Journal: Nature Communications

Article Title: SPACEL: deep learning-based characterization of spatial transcriptome architectures

doi: 10.1038/s41467-023-43220-3

Figure Lengend Snippet: a Spatial domains identified by Splane in slice S2 and S5 from Wu et al. dataset, slice S10 from Zhao et al. dataset, and slice S11 released by 10X Genomics. b , c Spatial distribution of chromosome 1q&8q copy number gains ( b ) and 1p copy number losses ( c ) of ST spots in slices S11, calculated by inferCNV. Dashed lines represent the tumor domain. d , e CNVs of chromosome 1q & 8q ( d ) and chromosome 1p ( e ) in each spatial domain calculated by inferCNV. CNVs, copy number variations; center line, median value; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range; n = 11 slices. f From left to right: Splane predicted spatial domains in slice S5, distribution of Splane predicted immune domains D7/D8/D9, distribution of Spoint predicted immune cells, and distribution of H&E staining marked immune spots. g Percentage of H&E staining marked immune spots in each domain of slice S1, S2, S5, and S6. The four slices were H&E stained in the original study. Bar height, mean value; whiskers, mean values ± 95% confidence intervals; n = 4 slices. h From left to right: Splane predicted spatial domains in slice S10, distribution of Splane predicted immune domains D7, D8, and D9, distribution of Spoint predicted immune cells, and distribution of CD3 + immunofluorescence (IF) staining marked immune spots. i Percentage of CD3 + IF staining marked immune spots in each domain of slice S10. Source data are provided as a Source Data file.

Article Snippet: The raw data of 11 ST datasets and five paired single-cell/nucleus RNA sequence datasets are available from the following studies: (1) 12 slices of human DLPFC 10X Visium data at http://research.libd.org/spatialLIBD/ ; (2) six slices of human breast cancer 10X Visium data at 10.5281/zenodo.4739739 ; (3) four slices of human breast cancer 10X Visium data: Parent_Visium_Human_BreastCancer, V1_Breast_Cancer_Block_A_Section_1, V1_Breast_Cancer_Block_A_Section_2 and Visium_FFPE_Human_Breast_Cancer at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (4) one slice of human breast cancer 10X Visium data: Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody at https://support.10xgenomics.com/spatial-gene-expression/datasets ; (5) Mouse brain STARmap data at https://www.starmapresources.org/data ; (6) 33 slices of Mouse MOp MERFISH data at https://doi.brainimagelibrary.org/doi/10.35077/g.21 ; (7) one slice of mouse E16.5 embryo brain Stereo-seq data, one slice of mouse brain Stereo-seq data, and 13 slices of mouse E16.5 whole embryo Stereo-seq data at https://db.cngb.org/stomics/mosta/download/ ; (8) ten slice of human brain MERFISH data at https://datadryad.org/stash/dataset/doi:10.5061/dryad.x3ffbg7mw ; (9) 75 slice of mouse whole brain Spatial Transcriptomics data are available in the GEO database under accession number GSE147747 ; (10) single-nucleus transcriptomics data across multiple human cortical areas at https://portal.brain-map.org/atlases-and-data/rnaseq/human-multiple-cortical-areas-smart-seq ; (11) single-cell transcriptomics data of human breast cancer data at https://singlecell.broadinstitute.org/single_cell/study/SCP1039 ; (12) single-cell transcriptomics data of mouse embryo brain at http://mousebrain.org/development/downloads.html ; (13) single-cell transcriptomics data of mouse whole cortex and hippocampus at https://portal.brain-map.org/atlases-and-data/rnaseq/mouse-whole-cortex-and-hippocampus-10x ; (14) single-cell transcriptomics data of mouse whole brain at mousebrain.org/adolescent/downloads.html .

Techniques: Staining, Immunofluorescence

Journal:

Article Title: Increased RNA-Induced Silencing Complex (RISC) Activity Contributes to Hepatocellular Carcinoma

doi: 10.1002/hep.24216

Figure Lengend Snippet: Inhibition of SND1 enzymatic activity inhibits cell viability and AEG-1 function. A. Hep-pc-4 and Hep-AEG-1-14 cells were treated or not with 50, 100 and 200 μM pdTp for 1 to 4 days and cell viability was measured by standard MTT assay. B. Hep-pc-4, Hep-AEG-1-14, Hep3B and QGY-7703 cells were treated with 100 μM pdTp and colony formation assay was performed. The colonies were scored after two weeks. Data represent mean± SEM of three independent experiments. C. Analysis of SND1 expression in tissue microarray by immunohistochemistry. ˆ: p<0.05, #: p<0.02 and *: p<0.01 vs the corresponding data point in Hep-pc-4 cells.

Article Snippet: Tissue microarray and immunostaining Human HCC tissue microarrays were obtained from Imgenex Corp. Two tissue microarrays were used: one containing 40 primary HCC, 10 metastatic HCC and 9 normal adjacent liver samples (Imgenex; IMH-360), the other containing 46 primary HCC and 13 metastatic HCC (Imgenex; IMH-318).

Techniques: Inhibition, Activity Assay, MTT Assay, Colony Assay, Expressing, Microarray, Immunohistochemistry

Journal:

Article Title: Increased RNA-Induced Silencing Complex (RISC) Activity Contributes to Hepatocellular Carcinoma

doi: 10.1002/hep.24216

Figure Lengend Snippet: Immunoperoxidase staining of normal liver and different stages of HCC by tissue microarray using anti-SND1 antibody

Article Snippet: Tissue microarray and immunostaining Human HCC tissue microarrays were obtained from Imgenex Corp. Two tissue microarrays were used: one containing 40 primary HCC, 10 metastatic HCC and 9 normal adjacent liver samples (Imgenex; IMH-360), the other containing 46 primary HCC and 13 metastatic HCC (Imgenex; IMH-318).

Techniques: Immunoperoxidase Staining, Microarray, Staining

Journal: Clinical 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. 1. Expression of CLIC4 is altered in several human cancer types. A, tumor array representing cDNAs derived from the ‘‘matched’’normal (N) and tumor (T) tissues (paired horizontally) of multiple human cancer types is probed with radioactively labeled CLIC4 or ubiquitin (inset) DNA probes. B, oncomine database (University of Michigan Comprehensive Cancer Center) was searched with‘‘CLIC4’’ as a query.Two examples of statistically significant changes (prostate/Lapointe/ Stanford University/P = 1.8 1021and lung/Bhattacharjee/Harvard Medical School/P = 3 109). Blue columns, normal tissues; red columns, cancerous tissues. Brackets,1.5 times interquartile range; dots, outliers; line within box, median; box boundaries, upper and lower quartiles.Two independent studies. C, tumor lysate dot blot representing 200 tumor samples (600 ng per spot) is probed with NH2-terminal CLIC4 antibody. ‘‘Matched’’normal (solid gray arrowhead) and tumor (solid black arrowhead) tissue samples are spotted vertically as a pair. Open circles are marker spots for an orientation.The experiment was repeated twice, and independent experiments with 10-fold less amount of lysate loaded per spot showed similar results.

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, Derivative Assay, Labeling, Ubiquitin Proteomics, Dot Blot, Marker

Journal: Clinical 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