Journal: Journal of Experimental & Clinical Cancer Research : CR

Article Title: Integrated multi-omics profiling reveals the role of the DNA methylation landscape in shaping biological heterogeneity and clinical behaviour of metastatic melanoma

doi: 10.1186/s13046-025-03474-9

Figure Lengend Snippet: Infiltrating T cells, T PEX and T EX are enriched in LOW melanomas compared to CIMP melanomas. A Violin plots showing expression, by semi-quantitative IHC, of CD3, CD4, CD8, PD-1, PD-L1, CD68 and CD163 in extra-tumor or intra-tumor compartments of n = 191 EPICA lesions classified according to DEM ( n = 39), LOW ( n = 50), INT ( n = 60), CIMP ( n = 42) methylation classes. Data expressed as IHC score (see Supplemental Methods). B , C Multiplex immunofluorescence analysis of a representative LOW ( B ) and CIMP ( C ) lesions. In B and C , the H&E image (top) shows the area used for tissue segmentation (bottom) with tumor and stroma identified in dark red and black, respectively. A higher magnification field of the same area shows the density and position of 5 main CD8 + T cell phenotypes identified based on differential expression of TCF-1, PD-1 and TIM-3 and color-coded as indicated. Visualization of tumor cells was omitted in B , C . D Density (cells/mm 2 ) in tumor, stroma and whole tissue (tumor + stroma) of the 5 CD8 + subsets defined by differential expression of TCF1, PD-1 and TIM-3 in LOW ( n = 17) and CIMP ( n = 16) lesions. Statistical analysis: in A by Kruskal Wallis test followed by Dunn’s multiple comparison test; in D , by Mann Whitney test for LOW vs CIMP comparisons in each microenvironment compartment and by Friedman multiple comparison test for tumor vs stroma vs tumor + stroma comparisons within each methylation subset. *: p < 0.05; **: p < 0.01; ***: p < 0.001; ****: p < 0.0001

Article Snippet: The following antibodies were used: CD8 (Leica Biosystems, clone 4B11), TCF-1/TCF7 (clone C63D9, Cell Signaling, MA, USA), TIM-3 (Cell Signaling, clone D5D5R) as well as PD-1 (clone EPR4877(2)) and S100/SOX10 (Clone EP268 1/4C4.9) ready-to-use antibodies all included in the Opal 6-Plex detection kit (Akoya Biosciences, Marlborough, MA, USA).

Techniques: Expressing, Methylation, Multiplex Assay, Immunofluorescence, Quantitative Proteomics, Comparison, MANN-WHITNEY

Journal: iScience

Article Title: T cell factor 1 (TCF-1) defines T cell differentiation in colorectal cancer

doi: 10.1016/j.isci.2024.110754

Figure Lengend Snippet: Differences in CD8 + T cell and γδ T cell spatial distribution in stage III CRC (A) Representative hematoxylin and eosin (H&E) staining of a stage III CRC tumor whole tissue section. Areas of interest for analysis include tumor stroma, tumor core, normal-adjacent tissue, lymphoid aggregates and invasive front. Scale bar: 2000 μm. (B–F) Representative images of mIHC staining of the five compartments of interest, i.e., B) tumor core (T), C) invasive front (IF), D) lymphoid aggregate (LA), E) tumor stroma (S) and F) normal-adjacent tissue (N). Staining represented as merged and single channel staining for CD3, CD8, TCRδ and PanCK and are shown with DAPI staining. White square boxes are magnified to the right (middle panel). Scale bar: 50 μm. (G–I) Densities (mm 2 , upper panel) and frequencies (lower panel) of G) total CD3 + , H) CD3 + CD8 + TCRδ − and I) CD3 + CD8 − TCRδ + cells across the five tumor areas of interest. Orange data points show dMMR cases, blue data points show pMMR cases. Each point represents the average of five multispectral images per patient. Error bars represent SEMs. p -values calculated using one-way ANOVA test and only p -values < 0.05 are displayed.

Article Snippet: CD8 [4B11] , GeneTex , Cat #: GTX75394; RRID: AB_376778.

Techniques: Staining

Journal: iScience

Article Title: T cell factor 1 (TCF-1) defines T cell differentiation in colorectal cancer

doi: 10.1016/j.isci.2024.110754

Figure Lengend Snippet: TCF-1-expressing CD8 + T cells predict improved survival in stage III CRC (A) Flowchart depicting overview of experiment setup. (B and C) Percentage disease-free and C) overall survival of stage III CRC patients with high or low CD3 + CD8 + TCF-1 + , total CD3 + or total CD3 + CD8 + T cell infiltration. Staining and analysis is performed on 3 replicate tissue microarray samples per tumor from 63 stage III CRC patients. p -values calculated using Log rank Mantel-Cox test.

Article Snippet: CD8 [4B11] , GeneTex , Cat #: GTX75394; RRID: AB_376778.

