing, Control, Software

Journal: RSC Advances

Article Title: pH-responsive niosome-based nanocarriers of antineoplastic agents †

doi: 10.1039/d4ra01334d

Figure Lengend Snippet: Changes in expression levels of inflammation-related proteins in MJ cells following treatment with: curcumin (B); Tw60 : Sp60 : Ch – S4 (C); Tw60 : Sp60 : Ch : PAA 17 – S19 (D), as compared to untreated control (A). Cells were exposed to equieffective concentrations (IC 50 ) of free curcumin and its niosome formulations for 24 h, following which a human cytokine profiler assay was performed according to manufacturer instructions. Further densitometric analysis of the array spots was conducted using ImageJ software and the most prominent changes in the proteome were expressed graphically (E). Legend: 1 – CCL2/MCP-1; 2 – CXCL11/I-TAC; 3 – CXCL12/SDF-1; 4 – IL-13; 5 – IL-16; 6 – MIF; 7 – SERPIN E1/PAI-1; 8 – CCL5/RANTES; 9 – GM-CSF; 10 – IL-5; 11 – ICAM1/CD54; 12 – IL-6; 13 – IL-18; 14 – IL-21; 15 – IL-1α; 16 – IL-32α.

Article Snippet: Proteome Profiler Human Apoptosis Array Kit, R&D Systems and a Proteome Profiler Human Cytokine Array Kit, R&D Systems were used for the parallel determination of multiple apoptosis- and inflammation-related protein endpoints.

Techniques: Expressing, Control, Software