Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 1. The relative expression of MBD3 in pan-cancer and COAD. (A,B) Different types of tumors compared with normal tissues in TCGA and GTEx databases. (C,D) Relative expression of MBD3 in colon cancer and colon cells. (E) Relative expression of MBD3 in single cells of COAD (* p < 0.05, ** p < 0.01, *** p < 0.001).

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Expressing

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 2. Clinical indicators of MBD3 in colon cancer. (A) Overall survival analyses of MBD3 in COAD. (B) Risk score of MBD3 in COAD. (C,D) Nomogram and calibration curves for prediction of one-, two-, and three-year overall survival rates of patients with COAD with high expression of MBD3. (E) Prognostic values of MBD3 expression by univariate analysis in COAD. (F) Prognostic values of MBD3 expression by multivariate analysis in COAD.

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Expressing

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 3. The immune mutational landscape, MSI and MATH of MBD3 in pan-cancer. (A) Immune mutational landscape of MBD3 in pan-cancer. (B,C) MSI and MATH of MBD3 in pan-cancer.

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques:

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 4. Function enrichment of MBD3 in single cells and DEGs. (A,B) Relationship between MBD3 expression and different functional states in tumors explored by the CancerSEA tool. * p < 0.05, ** p < 0.01. (C–E) Volcano plot of logFc > 1.5 and the top ten related differentially expressed genes of MBD3 from the TCGA database. (F–H) KEGG, GO and GSEA analysis of MBD3 and their co- expression genes.

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Expressing, Functional Assay

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 5. Representative images of MBD3 expression in COAD tissues and their matched paracancer- ous tissues. Original magnifications 20× and 40× (inset panels). (A–C) were representative images.

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Expressing

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 6. Cytological experiments regarding MBD3 (ns, (D) * p ≥0.05; (E) * p < 0.05; (H,L) * p < 0.01; (J,N) * p < 0.001). (A,D) The relative expression of MBD3 in COAD cell lines. (B,C,F) Plasmid transfection efficiency of MBD3 in COAD cell lines. (G) Cell migration assay of MBD3 in SW620, HCT116, SW480 and CaCO2. (H) Cell invasion assay of MBD3 in SW620, HCT116, SW480 and CaCO2. (I–L) show enhanced ability of MBD3 in COAD.

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Expressing, Plasmid Preparation, Transfection, Cell Migration Assay, Invasion Assay

Journal: Cancers

Article Title: MBD3 as a Potential Biomarker for Colon Cancer: Implications for Epithelial-Mesenchymal Transition (EMT) Pathways.

doi: 10.3390/cancers15123185

Figure Lengend Snippet: Figure 7. Effect of MBD3 on colon cancer proliferation and tumor formation experiment in nude mice. (A–D) Proliferative capacity of MBD3 in COAD. (E–H) Clone formation assay of MBD3 in COAD. (I–L) Tumor formation in nude mice (* p < 0.05).

Article Snippet: After deparaffinization, rehydration and microwave antigen retrieval, the slides were incubated with MBD3 (Proteintech Cat No. 14258-1-AP) antibody at 1:800 dilution at 4 ◦C overnight.

Techniques: Tube Formation Assay

Journal: Scientific Reports

Article Title: Empagliflozin reduces liver fibrosis by restoring catechol- O -methyltransferase activity associated with magnesium levels

