Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Function of liver activation-regulated chemokine/CC chemokine ligand 20 is differently affected by cathepsin B and cathepsin D processing.

doi: 10.4049/jimmunol.176.11.6512

Figure Lengend Snippet: FIGURE 4. Expression of CCL20 in melanoma cell lines and human malignant melanoma. A, RT-PCR analysis of CCL20 and G3PDH expres- sion in melanoma cell lines A375, A2058, and SK-MEL-2. Positive control RT-PCR products were obtained from primary keratinocytes (Prim. Ker- atin.), human keratinocyte cell line (NCTC 2544), and Caco-2 cells. A 100-base DNA ladder (ladder) and a negative control (no cDNA; control ) are shown. B, Localization of CCL20 transcripts in human malignant melanoma by in situ hybridization. Hybridization signals of antisense CCL20 riboprobes are identified in keratinocytes and melanoma cells. No signals were detected in serial sections hybridized with the sense probe.

Article Snippet: Human melanoma cell lines A375 (solid tumor metastatic line; ATCC CRL-1619), A2058 (lymph node metastatic line; ATCC CRL-11147), and SK-MEL-2 (skin metastatic line; ATCC HTB-68) were from American Type Culture Collection.

Techniques: Expressing, Reverse Transcription Polymerase Chain Reaction, Positive Control, Negative Control, Control, In Situ Hybridization, Hybridization

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Function of liver activation-regulated chemokine/CC chemokine ligand 20 is differently affected by cathepsin B and cathepsin D processing.

doi: 10.4049/jimmunol.176.11.6512

Figure Lengend Snippet: FIGURE 6. Cathepsins in melanoma cell lines and human malignant melanoma. A375, A2058, and SK-MEL-2 melanoma cells were stimulated with IL-1 and TNF- for 48 h before isolation of subcellular fractions. A, Upper panel, Membranes, cytosol, and conditioned medium were incu- bated for 4 h with 30 mM d-F-S(benzoyl)-F-F-A-A-pAB to assess Cath-D activity. Results are expressed as picomoles of pAB released per minute per 105 cells. Cath-D activity was also measured in the presence of pep- statin A (data not shown). A, Lower panel, Intact cells, cells lysed with Triton X-100, membranes, and cytosol were incubated for 50 min with 100 M Z-Arg-Arg-AMC to assess Cath-B activity. Results are expressed as nanomoles of AMC released per minute per 105 cells. No Cath-B activity was detected in conditioned medium or in the presence of CA-074 (data not shown). Statistically significant increases in activities above controls in the presence of inhibitor are indicated by asterisks (, p 0.05; and , p 0.01). B, Membranes, cytosol, and conditioned medium of A375 (1), A2058 (2), and SK-MEL-2 (3) cells were immunoblotted with anti-Cath-D or anti-Cath-B Ab. Purified Cath-D and Cath-B from human liver were used as controls (Cathepsin). A Coomassie blue staining of similar samples is given as a control for equal loading of the samples. C, Cath-D was immunochemically detected in paraffin sections of human melanoma (left panel); the negative control was obtained by omitting the primary Ab (right panel).

Article Snippet: Human melanoma cell lines A375 (solid tumor metastatic line; ATCC CRL-1619), A2058 (lymph node metastatic line; ATCC CRL-11147), and SK-MEL-2 (skin metastatic line; ATCC HTB-68) were from American Type Culture Collection.

Techniques: Isolation, Activity Assay, Incubation, Staining, Control, Negative Control

Journal: Journal of immunology (Baltimore, Md. : 1950)

Article Title: Function of liver activation-regulated chemokine/CC chemokine ligand 20 is differently affected by cathepsin B and cathepsin D processing.

