Journal: Clinical cancer research : an official journal of the American Association for Cancer Research

Article Title: Reciprocal modifications of CLIC4 in tumor epithelium and stroma mark malignant progression of multiple human cancers.

doi: 10.1158/1078-0432.CCR-06-1562

Figure Lengend Snippet: Fig. 2. CLIC4 expression and subcellular localization are altered in human tumors. Human normal and matched tumor (roman numerals, tumor stage) tissue sections representing (A) esophagus, (B) kidney, and (C) colon from the tissue microarrays are immunostained with anti-CLIC4 antibody and visualized by bright-field microscopy under 40 magnification. Inset, lower magnification (10). Black arrows, CLIC4 localized to the nucleus in the normal tissues. Similar staining patterns of CLIC4 were found in multiple human tumor types. Representative immunohistochemical stainings.

Article Snippet: Immunohistochemistry, immunofluorescence, and tissue microarray staining Human tissue microarrays were obtained from multiple sources: TARP tissue arrays (National Cancer Institute), ‘‘matched’’ human tumor tissue arrays (Imgenex, San Diego, CA), Food and Drug Administration–standard normal and tumor tissue arrays (Biochain, Hayward, CA) and human cancer screen tissue arrays (Clinomics), prostate tumor arrays (Baylor Specialized Programs of Research Excellence), and human tissue arrays (Accumax) were used for CLIC4 expression and localization studies.

Techniques: Expressing, Microscopy, Staining, Immunohistochemical staining

Journal: bioRxiv

Article Title: Antagonizing the serotonin receptor HTR2B drives antigen-specific cytotoxic T-cell responses and controls colorectal cancer growth

doi: 10.1101/2025.02.26.640476

Figure Lengend Snippet: TCGA-COAD data were analyzed. (A) Kaplan-Meier survival analysis of HTR 2B expression (derived from TCGA data) in 220 colon adenocarcinomas patient’s cohort. “HTR 2B -high” versus “HTR 2B -low” data were segregated based on the cohort’s top or bottom 25% with intratumoral HTR 2B expression. Mantel-cox log rank test. (B) Representative images of HTR 2B and Ki67 in the control (lamina propria) and lamina propria of colon adenocarcinoma (COAD) tissue. The original magnification is 200X, and the inset images are 600X. (C) Representative images of serotonin (5-HT), neurofilament-A (NF-A) in the control (lamina propria) and lamina propria of colon adenocarcinoma (COAD) tissue IHC. Original magnification 200X. (D) RNA-seq datasets (n=30 samples) were segregated into “HTR 2B -high” and “HTR 2B -low” (highest fifteen and lowest fifteen intra-tumoral HTR 2B expression), and the differential expression of selected genes was analyzed. (E) Principal component analysis (PCA) of “HTR 2B -high” versus “HTR 2B -low” datasets (n=15 patients/group). (F) Venn diagram showing numbers of mutually exclusive or shared genes in each group. (G) A volcano plot shows differentially expressed genes (DEGs) of “HTR 2B -high” versus “HTR 2B -low” datasets (n=15 patients/groups) are shown. (H) Heatmap statistics differentially expressed selected gene sets. (I) Gene ontology of altered biological processes. (J) Gene set enrichment analysis (GSEA) of the curated gene sets that affect the regulatory and effector functions of the T cells. (K) Intra-tumoral immune cell signatures were analyzed by deconvolution using TIMER2.0 of HTR 2B -high and -low datasets. (L) A TIDE computational analysis of the association between the tumor-infiltrating CD8 T cells (CTL) level (expression of CD8A, CD8B, GZMA, GZMB, and PRF1. Overall, patient survival with the intratumoral HTR 2B gene expression level. For each patient cohort, tumor samples were divided into HTR 2B -high (samples with HTR 2B expression one standard deviation above the average, shown in the left survival plot) and HTR 2B -low (remaining samples shown in the right survival plot) groups.

Article Snippet: The human colon adenocarcinoma tissue microarray (Novus Biological, Catalog # NBP2-78088) was stained with the antibodies and detected using chromogenic reagent DAB.

Techniques: Expressing, Derivative Assay, Control, RNA Sequencing, Gene Expression, Standard Deviation

Journal: Genome biology

Article Title: Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation.

doi: 10.1186/s13059-021-02375-2

Figure Lengend Snippet: Fig. 2 CBS epimutations associate with CIMP in primary GCs. a Overlap of genes that are promoter hypermethylated and downregulated at the RNA level in the discovery GC cell line panel, TCGA-stomach adenocarcinoma [STAD] and Singapore [SG] cohorts (β-value difference ≥0.3 and q-value < 0.05) [left panel]. Average promoter methylation β-values and gene expression of CBS gene in STAD according to CIMP subtypes (*P < 0.001, two-tailed Wilcoxon rank sum test, each CIMP group vs. non-CIMP group) [right panel]. b Immunohistochemistry of CBS in a normal human stomach with black arrow indicating cytoplasmic staining in epithelial cells. Control sections were not treated with the primary antibody. c Summary of CBS staining in 66 cases of matched normal and gastric adenocarcinomas (*P < 0.05, two- tailed Fisher’s exact test) [left panel] and an example of a matched normal vs. tumor case with a negative score [right panel]. d Summary of somatic and germline genetic alterations at CBS in STAD. PALP, pyridoxal- phosphate dependent enzyme domain; CBS, cystathionine beta-synthase domain; aa, amino acid

Article Snippet: Normal human stomach antrum and fundus tissue slides were purchased from Novus Biologicals (NBP2-30203, NBP230204).

Techniques: Methylation, Gene Expression, Two Tailed Test, Immunohistochemistry, Staining, Control