doi: 10.1038/s41598-025-12813-x

Figure Lengend Snippet: Empagliflozin (EMPA) increased liver catechol- O -methyltransferase (COMT) activity and ameliorated liver fibrosis in diabetic mice. ( a ) A methyltransferase assay kit, which detects the S -adenosylhomocysteine (SAH) reaction product, was used to measure the liver SAH concentration in db/ +, db/db control and db/db EMPA mice. Norepinephrine (NE) was used as a substrate, and tolcapone was used as a COMT inhibitor. ( b ) The difference in liver SAH between samples with and without NE (ΔSAH), which represents liver COMT activity, was calculated. ( c ) Liver membrane-bound (MB), soluble (S), and total COMT protein levels were analysed using western blotting. The data were normalised to those of β-actin. Original blots are presented in Supplementary Fig. S5. ( d ) Immunohistochemistry analysis was performed on the liver. The scale bar represents 200 µm. ( e ) Sirius red staining was performed on the liver. The scale bar represents 100 µm. ( f ) Liver α-smooth muscle actin (αSMA) protein levels were analysed using western blotting. Original blots are presented in Supplementary Fig. S6. db/ +, n = 5. db/db control, n = 6. db/db EMPA, n = 6. The data are presented as the mean ± SEM. The data were analysed using one-way ANOVA followed by Tukey’s test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: Deparaffinized sections were subjected to COMT staining using an anti-COMT antibody (Proteintech, Cat# 14754-1-AP, Rosemont, IL).

Techniques: Activity Assay, Concentration Assay, Control, Membrane, Western Blot, Immunohistochemistry, Staining

Journal: BMC Cancer

Article Title: Identifying NDUFB2 as a prognostic biomarker for glioblastoma through an exploratory analysis of an anesthesia-related gene signature

doi: 10.1186/s12885-025-15312-4

Figure Lengend Snippet: Flowchart of the study. The diagram illustrates the comprehensive workflow of this study. The process includes (1) data acquisition from public databases, (2) identification of differentially expressed anesthesia-related genes (ARGs) between glioblastoma (GBM) and normal tissues, (3) functional enrichment analyses (GO and KEGG), (4) consensus clustering to identify molecular subgroups, (5) construction and validation of an ARG-based prognostic model, (6) identification and multi-level analysis of the hub gene NDUFB2, and (7) experimental validation of NDUFB2 expression

Article Snippet: The samples, embedded in paraffin, were treated with NDUFB2 antibody (1:200, Proteintech, Cat# 17614-1-AP) overnight following deparaffinization and antigen retrieval via microwave.

Techniques: Functional Assay, Biomarker Discovery, Expressing

Journal: BMC Cancer

Article Title: Identifying NDUFB2 as a prognostic biomarker for glioblastoma through an exploratory analysis of an anesthesia-related gene signature

doi: 10.1186/s12885-025-15312-4

Figure Lengend Snippet: Identification and characterization of NDUFB2 as a hub gene. A PPI network highlighting the top 15 hub genes identified by the MCC algorithm in cytoHubba. NDUFB2 was identified as the key hub gene present in the prognostic model. B Pan-cancer analysis showing the hazard ratio (HR) of NDUFB2 across various cancers, indicating its risk-associated role in GBM. C Boxplot of NDUFB2 expression in GBM tumors vs. normal tissues from the TCGA and GTEx databases ( p = 0.017, Wilcoxon test). D Boxplot of NDUFB2 expression in gliomas vs. normal tissues ( p = 0.014, Wilcoxon test). E , F Kaplan-Meier curves showing that high NDUFB2 expression is associated with poorer ( E ) overall survival (OS) and ( F ) progression-free survival (PFS) in GBM patients ( n = 150, log-rank test, p < 0.001 for both). G Correlation plot illustrating the relationship between NDUFB2 expression and Tumor Inflammation Signature (TIP) scores. H Bubble plot showing the correlation between NDUFB2 expression and the infiltration levels of various immune cells. The size of the bubble represents the p -value, and the color represents the correlation coefficient. I Scatter plot showing the specific correlation between NDUFB2 expression and macrophage infiltration

Article Snippet: The samples, embedded in paraffin, were treated with NDUFB2 antibody (1:200, Proteintech, Cat# 17614-1-AP) overnight following deparaffinization and antigen retrieval via microwave.

