Journal: Investigative Ophthalmology & Visual Science

Article Title: Transvitreal Retinochoroidal Biopsies of Primary Uveal Melanoma Reveal an Association of Low HLA Class I and High NK Cell Abundance in Low-Risk Disease

doi: 10.1167/iovs.66.2.24

Figure Lengend Snippet: HLA class I expression inversely associates with intratumoral NK cell percentages. ( A ) Bar plots showing the percentages of HLA class I–positive tumor cells ( top ) and the NK cells ( middle ) and CD8 T cells ( bottom ) of all immune cells per patient. ( B ) Box plot showing the percentage of HLA class I–positive tumor cells versus the BAP1 staining that was performed on tissue. ( C ) Box plot showing the percentage of HLA class I–positive tumor cells versus the risk group. ( D ) Kaplan–Meier plot showing the RFS of two groups of patients, separated by the median percentage of NK cells into NK high and NK low groups.

Article Snippet: To identify the BRCA-1 associated protein 1 (BAP1) status of tumors, a standard immunohistochemistry (IHC) staining using 1:100 anti-BAP1 (clone C-4, sc-28383; Santa Cruz Biotechnology, Dallas, TX, USA) was performed.

Techniques: Expressing, Staining

Journal: Investigative ophthalmology & visual science

Article Title: Transvitreal Retinochoroidal Biopsies of Primary Uveal Melanoma Reveal an Association of Low HLA Class I and High NK Cell Abundance in Low-Risk Disease.

doi: 10.1167/iovs.66.2.24

Figure Lengend Snippet: FIGURE 6. HLA class I expression inversely associates with intratumoral NK cell percentages. (A) Bar plots showing the percentages of HLA class I–positive tumor cells (top) and the NK cells (middle) and CD8 T cells (bottom) of all immune cells per patient. (B) Box plot showing the percentage of HLA class I–positive tumor cells versus the BAP1 staining that was performed on tissue. (C) Box plot showing the percentage of HLA class I–positive tumor cells versus the risk group. (D) Kaplan–Meier plot showing the RFS of two groups of patients, separated by the median percentage of NK cells into NKhigh and NKlow groups.

Article Snippet: To identify the BRCA1 associated protein 1 (BAP1) status of tumors, a standard immunohistochemistry (IHC) staining using 1:100 anti-BAP1 (clone C-4, sc-28383; Santa Cruz Biotechnology, Dallas, TX, USA) was performed.

Techniques: Expressing, Staining

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Histological characteristics of mesothelioma patients’ biopsies relative to BAP1, p16 and MTAP.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques:

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Kaplan–Meier survival of patients with peritoneal mesothelioma. In ( A ), survival data is shown based on TERT score: patients with high TERT mRNA expression showed shorter survival times than their counterparts (violet lines); not statistically significant. In ( B ), survival data is shown based on histological type: epithelioid type (line blue), biphasic type (line red); differences are not significant. In ( C ), survival data based on mitotic index adjusted is shown: 2–4 (line red), 5–9 (line blue) or >10 (line green) mitosis expressed on 2 mm 2 ; p ≤ 0.0001. In ( D ), survival data based on sex is shown: male (line blue) and female (line red); p = 0.0152. In ( E ), survival data based on BAP1 is shown: positive (line blue) and negative (line orange); p = 0.0152. The dashed lines indicate SE.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques: Expressing

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Spearman’s correlation graphs between the customized score relative to the percentage of cells containing TERT mRNA (1+–4+ on the x -axis) and the score for a series of parameters obtained from morphological and cytogenetic analyses ( y -axis). In ( A ), TERT mRNA correlation with BAP1, p16 and MTAP protein expression, and with p16 cytogenetic alterations. In ( B ), TERT mRNA correlation with histotype, atypia and inflammatory infiltrate. In ( C ), TERT mRNA correlation with asbestous exposure type and time, sex, age and survival month. In ( D ), TERT mRNA correlation with necrosis, mitotic indexes, nuclear grade and ki-67. Statistical significance was determined by linear regression analysis. Only the significant r and p -values are reported.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques: Expressing

Journal: Cancers

Article Title: Analysis of TERT mRNA Levels and Clinicopathological Features in Patients with Peritoneal Mesothelioma

doi: 10.3390/cancers17020252

Figure Lengend Snippet: Pathological factors predictive of peritoneal mesothelioma patient survival. Univariate analysis using log-rank test.