Techniques: Expressing, Staining, Microarray

Journal: iScience

Article Title: T cell factor 1 (TCF-1) defines T cell differentiation in colorectal cancer

doi: 10.1016/j.isci.2024.110754

Figure Lengend Snippet: CD8 + TCF-1 + PD-1 + T pex cells are more abundant in lymphoid aggregates in stage III CRC (A) Representative CD8 + TCF-1 + PD-1 + T pex (upper panel) and CD8 + TCF-1 − PD-1 + T cells (lower panel) mIHC staining in a lymphoid aggregate and tumor core of stage III CRC whole tumor section. Merged images display overlay of CD3, CD8, TCRδ, PD-1, TCF-1, PanCK and DAPI staining. Single stains of CD3, CD8, TCRδ, PD-1, TCF-1 and PanCK are shown with DAPI staining. White square boxes are magnified to the right (middle panel). Scale bar: 50 μm. (B–E) Percentage frequencies of B) T pex (CD8 + TCF-1 + PD-1 + ), C) CD8 + TCF-1 − PD-1 + , D) CD8 + TCF-1 − PD-1 - and E) CD8 + TCF-1 + PD-1 - T cell subsets across the five tumor areas of interest; tumor core (T), invasive front (IF), lymphoid aggregates (LA), tumor stroma (S) and normal-adjacent tissue (N). Percentage frequencies for each CD8 + T cell subset is calculated based on the total CD3 + T cell count. Orange data points represent dMMR cases, blue data points represent pMMR cases. Each point represents the average of five multispectral images per patient. Error bars represent SEMs. p -values calculated using one-way ANOVA test and only p -values < 0.05 are shown.

Article Snippet: CD8 [4B11] , GeneTex , Cat #: GTX75394; RRID: AB_376778.

Techniques: Staining, Cell Counting

Journal: iScience

Article Title: T cell factor 1 (TCF-1) defines T cell differentiation in colorectal cancer

doi: 10.1016/j.isci.2024.110754

Figure Lengend Snippet:

Article Snippet: CD8 [4B11] , GeneTex , Cat #: GTX75394; RRID: AB_376778.

Techniques: Immunohistochemistry, Software, Plasmid Preparation

Journal: Frontiers in Immunology

Article Title: ITGAL expression in non-small-cell lung cancer tissue and its association with immune infiltrates

doi: 10.3389/fimmu.2024.1382231

Figure Lengend Snippet: Multicolor immunofluorescence labeling of antibodies and the cells they recognize.

Article Snippet: Next, the slides were stained with markers of CD20 (E7B7T) XP ® rabbit monoclonal antibody (mAb) (48750S, Cell Signaling Technology), recombinant anti-CD4 antibody [EPR6855, (ab133616), Abcam], anti-CD8 monoclonal antibody [4B11, (MA1-80231), Thermo Fisher Scientific], CD11a/integrin alpha L polyclonal antibody (15574-1-AP, Proteintech), anti-CD68 [KP1, (ZM-0060), ZSGB-Bio], anti-pan cytokeratin antibody [KRT/1877R, (ab234297), Abcam], followed by incubation with blocking proteins for 10 minutes.

Techniques: Immunofluorescence, Labeling

Journal: Frontiers in Immunology

Article Title: ITGAL expression in non-small-cell lung cancer tissue and its association with immune infiltrates

doi: 10.3389/fimmu.2024.1382231

Figure Lengend Snippet: Relationship between ITGAL expression and pattern of immune infiltration in NSCLC tumor tissue. (A, B) Multicolor immunofluorescence assay to detect the location of ITGAL expression and immune cells in lung cancer tissue microarray tumor tissues. (C) Patients with lung cancer were categorized into inflamed, excluded, and deserted immunophenotypes according to the degree of infiltration of CD20, CD8, CD4, and CD68-positive cells. (D–G) Comparison of ITGAL-positive cell infiltration in patients with different immunophenotypes. (H–L) Relationship between different immune cell surface markers and ITGAL expression in the TCGA database.

Article Snippet: Next, the slides were stained with markers of CD20 (E7B7T) XP ® rabbit monoclonal antibody (mAb) (48750S, Cell Signaling Technology), recombinant anti-CD4 antibody [EPR6855, (ab133616), Abcam], anti-CD8 monoclonal antibody [4B11, (MA1-80231), Thermo Fisher Scientific], CD11a/integrin alpha L polyclonal antibody (15574-1-AP, Proteintech), anti-CD68 [KP1, (ZM-0060), ZSGB-Bio], anti-pan cytokeratin antibody [KRT/1877R, (ab234297), Abcam], followed by incubation with blocking proteins for 10 minutes.

Techniques: Expressing, Immunofluorescence, Microarray, Comparison

Journal: Frontiers in Immunology

Article Title: ITGAL expression in non-small-cell lung cancer tissue and its association with immune infiltrates

doi: 10.3389/fimmu.2024.1382231

Figure Lengend Snippet: Immunohistochemical results of ITGAL immunohistochemistry of lung cancer tissue microarrays and their relationship with staining results of various indicators in tumor tissues.

