Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: Primer sequences of OCT2, OAT1, OAT3, P-gp, MATE1, MATE2K, MRP2 genes.

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Sequencing

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: Values of the binding energies of berberine and berberrubine to seven transporter proteins in the kidney (Kcal/mol).

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Binding Assay

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: Molecular docking illustrations of BBR and BBRR with seven transport proteins respectively. (A) BBR docked with OAT1. (B) BBR docked with OAT3. (C) BBR docked with OCT2. (D) BBR docked with MATE1. (E) BBR docked with MATE2K. (F) BBR docked with P‐gp. (G) BBR docked with MRP2. (H) BBRR docked with OAT1. (I) BBRR docked with OAT3. (J) BBRR docked with OCT2. (K) BBRR docked with MATE1. (L) BBRR docked with MATE2K. (M) BBRR docked with P‐gp. (N) BBRR docked with MRP2.

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques:

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: Trends of metformin, methotrexate, estrone-3-sulfate, topotecan, rhodamine 123, and vinblastine concentration under different dosing time conditions in cells lysates or extracellular medium from HEK-293 cells. Blank control (BC), raw Phellodendri Chinensis cortex (RPC), Phellodendri Chinensis Cortex with salt-water processing (SPC), berberine (BBR), berberrubine (BBRR). (A) The trend of MET concentration changes mediated by OCT2. (B) The trend of MTX concentration changes mediated by OAT1. (C) The trend of E3S concentration changes mediated by OAT3. (D) The trend of Rho123 concentration changes mediated by P-gp. (E) The trend of TOP concentration changes mediated by MATE1 and MATE2K. (F) The trend of VBL concentration changes mediated by MRP2 (n = 3).

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Concentration Assay, Control

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: The effect of various solutions on each substrate accumulation transported by renal transport proteins. Blank control (BC), raw Phellodendri Chinensis cortex (RPC), Phellodendri Chinensis Cortex with salt-water processing (SPC), berberine (BBR), berberrubine (BBRR) (A) The effect of various solutions on the accumulation of MET transported by OCT2. (B) The effect of various solutions on the accumulation of MTX transported by OAT1. (C) The effect of various solutions on the accumulation of E3S transported by OAT3. (D) The effect of various solutions on the accumulation of Rho123 transported by P-gp. (E) The effect of various solutions on the accumulation of TOP transported by MATE1 and MATE2K. (F) The effect of various solutions on the accumulation of VBL transported by MRP2. Compared with the RPC group, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001; compared with the SPC group, # p < 0.05, ## p < 0.01, ### p < 0.001, #### p < 0.0001 (n = 3).

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Control

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: The effect of various solutions on the protein expression of MATE1, MATE2K, P-gp, MRP2. Blank control (BC), raw Phellodendri Chinensis cortex (RPC), Phellodendri Chinensis Cortex with salt-water processing (SPC), berberine (BBR), berberrubine (BBRR). (A) MATE1, MATE2K, P-gp, MRP2 protein expression bands in HEK-293 cells. (B) The effect of various solutions on MATE1 protein expression level. (C) The effect of various solutions on MATE2K protein expression level. (D) The effect of various solutions on P-gp protein expression level. (E) The effect of various solutions on MRP2 protein expression level. Compared with the BC group, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001; compared with the RPC group, □ p < 0.05, □□ p < 0.01, □□□ p < 0.001, □□□□ p < 0.0001; compared with the BBR group, △ p < 0.05, △△ p < 0.01, △△△ p < 0.001, △△△△ p < 0.0001.

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Expressing, Control

Journal: Frontiers in Pharmacology

Article Title: A strategy for evaluating the impact of processing of Chinese meteria medica on meridian tropism: the influence of salt-water processing of phellodendri chinensis cortex on renal transport proteins

doi: 10.3389/fphar.2025.1558298

Figure Lengend Snippet: The effect of various solutions to MATE1, MATE2K, P-gp, MRP2 mRNA expression level. Blank control (BC), raw Phellodendri Chinensis cortex (RPC), Phellodendri Chinensis Cortex with salt-water processing (SPC), berberine (BBR), berberrubine (BBRR). (A) The effect of various solutions on MATE1 mRNA expression level. (B) The effect of various solutions on MATE2K mRNA expression level. (C) The effect of various solutions on P-gp mRNA expression level. (D) The effect of various solutions on MRP2 mRNA expression level Compared with the BC group, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001; compared with the RPC group, □ p < 0.05, □□ p < 0.01, □□□ p < 0.001, □□□□ p < 0.0001; compared with the BBR group, △ p < 0.05, △△ p < 0.01, △△△ p < 0.001, △△△△ p < 0.0001.

