Journal: bioRxiv

Article Title: Spatial transcriptomic analysis of progressing oral epithelial dysplasia reveals unique differentially expressed genes and microenvironmental changes

doi: 10.64898/2026.01.07.697832

Figure Lengend Snippet: Differential gene expression in progressors (biopsy 1) and non-progressors (biopsy 1) within PanCK-positive (A-C) and PanCK-negative (D) regions of interest (ROI). (A) Heatmap depicting unsupervised clustering of samples into two groups based on differentially expressed (DE) genes. (B) Volcano plot highlighting significantly DE genes with yellow dots. (C) Violin plots illustrating the most prominently downregulated gene (CDKN2A) and upregulated gene (STOM) in progressing oral epithelial dysplasia (OED). (D) Volcano plot displaying significantly DE genes with yellow dots, alongside violin plots showing downregulated genes (S100A10 and KL4) and upregulated gene (ZFAT) in progressing OED.

Article Snippet: Slide preparation was performed according to the manufacturer’s protocol (Nanostring GeoMx) with the following digestion and heat-induced epitope retrieval (HIER) conditions: 0.1 μg/ml Proteinase K for 15 min and ER for 20 min. ROI selection (PanCK+/PanCK-) was performed in the GeoMx Digital Spatial Profiler (DSP) based on morphology and immunofluorescence staining with PanCK (Novus Biologicals, clone AE1/AE3, NBP2-33200AF488), SMA (Abcam, clone 1A4, ab202368), CD45 (CST, clone D9M8I, 13917BF), and SYTO 83 DNA staining (ThermoFisher, S11364).

Techniques: Gene Expression

Journal: bioRxiv

Article Title: Spatial transcriptomic analysis of progressing oral epithelial dysplasia reveals unique differentially expressed genes and microenvironmental changes

doi: 10.64898/2026.01.07.697832

Figure Lengend Snippet: (A) Bar graph showing the most enriched pathways in Progressors, indicating the number of enriched pathways within each category. (B) Heatmap illustrating clustering of PanCK-positive (PanCK+) regions of interest (ROI) in progressing and non-progressing oral epithelial dysplasia (OED). (C) Volcano plot displaying differentially expressed (DE) pathways, with yellow dots representing significant pathways in PanCK+ ROI of progressors and non-progressors. (D) Heatmap showing clustering of PanCK-negative (PanCK-) ROI in progressing and non-progressing OED. (E) Heatmap illustrating clustering of PanCK+ ROI in precursor lesions and subsequent oral squamous cell carcinoma (OSCC) samples. (F) Heatmap depicting clustering of PanCK- ROI in precursor lesions and subsequent OSCC samples. (G) Volcano plot with yellow dots indicating DE pathways in PanCK+ ROI of precursor lesions and subsequent OSCC.

Article Snippet: Slide preparation was performed according to the manufacturer’s protocol (Nanostring GeoMx) with the following digestion and heat-induced epitope retrieval (HIER) conditions: 0.1 μg/ml Proteinase K for 15 min and ER for 20 min. ROI selection (PanCK+/PanCK-) was performed in the GeoMx Digital Spatial Profiler (DSP) based on morphology and immunofluorescence staining with PanCK (Novus Biologicals, clone AE1/AE3, NBP2-33200AF488), SMA (Abcam, clone 1A4, ab202368), CD45 (CST, clone D9M8I, 13917BF), and SYTO 83 DNA staining (ThermoFisher, S11364).

