Journal: PLoS ONE

Article Title: An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

doi: 10.1371/journal.pone.0139808

Figure Lengend Snippet: GISTIC-defined peaks associated with altered expression in ESCC.

Article Snippet: ERBB2 and GRB7 proteins were detected using an anti-ERBB2 rabbit monoclonal antibody (Epitomics, Inc) at a 1:5000 dilution and an anti-GRB7 rabbit monoclonal antibody (Gene Tex International Corporation) at a 1:1000 dilution.

Techniques: Expressing, Amplification

Journal: PLoS ONE

Article Title: An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

doi: 10.1371/journal.pone.0139808

Figure Lengend Snippet: Results of analysis on RNA interference screening data of Project Achilles.

Article Snippet: ERBB2 and GRB7 proteins were detected using an anti-ERBB2 rabbit monoclonal antibody (Epitomics, Inc) at a 1:5000 dilution and an anti-GRB7 rabbit monoclonal antibody (Gene Tex International Corporation) at a 1:1000 dilution.

Techniques: Virus

Journal: PLoS ONE

Article Title: An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

doi: 10.1371/journal.pone.0139808

Figure Lengend Snippet: (a) Reductions in mRNA and protein levels of GRB7 at 48 hours after siRNA transfection in KYSE410 and TE4 cells. The results are the mean ± SD from 3 replicates of a single experiment. (b) GRB7 inactivation reduced proliferation of KYSE410 and TE4 cells. Cell growth was measured on days 2, 3, and 4 by MTT assay. Absorbance at day 0 was assigned a value of 1. The results are the mean ± SD from 6 replicates of a single experiment. (c) Migration and invasion assays using GRB7 -knockdown cells. Each bar represents the average of 3 measurements. (d) Inhibitory effects of siRNA targeting GRB7 in combination with trastuzumab. Cells were transfected with siRNA targeting GRB7 or negative control siRNA and treated with or without trastuzumab (0.1 and 1.0 μg/mL). Cells were then seeded in 96-well plates, and cell growth was monitored every 24 hours using MTT assays. Absorbance at day 0 was assigned a value of 1. The results are the mean ± SD from 6 replicates of a single experiment.

Article Snippet: ERBB2 and GRB7 proteins were detected using an anti-ERBB2 rabbit monoclonal antibody (Epitomics, Inc) at a 1:5000 dilution and an anti-GRB7 rabbit monoclonal antibody (Gene Tex International Corporation) at a 1:1000 dilution.

Techniques: Transfection, MTT Assay, Migration, Knockdown, Negative Control

Journal: PLoS ONE

Article Title: An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

doi: 10.1371/journal.pone.0139808

Figure Lengend Snippet: (a) Analysis of GRB7 mRNA expression in tumor tissues and the corresponding normal mucosa by real-time RT-PCR. (b) Kaplan-Meier survival curves for ESCC patients according to GRB7 mRNA expression.

Article Snippet: ERBB2 and GRB7 proteins were detected using an anti-ERBB2 rabbit monoclonal antibody (Epitomics, Inc) at a 1:5000 dilution and an anti-GRB7 rabbit monoclonal antibody (Gene Tex International Corporation) at a 1:1000 dilution.

Techniques: Expressing, Quantitative RT-PCR

Journal: PLoS ONE

Article Title: An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma

doi: 10.1371/journal.pone.0139808

Figure Lengend Snippet: Results of univariate and multivariate analysis of clinicopathlogical factors for 5-year overall survival in the validation set.

Article Snippet: ERBB2 and GRB7 proteins were detected using an anti-ERBB2 rabbit monoclonal antibody (Epitomics, Inc) at a 1:5000 dilution and an anti-GRB7 rabbit monoclonal antibody (Gene Tex International Corporation) at a 1:1000 dilution.