Techniques: Expressing

Journal: BMC Cancer

Article Title: Identifying NDUFB2 as a prognostic biomarker for glioblastoma through an exploratory analysis of an anesthesia-related gene signature

doi: 10.1186/s12885-025-15312-4

Figure Lengend Snippet: Single-cell and drug sensitivity analysis of NDUFB2. A t-SNE plot of single cells from GBM tissue (dataset GSE102130 ), colored by identified cell type. B-F Violin and t-SNE plots showing NDUFB2 expression is predominantly localized in malignant tumor cells compared to other cell types in the tumor microenvironment ( p < 0.001). G-J Scatter plots showing the correlation between NDUFB2 expression and drug sensitivity (IC50) from GDSC, CTRP, and PRISM databases. A positive correlation indicates resistance (all p < 0.001). K ROC curves showing the AUC values for NDUFB2 expression in predicting immunotherapy response in datasets GSE126044 and GSE67501 . L ROC curve for NDUFB2 expression predicting immunotherapy response in the GBM dataset PRJNA482620 (AUC = 0.623, 95% CI = 0.415–0.803). M Boxplot of NDUFB2 expression in responders vs. non-responders to immunotherapy from the PRJNA482620 dataset ( p = 0.231, Wilcoxon test)

Article Snippet: The samples, embedded in paraffin, were treated with NDUFB2 antibody (1:200, Proteintech, Cat# 17614-1-AP) overnight following deparaffinization and antigen retrieval via microwave.

Techniques: Expressing

Journal: BMC Cancer

Article Title: Identifying NDUFB2 as a prognostic biomarker for glioblastoma through an exploratory analysis of an anesthesia-related gene signature

doi: 10.1186/s12885-025-15312-4

Figure Lengend Snippet: Spatial transcriptome analysis of NDUFB2 in GBM. A-J Spatial distribution plots showing the abundance of ten different deconvoluted cell types across the GBM tissue section. Color intensity indicates cell abundance per spot. K Spatial plot showing the predominant cell type assigned to each spot after deconvolution. L Spatial feature plot showing the distribution and abundance of macrophages. M Spatial feature plot showing the expression level of NDUFB2 , primarily localized in tumor cell regions. N Scatter plot demonstrating a significant inverse spatial correlation between NDUFB2 expression and macrophage abundance per spot (Pearson’s r = −0.4, p < 0.001)

Article Snippet: The samples, embedded in paraffin, were treated with NDUFB2 antibody (1:200, Proteintech, Cat# 17614-1-AP) overnight following deparaffinization and antigen retrieval via microwave.

Techniques: Expressing

Journal: BMC Cancer

Article Title: Identifying NDUFB2 as a prognostic biomarker for glioblastoma through an exploratory analysis of an anesthesia-related gene signature

doi: 10.1186/s12885-025-15312-4

Figure Lengend Snippet: Experimental validation of NDUFB2 expression. A RT-qPCR analysis of NDUFB2 mRNA levels in GBM tissues ( n = 4) and non-tumorous brain tissues ( n = 4). B Representative Western blot images showing NDUFB2 protein expression in GBM ( n = 4) and normal tissue ( n = 4) samples. GAPDH was used as a loading control. (C) Quantification of Western blot band intensities from ( B ). D , E Representative immunohistochemistry (IHC) images from the Human Protein Atlas (HPA) database showing NDUFB2 protein staining in normal brain and GBM tissue. F , G Validation of NDUFB2 protein expression in an in-house cohort of 22 GBM patients (GXMU-cohort). Scale bars = 200 μm. H Western blot analysis confirmed the knockdown efficiency of NDUFB2 protein expression in U251 cells transfected with si-NC, si-NDUFB2#1, si-NDUFB2#2, and si-NDUFB2#3. I Representative images from the Transwell assays showing cells that invaded through the Matrigel-coated membrane (Invasion) and migrated through the uncoated membrane (Migration). Cells were stained with crystal violet. (Scale bar = 100 μm). J Quantitative analysis of the number of invaded and migrated cells per field of view. The results demonstrate a significant reduction in both invasion and migration in the si-NDUFB2#1 group compared to the si-NC group. K Representative images from the wound healing assay at 0 h and 24 h after scratching the confluent monolayer of U251 cells transfected with si-NC. L Representative images from the wound healing assay at 0 h and 24 h after scratching the confluent monolayer of U251 cells transfected with si-NDUFB2#1

Article Snippet: The samples, embedded in paraffin, were treated with NDUFB2 antibody (1:200, Proteintech, Cat# 17614-1-AP) overnight following deparaffinization and antigen retrieval via microwave.

