Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Representative photographs of APEX1 immunohistochemical staining in hepatocellular carcinoma (HCC) ( A – C ), cholangiocarcinoma (Cholangioca) ( D – F ), and clear cell renal cell carcinoma (ccRCC) ( G – I ). The three cancers show nuclear, cytoplasmic, or nuclear and cytoplasmic expression of APEX1. The nontumor proliferative biliary epithelium (*) expresses nuclear staining, while the cholangiocarcinoma cells show both nuclear and cytoplasmic expression ( F ). Inflammatory cells (**) exhibit cytoplasmic staining ( H ). No APEX1 expression in nontumor hepatocytes in contrast to the high nuclear expression in inflammatory cells (^) ( J ). Positive nuclear expression in nontumor bile duct epithelial cells (^^) ( K ). Positive nuclear expression in proximal convoluted tubular epithelial cells ( L ) (scale bar = 20 μm).

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Immunohistochemical staining, Staining, Expressing

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Summary of the clinicopathologic characteristics of patients with primary clear cell renal cell carcinoma ( n = 106).

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques:

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Summary of the clinicopathologic characteristics of patients with hepatocellular carcinoma ( n = 131).

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Infection

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Summary of the clinicopathologic characteristics of patients with primary intrahepatic cholangiocarcinoma ( n = 32).

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Infection

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Cytoplasmic expression of the APEX1 protein in 131 paired cases of hepatocellular carcinoma cells and the matched nontumor hepatocytes ( A ), 32 paired cases of intrahepatic cholangiocarcinoma cells and the matched nontumor bile duct epithelial cells ( B ), and 106 paired cases of clear cell renal cell carcinoma cells and the matched nontumor proximal convoluted tubular epithelial cells ( C ), using immunohistochemical staining for formalin-fixed, paraffin-embedded tissue (Wilcoxon signed-rank test: p < 0.001, each). The line in the middle of the boxes is the median. The box length indicates the interquartile range. The ends of the whiskers represent maximum and minimum values.

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Expressing, Immunohistochemical staining, Staining, Formalin-fixed Paraffin-Embedded

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Multivariate analysis of overall survival and disease-free survival in 131 patients with primary hepatocellular carcinoma (HCC).

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Infection

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Multivariate analysis of overall survival and disease-free survival in 32 patients with primary intrahepatic cholangiocarcinoma.

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Infection

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Comparison of the s-APEX1 levels among hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), clear cell renal cell carcinoma (ccRCC), HBV DNA (+) (HBV DNA ≥ 58 copies/mL), and heathy control groups (Kruskal–Wallis test: p < 0.001). The dark line in the middle of the boxes is the median. The box length indicates the interquartile range. The ends of the whiskers represent maximum and minimum values.

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Comparison, Control

Journal: Journal of Clinical Medicine

Article Title: APEX1 Expression as a Potential Diagnostic Biomarker of Clear Cell Renal Cell Carcinoma and Hepatobiliary Carcinomas

doi: 10.3390/jcm8081151

Figure Lengend Snippet: Analysis of the diagnostic value of serum APEX1 for hepatocellular carcinoma (HCC), cholangiocarcinoma (CC), and clear cell renal cell carcinoma (ccRCC) by receiver operating characteristic (ROC) curves. ( A – C ) ROC curves for the serum APEX1 levels to separate the HCC, CC, or ccRCC group from the healthy control. ( D – F ) ROC curves for the serum APE1/Red-1 levels to separate HBV DNA (+) from the HCC, CC, or ccRCC group. ( A ) ROC curve: HCC (+) vs. healthy control group (−), 95% confidence interval: 0.869–0.976. ( B ) ROC curve: CC (+) vs. healthy control group (–), 95% confidence interval: 0.709–0.886. ( C ) ROC curve: ccRCC (+) vs. healthy control group (–), 95% confidence interval: 0.862–0.981. ( D ) ROC curve: HBV DNA (+) (+) vs. HCC (–), 95% confidence interval: 0.873–0.980. ( E ) ROC curve: HBV DNA (+) (+) vs. CC (–), 95% confidence interval: 0.631–0.835. ( F ) ROC curve: HBV DNA (+) (+) vs. ccRCC (–), 95% confidence interval: 0.778–0.942.

