xp 1 400 cell signaling technology 3579  (Cell Signaling Technology Inc)

Journal: Cell

Article Title: Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer.

doi: 10.1016/j.cell.2024.09.046

Figure Lengend Snippet: Figure 4. CAFs promote cell-state-specific reprogramming into a pro-invasive phenotype (A) Experimental design of scRNA-seq. (B) UMAP plot showing clustering of all cells analyzed by scRNA-seq. (C) Differential gene expression analysis in two patient-derived cell lines. Relevant differentially expressed genes (< 0.5 or >0.5 log2 fold change) are labeled. Note high expression of stem cell genes such as SOX2 in UTSCC76 and high expression of EMT-related ECM genes and AREG in UTSCC74. (D) UMAP plot of cancer cells re-clustered without CAFs. Note separation of UTSCC74 clusters upon co-culture with CAFs. (E) Differential gene expression analysis of the SCC cells upon co-culture with CAFs compared with the same cells cultured alone. (F) GO terms enriched among genes upregulated in UTSCC74 cells co-cultured with CAFs compared with the same SCC cells cultured alone.

Article Snippet: The remainingparameterswere formattedasa ‘‘count Antibody target Supplier and catalogue number Dilution, staining time and temperature AREG LSBio LS-B13911 1:100, 1h Room temperature (RT) aSMA Dako M0851 1:500, 2h RT ß-catenin Cell Marque 224M-14 1:500, 1.5h RT Bmi-1 Cell Signalling Technologies 6964 1:100, 1.5h RT CD11b Bio SB 6441 1:200, Overnight 4 C CD3 Invitrogen MA5-14482 1:750, Overnight 4 C CD34 Dako M716529-2 1:200, Overnight 4 C E-cadherin BD 610182 1:200, 2h RT EGFR Cell Signalling Technologies 4267 1:200, 2h RT Epcam Abcam 71916 1:500, 2h RT FAP Abcam 207178 1:1000, 2h RT Keratin 14 Progen GP-CK14 1:200, 2h RT Keratin 18/8 Cell Signalling Technologies 4546 1:50, 2h RT Myh9 Biolegend Poly 909801 1:2000, 1h RT Pan-cytokeratin Abcam 7753 1:150, 2h RT Pan-cytokeratin Invitrogen MA5-13156 1:100, 2h RT PDGFRB Cell Signalling Technologies 3169 1:100, 1.5h RT Slug Cell Signalling Technologies 9585 1:50, 1.5h RT Sox2 Cell Signalling Technologies 3579 1:100, 2h RT Tenascin C R&D MAB 2138 1:100, 1.5h RT Vimentin Santa Cruz Biotechnology SC6260 1:200, 2h RT Parameter Epithelial panel Stromal panel Nuclear mean intensity DAPI, Slug, Bmi1, Sox2 DAPI Cytoplasmic mean intensity ß-catenin, KRT8/18, KRT14, Epcam, Vimentin PDGFRB-ß, CD11b, CD34, CD3, a-SMA, FAP, Pan-cytokeratin, EGFR Morphometric parameters Area, circularity, roundness, perimeter, solidity, compactness, aspect ratio, EFC ratio Local neighborhood parameters Order, number of neighbors (nuclei within 85 pixels to each other in centroid-to-centroid distance), distance to nearest neighbor, distance to nearest epithelial/stromal cell ll OPEN ACCESS Cell 187, 1–18.e1–e9, December 12, 2024 e5 Please cite this article in press as: Punovuori et al., Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer, Cell (2024), https://doi.org/10.1016/j.cell.2024.09.046 Article matrix’’ and analyzed using the Seurat package in R.53 All parameter values were normalized to remove sampling effect and scaled to obtain relative parameter expression between cells.

Techniques: Gene Expression, Derivative Assay, Labeling, Expressing, Co-Culture Assay, Cell Culture