Techniques: Biomarker Discovery, Expressing, Quantitative RT-PCR, Western Blot, Control, Immunohistochemistry, Staining, Knockdown, Transfection, Membrane, Migration, Wound Healing Assay

Journal: Translational Oncology

Article Title: MTHFD1L, A Folate Cycle Enzyme, Is Involved in Progression of Colorectal Cancer ☆ ☆☆

doi: 10.1016/j.tranon.2019.07.011

Figure Lengend Snippet: Elevated expression of MTHFD1L in CRC tissues. (A) Gene expression analysis of CRC datasets showed upregulated expression of MTHFD1L in CRC tissues . (B) Dataset from Skrzypczak et al., 2010 showing overexpression of MTHFD1L in CRCs (n = 36) as compared to normal colon tissues (n = 24). (C) TCGA data acquired from UALCAN with MTHFD1L expression in normal colon (n = 41) and CRCs tissues (n = 286). (D) qRT-PCR analysis showing mRNA levels of MTHFD1L in CRCs (n = 110) and matched adjacent non-cancerous tissue (n = 110). (E) Stage-wise expression of MTHFD1L transcripts from UALCAN in CRC tissues Stage I (n = 45), Stage II (n = 110), Stage (n = 80), and Stage IV (n = 39) and normal (n = 41). (F) MTHFD1L mRNA expression in paired samples from different stages of CRC [(Stage 1 (n = 18), Stage 2 (n = 30), Stage 3 (n = 42), and Stage 4 (n = 20)].

Article Snippet: Deparaffinization, rehydration, antigen retrieval, reduction of endogenous activity, and blocking steps were performed sequentially before probing with an antibody against MTHFD1L (Cat# 16113–1-AP, Proteintech, Irvine, CA).

Techniques: Expressing, Gene Expression, Over Expression, Quantitative RT-PCR

Journal: Translational Oncology

Article Title: MTHFD1L, A Folate Cycle Enzyme, Is Involved in Progression of Colorectal Cancer ☆ ☆☆

doi: 10.1016/j.tranon.2019.07.011

Figure Lengend Snippet: MTHFD1L protein overexpression in CRC tissues. (A) Immunoblot analysis to showing MTHFD1L protein expression in different stages of CRCs by probing of lysates of paired CRCs and matched adjacent non-cancerous tissues with MTHFD1L antibody. β-Actin was used as a loading control. (B) Photographs of MTHFD1L immunostaining using MTHFD1L antibody in tissue containing CRC cells and normal cells.

Article Snippet: Deparaffinization, rehydration, antigen retrieval, reduction of endogenous activity, and blocking steps were performed sequentially before probing with an antibody against MTHFD1L (Cat# 16113–1-AP, Proteintech, Irvine, CA).

Techniques: Over Expression, Western Blot, Expressing, Control, Immunostaining

Journal: Translational Oncology

Article Title: MTHFD1L, A Folate Cycle Enzyme, Is Involved in Progression of Colorectal Cancer ☆ ☆☆

doi: 10.1016/j.tranon.2019.07.011

Figure Lengend Snippet: Silencing of MTHFD1L reduced malignant phenotypes of colon cancer. (A) Colon cancer cells, SW480 and HT29, were transiently transfected with MTHFD1L siRNA, and immunoblot analyses were performed to show knockdown of MTHFD1L. (B) Proliferation assay of cells transfected with MTHFD1L siRNA or control siRNA at 2, 4, and 6 days (∗ P < .001). (C) Representative images of colony formation after transfection of cells with control or MTHFD1L siRNA. (D) Cells transfected with MTHFD1L siRNA or control siRNA and plated in 8-μm pore invasion chambers with Matrigel. After 48 h, cells that invaded through the pores were fixed and stained. Photographs of invaded cells are shown. (E) Spheroid formation assay after transfection of MTHFD1L siRNA or control siRNA. (F) Wound healing assay after transfection with MTHFD1L siRNA or control siRNA.