Techniques:

Journal: Cancer Research

Article Title: Tissue Factor Regulation by Epidermal Growth Factor Receptor and Epithelial-to-Mesenchymal Transitions: Effect on Tumor Initiation and Angiogenesis

doi: 10.1158/0008-5472.can-08-2067

Figure Lengend Snippet: Figure 3. Changes in TF expression associated with multilineage differentiation of cancer cells in vivo. A, the majority of cells within the tumor mass were human cancer cells, as determined by staining with an antibody directed against human (tumor) cell nuclear antigen (green). Tumors grown in YFP/SCID mice were double-stained using anti-TF (human cancer cells, green) and anti-GFP (host, red) antibodies. Infiltration of YFP-positive host cells in A431 tumors is minimal (<10%) and many stroma-poor tumor regions remain negative for TF. Immunofluorescence staining of cytokeratin (red) reveals highly keratinized pearl structures within these tumors. B, some tumor cells have lost their epithelial phenotype and express the mesenchymal marker vimentin (green), indicative of cells undergoing EMT. H&E staining depicts which regions of the tumor are likely to express vimentin and undergo EMT (tumor periphery) and those that retain their epithelial phenotype and differentiate along an epithelial pathway (central tumor). Arrowhead, a keratin pearl. Cytokeratin immunofluorescence (red) shows regions of the tumor that have undergone epithelial differentiation. C, comparative Western blot analysis between A431 cells maintained in culture and those grown as tumors. A global decrease in TF protein levels were observed in tumors. Changes in EGFR were unremarkable whereas the expression of E-cadherin is reduced and the extracellular region is cleaved, leaving an 80 kDa protein that is unable to make cell-cell contacts. Consistent with this loss of E-cadherin and epithelial phenotype, some tumor regions express vimentin, whereas other regions of these tumors remain epithelial and express high levels of cytokeratin. Bars, 100 AM.

Article Snippet: All other tissue staining was performed on 4-Am paraffin sections which were incubated overnight at 4jC with the respective primary antibodies following heat antigen retrieval; except for cytokeratin (Novus Biological, Inc.) staining which required proteolytic digestion prior to a 60 min incubation with the prediluted antibody at room temperature.

Techniques: Expressing, In Vivo, Staining, Immunofluorescence, Marker, Western Blot

Journal: Cancer Communications

Article Title: Intratumoral CD103 + CD8 + T cells predict response to neoadjuvant chemoimmunotherapy in advanced head and neck squamous cell carcinoma

doi: 10.1002/cac2.12480

Figure Lengend Snippet: The increased CD103 + CD8 + TIL density is associated with better therapeutic response in NACI‐treated HNSCC patients. (A) mIHC image of DAPI, Cytokeratin (CK), CD103, and CD8 staining of advanced HNSCC tissues in the responders and non‐responders. Scale bar, 100 μm. (B) Density of intratumoral CD103 + CD8 + TILs and CD103 − CD8 + TILs in tumors was assessed in the MPR group ( n = 22) and IPR group ( n = 17) patients to NACI via mIHC assay. Density of intratumoral CD103 + CD8 + TILs and CD103 − CD8 + TILs in tumors was assessed in the responders (R; n = 19) and non‐responders (NR; n = 20) patients to NACI. Image shows CD103 + CD8 + (yellow), CD103 − CD8 + (red), and CD8 + (red) cells in advance HNSCC (lower panel). Scale bar, 10 μm. (C) MRI showing the tumor size in responders and non‐responders before and after NACI, respectively. (D) mIHC image shows the density of CD103 + CD8 + TILs in tumors from responders and non‐responders before and after NACI. Scale bar, 200 μm. (E) The temporal alterations of the density of CD103 + CD8 + TILs and CD103 − CD8 + TILs from pre‐ and post‐NACI in the responders ( n = 19) and non‐responders ( n = 20) via mIHC assay. (F) Distribution of CD103 + CD8 + TILs between different clinical characteristics in patients with advanced HNSCC. Horizontal lines indicate the mean ± SEM. Significance was determined with a 2‐tailed Mann‐Whitney U test. Pearson's chi‐square test was used for studying the distribution of intraepithelial CD103 + CD8 + TILs across different subgroups. Abbreviations: TIL, tumor‐infiltrating cell; HNSCC, head and neck squamous cell carcinoma; mIHC, multiplex immunofluorescent; MRI, Magnetic resonance imaging; MPR, major pathologic response; IPR, incomplete pathologic response; R, responders; NR, non‐responders; SEM, standard error of the mean; NACI, neoadjuvant chemoimmunotherapy; MRI, magnetic resonance imaging.

