Journal: World Journal of Gastroenterology : WJG

Article Title: Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori

doi: 10.3748/wjg.v18.i48.7212

Figure Lengend Snippet: Differentially expressed genes with a fold change of > 2.0 or < 0.5 in GES-1 cells co-cultured with the most virulent gastric carcinoma-derived strain vs the least virulent chronic gastritis-derived strain

Article Snippet: Briefly, goat-anti-HDAC6 (1:100; Santa Cruz Biotechnology, Inc., Heidelberg, Germany) and rabbit-anti-TRAF1 (1:100; BIOSS, Beijing, China) were used as primary antibodies.

Techniques: DNA Synthesis, Transduction, Cell Differentiation

Journal: World Journal of Gastroenterology : WJG

Article Title: Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori

doi: 10.3748/wjg.v18.i48.7212

Figure Lengend Snippet: Most differentially expressed genes in GES-1 cells co-cultured with the most virulent gastric carcinoma-derived strain vs the least virulent chronic gastritis-derived strain

Article Snippet: Briefly, goat-anti-HDAC6 (1:100; Santa Cruz Biotechnology, Inc., Heidelberg, Germany) and rabbit-anti-TRAF1 (1:100; BIOSS, Beijing, China) were used as primary antibodies.

Techniques: Transduction, Histone Deacetylase Assay

Journal: World Journal of Gastroenterology : WJG

Article Title: Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori

doi: 10.3748/wjg.v18.i48.7212

Figure Lengend Snippet: Verification of HDAC6 and TRAF1 up-regulation in GES-1 cells in response to the most and least virulent Helicobacter pylori strains as determined by quantitative real-time polymerase chain reaction analysis. A: Representative quantitation of mRNA expression of GAPDH, HDAC6 and TRAF1 in GES-1 cells (a), GES-1 cells co-cultured with the CG-derived Helicobacter pylori (H. pylori) strain (b) and GES-1 cells co-cultured with the GC-derived H. pylori strain (c); B: Graphic analysis showing mRNA expression of HDAC6 and TRAF1 expressions in GES-1 cells in GES-1 cells, GES-1 cells co-cultured with the CG-derived H. pylori strain and GES-1 cells co-cultured with the GC-derived H. pylori strain. bP < 0.01 vs the control; dP < 0.01 vs cells co-cultured with the CG-derived H. pylori strain.

Article Snippet: Briefly, goat-anti-HDAC6 (1:100; Santa Cruz Biotechnology, Inc., Heidelberg, Germany) and rabbit-anti-TRAF1 (1:100; BIOSS, Beijing, China) were used as primary antibodies.

Techniques: Real-time Polymerase Chain Reaction, Quantitation Assay, Expressing, Cell Culture, Derivative Assay

Journal: World Journal of Gastroenterology : WJG

Article Title: Comparative genomic study of gastric epithelial cells co-cultured with Helicobacter pylori

doi: 10.3748/wjg.v18.i48.7212

Figure Lengend Snippet: Histology and immunohistochemistry (400 ×, scale bar = 50 μm) of HDAC6 and TRAF1 in gastric specimens of patients with chronic gastritis (CG, n = 23), intestinal metaplasia (IM, n = 30), dysplasia (n = 33), and gastric carcinoma (GC, n = 27).

Article Snippet: Briefly, goat-anti-HDAC6 (1:100; Santa Cruz Biotechnology, Inc., Heidelberg, Germany) and rabbit-anti-TRAF1 (1:100; BIOSS, Beijing, China) were used as primary antibodies.

Techniques: Immunohistochemistry

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 expression in pentamer+/CD8+ cells. (A and B) MFI of TRAF1 in peripheral total CD8+ and pentamer+/CD8+ cells after 3 h (A) and after 10 days (B) of specific in vitro challenge, depending on the viral control. According to the MFI, TRAF1 expression was categorized as negative (Neg), dim, and high. The box plots summarize the distribution of the TRAF1 MFI in total and pentamer-binding CD8+ cells in each category. (C) Representative dot plots showing TRAF1 expression in pentamer+/CD8+ cells after 3 h and 10 days of specific in vitro challenge in patients with resolved and persistent infections. The data represent the percentage of cells in each area in reference to the number of total CD8+ and pentamer+/CD8+ cells. (D) Histograms of TRAF1 expression by pooled HCV and CMV specific pentamer+/CD8+ cells from all patients with resolved infection after treatment and persistent infection after 3 h of specific stimulation. (E) Difference in TRAF1 expression according to the MFI between NS3 pentamer+/CD8+ and total CD8+ cells from patients with PI infected by wild-type HCV NS3 or an escape variant. Bold lines, median values of the distribution; #, Mann-Whitney U test; ¤, Wilcoxon test. ○, outlier value; *, extreme value; Ag, antigen; MFI, mean fluorescence intensity; ND, not done; Negative Control, T cell labeling with the secondary antibody only; NS, nonsignificant; Pent, pentamer.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, In Vitro, Control, Binding Assay, Infection, Variant Assay, MANN-WHITNEY, Fluorescence, Negative Control, Labeling

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Pilot analysis of TRAF1 expression in pentamer+/CD8+ cells from patients with resolved and persistent infections performed directly ex vivo and after 3 h of specific stimulation. Box plots (A) and representative dot plots (B) from a preliminary analysis show the level of TRAF1 expression in HCV pentamer-binding CD8+ cells determined directly ex vivo and after 3 h of specific stimulation in patients with a resolved infection after treatment and patients with persistent infection. Negative control, T cell labeling with the secondary antibody only; MFI, mean fluorescence intensity; NS, nonsignificant; st, stimulation; §, Mann-Whitney U test; ¥, Wilcoxon test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, Binding Assay, Infection, Negative Control, Labeling, Fluorescence, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Correlation between TRAF1 expression, exhaustion phenotype, and reactivity of HCV pentamer+/CD8+ cells. Tests for TRAF1 and Mcl-1 were performed after 3 h of specific peptide stimulation, while PD-1 and CD127 were assessed directly ex vivo. (A) Correlation between TRAF1 level and CD127, PD-1, and Mcl-1 expression on pentamer+/CD8+ cells pooled from patients with persistent and resolved infections. (B) PD-1, CD127, and Mcl-1 expression on HCV pentamer+/CD8+ cells from HCV patients, according to the TRAF1 level. (C) Rates of HCV pentamer+/CD8+ cell proliferation after 10 days of specific in vitro challenge, depending on the level of TRAF1 expression. (D) Representative dot plots showing the PD-1, CD127, and Mcl-1 phenotype (as the MFI) and the expansion ability (as the percentage of pentamer-binding CD8+ cells out of the number of total CD8+ cells) according to the TRAF1 level in pentamer+/CD8+ cells. (E) Histograms of PD-1, CD127, and Mcl-1 expression on pooled pentamer+/CD8+ cells in relation to the TRAF1 level. *, Spearman correlation test; ¥, Mann-Whitney U test; negative control, T cell labeling with the nonspecific isotype antibody; ○, outlier values; LOD, limit of detection; MFI, mean fluorescence intensity.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, In Vitro, Binding Assay, MANN-WHITNEY, Negative Control, Labeling, Fluorescence