Article Snippet: Deparaffinization, rehydration, antigen retrieval, reduction of endogenous activity, and blocking steps were performed sequentially before probing with an antibody against MTHFD1L (Cat# 16113–1-AP, Proteintech, Irvine, CA).

Techniques: Transfection, Western Blot, Knockdown, Proliferation Assay, Control, Staining, Tube Formation Assay, Wound Healing Assay

Journal: Frontiers in Immunology

Article Title: Integrated bioinformatic analysis of mitochondrial metabolism-related genes in acute myeloid leukemia

doi: 10.3389/fimmu.2023.1120670

Figure Lengend Snippet: Cox regression to prognosis MMRGs associated with OS in TCGA-LAML.

Article Snippet: Tissue sections were deparaffinized and rehydrated, and then stained with H&E, or incubated with antibodies, specifically ECHS1 (Cat No. 11305-1-AP; proteintech, China), and NUDFS2 (Cat No. R27071; Zenbioscience, China).

Techniques:

Journal: Frontiers in Immunology

Article Title: Integrated bioinformatic analysis of mitochondrial metabolism-related genes in acute myeloid leukemia

doi: 10.3389/fimmu.2023.1120670

Figure Lengend Snippet: Validation of the expression levels of key MMRGs by IHC. A-B. H&E and ECHS1 (A) and NDUFS2 (B) IHC staining of BM samples from nonneoplastic patients and AML patients. Original magnification, 400X. (C-D) . Statistics of ECHS1 (C) and NDUFS2 (D) mean IOD from IHC images of nonneoplastic patients (n = 10) and AML patients (n = 10). ****P-value< 0.0001.

Article Snippet: Tissue sections were deparaffinized and rehydrated, and then stained with H&E, or incubated with antibodies, specifically ECHS1 (Cat No. 11305-1-AP; proteintech, China), and NUDFS2 (Cat No. R27071; Zenbioscience, China).

Techniques: Biomarker Discovery, Expressing, Immunohistochemistry

Journal: Clinical Epigenetics

Article Title: Promoter methylation changes in ALOX12 and AIRE1 : novel epigenetic markers for atherosclerosis

doi: 10.1186/s13148-020-00846-0

Figure Lengend Snippet: Immunofluorescence staining for AIRE1 and infiltrated CD4(+)-T cells and CD14(+)-monocytes in atherosclerotic plaque and non-plaque intima of common carotid artery of a 54-year-old man. White arrow, cells co-stained with CD14 and AIRE1 antibodies

Article Snippet: After deparaffinization in xylene and rehydration in an alcohol series, the sections were incubated overnight at 4 °C with primary antibodies including CD4 (Cat. No. ab133616, Abcam, 1:100) for T cell, CD14 (Cat. No. 17000-1-AP, Proteintech, 1:100) for monocytes, and ALOX12 (Cat. No. ab167372, Abcam, 1:100) and AIRE1 (Cat. No. sc-373703, Santa cruz biotechnology, 1:100) for the target genes.

Techniques: Immunofluorescence, Staining

Journal: Clinical Epigenetics

Article Title: Promoter methylation changes in ALOX12 and AIRE1 : novel epigenetic markers for atherosclerosis

doi: 10.1186/s13148-020-00846-0

Figure Lengend Snippet: Immunofluorescence staining for ALOX12 and infiltrated CD4(+)-T cells and CD14(+)-monocytes in atherosclerotic plaque and non-plaque intima of common carotid artery of a 54-year-old man. White arrow, cells co-stained with CD14 and ALOX12 antibodies

Article Snippet: After deparaffinization in xylene and rehydration in an alcohol series, the sections were incubated overnight at 4 °C with primary antibodies including CD4 (Cat. No. ab133616, Abcam, 1:100) for T cell, CD14 (Cat. No. 17000-1-AP, Proteintech, 1:100) for monocytes, and ALOX12 (Cat. No. ab167372, Abcam, 1:100) and AIRE1 (Cat. No. sc-373703, Santa cruz biotechnology, 1:100) for the target genes.

Techniques: Immunofluorescence, Staining