Article Snippet: DMEM high glucose medium (Cat. No.: 8123207), PBS buffer salt solution (Cat. No.: 20210927) were purchased from Gibco (Waltham, Massachusetts, United States), fetal bovine serum (Cat. No.: ST200913) was purchased from PAN (Aden Bach, Free State of Bavaria, Germany), penicillin-streptomycin-Amphotericin B Mixed Triple Antibody Solution (Cat. No.: 20220519JH), 20×TBST buffer (Cat. No.: T1082), Whole Protein Lysis Kit (Cat. No.: BC3710), TRIzol Lysis Solution (Cat. No.: 15596018CN), ECL PLUS Ultra-Sensitive Luminescent Solution (Cat. No.: PE0010), dimethyl sulfoxide (Cat. No.: 710N0310), metformin (Cat. No.: D9351, purity≥98%), methotrexate (Cat. No.: M8971, purity≥98%), rhodamine123 (Cat. No.: R8030, purity≥98%), topotecan (Cat. No.: IT1030, purity≥98%) were purchased from Solarbio Science and Technology Co. Ltd (Beijing, China), SDS-PAGE Protein Sampling Buffer 5× (Cat. No.: P0015L) was purchased from Beyotime Bio-Tech Ltd (Shanghai, China), OCT2 rabbit anti-polyclonal antibody (Cat. No.: 10867-2-AP), OAT1 rabbit anti-polyclonal antibody (Cat. No.: 26574-1-AP), OAT3 rabbit anti-polyclonal antibody (Cat. No.: 16844-1-AP), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20,898), P-gp rabbit anti-polyclonal antibody (Cat. No.: 22336-1-AP), MATE1 rabbit anti-polyclonal antibody (Cat. No.: 20898-1-AP), MATE2K rabbit anti-polyclonal antibody (Cat. No.: 26873-1-AP), MRP2 rabbit anti-polyclonal antibody (Cat. No.: 29261-1-AP), Goat Anti-Rabbit IgG II Antibody (Cat. No.: 20001097) were purchased from the Proteintech (Wuhan, China).

Techniques: Expressing, Control

Journal: bioRxiv

Article Title: Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

doi: 10.1101/2024.06.12.598635

Figure Lengend Snippet: (A) Proteins ranked by their expression differences in HRS compared to GC. The top ten differentially expressed proteins in HRS are listed, with known lymphoma-related markers in bold. (B) Same as A but for SLL compared to GC. (C) Principal component analysis of GC/HRS/SLL cell proteomes. (D) Volcano plot of the proteomic comparison between HRS and SLL. Red dots represent significantly differentially expressed proteins. Proteins with largest fold-change are annotated with their names. Statistical significance was determined using two-sided t -test (FDR<0.05, S0=0.1). (E) The scatter plot of the differential enrichment of proteins in the HRS and SLL populations in comparison to GC. Proteins that show significant expression in HRS (orange), SLL (magenta), and both populations (blue) are highlighted. (F) Expression of IRF4 determined by MS analysis. The box plot displays the distribution of the data from the minimum to the maximum intensity. The horizontal line within each box represents the mean value of the intensity. Statistical significance was determined using one-way ANOVA. F-value (2, 9) = 92.55; **** P < 0.0001. * P < 0.05. (G) Representative images illustrating immunofluorescence staining of CD20, CD30 and IRF4 in non-lesional germinal center regions and tumor areas. Arrows indicate HRS cells. (H) Quantification of staining intensity of IRF4 in GC, HRS and SLL (similar as in F). The horizontal line within each box represents the median value of the intensity. Statistical significance was determined using one-way ANOVA. F (2, 41786) = 4132, **** P < 0.0001. (I) Representative images illustrating immunofluorescence staining of CD20, CD30 and LENG1 in non-lesional germinal center regions and tumor areas. Arrows indicate HRS cells. (J) Quantification of staining intensity of LENG1 in GC, HRS and SLL as (H). F (2, 40108) = 3054, **** P < 0.0001. (K) Expression of LENG1 determined by MS analysis (similar as in F). F (2, 9) = 217.7. (L) Representative immunohistochemistry images of LENG1 in human lymph node tissues, including both normal and lymphoma cases, sourced from the HPA database. (M) Kaplan-Meier analysis to pan-cancer in TCGA using UCSC Xena, with a focus on LENG1 (see main text). The p-values reflect comparisons between two groups through univariate analysis using the log-rank test.