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 expression in pentamer+/CD8+ cells from resolved infection cases after interferon-free and interferon-containing regimens. Box plots (A) and representative dot plots (B) showing the level of TRAF1 expression after 3 h of antigen-specific stimulation in HCV pentamer-binding CD8+ cells from sustained virologic responders to interferon (IFN)-containing and -free regimens. MFI, mean fluorescence intensity; NS, nonsignificant; §, Mann-Whitney U test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Infection, Binding Assay, Fluorescence, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 kinetics in pentamer+/CD8+ cells during treatment with direct-acting antivirals. Longitudinal dot plots show the peripheral ex vivo frequency, the proliferation intensity after specific in vitro challenge, the PD-1/CD127 level obtained directly ex vivo, and the level of TRAF1 expression after 3 h of specific stimulation in pentamer+/CD8+ cells from two HCV genotype 1-infected patients during treatment with direct-acting antivirals. ALT, alanine aminotransferase; EOT, end of treatment; OMB-PAR/rt/DAS+RBV, ombitasvir-paritaprevir-ritonavir-dasabuvir plus ribavirin; MFI, mean fluorescence intensity; PBL, peripheral blood lymphocyte; SOF-LED, sofosbuvir plus ledipasvir.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Ex Vivo, In Vitro, Expressing, Infection, Fluorescence

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: CD107a-mobilizing and gamma interferon (IFN-γ)-secreting HCV pentamer+/CD8+ cells according to the level of TRAF1 expression. Box plots (A) and representative dot plots (B) show the percentage of IFN-γ-secreting and CD107a-mobilizing pentamer+/CD8+ cells ex vivo and after 10 days of specific in vitro challenge, according to the TRAF1 level, among cells with a preserved expansion ability. ○, outlier value; *, extreme value. The data in each dot plot represent the percentage of positive cells out of the number of either total CD8+ cells or pentamer+/CD8+ cells. NS, nonsignificant; #, Wilcoxon test; *, Mann-Whitney U test.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, Ex Vivo, In Vitro, MANN-WHITNEY

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: Clinical features of recruited patients with CD8 + /pentamer + cells directly detectable ex vivo according to TRAF1 expression a

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Ex Vivo, Expressing, Infection

Journal: Journal of Virology

Article Title: According to Hepatitis C Virus (HCV) Infection Stage, Interleukin-7 Plus 4-1BB Triggering Alone or Combined with PD-1 Blockade Increases TRAF1 low HCV-Specific CD8 + Cell Reactivity

doi: 10.1128/JVI.01443-17

Figure Lengend Snippet: TRAF1 regulation by IL-7 and TGF-β1 in pentamer+/CD8+ cells. (A) Levels of TRAF1 expression in pentamer+/CD8+ cells after β-galactosidase (β-Gal), IL-7, and TGF-β1 treatments in vitro. Box plots summarize the distribution of the level of TRAF1 expression in each category. (B) Representative dot plots and histograms showing TRAF1 levels in pentamer+/CD8+ cells after IL-7, TGF-β1, and β-galactosidase treatments in vitro. (C) In selected patients with PI, the dynamics of the TGF-β1 levels in PBL culture supernatants between day 2 and day 9 of NS3-specific in vitro challenge, according to cell expansion status. (Top) Global variation in TGF-β1 levels; (bottom) individual variation in TGF-β1 levels. Box plots summarize the distribution of either the absolute value or the relative variation in the TGF-β1 level in each category. (D) (Left) Serum TGF-β1 level in patients with persistent infection and resolved infection after treatment. Box plots represent the distribution of the TGF-β1 levels in each group. (Right) Correlation between the serum TGF-β1 level and TRAF1 expression in HCV pentamer+/CD8+ cells after 3 h of specific stimulation. (E) Serum TGF-β1 concentration according to the TRAF1 phenotype of HCV pentamer+/CD8+ cells after 3 h specific stimulation. Box plots summarize the distribution of the TGF-β1 level in every group. ¤, Wilcoxon test; #, Mann-Whitney U test; ¥, Spearman correlation test; ○, outlier value; MFI, mean fluorescence intensity.

Article Snippet: The following unlabeled MAb were also used: TRAF1 rabbit anti-human immunoglobulin (clone 45D3; Cell Signaling, Boston, MA) and myeloid cell leukemia 1 protein (Mcl-1) rabbit anti-human immunoglobulin (clone Y37; Epitomics, Burlingame, CA).

Techniques: Expressing, In Vitro, Infection, Concentration Assay, MANN-WHITNEY, Fluorescence