Article Snippet: Next, the slides were stained with markers of CD20 (E7B7T) XP ® rabbit monoclonal antibody (mAb) (48750S, Cell Signaling Technology), recombinant anti-CD4 antibody [EPR6855, (ab133616), Abcam], anti-CD8 monoclonal antibody [4B11, (MA1-80231), Thermo Fisher Scientific], CD11a/integrin alpha L polyclonal antibody (15574-1-AP, Proteintech), anti-CD68 [KP1, (ZM-0060), ZSGB-Bio], anti-pan cytokeratin antibody [KRT/1877R, (ab234297), Abcam], followed by incubation with blocking proteins for 10 minutes.

Techniques: Immunohistochemical staining, Immunohistochemistry, Staining

Journal: Frontiers in Oncology

Article Title: VISTA/CTLA4/PD1 coexpression on tumor cells confers a favorable immune microenvironment and better prognosis in high-grade serous ovarian carcinoma

doi: 10.3389/fonc.2024.1352053

Figure Lengend Snippet: Immunohistochemical staining of checkpoints and tumor-infiltrating lymphocytes in HGSOC. (A) VISTA expression in placenta: positive control; (B) Normal ovarian tissue: negative control; (C) CTLA4 expression in HGSOC; (D) VISTA expression in HGSOC; (E) PDL1 expression in HGSOC; (F) PD1expression in HGSOC. Representative staining densities of tumor-infiltrating lymphocytes expressing: (G) CD3; (H) CD4; (I) CD8 and (J) FOXP3 in HGSOC samples. Magnification (×200), scale bare (100 µm). VISTA, V-domain Ig-containing suppressor of T cell activation; CTLA4, Cytotoxic T- lymphocyte- associated protein 4; PD1, Programmed death PD-1; PDL1, Programmed death ligand PDL-1.

Article Snippet: TILs were evaluated using labeling by the following mouse monoclonal antibodies: CD8 (NCL-L-CD8 clone 4B11,1:50, pH9, Novocastra); CD3 (NCL-L-CD3-565, clone LN10, 1:500, pH6, Novocastra); CD4 (NCL-L-CD4-368, clone 4B12, 1:100, pH9, Novocastra), CD56 (Ou NCL-L-504, Clone66556, 1:400, Novocastra), and FOXP3 [clone 236A(E7)], 1:400, pH, Bioscience).

Techniques: Immunohistochemical staining, Staining, Expressing, Positive Control, Negative Control, Activation Assay

Journal: Frontiers in Oncology

Article Title: VISTA/CTLA4/PD1 coexpression on tumor cells confers a favorable immune microenvironment and better prognosis in high-grade serous ovarian carcinoma

doi: 10.3389/fonc.2024.1352053

Figure Lengend Snippet: Correlation between VISTA, PD1, PDL1, CTLA4 expression and tumor infiltrating lymphocytes.

Article Snippet: TILs were evaluated using labeling by the following mouse monoclonal antibodies: CD8 (NCL-L-CD8 clone 4B11,1:50, pH9, Novocastra); CD3 (NCL-L-CD3-565, clone LN10, 1:500, pH6, Novocastra); CD4 (NCL-L-CD4-368, clone 4B12, 1:100, pH9, Novocastra), CD56 (Ou NCL-L-504, Clone66556, 1:400, Novocastra), and FOXP3 [clone 236A(E7)], 1:400, pH, Bioscience).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: VISTA/CTLA4/PD1 coexpression on tumor cells confers a favorable immune microenvironment and better prognosis in high-grade serous ovarian carcinoma

doi: 10.3389/fonc.2024.1352053

Figure Lengend Snippet: Univariate and Multivariate analyses of TILs correlated with VISTA + /CTLA4 + /PD1 + .

Article Snippet: TILs were evaluated using labeling by the following mouse monoclonal antibodies: CD8 (NCL-L-CD8 clone 4B11,1:50, pH9, Novocastra); CD3 (NCL-L-CD3-565, clone LN10, 1:500, pH6, Novocastra); CD4 (NCL-L-CD4-368, clone 4B12, 1:100, pH9, Novocastra), CD56 (Ou NCL-L-504, Clone66556, 1:400, Novocastra), and FOXP3 [clone 236A(E7)], 1:400, pH, Bioscience).

Techniques:

Journal: Frontiers in Oncology

Article Title: VISTA/CTLA4/PD1 coexpression on tumor cells confers a favorable immune microenvironment and better prognosis in high-grade serous ovarian carcinoma

doi: 10.3389/fonc.2024.1352053

Figure Lengend Snippet: Tumor microenvironment model correlated with Overall survivalin HGSOC.

Article Snippet: TILs were evaluated using labeling by the following mouse monoclonal antibodies: CD8 (NCL-L-CD8 clone 4B11,1:50, pH9, Novocastra); CD3 (NCL-L-CD3-565, clone LN10, 1:500, pH6, Novocastra); CD4 (NCL-L-CD4-368, clone 4B12, 1:100, pH9, Novocastra), CD56 (Ou NCL-L-504, Clone66556, 1:400, Novocastra), and FOXP3 [clone 236A(E7)], 1:400, pH, Bioscience).

Techniques: