Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: The predominant methodical workflow in the current study. PDHB: Pyruvate dehydrogenase E1 subunit β; ROC: Receiver operating characteristic; TMB: Tumor mutation burden; MSI: Microsatellite instability; qRT-RCR: Real-time quantitative PCR.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Mutagenesis, Real-time Polymerase Chain Reaction

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Expression levels of pyruvate dehydrogenase E1 subunit β in pan-cancer. A: Comparison of pyruvate dehydrogenase E1 subunit β (PDHB) expression levels in different cancers based on The Cancer Genome Atlas (TCGA) database; B: Expression of PDHB in cancer vs normal tissues in the TCGA database; C: Differential expression of PDHB in cancer and normal tissues in the TCGA joint Genotype Tissue Expression Dataset database; D: Protein levels of PDHB in tumors and normal tissues from the UALCAN database. a P < 0.05, b P < 0.01, c P < 0.001. PDHB: Pyruvate dehydrogenase E1 subunit β; ACC: Adrenocortical carcinoma; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and Endocervical adenocarcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; DLBC: Lymphoid neoplasm diffuse large B-cell lymphoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LAML: Acute myeloid leukemia; LGG: Brain lower grade glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PCPG: Pheochromocytoma and Paraganglioma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine corpus endometrial carcinoma; UCS: Uterine carcinosarcoma; UVM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing, Comparison, Quantitative Proteomics

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Correlation of pyruvate dehydrogenase E1 subunit β expression with tumor stage in multiple cancers and receiver operating characteristic diagnostic analysis. A: Correlation between pyruvate dehydrogenase E1 subunit β (PDHB) gene expression and tumor staging; B: Receiver operating characteristic curve analysis of PDHB in various cancers (AreaUnderROC > 0.7). ACC: Adrenocortical carcinoma; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; ESCA: Esophageal carcinoma; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; PAAD: Pancreatic adenocarcinoma; PRAD: Prostate adenocarcinoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; UVM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing, Diagnostic Assay, Gene Expression

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Mutation frequency of pyruvate dehydrogenase E1 subunit β in pan-cancer. A: Somatic mutation analysis of pyruvate dehydrogenase E1 subunit β (PDHB) in different cancers; B: CBioPortal shows the mutation type and mutation frequency of PDHB sequences.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Mutagenesis

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Correlation analysis of pyruvate dehydrogenase E1 subunit β gene expression with DNA methylation levels in tumor mutation burden, microsatellite instability and pan-cancer. A: Radar plot demonstrating the relationship between tumor mutation burden and pyruvate dehydrogenase E1 subunit β (PDHB) gene expression in various malignancies. Correlation coefficients are indicated by red curves and ranges are indicated by blue values; B: Radar plot showing the relationship between microsatellite instability and PDHB gene expression and various malignancies. Correlation coefficients are shown by blue curves and ranges are shown by green values; C: PDHB methylation levels in the UALCAN database on different cancers. a P < 0.05, b P < 0.01, c P < 0.001. ACC: Adrenocortical carcinoma; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and Endocervical adenocarcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; DLBC: Lymphoid neoplasm diffuse large B-cell lymphoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LAML: Acute myeloid leukemia; LGG: Brain lower grade glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PCPG: Pheochromocytoma and Paraganglioma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine corpus endometrial carcinoma; UCS: Uterine carcinosarcoma; UVM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Gene Expression, DNA Methylation Assay, Mutagenesis, Methylation