Article Snippet: Immunohistochemical staining of the FFPE tissue section was conducted as previously described [ ] using a primary rabbit polyclonal antibody against human APEX1 (product # MR-PAAPE, diluted 1:50, incubation at 31 °C for 32 min; MediRedox, Daejeon, South Korea).

Techniques: Diagnostic Assay, Control

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: BAP1 expression of the GBC cell line G-415 was down-regulated by siRNA and the proliferative ability was measured by MTS assay. No significant difference was observed between each siRNA group and the control. The vertical axis shows the relative intensity compared to the intensity at day 1, and the horizontal axis shows the number of cell culture days.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Expressing, MTS Assay, Control, Cell Culture

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: (a) A diagram immediately after scratching in the confluently cultured cells (day 1) and the narrowed gap by migrating cells (day 2) are shown. (b) The relative increase of the migration area compared to the control group after 24 hours was significantly higher in the BAP1 knocked-down cells.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Cell Culture, Migration, Control

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: (a) The GBC cell line G-415 was transfected with siRNA against BAP1 and was seeded on a Matrigel invasion chamber and the infiltrated cells on the lower surface of the chamber were stained. (b) Compared to the control group, the number of infiltrated cells tended to increase in both siRNA1 and siRNA2, and the number of infiltrated cells was significantly higher in the siRNA1.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Transfection, Staining, Control

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: Cell viability of BAP1 knocked-down GBC cell line G-415 under the agents of gemcitabine (GEM), cisplatin (CDDP), fluorouracil (5-FU), sodium valproate, 5-azacytidine, and bortezomib was measured by MTS assay. No change in sensitivity was observed in GEM, CDDP, 5-FU, sodium valproate or 5-azacytidine. Bortezomib showed a significant decrease in sensitivity in the siRNA1 and siRNA2 group compared to the control.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: MTS Assay, Control

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: Kaplan–Meier survival curves for 41 GBC cases except for in-hospital deaths and deaths from other diseases show a significantly poorer prognosis in the BAP1 low expression group.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Expressing

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: Summary of clinical characteristics, BAP1 expression, mutation, homozygous deletion and methylation in the GBC patients.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Expressing, Mutagenesis, Methylation

Journal: PLoS ONE

Article Title: Loss of BAP1 expression is associated with genetic mutation and can predict outcomes in gallbladder cancer

doi: 10.1371/journal.pone.0206643

Figure Lengend Snippet: (a) Since the BAP1 staining concentration was low in the cancer part (Ca 40.4 < Liver 70.3), ID12 was categorized to the BAP1 low expression group. (b) The nonsense mutation on exon 8 (c.587G>A (p.Trp96Ter)) and the missense mutation on exon 4 (c.128T>A (p.Val43Glu), c.197T>A (p.Val66Glu)) were observed.

Article Snippet: Antibodies used for western blotting were as follows: as primary antibodies, mouse anti-human BAP1 monoclonal antibodies (sc-28383) were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA), and rabbit monoclonal antibodies against human E-cadherin (#3195), vimentin (#5741) and GAPDH (#2118) were obtained from Cell Signaling Technology (Danvers, MA, USA); as secondary antibodies, anti-mouse IgG HRP-conjugated secondary antibody (#7076) and anti-rabbit IgG HRP-conjugated secondary antibody (#7074) were also purchased from Cell Signaling Technology.

Techniques: Staining, Concentration Assay, Expressing, Mutagenesis

Journal:

Article Title: Base Excision Repair Is Limited by Different Proteins in Male Germ Cell Nuclear Extracts Prepared from Young and Old Mice

doi: 10.1128/MCB.22.7.2410-2418.2002

Figure Lengend Snippet: Western blot analysis of BER proteins in nuclear extracts prepared from enriched populations of primitive type A spermatogonia (PA), type A spermatogonia (A), type B spermatogonia (B), pachytene spermatocytes (P), and round spermatids (R). Bands corresponding to DNA ligase I (130 kDa), DNA ligase III (93 kDa), Xrcc-1 (69 kDa), β-pol (39 kDa), and Ape/Ref-1 (37 kDa) proteins were visualized. Triplicate assays for each of three independent nuclear extract preparations were performed. Some variation between replicates was noted. A summary of all data is shown in Table ​Table1.1. Molecular mass protein standards and purified DNA ligases I and III, β-pol, and Ape/Ref-1 (lane STD) are shown for comparison.

Article Snippet: Rabbit anti-human APE/REF-1 (hAPE/REF-1; Novus Biologicals, Littleton, Colo.) and rabbit polyclonal anti-β-pol (S. Wilson, NIEHS, Research Triangle Park, N.C.) were used to detect Ape/Ref-1 and β-pol, respectively.

Techniques: Western Blot, Purification, Comparison

Journal:

Article Title: Base Excision Repair Is Limited by Different Proteins in Male Germ Cell Nuclear Extracts Prepared from Young and Old Mice

doi: 10.1128/MCB.22.7.2410-2418.2002

Figure Lengend Snippet: Western blot analysis of BER proteins in MGC nuclear extracts prepared from 3-month-old, 16-month-old, and 28-month-old mice. Bands corresponding to DNA ligase I (130 kDa), DNA ligase III (93 kDa), Xrcc-1 (69 kDa), β-pol (39 kDa), and Ape/Ref-1 (37 kDa) proteins were visualized. Triplicate assays were performed for each of three independent nuclear extract preparations. Some variation in signal intensities was observed among Western blots. A summary of all data is shown in Table ​Table2.2. Molecular mass protein standards and purified DNA ligases I and III, β-pol, and APE/REF-1 (lane STD) are shown for comparison.

Article Snippet: Rabbit anti-human APE/REF-1 (hAPE/REF-1; Novus Biologicals, Littleton, Colo.) and rabbit polyclonal anti-β-pol (S. Wilson, NIEHS, Research Triangle Park, N.C.) were used to detect Ape/Ref-1 and β-pol, respectively.

Techniques: Western Blot, Purification, Comparison

Journal:

Article Title: Base Excision Repair Is Limited by Different Proteins in Male Germ Cell Nuclear Extracts Prepared from Young and Old Mice

doi: 10.1128/MCB.22.7.2410-2418.2002

Figure Lengend Snippet: UDG-BER activities for MGC nuclear extracts prepared from 3-month-old B6D2F1 (open), 28-month-old B6D2F1 (solid), and 3-month-old Apex heterozygous knockout mice (striped). Results are presented as means ± SEM of three replicate assays for each of three independent nuclear extract preparations. ∗, significantly (P < 0.05) different from addition of 0 ng of protein within a specific group. †, amount of purified APE/REF-1 required to restore activity to that of 3-month-old mice with 0 ng of protein added.

Article Snippet: Rabbit anti-human APE/REF-1 (hAPE/REF-1; Novus Biologicals, Littleton, Colo.) and rabbit polyclonal anti-β-pol (S. Wilson, NIEHS, Research Triangle Park, N.C.) were used to detect Ape/Ref-1 and β-pol, respectively.

Techniques: Knock-Out, Purification, Activity Assay

Journal: Science (New York, N.Y.)

Article Title: Loss of the tumor suppressor BAP1 causes myeloid transformation

doi: 10.1126/science.1221711

Figure Lengend Snippet: BAP1 deficiency results in MDS/CMML-like disease.

Article Snippet: Anti-BAP1 and anti-HCF1 antibodies were from Bethyl laboratories.

Techniques:

Journal: Science (New York, N.Y.)

Article Title: Loss of the tumor suppressor BAP1 causes myeloid transformation

doi: 10.1126/science.1221711

Figure Lengend Snippet: BAP1 deficiency in hematopoietic cells is sufficient for MDS/CMML-like disease.

Article Snippet: Anti-BAP1 and anti-HCF1 antibodies were from Bethyl laboratories.

Techniques:

Journal: Science (New York, N.Y.)

Article Title: Loss of the tumor suppressor BAP1 causes myeloid transformation

doi: 10.1126/science.1221711

Figure Lengend Snippet: Identification and characterization of BAP1-associated proteins in mouse brain and spleen.

Article Snippet: Anti-BAP1 and anti-HCF1 antibodies were from Bethyl laboratories.

Techniques:

Journal: Science (New York, N.Y.)

Article Title: Loss of the tumor suppressor BAP1 causes myeloid transformation

doi: 10.1126/science.1221711

Figure Lengend Snippet: Identification of BAP1-regulated genes.

Article Snippet: Anti-BAP1 and anti-HCF1 antibodies were from Bethyl laboratories.

