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: 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: mSphere

Article Title: Differential innate immune responses of human macrophages and bronchial epithelial cells against Talaromyces marneffei

doi: 10.1128/msphere.00258-22

Figure Lengend Snippet: Cytokine responses of human and murine macrophages cultured in the presence or absence of plasma/serum upon Talaromyces marneffei infection. Upon T. marneffei infection, the relative expression of ( A ) TNF and ( B ) CXCL8 mRNAs in hPBDMs could only be stimulated in the presence of autologous plasma; whereas no significant change in the mRNA expression of these two cytokines was observed when the culture medium was not supplemented with autologous plasma. The infection experiment was conducted in triplicate using blood cells isolated from three independent donors. The inability of T. marneffei to induce ( C ) TNF and ( D ) CXCL8 mRNAs upon infection was also observed in the murine macrophage cell lines J774A.1 and RAW264.7. Data are presented as mean ± SD and comparisons were analyzed using unpaired t -test (two-tailed). **, P < 0.01; ***, P < 0.001.

Article Snippet: Expression of cytokines were measured semi-quantitatively using the Proteome Profiler Human XL Cytokine Array Kit (R&D Systems, Minneapolis, MN, USA) according to the manufacturer’s instruction; and all samples were tested in duplicates.

Techniques: Cell Culture, Clinical Proteomics, Infection, Expressing, Isolation, Two Tailed Test

Journal: mSphere

Article Title: Differential innate immune responses of human macrophages and bronchial epithelial cells against Talaromyces marneffei

doi: 10.1128/msphere.00258-22

Figure Lengend Snippet: Changes of cytokine mRNA expression in hPBDMs upon Aspergillus fumigatus and Talaromyces marneffei infections. Relative mRNA expressions of CXCL8 and TNF in hPBDMs infected with both fungi were significantly induced mainly after 4 h post-infection and the expression of CXCL10 mRNA in hPBDMs was only significantly induced by T. marneffei infection, in which the expression level reached the peak at 8 h post-infection. The infection experiment was conducted in triplicate using blood cells isolated from three independent donors. The relative mRNA expression levels of CXCL8 , CXCL10 , and TNF were detected by qRT-PCR. Data are presented as mean ± SD and comparisons were analyzed using unpaired t -test (two-tailed). *, P < 0.05; †, P < 0.01; ‡, P < 0.001; ×, undetectable.

Article Snippet: Expression of cytokines were measured semi-quantitatively using the Proteome Profiler Human XL Cytokine Array Kit (R&D Systems, Minneapolis, MN, USA) according to the manufacturer’s instruction; and all samples were tested in duplicates.

Techniques: Expressing, Infection, Isolation, Quantitative RT-PCR, Two Tailed Test

Journal: Phytomedicine : international journal of phytotherapy and phytopharmacology

Article Title: Caffeic acid selectively eliminates teratogenic human-induced pluripotent stem cells via apoptotic cell death.

doi: 10.1016/j.phymed.2022.154144

Figure Lengend Snippet: Fig. 3. Increase of caspase activities by CAA treatment in iPSCs. (A) Apoptosis-related proteins were detected by Western blotting in CAA-treated iPSCs and hDFs. Relative band intensities were calculated after normalization to β-actin expression. (B) iPSCs and hDFs were treated with 50 and 100 μM CAA for 24 h, and the caspase-3, −8, and −9 activities were determined. Relative caspase activity compared with CAA-untreated iPSCs and hDFs was expressed as the means ± SD (n = 3). (C) iPSCs were pre-treated with or without 10 μM of caspase-3 inhibitor (z-DEVD), caspase-8 inhibitor (z-IETD), caspase-9 inhibitor (z-LEHD), and pan-caspase inhibitor (z-VAD) for 30 min and then treated with 50 and 100 μM CAA. DMSO was treated as vehicle control. After 24 h, cells were stained with crystal violet solution and relative cell viability compared with CAA-untreated control iPSCs were expressed as the means ± SD (n = 3). **p < 0.01 vs. CAA-untreated control. ##p < 0.01 vs. Inhibitor-untreated control. Scale bar = 100 μM.

Article Snippet: The expression profile of human apoptosis-related proteins in CAA-treated or -untreated iPSCs was analyzed using a Proteome Profiler Human Apoptosis Array Kit A. Kim et al. Phytomedicine 102 (2022) 154144 (ARY009, R&D System, Minneapolis, MN, USA) according to the manufacturer’s instruction.

Techniques: Western Blot, Expressing, Activity Assay, Control, Staining

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

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