Article Snippet: The following antibodies were purchased from Cell Signaling Technology (CST, Danvers, MA, USA) or Abcam (Waltham, MA, USA): CD8 (1:200, #85336, CST), CD103 (1:200, EPR22590‐27, Abcam), cytokeratin (1:250, #67306, CST), CD68 (1:1000, #76437, CST), and TREM2 (1:500, #91068, CST).

Techniques: Clinical Proteomics, Staining, MANN-WHITNEY, Multiplex Assay, Magnetic Resonance Imaging

Journal: Cancer Communications

Article Title: Intratumoral CD103 + CD8 + T cells predict response to neoadjuvant chemoimmunotherapy in advanced head and neck squamous cell carcinoma

doi: 10.1002/cac2.12480

Figure Lengend Snippet: Intraepithelial CD103 + CD8 + TIL density has a strong predictive value for therapeutic response in HNSCC patients treated with NACI. (A) Overview of the automated image analysis pipeline via inform analysis (upper panel). The spatial distribution of CD103 + CD8 + TILs in the responders and non‐responders (lower panel). Digital markup image shows tumor (red) and stromal (green) zones of the tumor section defined by cytokeratin staining. Digital markup image shows CD103 + CD8 + TILs (red). Scale bar, 100 μm. (B) Density of intraepithelial and stromal CD103 + CD8 + TILs in tumors were assessed in the MPR group ( n = 22) and IPR group ( n = 17) patients to NACI via inform analysis. Density of intraepithelial and stromal CD103 + CD8 + TILs in tumors were assessed in the responders (R; n = 19) and non‐responders (NR; n = 20) with NACI. (C) HALO® spatial analyses demonstrate the spatial distribution of CD103 + CD8 + TILs in the responders and non‐responders. Digital markup image shows tumor (red) and stromal (green) zones of the tumor section defined by cytokeratin staining. Digital markup image shows the density of intratumoral CD103 + CD8 + TILs (blue), intraepithelial CD103 + CD8 + TILs (red), and stromal CD103 + CD8 + TILs (green). Scale bar, 1 mm, 200 μm. Proximity analysis histograms of CD103 + CD8 + TILs within an 800 μm radius by progressive segments of 200 μm bands in advanced HNSCC tissues. (D) Temporal alterations in the density of intraepithelial CD103 + CD8 + TILs from pre‐ and post‐NACI in the responders ( n = 19) and non‐responders via inform analysis ( n = 20). (E) Predictive value of intratumoral CD103 + CD8 + TILs, intraepithelial CD103 + CD8 + TILs, and stromal CD103 + CD8 + TILs via ROC analysis. (F) Distribution of intraepithelial CD103 + CD8 + TILs between different clinical characteristics in patients with advanced HNSCC. Horizontal lines indicate the mean ± SEM. Significance was determined with a 2‐tailed Mann‐Whitney U test. Pearson's chi‐square test was used for studying the distribution of intraepithelial CD103 + CD8 + TILs across different subgroups. Abbreviations: TIL, tumor‐infiltrating cell; HNSCC, head and neck squamous cell carcinoma; MPR, major pathologic response; IPR, incomplete pathologic response; ROC, Receiver Operating Characteristic; R, responders; NR, non‐responders; SEM, standard error of the mean; NACI, neoadjuvant chemoimmunotherapy.

Article Snippet: The following antibodies were purchased from Cell Signaling Technology (CST, Danvers, MA, USA) or Abcam (Waltham, MA, USA): CD8 (1:200, #85336, CST), CD103 (1:200, EPR22590‐27, Abcam), cytokeratin (1:250, #67306, CST), CD68 (1:1000, #76437, CST), and TREM2 (1:500, #91068, CST).

Techniques: Clinical Proteomics, Staining, MANN-WHITNEY