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Correlation of pyruvate dehydrogenase E1 subunit β gene expression with stromal and immune scores in different cancers. A: Correlation analysis of pyruvate dehydrogenase E1 subunit β (PDHB) gene expression with immune scores of bladder urothelial carcinoma (BLCA), breast invasive carcinoma (BRCA), brain lower grade glioma (LGG), lung adenocarcinoma (LUAD), lung squamous cell carcinoma, pancreatic adenocarcinoma (PAAD), thyroid carcinoma (THCA), uterine corpus endometrial carcinoma (UCEC); B: Correlation analysis of PDHB gene expression with stromal scores of BLCA, BRCA, LGG, liver hepatocellular carcinoma, LUAD, mesothelioma, ovarian serous cystadenocarcinoma, PAAD, prostate adenocarcinoma, sarcoma, testicular germ cell tumors, THCA, thymoma, UCEC. a P < 0.05, b P < 0.01, c P < 0.001. BRCA: Breast invasive carcinoma; BLCA: Bladder urothelial carcinoma; LGG: Brain lower grade glioma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; PAAD: Pancreatic adenocarcinoma; THCA: Thyroid carcinoma; UCEC: Uterine corpus endometrial carcinoma; BRCA: Breast invasive carcinoma; LIHC: Liver hepatocellular carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PRAD: Prostate adenocarcinoma; SARC: Sarcoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine corpus endometrial carcinoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Gene Expression

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Correlation analysis of pyruvate dehydrogenase E1 subunit β expression and tumor immunity. A: TIMER method to analyze the correlation between pyruvate dehydrogenase E1 subunit β (PDHB) and immune cell infiltration; B: CIBERSORT method to analyze PDHB correlation with immune cell infiltration; C: Co-expression analysis of PDHB with tumor chemokines; D: Co-expression analysis of PDHB with tumor chemokine receptors; E: Co-expression analysis of PDHB with immune checkpoint gene. a P < 0.05, b P < 0.01, c P < 0.001. PDHB: Pyruvate dehydrogenase E1 subunit β. ACC: Adrenocortical carcinoma; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and Endocervical adenocarcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; DLBC: Lymphoid neoplasm diffuse large B-cell lymphoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LAML: Acute myeloid leukemia; LGG: Brain lower grade glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PCPG: Pheochromocytoma and Paraganglioma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine corpus endometrial carcinoma; UCS: Uterine carcinosarcoma; UVM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Pyruvate dehydrogenase E1 subunit β expression levels at the single-cell sequencing level. A and B: CancerSEA database demonstrates the correlation of pyruvate dehydrogenase E1 subunit β (PDHB) expression with multiple biological functions in pan-cancer; C: t-Distributed Stochastic Neighbor Embedding plots showing the distribution of PDHB in ovarian serous cystadenocarcinoma, retinoblastoma, and uveal melanoma at the single-cell level. a P < 0.05, b P < 0.01, c P < 0.001. OV: Ovarian serous cystadenocarcinoma; RB: Retinoblastoma; UM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing, Sequencing

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Enrichment analysis of pyruvate dehydrogenase E1 subunit β-associated genes in pan-cancer. A: Interaction network of pyruvate dehydrogenase E1 subunit β (PDHB)-associated biomarkers derived from the BioGRID database; B: GEPIA2.0 showed that PDHB expression was positively correlated with actin related protein 8 (ACTR8), potassium channel tetramerization domain containing 6 (KCTD6), mutl homolog 1 (MLH1), proteasome 26s subunit, non-ATPase 6 (PSMD6), ribonuclease P/MRP subunit p14 (RPP14), and ubiquitin specific peptidase 19 (USP19) genes; C: Heat map showing PDHB expression positively correlated with 6 genes (ACTR8, KCTD6, MLH1, PSMD6, RPP14, USP19); D: Enrichment analysis of PDHB-related genes. PDHB: Pyruvate dehydrogenase E1 subunit β. ACC: Adrenocortical carcinoma; BLCA: Bladder urothelial carcinoma; BRCA: Breast invasive carcinoma; CESC: Cervical squamous cell carcinoma and Endocervical adenocarcinoma; CHOL: Cholangiocarcinoma; COAD: Colon adenocarcinoma; DLBC: Lymphoid neoplasm diffuse large B-cell lymphoma; ESCA: Esophageal carcinoma; GBM: Glioblastoma multiforme; HNSC: Head and Neck squamous cell carcinoma; KICH: Kidney chromophobe; KIRC: Kidney renal clear cell carcinoma; KIRP: Kidney renal papillary cell carcinoma; LAML: Acute myeloid leukemia; LGG: Brain lower grade glioma; LIHC: Liver hepatocellular carcinoma; LUAD: Lung adenocarcinoma; LUSC: Lung squamous cell carcinoma; MESO: Mesothelioma; OV: Ovarian serous cystadenocarcinoma; PAAD: Pancreatic adenocarcinoma; PCPG: Pheochromocytoma and Paraganglioma; PRAD: Prostate adenocarcinoma; READ: Rectum adenocarcinoma; SKCM: Skin cutaneous melanoma; STAD: Stomach adenocarcinoma; TGCT: Testicular germ cell tumors; THCA: Thyroid carcinoma; THYM: Thymoma; UCEC: Uterine corpus endometrial carcinoma; UCS: Uterine carcinosarcoma; UVM: Uveal melanoma.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Derivative Assay, Expressing, Ubiquitin Proteomics

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Drug sensitivity analysis. Correlation of IC 50 with pyruvate dehydrogenase E1 subunit β expression for different drugs. A: Chelerythrine; B: Nelarabine; C: Fludarabine; D: Fenretinide; E: Lapachone; F: Vorinostat; G: Dasatinib; H: Dolastatin 10. PDHB: Pyruvate dehydrogenase E1 subunit β.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Results of pyruvate dehydrogenase E1 subunit β expression validation. A: Pyruvate dehydrogenase E1 subunit β (PDHB) expression in the human normal hepatocyte cell line (L-O2) and human hepatoma cell lines (SMMC-7721, HepG2, Huh7, H-97); B: PDHB expression in the human normal gastric mucosal cell line (GES-1) and human gastric cancer cell lines (HGC-27, MGC-803, MKN-45); C: PDHB expression in the human normal colonic epithelial cell line (NCM460) and human colon cancer cell lines (SW620, HCT116); D: PDHB expression in the human normal breast cell line (MCF-10A) and breast cancer cell lines (MDA-MB-231, MCF-7); E: PDHB expression in the human normal prostate cell line (RWPE-2) and prostate cancer cell lines (PC-3, 22Rv1 and DU145); F: Validation of PDHB protein expression in the L-O2 and hepatoma cell lines (HepG2, SMMC-7721, Huh7, H-97); G: Quantitative plots; H: Validation of PDHB protein expression in the GES-1 and gastric cancer cell lines (MKN-45, AGS, HGC-27, MGC-803); I: Quantitative plots. a P < 0.05, b P < 0.01, c P < 0.001. PDHB: Pyruvate dehydrogenase E1 subunit β; L-O2: Human normal hepatocyte cell line; GES-1: Gastric mucosal cells; NS: Not significant.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Expressing, Biomarker Discovery

Journal: World Journal of Gastrointestinal Oncology

Article Title: Analysis of the potential biological value of pyruvate dehydrogenase E1 subunit β in human cancer

doi: 10.4251/wjgo.v16.i1.144

Figure Lengend Snippet: Effects of siRNA-pyruvate dehydrogenase E1 subunit β on proliferation, migration and invasion of Huh7 hepatoma cells. A: Transfection efficiency of siRNA-pyruvate dehydrogenase E1 subunit β (PDHB) in Huh7 cell lines; B: The relative expression of mRNA reflects the efficiency of siRNA-PDHB transfection; C: siRNA-PDHB transfection efficiency by protein expression level; D: The CCK-8 method detected the proliferation capacity of Huh7 cell lines; E: Colony formation assay to determine the proliferation capacity of Huh7 cell lines; F: The histogram shows the number of colonies formed; G: Cell scratch assay to detect the migration capacity of Huh7 cell lines; H: Histogram of quantification of cell scratch assay results; I: Transwell method was used to detect the migration and invasion capacity of Huh7 cell lines; J: The histogram shows the number of migrating cells; K: The histogram shows the number of invading cells. a P < 0.05, b P < 0.01, c P < 0.001. PDHB: Pyruvate dehydrogenase E1 subunit β.

Article Snippet: The membranes were incubated with primary antibodies of PDHB (Proteintech Group, Wuhan) and β-Tubulin (Boster, Wuhan) overnight on a 4 °C shaker, followed by incubation with secondary antibodies for 1 h, three rinses with TBST rinse solution for 10 min each time and then with an enhanced chemiluminescence kit (Boster, Wuhan) to visualize the blots.

Techniques: Migration, Transfection, Expressing, CCK-8 Assay, Colony Assay, Wound Healing Assay

Journal: Journal of Hematology & Oncology

Article Title: The LINC00623/NAT10 signaling axis promotes pancreatic cancer progression by remodeling ac4C modification of mRNA

doi: 10.1186/s13045-022-01338-9

Figure Lengend Snippet: NAT10 functions as a downstream mediator of LINC00623by remodeling N4-acetylcytidine (ac4C) modification of mRNA. a Representative images of IHC staining with an anti-NAT10 antibody in PDAC, pancreatic intraepithelial neoplasia (PanIN) or matched adjacent normal pancreatic tissues (NP). b The mRNA level of LINC00623 was positively correlated with the protein level of NAT10 in PDAC tissues ( n = 93). c Kaplan‒Meier survival curve of two groups of patients with PDAC ( n = 93): NAT10 (+), patients with high NAT10 expression; NAT10 (-), patients with low NAT10 expression. The expression of NAT10 was determined by IHC staining. d Schematic diagram of the effects of NAT10 on the stability and translation efficiency of mRNA by catalyzing ac4C modification. e Metagene profile showing the distribution of NAT10 peaks across full-length transcripts containing the 5′UTR, CDS, and 3′UTR. BxPC-3 cell lysates were used for the NAT10 RIP assay. f Metagene profile showing the distribution of ac4C peaks across full-length transcripts containing the 5′UTR, CDS, and 3′UTR. BxPC-3 cell lysates were also used for acRIP. g Venn diagram showing the downstream target genes regulated by NAT10 via ac4C modification in BxPC-3 cells. Group 1: The gene set enriched in NAT10 RIP-seq (RIP-seq); Group 2: The set of target genes enriched in parental cells but not in NAT10-silenced cells according to acRIP-seq (acRIP-seq); Group 3: The genes upregulated or downregulated in NAT10-silenced cells compared with control cells (RNA-seq); Group 4: The mRNA transcripts displaying differences in translation efficiency in NAT10-silenced cells (Ribo-seq). h Functional annotation and pathway enrichment analysis of the predicted downstream target genes of NAT10 according to the Metascape database. i The relative mRNA levels of NAT10, KCNN4, LAMB3 and PHGDH were measured by RT-qPCR. j The protein levels of KCNN4, LAMB3 and PHGDH were determined by Western blotting. k RT-qPCR was used to detect the relative enrichment of KCNN4 , LAMB3 and PHGDH mRNAs in NAT10 RIP products. l RT-qPCR was used to detect the relative enrichment of KCNN4, LAMB3 and PHGDH mRNAs in acRIP products. i – l BxPC-3 cells were transfected with NAT10 silencing and control plasmids. Cell lysates were harvested for RIP assays. IgG was used as the isotype control. The values indicate the mean ± SD of three independent experiments. P values are shown as * P < 0.05; ** P < 0.01; *** P < 0.001. Independent Student’s t test

Article Snippet: The sections were then incubated with specific primary antibodies against PCNA (1:200 dilution, ab15497, Abcam, Cambridge, UK), NAT10 (1:500 dilution, ab194297, Abcam), Vimentin (1:500 dilution, ab92547, Abcam), E-cadherin (1:500 dilution, 20874-1-AP, Proteintech), N-cadherin (1:100 dilution, ab76011, Abcam), LAMB3 (1:500 dilution, 26795-1-AP, Proteintech), PHGDH (1:500 dilution, 14719-1-AP, Proteintech) and KCNN4 (1:200 dilution, 23271-1-AP, Proteintech) at 4 °C overnight.

