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: bioRxiv

Article Title: Persistent SARS-CoV-2 Spike is Associated with Localized Immune Dysregulation in Long COVID Gut Biopsies

doi: 10.64898/2026.03.09.707564

Figure Lengend Snippet: (A) Representative staining images of the left colon and terminal ileum between healthy and Long COVID participants used for ROI collection. Tissue sections were stained with SYTO-13 (Blue), anti-SARS-CoV-2 Spike ( CR3022 ) (Yellow), anti-PanCK (Green), and anti -CD19 (CB19) (red) and visualized using the GeoMx DSP (Long COVID = 8; Healthy = 3). (B) SARS-COV-2 Spike protein positive cell detection based on a QuPath pipeline comparing condition and tissue type between tissue compartments. Cell detection was performed using an adapted StarDist script followed by cell classification based on a supervised ML model. Kruskal-Wallis with multiple comparisons was performed ( p ≤ 0.05 (*), p ≤ 0.01 (**), p ≤ 0.001 (***)). (D) ROI selection and differential expression strategies comparing detected Spike protein positive ROI’s in colon tissue between Long COVID and healthy participants. (D) Differential analysis was performed using the limma-voom pipeline, correcting for replicate samples and variation in the frequency of detected SARS-CoV-2 Spike by ROI. 18,582 transcript targets were plotted. The main volcano plot highlights 26 and 31 genes that are upregulated and downregulated, respectively, at an unadjusted p -value threshold of 0.05 and an absolute log 2 FC > 1. Points with a triangular shape passed the adjusted p-value threshold based on a Benjamini-Hochberg correction. Smaller volcano plots show differentially expressed genes belonging to GeneOntology (GO) panels (GO:0002376 & GO:0006954) at an unadjusted p -value threshold of 0.05 and a Fold-Change value of 1.5. (E) Gene-Set Enrichment Analysis was performed on a ranked list of log 2 FC values with GeneOntology and KEGG ( 54 and 38 statistically significant pathways, respectively ) . Representative categories were selected, and pathways/ gene sets were plotted using the normalized enrichment score (NES) alongside the ratio of genes in the leading edge to total genes in the gene set (GeneRatio) and the adjusted p-value. (F) Spatial deconvolution was performed using a safeTME reference expression profile. Statistical significance was assessed using the propeller framework, a moderated two-tailed Mann-Whitney U test with BH FDR correction ( FDR ≤ 0.05 (*), FDR ≤ 0.01 (**), FDR ≤ 0.001 (***)).

Article Snippet: NBP2-76425AF594), and anti-CD19 (Novus; Ca.

Techniques: Staining, Selection, Quantitative Proteomics, Expressing, Two Tailed Test, MANN-WHITNEY

Journal: Cell reports

Article Title: Insights into Gonadal Sex Differentiation Provided by Single-Cell Transcriptomics in the Chicken Embryo.

doi: 10.1016/j.celrep.2020.03.055

Figure Lengend Snippet: Figure 5. PAX2 Marks a Mesenchymal Cell Population in the Embryonic Chicken Gonad (A) Time series of PAX2 protein expression in male and female gonads by immunofluorescence. Cytokeratin marks the coelomic epithelium (arrowheads). PAX2+

Article Snippet: Sections were blocked in 2% BSA/PBS for 1hr at room temperature followed by primary antibody incubation overnight at 4 C. The following antibodies were used: goat anti-GFP antibody (Rockland, 1;500), anti-acetylated tubulin as counter-strain (T6793, Sigma; 1:500); rabbit anit-PAX2 (Biolegend, 1;500), mouse anti-pan cytokeratin (Novus Bio, 1:200), rabbit anti-DMRT1 (in house antibody; 1:2000), mouse anti-Steroidogenic Factor-1 (Sf1) (Life Technologies; 1:10).

Techniques: Expressing