hnscc cell lines fadu  (ATCC)

Journal: Genome Medicine

Article Title: Spatial transcriptomics reveals a molecular tumor budding signature in head and neck cancer

doi: 10.1186/s13073-026-01612-2

Figure Lengend Snippet: Molecular characterization of tumor buds in HNSCC. a Study overview. b Representative H&E-stained image of a selected ROI containing tumor buds with the sampled tumor buds outlined. c The same ROI visualized in the GeoMx DSP platform. d Segmentation of the tumor compartment of the ROI showing the cells selected for profiling. e Intertumoral and f intratumoral DGEA volcano plots. g Intertumoral and h intratumoral enrichment analyses using the MSiGDB HALLMARK gene sets and the differentially expressed genes. i-k PI3K, EGFR, and MAPK PROGENy pathway activation scores by compartment and segment type. Groups with significantly different distributions of PROGENy scores than the tumor buds PROGENy scores after multiple testing correction are marked with an asterisk

Article Snippet: HNSCC cell line FaDu was purchased from ATCC (Manassas, VA, USA), regularly mycoplasma-tested, and verified via short-tandem repeat analysis.

Techniques: Staining, Activation Assay

Journal: Genome Medicine

Article Title: Spatial transcriptomics reveals a molecular tumor budding signature in head and neck cancer

doi: 10.1186/s13073-026-01612-2

Figure Lengend Snippet: TBS correlates with EGFR-activity subtypes and is enhanced at the tumor leading edge. a EGFR-activity subtypes were inferred in HPV-neg. single malignant cells of GSE181919 by NMF using the REACTOME EGFR activity signature ( n = 50 genes). Subtypes are depicted in a uMAP along with inferred EGFR activity, EMT score, and TBS. b The TBS (centered, SD-normalized) is depicted across HPV-neg. single malignant cells within the indicated EGFR-subtypes. *** indicates a p -value < 0.001 (one-way ANOVA). c EMT scores, EGFR-activity, TBS (centered, SD-normalized), and EpCAM and LAMC2 expression are depicted for all HPV-neg. malignant cells of GSE181919 . d Correlation of the TBS (centered, SD-normalized) with EGFR signaling (left) and EMT (right) are shown as dot plots with Pearson correlation values. e Shown is a Venn representation of the intersection of genes from the TBS, the invasive cell signature (invCell-sig, and the invasive gene regulatory network (invGRN) (both described in Zhou et al. 2025 ). f Representative example of the TBS distribution within the tumor core, the leading edge, and the transitory regions of HNSCC. Shown are an H&E staining, a heatmap of the TBS, and a spot annotation for patient 32 of GSE208253 . g The TBS (centered, SD-normalized) for tumor core, the leading edge, and the transitory regions of HNSCC ( n = 11) of GSE208253 are depicted as raincloud plots

Article Snippet: HNSCC cell line FaDu was purchased from ATCC (Manassas, VA, USA), regularly mycoplasma-tested, and verified via short-tandem repeat analysis.

Techniques: Activity Assay, Expressing, Staining

Journal: Genome Medicine

Article Title: Spatial transcriptomics reveals a molecular tumor budding signature in head and neck cancer

doi: 10.1186/s13073-026-01612-2

Figure Lengend Snippet: Evaluation of partial EMT (pEMT) phenotypes. a Epithelial and mesenchymal profiling of the spatial transcriptomics compartments and b the primary cancer cells from the scRNA-seq HNSCC dataset. Genes in red were overexpressed DEGs in tumor buds (spatial transcriptomics intratumoral comparison) or in TBS high cells (scRNAseq), while genes in green were underexpressed DEGs. c Correlation of TBS and the 15-gene pEMT score of tumor ROIs/AOIs in the spatial transcriptomics dataset. d Correlation of TBS and the 15-gene pEMT score of primary tumor cells in the scRNAseq dataset ( GSE103322 )

Article Snippet: HNSCC cell line FaDu was purchased from ATCC (Manassas, VA, USA), regularly mycoplasma-tested, and verified via short-tandem repeat analysis.

Techniques: Spatial Transcriptomics, Comparison

Journal: Genome Medicine

Article Title: Spatial transcriptomics reveals a molecular tumor budding signature in head and neck cancer

doi: 10.1186/s13073-026-01612-2

Figure Lengend Snippet: Drug responses of SCC cell lines by tumor budding signature (TBS). a Overview of the Spearman correlation coefficients for the pooled SCCs and for each cancer entity separately. MEK inhibitors are marked with a grey bar. Asterisks indicate significance after multiple testing correction (FDR 5%). b-d Selected examples of drugs for which the cell lines’ TBS correlated with their responses to the drug. The x axis refers to the log2-fold-change viability values from PRISM. The circles refer to HNSCC, the triangles to esophageal squamous cell carcinoma, and the squares to lung squamous cell carcinoma cell lines. The FaDu cell line is marked in blue. e TBS score of the FaDu cell line under serum-free (FaDu control) and EGF-treated (FaDu EGF 9nM) conditions after six and 72 h. f Local invasion induced by EGF treatment was assessed in a 3D-model of FaDu cell spheroid embedded in collagen I. Shown are representative micrographs of FaDu spheroids in the absence of growth factors (SF; serum-free) and after treatment with 9 nM EGF. Co-treatment with cetuximab and avutometinib are indicated. Yellow lines denote the original spheroid, invasive area, and invasive distance. The viability of FaDu cells after avutometinib treatment at increasing concentrations was assessed by WST-8 assay. Shown are mean with SD from n = 3 independent experiments. g Invasive area and distance of FaDu cell spheroid treated with the indicated compounds was quantified and is represented as mean with SD from n = 3 independent experiments performed with minimum five spheroids per treatment and experiment. SF: serum-free; EGF: EGF treatment only; EGF + Cet: EGF and cetuximab co-treatment; EGF + Avo 10 nM: EGF and avutometinib (10nM) co-treatment; EGF + Avo 25 nM: EGF and avutometinib (25nM) co-treatment. P -value ** < 0.01, *** < 0.001, **** < 0.0001

Article Snippet: HNSCC cell line FaDu was purchased from ATCC (Manassas, VA, USA), regularly mycoplasma-tested, and verified via short-tandem repeat analysis.

Techniques: Control