Article Snippet: BRCA1-associated protein 1 (BAP1) (clone C4, Santa Cruz Biotechnology, Santa Cruz, CA, USA) was classified as negative only if a complete absence of nuclear staining was observed in the presence of nuclear-positive lymphocytes.

Techniques:

Journal: Cell Death Discovery

Article Title: BAP1 inactivation promotes lactate production by leveraging the subcellular localization of LDHA in melanoma

doi: 10.1038/s41420-024-02250-6

Figure Lengend Snippet: A Cell culture medium pH decreased after BAP1 knockdown. Samples are cell culture medium of BAP1 knockdown group and control group in UVM cell line (MEL290). B Changes in lactic acid, citric acid and succinic acid levels after BAP1 knockdown. Samples are cell culture medium from BAP1 knockdown group and control group, and values were determined using the corresponding kits respectively. C Changes in lactic acid, citric acid and succinic acid content after reintroduction with BAP1. Exogenous BAP1 (wild type, enzyme active site mutants C91G and G185R) was complemented in the BAP1 knockdown MEL290 cell line, and the extracellular lactate levels were measured after the complementation. D Increase in cellular glycolytic capacity after BAP1 knockdown. Glycolytic capacity of BAP1 knockdown and control groups in MUM2B and B16F10 was detected using a hippocampal extracellular flux analyzer and analyzed by Agilent Seahorse XF reporter generator. *p < 0.05, **<0.01, ***<0.001, and no significance (ns).

Article Snippet: Cell samples were lysed using buffer containing NP-40, the supernatant was collected after centrifugation, and proteins were separated using BAP1 antibody and magnetic beads (#70024, Cell Signaling Technology).

Techniques: Cell Culture, Knockdown, Control

Journal: Cell Death Discovery

Article Title: BAP1 inactivation promotes lactate production by leveraging the subcellular localization of LDHA in melanoma

doi: 10.1038/s41420-024-02250-6

Figure Lengend Snippet: A Heat map showing the mean expression values of genes related to glucose metabolism, data from RNA-seq data of BAP1 knockdown group and control group in MEL290, MUM2B cell lines. B Fluorescence quantitative PCR was performed on differentially expressed genes, and the samples were MEL290 cell lines. C Western blot of differentially expressed genes to detect protein expression levels in the BAP1 knockdown and control groups of MEL290 cell lines. D Immunoprecipitation of BAP1 was performed on the MEL290 cell line, and protein characterization was performed using triple quadrupole tandem mass spectrometry and compared with published mass spectrometry data (PXD030044, PXD023676). E Immunoprecipitation of LDHA was used to detect its interaction with endogenous BAP1. F Immunoprecipitation of exogenous BAP1 was used to detect its interaction with LDHA. G Simultaneous knockdown of LDHA in the BAP1 knockdown and control groups, respectively, and detection of changes in extracellular lactate levels. *p < 0.05, **<0.01, ***<0.001, and no significance (ns).

Article Snippet: Cell samples were lysed using buffer containing NP-40, the supernatant was collected after centrifugation, and proteins were separated using BAP1 antibody and magnetic beads (#70024, Cell Signaling Technology).

Techniques: Expressing, RNA Sequencing, Knockdown, Control, Fluorescence, Real-time Polymerase Chain Reaction, Western Blot, Immunoprecipitation, Targeted Proteomics, Mass Spectrometry

Journal: Cell Death Discovery

Article Title: BAP1 inactivation promotes lactate production by leveraging the subcellular localization of LDHA in melanoma

doi: 10.1038/s41420-024-02250-6

Figure Lengend Snippet: A Human-derived full-length LDHA and full-length BAP1 were expressed in E. coli, and the proteins were purified using Ni column affinity chromatography and GST column affinity chromatography, respectively. B Examination of the direct interaction between GST-BAP1 and LDHA in vitro by GST-Pulldown. C – E The purified LDHA proteins were used for kinetic assays of enzyme activity, and the absorbance was measured at 340 nm to determine the amount of NADH. C Only substrate was added in the Control group, and LDHA was added in the LDHA group. D The enzymatic activity of LDHA was completely inhibited after the addition of 50 mM oxamate to LDHA. E The enzymatic activity of LDHA was not significantly changed after the addition of an equal amount of BAP1 protein to LDHA.