Techniques: Modification, Immunohistochemistry, Expressing, Control, RNA Sequencing, Functional Assay, Quantitative RT-PCR, Western Blot, Transfection

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 1 Immunoproteasome expression profile in muscle-invasive bladder cancer (MIBC). A Expression of immunoproteasome subunits PSMB8, PSMB9 and PSMB10 in pan-tumor tissues and corresponding normal tissues derived from the TCGA dataset. Red boxes outline upregulation of PSMB8, PSMB9 and PSMB10 in bladder cancer tissues in contrast to normal tissues. Data are expressed as individual spots per subject with mean of the logarithm of transcripts per million. *p < 0.05, **p < 0.01, ***p < 0.001. B Expression of PSMB8, PSMB9 and PSMB10 in MIBC (n = 369) and normal tissues (n = 19) from the TCGA cohort. Data are expressed as individual spots per subject with mean ± SEM of the logarithm of transcripts per million. P-values are indicated in each graph. C Immunohistochemistry staining scores of PSMB8, PSMB9 and PSMB10 in MIBC (n = 67) and normal tissues (n = 18) derived from the CQUCH cohort. Data are expressed as individual spots per subject with mean ± SEM of each group. P-values are indicated in each graph. D Representative positive and negative immunohistochemistry stainings of PSMB8, PSMB9 and PSMB10 in MIBC and normal tissues derived from the CQUCH cohort. Scale bar: 40 μm. Positive stainings are divided into low and high expression by an average immunohistochemistry staining score

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing, Derivative Assay, Immunohistochemistry, Staining

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 2 Association of the expression of immunoproteasome subunits with survival prognosis in MIBC patients. A Kaplan–Meier curve of progression-free survival (upper panel) and overall survival (lower panel) for MIBC patients in the CQUCH cohort with high and low expression of PSMB8, PSMB9 and PSMB10. B Kaplan–Meier curve of progression-free survival (upper panel) and overall survival (lower panel) for MIBC patients in the TCGA cohort with high and low expression of PSMB8, PSMB9 and PSMB10

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 3 Association of the expression of immunoproteasome subunits with survival prognosis in MIBC patients receiving immunotherapy. A Kaplan–Meier curve of overall survival for MIBC patients receiving immune checkpoint inhibitor treatment in the IMvigor210 cohort with high and low expression of PSMB8, PSMB9 and PSMB10. B Kaplan–Meier curve of progression-free survival (upper panel) and overall survival (lower panel) for MIBC patients receiving immune checkpoint inhibitor treatment in the CQUCH cohort with high and low expression of PSMB8, PSMB9 and PSMB10

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 4 Effect of immunotherapy (IMT) on survival prognosis in MIBC patients with different expression levels of immunoproteasome subunits. A Kaplan–Meier curve of progression-free survival (upper panel) and overall survival (lower panel) for MIBC patients receiving IMT or not receiving (non-IMT) immune checkpoint inhibitor treatment in the CQUCH cohort with high expression of PSMB8, PSMB9 and PSMB10. B Kaplan–Meier curve of progression-free survival (upper panel) and overall survival (lower panel) for MIBC patients receiving IMT or not receiving (non-IMT) immune checkpoint inhibitor treatment in the CQUCH cohort with low expression of PSMB8, PSMB9 and PSMB10