doi: 10.4049/jimmunol.176.11.6512

Figure Lengend Snippet: FIGURE 7. Cleavage of CCL20 by melanoma cell lines. A, Processing of CCL20 by membranes of A375 (1), A2058 (2), and SK-MEL-2 (3) cells. CCL20 (5 M) was incubated for 4 h at 37°C with membrane equivalents of 3 105 cells in 50 mM sodium citrate, 50 mM NaCl (pH 4.0), and pepstatin A as indicated. The cleavage products were separated by SDS-PAGE and stained with Coomassie blue. The molecular masses of intact CCL201–70 and CCL201–55 after Cath-D cleavage are 8025 and 6224 Da, respectively (arrows). B, Processing of CCL20 by purified Cath-B (left panel) or Cath-D (middle panel) for 1.5 h or membranes of SK-MEL-2 cells (right panel) for 4 h at pH 4.0 in presence of CA-074 and pepstatin A as indicated. The molecular masses of intact CCL201–70, CCL201–66 after Cath-B cleavage and CCL201–55 after Cath-D cleavage are 8025, 7552, and 6224 Da, respectively (arrows). C, As in A but incubation was with PBS containing 4 mM EDTA, 2 mM L-cysteine, 0.1% Triton X-100 (pH 6.8). D, Processing of CCL20 by conditioned medium of SK-MEL-2 cells. Conditioned medium was concentrated (2.5) and incubated with CCL20 (5 M) at pH 4.0 for the indicated times and in the presence of pepstatin A (left panel). Coomassie blue staining of CCL20 incubated for 8 h with purified Cath-D or conditioned medium is shown in the middle panel. The right panel shows migration in response to increasing concentrations of CCL20 after incubation for 8 h in conditioned medium with or without pepstatin A. Results are expressed as means SD of the numbers of cells observed per five high-power fields. A representative experiment of three is shown. IB, Immunoblotting; Cond. medium, conditioned medium.

Article Snippet: Human melanoma cell lines A375 (solid tumor metastatic line; ATCC CRL-1619), A2058 (lymph node metastatic line; ATCC CRL-11147), and SK-MEL-2 (skin metastatic line; ATCC HTB-68) were from American Type Culture Collection.

Techniques: Incubation, Membrane, SDS Page, Staining, Migration, Western Blot

Journal: bioRxiv

Article Title: Exploiting pair correlation function to describe biological tissue structure

doi: 10.64898/2025.12.19.695425

Figure Lengend Snippet: (A) Analytical workflow. (B) Example of pcf fit. Grey dots correspond to the empirical pcf. Each colored curve corresponds to the fit of a different model. The dashed line corresponds to the line of equation y=1. (C) Distribution of R 2 values for the different model fits to the IMC Lymph node dataset. The thick line corresponds to the median, and the bottom and upper limits of the box correspond to the first and third quartiles, respectively. The lower and upper whiskers correspond to the lowest and highest values, respectively, within the range of the first and third quartiles ±1.5 times the interquartile range (IQR). All boxplots shown in this manuscript are using the same graphical code. The boxplot is based on N = 17 cell types. (D) Distribution of R 2 values for the different model fit to the Xenium Lymph node dataset. The boxplot is based on N = 18 cell types. (E) Distribution of R 2 values for the different model fit to the MERIFSH Tonsil dataset. The boxplot is based on N = 24 cell types. (F) Distribution of R 2 values for the different model fit to the CosMX Prefrontal cortex dataset. The boxplot is based on N = 14 cell types. ( G ) Comparison of the inferred τ parameter with the scale parameter of the simulated Thomas point pattern. Each dot is the average result of 50 simulations. The dashed line corresponds to a linear regression. The black bars correspond to standard deviation observed across simulations. ( H ) Comparison of the inferred C normalised parameter with the noise parameter of the simulated noisy Thomas point pattern. Each dot is the average result of 50 simulations. The dashed line corresponds to a linear regression. The black bars correspond to standard deviation observed across simulations. (I) Spatial pattern of 9 cell types from the MERFISH Tonsild dataset. For each PCF-SiM parameter, 3 patterns are shown with an increasing parameter value from to to bottom.

Article Snippet: The three spatial transcriptomic datasets were obtained using the following procedure: – We obtained the Xenium human lymph node dataset from the 10X Genomics website ( https://www.10xgenomics.com/datasets/human-lymph-node-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard ).

Techniques: Comparison, Standard Deviation

Journal: bioRxiv

Article Title: Exploiting pair correlation function to describe biological tissue structure