Techniques:

Journal: iScience

Article Title: CD2 costimulation strength: A key regulator of T cell function and anti-tumor immunity that is epigenetically regulated

doi: 10.1016/j.isci.2025.113977

Figure Lengend Snippet: Genome-scale CRISPR-CAS9 screen identifies regulators of CD2 expression (A) Diagram shows the experimental design used for identifying positive regulators of CD2 using a GW CRISPR-CAS9 KO screen in the human Jurkat T cell line. CD2lo expressing cells were FACsorted (step 3) at 5 separate timepoints during the cell library screen culture. (B) A representative example plot from one of the five timepoints, showing the distribution of target gene enrichment within the CD2lo population compared to the total unsorted population based on log2 fold change of gene enrichment and p -value for enrichment generated by using the MAGeCK algorithm. (C) Bar chart shows the log2 fold change enrichment of targeting sgRNAs in CD2lo against the unsorted control population, which were reproduced in more than 1 of the 5 screen timepoints tested; each dot represents a separate timepoint. Data represent mean ± SD. (D) Flow cytometry histograms of surface CD2 expression, representative of two independent experiments, upon using two different sgRNA targeting BAP1 for knock out (BAP1 KO1 and KO2) and one sgRNA targeting CD2 (CD2 KO) compared to WT control and the corresponding geometric mean fluorescence intensity of each total population (gMFI). (E) A Western blot and corresponding bar charts show the total amount of BAP1 and CD2 protein normalized to beta-actin (b-actin) expression in experiments as in (D) using two different sgRNAs to knock out BAP1. (F) Histograms from two independent experiments are presented, here, show the surface CD2 expression upon three different sgRNA targeting SUZ12 for knock out (SUZ1 KO1, KO2, and KO3) compared to CD2 KO and WT control with corresponding gMFI of each total population. (G) A Western blot and corresponding bar charts show the total amount of SUZ12 protein normalized to GAPDH protein expression from experiments shown in (F). (H) Bar charts show the relative CD2 mRNA expression upon BAP1, SUZ12, and CD2 KO from experiments in D and F, compared to WT controls as quantified by real-time quantitative PCR; results from two different sgRNAs targeting each gene are shown. Also see and .

Article Snippet: BAP1 (D7W7O) Rabbit , Cell Signaling Technology , Cat# 13271S.

Techniques: CRISPR, Expressing, Generated, Control, Flow Cytometry, Knock-Out, Fluorescence, Western Blot, Real-time Polymerase Chain Reaction

Journal: iScience

Article Title: CD2 costimulation strength: A key regulator of T cell function and anti-tumor immunity that is epigenetically regulated

doi: 10.1016/j.isci.2025.113977

Figure Lengend Snippet: CD2 expression is coregulated with the expression of markers associated with T cell development, stemness, exhaustion, and metabolism (A) Volcano plot shows p values and fold changes in the expression of genes detected in BAP1 KO Jurkats relative to WT Jurkats. (B and C) Heatmaps of the log2 fold change (FC) expression of selected differentially expressed genes (DEGs) and their corresponding gene names identified in BAP1 KO Jurkats relative to WT control; these are categorized in T cell surface signaling molecules, adhesion molecules, transcription factors (TFs), and solute transporters in (B) and in factors associated with stemness and exhaustion of T cells in (C) categorized in two groups A and B as explained in section. (D and E) Bubble plots shows a selection of enriched pathways determined by performing gene ontology analysis (biological process pathways) in (D) and KEGG pathway analysis in (E) of DEGs in BAP1 KO T cells with a padjust<0.05. The gene count per pathway is represented by the size of the dot and the p value by the color of the dot. (F) A bar chart shows a selection of enriched pathways and the corresponding normalized enrichment score (NES) determined by performing gene set enrichment analysis (GSEA) using the C5 gene sets of the Molecular Signatures Database (MSigDB) and the same DEGs as in (D-E). (G) A selection of enriched gene signatures in BAP1 KO was identified upon GSEA using the C7 immunological signature gene sets in MSigDB. (H) GSEA in BAP1 KO T cells for a progenitor exhausted T cell gene signature generated from. Also see and .

Article Snippet: BAP1 (D7W7O) Rabbit , Cell Signaling Technology , Cat# 13271S.