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 6 Association of immunoproteasome subunits with inflammatory factors in MIBC. Expression correlation heatmap of the association of IFN-γ and TNF with the immunoproteasome subunits PSMB8, PSMB9 and PSMB10 in MIBC of the TCGA cohort (A) and the IMvigor210 cohort (B). Correlation coefficient between each two molecules is written in each square. Color bar on the right side of each heatmap shows the correlation coefficient. Positive correlation is shown in red, negative and blue. C, D Kaplan–Meier curve of overall survival of MIBC patients receiving immune checkpoint inhibitor treatment in the IMvigor210 cohort with high and low expression of IFN-γ or TNF

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 7 Association of immunoproteasome subunits with tumor infiltrating immune cells in MIBC. Correlation lollipop charts of tumor infiltrating immune cells which were associated with the expression of the immunoproteasome subunits PSMB8, PSMB9 and PSMB10 in MIBC of the TCGA cohort (A) and the IMvigor210 cohort (B). Lollipop size shows the correlation coefficient between each infiltrating immune cell type and each immunoproteasome subunit. P values were labeled on the right side of each chart. Values of P < 0.05 were considered statistically significant and marked in red

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques: Expressing, Labeling

Journal: Journal of translational medicine

Article Title: Immunoproteasome subunits are novel signatures for predicting efficacy of immunotherapy in muscle invasive bladder cancer.

doi: 10.1186/s12967-025-06207-w

Figure Lengend Snippet: Fig. 8 Association of immunoproteasome subunits with different immune-related functions and signaling in MIBC. A GO analysis of the association of the immunoproteasome subunits PSMB8, PSMB9 and PSMB10 with immune-related functions in MIBC of the TCGA cohort. Color bar shows the p-value on the right side of each chart. The number of related genes were shown as the length of the column of each chart. B KEGG analysis of the association of the immunoproteasome subunits PSMB8, PSMB9 and PSMB10 with immune-related signaling in MIBC of the TCGA cohort. Color bar shows the p-value on the right side of each chart. The number of related genes were shown by dot size. C GSEA analysis of the association of the immunoproteasome subunits PSMB8, PSMB9 and PSMB10 with different immune cell functions in MIBC of the TCGA cohort

Article Snippet: Following incubation in phosphate-buffered saline containing 10% species-appropriate normal serum to block non-specific binding at room temperature for 1 h, sections were incubated in a humidified chamber with primary antibodies against PSMB8 (1:100; proteintech, Wuhan, China), PSMB9 (1:100; proteintech), PSMB10 (1:100; proteintech) and PD-L1 (1:100; proteintech) using isotype-matched IgGs as negative controls at 4 °C overnight.

Techniques:

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

Article Title: Role of IL-6-IL-27 Complex in Host Antiviral Immune Response.

doi: 10.4049/jimmunol.2100179

Figure Lengend Snippet: FIGURE 1. Interactions between the subunits of IL-6 and IL-27 in vivo and in vitro. (AC) CoIP and immunoblotting of serum samples were performed with the indicated Abs. IL-6 interacted with IL-27A (A), IL-6 interacted with EBi3 (B), and IL-27A interacted with EBi3 (C). (DG) HEK293T cells were transfected with the indicated plasmids for 24 h. CoIP and immunoblotting were performed with the indicated Abs. IL-6-3HA interacted with IL-27A-V5 (D), IL-6-3HA interacted with EBi3-Myc (E), IL-27A-V5 interacted with EBi3-Myc (F), and IL-6-3HA interacted with IL-27-V5 (G). (H) Colocalization of IL-6 and IL-27 was detected by confocal microscopy. A549 cells were transfected with IL-6-eGFP-KDEL and IL-27-DsRed-KDEL for 24 h, and the nuclei were stained with DAPI before observation using confocal microscopy. All experiments were repeated at least three times with consistent results.

Article Snippet: Abs against V5 tag (66007-1-Ig), EBi3 (12371-1-AP), myxovirus resistance A (MxA; 13750-1-AP), MAVS (14341-1-AP), TGFb-activated kinase 1 (12330-2-AP), IRF3 (11312-1-AP), NF-kB p65 (10745- 1-AP), NF-kB p50 (14220-1-AP), Lamin A/C (10298-1-AP), GAPDH (60004-1-Ig), and b-actin (60008-1-Ig) were purchased from ProteinTech Group (Wuhan, China).

