Journal: Cell Reports

Article Title: Aryl Hydrocarbon Receptor Contributes to the Transcriptional Program of IL-10-Producing Regulatory B Cells

doi: 10.1016/j.celrep.2019.10.018

Figure Lengend Snippet:

Article Snippet: Negative CD43- Isolation Kit , Miltenyi Biotec , Cat# 130-049-801.

Techniques: Western Blot, Recombinant, Methylation, Adjuvant, Enzyme-linked Immunosorbent Assay, Isolation, cDNA Synthesis, SYBR Green Assay, DNA Library Preparation, Purification, Bicinchoninic Acid Protein Assay, Microarray, Ex Vivo, Generated, Software, Red Blood Cell Lysis, Staining, Lysis

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 1. Expression of NQO1 in pan‑cancer. mRNA expression levels of NQO1 in normal and tumor tissues were analyzed using (A) TIMER, (B) UCSC, (C) GEPIA and (D) TCGA databases. (E) Protein expression levels of NQO1 in normal and tumor tissues were analyzed using CTPAC database. The expres‑ sion of NQO1 in different cancer stages was analyzed using (F) GSCA and (G) UCSC databases. (H) Overall survival and disease‑free survival of patients with cancer split according to NQO1 expression were detected using the GEPIA database. n.s., P>0.05, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; TIMER, Tumor Immune Estimation Resource; UCSC, University of California Santa Cruz; GSCA, Gene Set Co‑Expression Analysis; UALCAN, University of ALabama at Birmingham Cancer; TCGA, The Cancer Genome Atlas; GEPIA, Gene Expression Profiling Interactive Analysis.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: Expressing, Gene Expression

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 2. NQO1 expression is upregulated and associated with poor outcome in patients with GBM. (A) Correlation between NQO1 expression level and ploidy, MATH, purity, HRD and TMB were analyzed using TCGA database. (B) Intersection analysis of NQO1 and ploidy, MATH, purity, HRD and TMB was determined using a Venn diagram. (C) Correlation between NQO1 and cancer subtype was assessed using the GSCA database. (D) mRNA expression levels of NQO1 in GBM subtypes were assessed using GSCA and TISIDB databases. (E) The mRNA expressions of differentially expressed genes in GBM were analysed by using GEO database. (F) mRNA expression levels of NQO1 were assessed using the Oncomine database in brain and GBM tissues. (G) Positive rate of NQO1 protein expression in adjacent non‑tumor (n=29) and GBM (n=195) tissues. (H) Representative images of immunohistochemistry staining of the tissue microarray from patients with GBM. Scale bars, upper: 50 µm; lower: 25 µm. (I) Kaplan‑Meier survival analysis of patients with GBM and low or high NQO1 expression in UALCAN and TCGA databases. (J) Diagnostic value of NQO1 in patients with GBM was determined using ROC curve analysis. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; MATH, mutant‑allele tumor heterogeneity; HRD, homologous recombination deficiency; TMB, tumor mutational burden; GBM, glioblastoma multiforme; ROC, receiver operating characteristic; UALCAN, University of ALabama at Birmingham Cancer; TCGA, The Cancer Genome Atlas; TISIDB, an integrated repository portal for tumor‑immune system interactions; GSCA, Gene Set Co‑Expression Analysis.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: Expressing, Immunohistochemistry, Staining, Microarray, Diagnostic Assay, Homologous Recombination

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 3. NQO1 regulates GBM cell proliferation in vitro and in vivo. (A) Expression levels of NQO1 in NHA and GBM cell lines were detected by western blotting. (B) Confirmation of NQO1 knockdown and overexpression were detected by western blotting in the sh‑Con, sh‑NQO1, vector and NQO1 overexpres‑ sion groups. β‑actin was used as a loading control. Effects of NQO1 on GBM cell proliferation were determined using (C) MTT, (D) EdU and (E) colony formation assays. Scale bar: 50 µm. (F) Expression levels of cell cyclin‑related proteins in the NQO1 knockdown or overexpression groups were detected by western blotting. (a) sh‑Con group, (b) shNQO1 group, (c) vector group (d) NQO1 overexpression group. (G) Representative images of GBM cell xenograft tumors in the four groups of nude mic. . (a) sh‑Con group, (b) shNQO1 group, (c) vector group (d) NQO1 overexpression group. Xenograft tumor weights are shown (n=4/group). In the images, each grid represents 1x1 mm. (H) Ki67 expression in tumor sections were determined by immunohistochemical analysis. Scale bar: 50 µm. In all panels, t‑tests for independent means were used for two group comparisons. *P<0.05, **P<0.01. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; NHA, normal human astrocytes; GBM, glioblastoma multiforme; sh, short hairpin; Con, control; CDK1, cyclin‑dependent kinase 1.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: In Vitro, In Vivo, Expressing, Western Blot, Knockdown, Over Expression, Plasmid Preparation, Control, Immunohistochemical staining