Techniques: Expressing, Control, Selection, Generated

Journal: iScience

Article Title: CD2 costimulation strength: A key regulator of T cell function and anti-tumor immunity that is epigenetically regulated

doi: 10.1016/j.isci.2025.113977

Figure Lengend Snippet: BAP1 expression levels tune the expression of surface receptors in T cells (A) Flow cytometry contour plots show CD2 − CD3e expression profile during sgRNA BAP1 KO2 in Jurkat T cells at different timepoints of the culture and the gating to define different populations from one of the three representative experiments performed. Double-positive, DP: CD3 + CD2 + , single positive, SP: CD3 − CD2+/high, double-negative DN: CD3 − CD2-/low T cell subsets. (B) A Western blot and corresponding bar charts show the total amount of BAP1 protein normalized to beta-actin (b-actin) expression in experiments as in (A) at endpoint when culture showed no further deviation in ratio of DP, SP, and DN subsets. This is representative of two independent experiments. (C) Flow cytometry histograms (left) of CD2, CD28, CD11a, CD49a, and CD58 in DN, SP, DP BAP1KO2 T cell subsets and WT T cells and the corresponding percentage positive T cells for each marker is shown in bar chart (right) . This is representative of two independent experiments. (D) Right and left bar charts present the percentage of WT and mutant DNA sequences and the percentage of WT and mutant protein sequences with in-frame mutations (MT-IF) and in frameshift-missense mutations as part of the total DNA and protein sequences, respectively. This is shown for the three Jurkat FACSorted populations defined based on their CD2 − CD3e expression profile as described above, DN, SP, and DP. (E) Images of the modeled protein structures of WT BAP1 and mutant A BAP1 (one of the top three mutant protein sequences between the three Jurkat clones DN, SP, and DP; see also C. At the top, it is the model structure of the whole protein sequence, and underneath a zoom-in image of the region of the exon 8 that was targeted by the CRISP-CAS9-sgRNA complex. Also see .

Article Snippet: BAP1 (D7W7O) Rabbit , Cell Signaling Technology , Cat# 13271S.

Techniques: Expressing, Flow Cytometry, Western Blot, Marker, Mutagenesis, Clone Assay, Sequencing

Journal: iScience

Article Title: CD2 costimulation strength: A key regulator of T cell function and anti-tumor immunity that is epigenetically regulated

doi: 10.1016/j.isci.2025.113977

Figure Lengend Snippet: BAP1 is required for full upregulation and sustained expression of CD2, TCR, and PD-1, but not CD28 or CD226, following T cell activation (A) Flow cytometry histograms of CD2, CD28, CD226 and TCR expression in WT and DN BAP1KO Jurkat T cells in resting conditions and two days post-chemical cell activation by-passing the need to engage the TCR-CD3 complex, with low (0.6 ng/mL) and high (20 ng/mL) concentrations of phorbol myristate acetate (PMA), with low (0.1 μg/mL) and high ((1 μg/mL)) concentrations of ionomycin (ION) or a combination of high concentration of PMA with low or high concentration of ION. (B) Same as in (a) but 11–12 days post-chemical activation that includes a resting period of cells cultured in no stimulation conditions. A and B are representative of two independent experiments. The dot lines are aligned on the resting or lowPMA conditions of WT as a visual aid comparison reference. Also see and .

Article Snippet: BAP1 (D7W7O) Rabbit , Cell Signaling Technology , Cat# 13271S.

Techniques: Expressing, Activation Assay, Flow Cytometry, Concentration Assay, Cell Culture, Comparison

Journal: iScience

Article Title: CD2 costimulation strength: A key regulator of T cell function and anti-tumor immunity that is epigenetically regulated

doi: 10.1016/j.isci.2025.113977

Figure Lengend Snippet: Pharmacological inhibition of histone deacetylases partially rescues BAP1 loss-mediated CD2 repression (A) Flow cytometry histograms show the surface CD2 expression in DN BAP1KO T cells in control condition and upon treatment with three different PRC2 inhibitors in a dose-dependent manner, seven days post-initiation of treatment (PRC2i-1, GSK126; PRC2i-2, A-395; PRC2i-3, Tazemetostat). Results are from one/or two independent experiments performed for each inhibitor. (B) Flow cytometry histograms show the surface CD2 expression in DN BAP1KO T cells in control conditions and upon treatment with HDAC inhibitor, LMK235, in a dose-dependent manner, three and seven days post-initiation of treatment; a representative experiment is shown from two independent ones. WT represents CD2 expression in WT T cells in control, untreated conditions. Also see .

Article Snippet: BAP1 (D7W7O) Rabbit , Cell Signaling Technology , Cat# 13271S.

Techniques: Inhibition, Flow Cytometry, Expressing, Control