Article Snippet: Cell samples were lysed using buffer containing NP-40, the supernatant was collected after centrifugation, and proteins were separated using BAP1 antibody and magnetic beads (#70024, Cell Signaling Technology).

Techniques: Derivative Assay, Purification, Affinity Column, Chromatography, In Vitro, Activity Assay, Control

Journal: Cell Death Discovery

Article Title: BAP1 inactivation promotes lactate production by leveraging the subcellular localization of LDHA in melanoma

doi: 10.1038/s41420-024-02250-6

Figure Lengend Snippet: A Immunofluorescence staining of BAP1 knockdown cell lines. Reduced nuclear localization of LDHA in the BAP1 knockdown group. Each datapoint represents the mean value of nuclear enrichment ratio of each condition from three experimental replicates. Scale bar is 20 µm. B Western blotting for nucleus and cytoplasm separation of BAP1 knockdown cell lines. C Immunofluorescence staining of BAP1 reintroduction cell lines. The nuclear translocation of LDHA was significantly increased after complementation back to exogenous BAP1. Quantification of nuclear localization of LDHA cells as a percentage of total cell numbers, respectively. Scale bar is 20 µm. D Western blotting for nucleus and cytoplasm separation of BAP1 reintroduction cell lines.

Article Snippet: Cell samples were lysed using buffer containing NP-40, the supernatant was collected after centrifugation, and proteins were separated using BAP1 antibody and magnetic beads (#70024, Cell Signaling Technology).

Techniques: Immunofluorescence, Staining, Knockdown, Western Blot, Translocation Assay

Journal: Cell Death Discovery

Article Title: BAP1 inactivation promotes lactate production by leveraging the subcellular localization of LDHA in melanoma

doi: 10.1038/s41420-024-02250-6

Figure Lengend Snippet: A Complementation of exogenous NLS-deleting BAP1 mutant (ΔNLS) and wild-type BAP1 (WT) in BAP1-knockdown MEL290 cell lines and performing Immunofluorescence staining. Each datapoint represents the mean value of nuclear enrichment ratio of each condition from three experimental replicates. Scale bar is 20 µm. B Measuring lactate content in cell lines with BAP1-WT and BAP1-ΔNLS. C Complementation of exogenous BAP1 truncations in BAP1-knockdown MEL290 cell lines and performing Immunofluorescence staining. Intranuclear localization of LDHA in cells did not change significantly after reintroduction of BAP1 truncation mutants. Scale bar is 20 µm. D Measuring lactate content in cell lines with BAP1 truncation mutants. E , F LDHA was detected at different sites by Western blotting after isolating the nucleus and cytoplasm.

Article Snippet: Cell samples were lysed using buffer containing NP-40, the supernatant was collected after centrifugation, and proteins were separated using BAP1 antibody and magnetic beads (#70024, Cell Signaling Technology).

Techniques: Mutagenesis, Knockdown, Immunofluorescence, Staining, Western Blot

Journal: Neuropathology

Article Title: Solitary subependymal giant cell astrocytoma lacking TSC1 /2 mutations and TTF ‐1 expression: A potential diagnostic pitfall

doi: 10.1111/neup.13013

Figure Lengend Snippet: Immunohistochemical features of the tumor on BAP1 immunostaining. Tumor cells show weak nuclear staining for BAP1.

Article Snippet: Immunohistochemistry for BAP1 protein (clone C4, dilution 1:100; Santa Cruz Biotechnology, Germany), performed due to the BAP1 mutation, showed nuclear staining for this protein with a milder intensity than that found in normal cells ( Fig. ) .

Techniques: Immunohistochemical staining, Immunostaining, Staining