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 4. NQO1 accelerates GBM cell metastasis via the EMT process in vitro and in vivo. (A) Representative images of wound healing at 0 and 24 h after wound scratch in the sh‑Con, sh‑NQO1, vector and NQO1 overexpression groups. Wound healing percentage was quantified as width at 24 h/width at 0 h using ImageJ. Scale bar: 50 µm. (B) Representative images and quantification of the Transwell (migration and invasion) assays in the four groups of GBM cells. Scale bar: 50 µm. (C) Association between NQO1 expression and EMT markers in GBM were presented by using Venn diagram. The data were obtained from GEPIA, LinkOmics, CHIPbase and cBioportal database. (D) Expression levels of EMT markers were detected using western blotting in the four groups of GBM cells. β‑actin was used as a loading control. Expression levels of EMT markers (E‑cadherin and Vimentin) in the four groups of GBM cells were detected using immunofluorescence staining. Scale bar: 50 µm (right), 25 µm (left). Red staining indicates Vimentin, green staining indicates E‑cadherin, blue staining indicates DAPI. (F) Representative images of H&E staining of the lung tissues. Scale bar: 100 µm. (G) Expression levels of E‑cadherin and Vimentin in the four groups of xenograft tumor tissues were detected using immunohistochemical staining. Scale bars, upper: 100 µm; lower: 50 µm. **P<0.01. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; EMT, epithelial‑mesenchymal transition; GBM, glioblastoma multiforme; sh, short hairpin; Con, control; HE, hematoxylin and eosin; Twist, twist‑related protein; GEPIA, Gene Expression Profiling Interactive Analysis.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: In Vitro, In Vivo, Plasmid Preparation, Over Expression, Migration, Expressing, Western Blot, Control, Immunofluorescence, Staining, Immunohistochemical staining, Gene Expression

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 5. NQO1 activates the PI3K/Akt/mTOR pathway to regulate cell proliferation, movement and the EMT process. (A) Expression of PI3K/Akt/mTOR pathway markers was detected by western blotting in the four groups of GBM cells. β‑actin was used as the loading control. Effects of LY294002 and Rapamycin on the proliferation of NQO1‑overexpressing cells were detected using (B) MTT, (C) colony formation and (D) EdU assays. Effects of LY294002 and Rapamycin on the mobilty of NQO1‑overexpressing cells were determined using (E) wound healing (scale bar: 50 µm) and (F) Transwell assays (scale bar: 25 µm). (G) Expression levels of EMT markers (E‑cadherin and Vimentin) in the four groups of GBM cells were detected using immunofluorescence staining. Scale bar: 50 µm (right), 25 µm (left). Red staining indicates Vimentin, green staining indicates E‑cadherin, blue staining indicates DAPI. (H) Expression levels of EMT markers and PAM pathway markers were detected using western blotting in the four groups of GBM cells. β‑actin was used as a loading control. *P<0.05, **P<0.01. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; EMT, epithelial‑mesenchymal transition; GBM, glioblastoma multiforme; sh, short hairpin; Con, control; p‑, phosphorylated; 4EBP1, eIF4E‑binding protein; S6, ribosomal protein S6; mTOR, mammalian target of rapamycin.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: Expressing, Western Blot, Control, Immunofluorescence, Staining

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 6. NQO1/Snail regulates GBM progression by activating the PI3K/Akt/mTOR signaling pathway. (A) Correlations between NQO1 expression, and Snail, COL1A1, FN1 and TWIST2 were analyzed using the ENCORI database. (B) Colocalization phenomena of NQO1 and Snail in GBM cells was confirmed using immunofluorescence analysis. Scale bar: 25 µm. (C) Interaction of NQO1 and Snail protein in GBM cells was analyzed using co‑IP. (D) T98G cells of the vector and NQO1 overexpression groups were treated with 10 µM MG132 for 6 h. The ubiquitination of Snail was examined by western blotting. (E) Snail expression in GBM cells in the Vector group, and in those co‑transfected with NQO1 and si‑Con or siSnail (si #1, si #2 and si #3), as determined using western blotting. (F) Proliferation of T98G and SHG44 cells were measured by colony formation assay. Migration of cells was determined using (G) wound healing (scale bar: 50 µm) and (H) Transwell assays (scale bar: 25 µm). (I) Expression levels of epithelial‑mesenchymal transition markers and PI3K/Akt/mTOR pathway markers were detected using western blotting. β‑actin was used as the loading control. *P<0.05, **P<0.01. NQO1, NAD(P)H:quinone acceptor oxido‑ reductase 1; GBM, glioblastoma multiforme; si, small interfering; Con, control; IP, immunoprecipitation; IB, immunoblot; V, Vector; N, NQO1.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: Expressing, Immunofluorescence, Plasmid Preparation, Over Expression, Ubiquitin Proteomics, Western Blot, Colony Assay, Migration, Control, Immunoprecipitation

Journal: International journal of oncology

Article Title: NQO1 drives glioblastoma cell aggressiveness through EMT induction via the PI3K/Akt/mTOR/Snail pathway.

doi: 10.3892/ijo.2023.5558

Figure Lengend Snippet: Figure 7. Mechanistic diagram depicting the role of NQO1 in GBM cell aggressiveness via the PI3K/Akt/mTOR/Snail pathway. NQO1 could promote GBM aggressiveness by activating the PI3K/Akt/mTOR signaling pathway via blocking Snail degradation. NQO1, NAD(P)H:quinone acceptor oxidoreductase 1; GBM, glioblastoma multiforme; 4EBP1, eIF4E‑binding protein; S6, ribosomal protein S6; mTOR, mammalian target of rapamycin.