doi: 10.64898/2025.12.19.695425

Figure Lengend Snippet: (A) Pearson’s correlation between the Clark-Evans index and the three PCF-SiM fitted parameters for the IMC Lymph node dataset. ( B ) Pearson’s correlation between the Clark-Evans index and the three PCF-SiM fitted parameters for the Xenium Lymph node dataset. ( C ) Pearson’s correlation between the Clark-Evans index and the three PCF-SiM fitted parameter for the MERFISH Tonsil dataset. ( D ) Pearson’s correlation between the Clark-Evans index and the three PCF-SiM fitted parameters for the CosMX Prefrontal cortex dataset. (E) Pearson’s correlation between the overdispersion index and the three PCF-SiM fitted parameters for the IMC Lymph node dataset. (F) Pearson’s correlation between the overdispersion index and the three PCF-SiM fitted parameters for the Xenium Lymph node dataset. (G) Pearson’s correlation between the overdispersion index and the three PCF-SiM fitted parameters for the MERFISH Tonsil dataset. (H) Pearson’s correlation between the overdispersion index and the three PCF-SiM fitted parameters for the MERFISH Tonsil dataset. (I) Comparison of the initially estimated C normalised parameter and the estimated C normalised parameter after label corruption. Each dot corresponds to a cell type and is the result of 100 simulations. Dashed line corresponds to the x=y line. The black bars correspond to the standard deviation observed across samples. (J) Comparison of the initially estimated p parameter and the estimated p parameter after label corruption. Each dot corresponds to a cell type and is the result of 100 simulations. Dashed line corresponds to the x=y line. The black bars correspond to the standard deviation observed across samples. (K) Comparison of the initially estimated τ parameter and the estimated τ parameter after label corruption. Each dot corresponds to a cell type and is the result of 100 simulations. Dashed line corresponds to the x=y line. The black bars correspond to the standard deviation observed across samples. ( L ) Estimated τ parameter for the different proteins of the Influenza data. The large horizontal lines correspond to the median while the two smaller horizontal bars correspond to the interquartile ranges. All “prism-like” plots in the manuscript are using the same graphical codes. P-values were computed using Tukey’s honestly significant difference test. ( M ) Estimated p parameter for the M2 protein according to the protein genotype. P-value was computed using a regular Welsh test. ( N ) Estimated PCF-SiM parameters for the different tree species from the Lansing Woods dataset.

Article Snippet: The three spatial transcriptomic datasets were obtained using the following procedure: – We obtained the Xenium human lymph node dataset from the 10X Genomics website ( https://www.10xgenomics.com/datasets/human-lymph-node-preview-data-xenium-human-multi-tissue-and-cancer-panel-1-standard ).

Techniques: Comparison, Standard Deviation

Journal: Briefings in Bioinformatics

Article Title: Cross-modality representation and multi-sample integration of spatially resolved omics data

doi: 10.1093/bib/bbag214

Figure Lengend Snippet: PRESENT facilitates accurate spatial domain identification in spatial RNA-ADT data. (a) spatial visualization of the 10x Genomics Visium RNA-protein human lymph node sample colored by ground truth domain labels. (b) Quantitative comparison of spatial domain identification performance between PRESENT and other baseline methods, shown as a bar plot for the human lymph node dataset. (c) Quantitative comparison between PRESENT utilizing both RNA and ADT data (RNA & ADT) and PRESENT using only RNA (RNA-only) or ADT data (ADT-only), shown as a radar plot in the human lymph node dataset. (d) UMAP visualization of latent embeddings from different methods, colored by ground truth domain labels in the human lymph node dataset. (e) UMAP visualization of latent embeddings, colored by cluster labels in the human lymph node dataset. (f) Spatial visualization of spots colored by cluster labels in the human lymph node dataset. The cluster labels in e and f were derived from latent embeddings of different methods using the Leiden algorithm. (g) Histology image of the SPOTS mouse spleen dataset and spatial visualization of spots colored by cluster labels in the SPOTS mouse spleen dataset. The cluster labels were derived from latent embeddings of PRESENT using Leiden algorithm. (h) Differentially expressed proteins of each spatial domain through one-versus-all Wilcoxon rank-sum test, shown as a dot plot. (i) DEGs of all the spatial domains through one-versus-all Wilcoxon rank-sum test, shown as a dot plot. (j) Volcano plot showing the DEGs of Mac1-enriched domain and Mac2-enriched domain through Mac1-versus-Mac2 Wilcoxon rank-sum test, where the x axis denotes the log(fold-change) (log(FC)), while the y axis denotes the significance measured by -log10(false discovery rate) (−log10(FDR)). The vertical dashed line represents the threshold for log(FC)= \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} $\pm$\end{document} 0.2, while the horizontal dashed line denotes the threshold for -log10(FDR) = 0.05. (k) Chord plot demonstrating the linkage of DEGs in the Mac1-enriched domain and the corresponding enriched pathways. The left semicircle represents DEGs while the right semicircle denotes the enriched biological processes. Bar plot is employed to demonstrate the significance of each pathway (x axis, −log10(FDR)). (l) The linkage of DEGs in the Mac2-enriched domain and corresponding pathways as well as the significance of each enriched pathway.

Article Snippet: To evaluate the spatial domain detection performance of PRESENT, we collected a spatial RNA-ADT human lymph node dataset generated by 10x Genomics Visium technology [ ], which simultaneously assessed transcriptomic and proteomic expression as well as the spatial locations of spots and was manually annotated by the clinician group according to the histological image [ ] ( ).

Techniques: Comparison, Derivative Assay