Techniques: In Vivo, In Vitro, Western Blot, Transfection, Confocal Microscopy, Staining

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

Article Title: Role of IL-6-IL-27 Complex in Host Antiviral Immune Response.

doi: 10.4049/jimmunol.2100179

Figure Lengend Snippet: FIGURE 2. Construction of the IL-6IL-27 complex and its antiviral activity. (A) A schematic of the IL-6IL-27 construction via flexible self-cleaved linker is shown. Immunoblotting analysis of IL-6, EBi3, IL-27A, and b-actin of HEK293T cells transfected with empty vector pcDNA3.1(1) or IL-6IL-27 complex expression plasmids for 24 h. (B) A549 cells were transfected with indicated plasmids for 24 h followed by H1N1 infection (MOI = 1) for 12 h. The NP-specific mRNA, cRNA, and vRNA levels were measured using QRT-PCR. (C) RD cells were transfected with the indicated plasmids for 24 h fol- lowed by EV71 infection (MOI = 1) for 24 h. The VP1 mRNA levels were measured using QRT-PCR. (D) Vero cells were (Figure legend continues)

Article Snippet: Abs against V5 tag (66007-1-Ig), EBi3 (12371-1-AP), myxovirus resistance A (MxA; 13750-1-AP), MAVS (14341-1-AP), TGFb-activated kinase 1 (12330-2-AP), IRF3 (11312-1-AP), NF-kB p65 (10745- 1-AP), NF-kB p50 (14220-1-AP), Lamin A/C (10298-1-AP), GAPDH (60004-1-Ig), and b-actin (60008-1-Ig) were purchased from ProteinTech Group (Wuhan, China).

Techniques: Activity Assay, Western Blot, Transfection, Plasmid Preparation, Expressing, Infection, Quantitative RT-PCR

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

Article Title: Role of IL-6-IL-27 Complex in Host Antiviral Immune Response.

doi: 10.4049/jimmunol.2100179

Figure Lengend Snippet: FIGURE 5. The IL-6IL-27 complex interacts with MAVS. (AC) A549 cells were transfected with increasing amounts of the indicated expression plas- mids (wedge; 100, 200, and 300 ng) of the IL-6IL-27 complex expression plasmid and luciferase reporter plasmids containing the IFN-b (A), NF-kB (B), and ISRE (C) promoter for 24 h followed by VSV infection (MOI = 1) for 24 h. Reporter assays were performed. pRL-TK was used as an internal control. (DI) HEK293T cells were transfected with the indicated plasmids for 24 h. CoIP and immunoblotting were performed with the indicated Abs. IL-6-3HA interacted with Flag-MAVS (D), IL-27A-V5 interacted with Flag-MAVS (E), EBi3-Myc interacted with Flag-MAVS (F), IL-6-HA interacted with Flag- TBK1 (G), IL-27A-V5 interacted with Flag-TBK1 (H), and EBi3-Myc interacted with Flag-TBK1 (I). All experiments were repeated at least three times with consistent results.

Article Snippet: Abs against V5 tag (66007-1-Ig), EBi3 (12371-1-AP), myxovirus resistance A (MxA; 13750-1-AP), MAVS (14341-1-AP), TGFb-activated kinase 1 (12330-2-AP), IRF3 (11312-1-AP), NF-kB p65 (10745- 1-AP), NF-kB p50 (14220-1-AP), Lamin A/C (10298-1-AP), GAPDH (60004-1-Ig), and b-actin (60008-1-Ig) were purchased from ProteinTech Group (Wuhan, China).

Techniques: Transfection, Expressing, Plasmid Preparation, Luciferase, Infection, Control, Western Blot