Article Snippet: For rescue experiments, the cells were divided into the following four groups: Vector, NQO1, NQO1 + LY294002 (50 μM; cat. no. S1105; Selleck Chemicals; treated at 37 ̊C for 48 h,) and NQO1 + Rapamycin (50 nM; cat. no. S1039; Selleck Chemicals; treated at 37 ̊C for 48 h).

Techniques: Blocking Assay

Journal: Microarrays

Article Title: Immune-Signatures for Lung Cancer Diagnostics: Evaluation of Protein Microarray Data Normalization Strategies

doi: 10.3390/microarrays4020162

Figure Lengend Snippet: Principal component analysis (PCA) plot showing the first three principal components of the microarray data set ( a ) unnormalized, ( b ) quantile normalized, ( c ) ComBat-adjusted, and ( d ) DWD-adjusted. Each sphere represents one sample; the color of the sphere indicates the different experimental runs. Run 1 to run 6 is represented by the following colors: run 1 = orange, run 2 = cyan, run 3 = dark blue, run 4 = yellow, run 5 = dark green, run 6 = pink.

Article Snippet: SU8 epoxide-coated glass slides were printed with contact printing technology using a NanoPrint TM LM210 (Dynamic Devices, Wilmington, DE, USA) with 48 SMP2 Stealth Microarray Printing Pins (TeleChem ArrayIt Microarray Division, Sunnyvale, CA, USA).

Techniques: Microarray

Journal: Microarrays

Article Title: Immune-Signatures for Lung Cancer Diagnostics: Evaluation of Protein Microarray Data Normalization Strategies

doi: 10.3390/microarrays4020162

Figure Lengend Snippet: ( a ) Study workflow including the production of 16k protein microarrays, array processing with 200 clinical samples, data pre-processing, data visualization, and statistical analysis of microarray data using BRB-ArrayTools. ( b ) Illustrated microarray processing workflow.

Article Snippet: SU8 epoxide-coated glass slides were printed with contact printing technology using a NanoPrint TM LM210 (Dynamic Devices, Wilmington, DE, USA) with 48 SMP2 Stealth Microarray Printing Pins (TeleChem ArrayIt Microarray Division, Sunnyvale, CA, USA).

Techniques: Microarray

Journal: Microarrays

Article Title: Immune-Signatures for Lung Cancer Diagnostics: Evaluation of Protein Microarray Data Normalization Strategies

doi: 10.3390/microarrays4020162

Figure Lengend Snippet: Principal variance components analysis (PVCA) of the microarray data set ( a ) unnormalized, ( b ) quantile normalized, ( c ) ComBat-adjusted, and ( d ) DWD-adjusted. Contribution to variance was estimated for the following factors: run = experimental runs (run 1 to run 6), type = sample type (cancer or control), sex = female/male, age = age group (0–56, 56–64, 64–70, 70–100 years), smoking = smoking habit (current, never, former smoker), resid = residual weighted average proportion variance. Single factors were investigated as well as combinations of factors.

Article Snippet: SU8 epoxide-coated glass slides were printed with contact printing technology using a NanoPrint TM LM210 (Dynamic Devices, Wilmington, DE, USA) with 48 SMP2 Stealth Microarray Printing Pins (TeleChem ArrayIt Microarray Division, Sunnyvale, CA, USA).

Techniques: Microarray

Journal: Current Cardiovascular Risk Reports

Article Title: Marine n-3 Fatty Acids and Gene Expression in Peripheral Blood Mononuclear Cells

doi: 10.1007/s12170-014-0412-7

Figure Lengend Snippet: PBMC transcriptome analyses in marine n-3 fatty acid intervention studies

Article Snippet: Bouwens et al, 2009 , Double-blind, randomized, placebo-controlled study. , 1.8 g/d EPA + DHA or HOSO (control) , 26 , 48 elderly healthy subjects , Human whole-genome NuGO Gene Chip arrays (Affymetrix) , Between groups: not shown within n-3 group: 1040 gene transcripts ( P < 0.05). Within HOSO group: 298 , Within n-3 group: pathways related to NF- κ B-signaling, eicosanoid synthesis, scavenger receptor activity, adipogenesis, and hypoxia signaling. ↓ Pathways related to cell cycle. ↑ , FFA and TG↓, CRP ↔ c.

Techniques: Microarray, Activation Assay, Activity Assay