wild type bap1  (Addgene inc)

Journal: Molecular Cancer Research

Article Title: Multi-omics Profiling Shows BAP1 Loss Is Associated with Upregulated Cell Adhesion Molecules in Uveal Melanoma

doi: 10.1158/1541-7786.mcr-21-0657

Figure Lengend Snippet: Figure 1. BAP1 mutations are correlated with increased expression of CAMs CDH1, CADM1, and SDC2. A, On the basis of BAP1 mutation and copy loss, TCGA uveal melanoma samples were strati- fied into BAP1 mutant and wild-type groups. Differential expression analy- sis was performed between BAP1 mutant (n ¼ 40) and wild-type (n ¼ 40) samples and used for performing GSEA. GSEA enrichment plots of the Hallmark epithelial to mesenchymal and KEGG CAMs) gene sets in BAP1 mutant versus wild-type groups are shown. B, A heatmap showing z-score values for the top 10 genes from the Hallmark EMT and KEGG CAMs gene sets in TCGA uveal mela- noma patient tumor samples. C, CDH1, CADM1, and SDC2 gene expression from TCGA RNA-seq data in BAP1 wild-type (n ¼ 40) and mutant sam- ples (n ¼ 40). D, Analysis of TCGA data for uveal melanoma patient progres- sion-free survival according to CDH1, CADM1, and SDC2 expression, strati- fied by high or low median RNA expression. Log-rank test was used to determine the significance of progres- sion-free survival (https://wiki.nci.nih. gov/plugins/servlet/mobile#content/ view/24279961).

Article Snippet: For BAP1 expression, wild-type BAP1 plasmid, pLVX-M-Flag-BAP1 was used; it was a gift from Boyi Gan (Addgene plasmid # 125840; http://n2t.net/addgene:125840; RRID: Addgene_125840; ref. 6).

Techniques: Expressing, Mutagenesis, Quantitative Proteomics, Gene Expression, RNA Sequencing, RNA Expression

Journal: Molecular Cancer Research

Article Title: Multi-omics Profiling Shows BAP1 Loss Is Associated with Upregulated Cell Adhesion Molecules in Uveal Melanoma

doi: 10.1158/1541-7786.mcr-21-0657

Figure Lengend Snippet: Figure 2. BAP1 mutant and wild-type uveal melanoma cell line panel shows dif- ferential expression of CDH1, CADM1, and SDC2. Differential expression analysis of RNA-seq data from tripli- cates of six BAP1 mutant (MM28, MP38, MP46, MP65, WM3618F, and PDX4) and two BAP1 wild-type cell lines (92.1 and MM66) was performed using DESeq2. A, A heatmap showing average expression of six BAP1 mu- tant and two wild-type cell lines for the top 10 positively enriched KEGG CAMs pathway genes. B, Box plots of CDH1, CADM1, and SDC2 mRNA expression in BAP1 mutant (n ¼ 18) versus wild-type (n ¼ 6) cell line samples. C, A volcano plot showing antibodies targeting genes from the KEGG CAM pathway from the RPPA data. D, A heatmap of median- centered, log2-transformed RPPA data for the top and bottom five proteins ranked by the product of the fold change and log10(Benjamini– Hochberg FDR), when comparing BAP1 mutant versus wild-type cell lines. Each cell line was done in triplicate. Proteins are ordered on the basis of hierarchical clustering. E, Uveal melanoma cell line panel showing expression of E-cadherin and CADM1 in BAP1 wild-type versus mutant cell lines. F, Dot plot showing the average expression and percent of cells expressing CDH1, CADM1, and SDC2 from patient tumor scRNA-seq data. Cells were separat- ed into nonmalignant and tumor- specific malignant cell groups.

Article Snippet: For BAP1 expression, wild-type BAP1 plasmid, pLVX-M-Flag-BAP1 was used; it was a gift from Boyi Gan (Addgene plasmid # 125840; http://n2t.net/addgene:125840; RRID: Addgene_125840; ref. 6).

Techniques: Mutagenesis, Expressing, Quantitative Proteomics, RNA Sequencing, Transformation Assay

Journal: Molecular Cancer Research

Article Title: Multi-omics Profiling Shows BAP1 Loss Is Associated with Upregulated Cell Adhesion Molecules in Uveal Melanoma

doi: 10.1158/1541-7786.mcr-21-0657

Figure Lengend Snippet: Figure 3. Changes in CAMs gene expression due to BAP1 reexpression. A, Scatter plots showing fold change mRNA expression values for BAP1 mutant versus BAP1 reexpression or BAP1 mutant versus BAP1 wild-type com- parisons from four independent datasets (14, 53) for the KEGG CAMs gene set. Red dots indicate genes with log2 fold changes greater than 1 and BHFDR value of less than 0.05. B, A BAP1-mutant uveal melanoma cell line (53) was transfected with wild-type or mutant BAP1 to pro- duce proficient and deficient reex- pressing samples, respectively. Each of the mutant reexpressing and parental samples were compared against the wild-type reexpressing samples. Rank list plots showing the fold change values for genes in the KEGG CAMs pathway for parental (left), mutant A95P reexpressing (middle), and mutant C91W reex- pressing (right) samples compared against BAP1 wild-type reexpressing samples. C, Expression of BAP1 in BAP1 mutant cell cline, MP46, was confirmed by Western blot analysis, and protein expression of E-cadherin decreased in MP46-BAP1 cells. MP46-GFP was used as a control. Representative Western blots from triplicate experiments are shown.

Article Snippet: For BAP1 expression, wild-type BAP1 plasmid, pLVX-M-Flag-BAP1 was used; it was a gift from Boyi Gan (Addgene plasmid # 125840; http://n2t.net/addgene:125840; RRID: Addgene_125840; ref. 6).

Techniques: Gene Expression, Expressing, Mutagenesis, Transfection, Western Blot, Control