Techniques: Biomarker Discovery, Expressing

Journal: bioRxiv

Article Title: CD4 + follicular helper-like T cells are key players in anti-tumor immunity

doi: 10.1101/2020.01.08.898346

Figure Lengend Snippet: ( A ) Canonical pathways (horizontal axis; bars in plot) for which CXCL13 -expressing TILs show enrichment, presented as the frequency of differentially expressed genes encoding components of each pathway that are upregulated (key) in CXCL13 -expressing TILs relative to their expression in CXCL13 -non-expressing TILs (left vertical axis), and adjusted P values (right vertical axis; grey squares; Benjamini-Hochberg test); P < 0.05. ( B ) Percentage (left margin) of CXCL13 -non-expressing or CXCL13 -expressing cells that express the indicated CD4 + help-related genes (left plot) and violin plots of expression of the same genes in CXCL13 -non-expressing or CXCL13 -expressing cells (right), presented as in . ( C ) Percentage (left margin) of CXCL13 -non-expressing or CXCL13 -expressing cells that express the indicated cytotoxicity-related genes (left plot) and violin plots (middle) of expression of the same genes in CXCL13 -non-expressing or CXCL13 -expressing cells, presented as in . GSEA (right) of cytotoxicity signature in the transcriptome of CXCL13 -expressing versus CXCL13-non-expressing cells, presented as in . ( D ) Flow-cytometric analysis (top panel) shows expression of CXCL13 and granzyme B in CXCR5 + and CXCR5 − subsets in live, singlet-gated, CD45 + CD3 + CD4 + TILs ( n = 9) from patients with NSCLC; numbers in quadrants indicate percentage of CD4 + TILs in each. ImageStream analysis (middle panel) shows expression of CXCL13 and granzyme B in live, singlet-gated, CD3 + CD4 + CXCR5 − TILs ( n = 3). Pan-CytoKeratin(CK) (DAB) IHC staining (bottom panel, left) shows invasive margin (black frame) of tumors ( n = 41); scale bar represent 200µm. PseudoIF image of MxIHC staining (bottom panel, right) shows CXCL13 (red), CD4 (green), granzyme B (cyan) in region indicated by arrow; scale bars represent 10µm. ( E ) Expression of transcripts differentially expressed in CXCL13 -expressing versus CXCL13 -non-expressing TILs, in various sorted subsets (above heatmap, right key). Each column represents the average expression (CPM) in a particular subset. Left margin, vertical colored lines indicate subset in which the genes are differentially expressed. Right margin, examples of key transcripts expressed uniquely or shared by corresponding subsets.

Article Snippet: The primary antibodies used for IHC includes anti-CD103 (EPR4166(2); 1:500; Abcam), anti-CXCL13 (polyclonal; 1:100; ThermoFisher Scientific), anti-CD8 (C8/144B; pre-diluted; Agilent Dako), anti-CD4 (4B12; pre-diluted; Agilent Dako), anti-granzyme B (GrB-7; 1:50; Dako) and anti-PanCK (AE1/AE3; pre-diluted; Agilent Dako).

Techniques: Expressing, Immunohistochemistry, Staining

Journal: bioRxiv

Article Title: CD4 + follicular helper-like T cells are key players in anti-tumor immunity

doi: 10.1101/2020.01.08.898346

Figure Lengend Snippet: ( A ) Pan-CK (DAB) IHC staining shows TLS (blue frame), invasive margin (black frame)(above, left image) and tumor core (red frame)(below, left image). PseudoIF image of MxIHC staining shows pan-CK (white), CD4 (green), CXCL13 (red), nuclei (blue) in regions indicated by arrows; scale bars represent 200µm. ( B ) Pan-CK (DAB) IHC staining shows invasive margin (black frame)(above, left image) and tumor core (red frame)(below, left image); scale bars represent 200µm. PseudoIF image of MxIHC staining shows CD8 (magenta), CD103 (blue), granzyme B (cyan), CXCL13 (red), CD4 (green) in regions indicated by arrows; scale bars represent 10µm. ( C ) Correlation of the number of CD4 + CXCL13 + cells and CD8 + CD103 + cells in lung tumors (quantified by IHC)(left). Correlation of the percentage of CXCL13 + cells in CD4 + cells and the number of CD8 + CD103 + cells in lung tumors (quantified by IHC)(right). Each symbol (key) represents an image; 3 images analyzed per patient ( n = 41); r values indicate the Spearman correlation coefficient; P values, Spearman correlation.

Article Snippet: The primary antibodies used for IHC includes anti-CD103 (EPR4166(2); 1:500; Abcam), anti-CXCL13 (polyclonal; 1:100; ThermoFisher Scientific), anti-CD8 (C8/144B; pre-diluted; Agilent Dako), anti-CD4 (4B12; pre-diluted; Agilent Dako), anti-granzyme B (GrB-7; 1:50; Dako) and anti-PanCK (AE1/AE3; pre-diluted; Agilent Dako).

Techniques: Immunohistochemistry, Staining