Article Snippet: The tissue was then blocked with 5% BSA for 20 minutes at room temperature and incubated overnight at 4°C with primary antibodies, including anti-CD30 clone Ber-H2 (1:50, M0751, Agilent) with anti-SKIL antibody (1:200, HPA008472, Sigma-Aldrich) / anti-IRF4 antibody (1:100, 11247-2-AP, Proteintech) / anti-LENG1 antibody (1:500, HPA043541, Sigma-Aldrich) / Alexa Fluor® 488 Collagen I (1:1000, ab275996, Abcam) / CD3 (1:500, A0452, Agilent).

Techniques: Expressing, Comparison, Immunofluorescence, Staining, Immunohistochemistry

Journal: bioRxiv

Article Title: Deep Visual Proteomics Unveils Precision Medicine Insights in Composite Small Lymphocytic and Classical Hodgkin Lymphoma

doi: 10.1101/2024.06.12.598635

Figure Lengend Snippet: (A) Volcano plot comparing the proteomes of HRS and GC. Orange dots represent significantly differentially expressed proteins, and proteins with largest fold-change are annotated with their names. Statistical significance was determined using two-sided t -test (FDR<0.05, S0=0.1). (B) Interaction between compounds and proteins using STITCH and STRING (see Methods). Interactions are visualized in Cytoscape, representing nodes with gray lines connecting them, where thicker lines signified stronger associations. IRF4 and related proteins appear as circles, while compounds appear as ovals in the visual representation. (C) Volcano plot comparing the proteomes of HRS and GC. Magenta dots represent significantly differentially expressed proteins as in (A). (D) Gene Ontology (GO) enrichment analysis on the upregulated pathways in HRS involving iterative comparisons and functional grouping of these pathways. The plot illustrates -log10 (FDR of term) values, with circle size denoting the percentage of associated upregulated entities in HRS compared to the background entities. (E) Heatmap illustrating entities participating in the cell cycle process pathway identified through GO enrichment analysis. GC, HRS, and SLL are represented with four replicates each, with Z-scores depicted using a gradient color scale. (F) Heatmap of the proteasome subunit proteins. (G) GO enrichment analysis of the upregulated pathways in SLL similar to (D). (H) Interaction between compounds and proteasome proteins.

Article Snippet: The tissue was then blocked with 5% BSA for 20 minutes at room temperature and incubated overnight at 4°C with primary antibodies, including anti-CD30 clone Ber-H2 (1:50, M0751, Agilent) with anti-SKIL antibody (1:200, HPA008472, Sigma-Aldrich) / anti-IRF4 antibody (1:100, 11247-2-AP, Proteintech) / anti-LENG1 antibody (1:500, HPA043541, Sigma-Aldrich) / Alexa Fluor® 488 Collagen I (1:1000, ab275996, Abcam) / CD3 (1:500, A0452, Agilent).

Techniques: Functional Assay

Journal: Stem Cell Research & Therapy

Article Title: NCAPH-YAP1 interaction promotes breast cancer stemness and tumor progression

doi: 10.1186/s13287-025-04648-0

Figure Lengend Snippet: Transcriptome sequencing analysis of BC cell lines after NCAPH overexpression. A Heatmap of DEGs following NCAPH overexpression. B GSEA analysis showing enrichment of the Hippo signaling pathway. C KEGG pathway analysis of DEGs. D KMplot database analysis of the impact of YAP1 expression levels on OS in BC patients

Article Snippet: The primary antibodies used were against NCAPH (1:5000, Cat# 67,655–1-Ig), CD133 (1:5000, Cat#18,470–1-AP), CD44 (1:5000, Cat#60,224–1-Ig), YAP1 (1:5000, Cat# 13,584–1-AP), phospho-YAP1 (Ser127, 1:5000, Cat#29,018–1-AP), OCT4 (1:5000, Cat#60,242–1-Ig), SOX2 (1:2000, Cat#66,411–1-Ig), Nanog (1:2000, Cat#67,255–1-Ig), Cyclin D1 (1:5000, Cat#26,939–1-AP), CDK1 (1:5000, Cat#67,575–1-Ig), CDK2 (1:5000, Cat#10,122–1-AP), CDK4 (1:5000, Cat#66,950–1-Ig), β-actin (1:5000, Cat#66,009–1-Ig), Flag (1:5000, Cat#66,008–4-Ig), α-Tubulin (1:5000, Cat#66,031–1-Ig), and GAPDH (1:5000, Cat#10,494–1-AP), all sourced from Proteintech (Rosemont, IL, USA).

Techniques: Sequencing, Over Expression, Expressing

Journal: Stem Cell Research & Therapy

Article Title: NCAPH-YAP1 interaction promotes breast cancer stemness and tumor progression

doi: 10.1186/s13287-025-04648-0

Figure Lengend Snippet: NCAPH interacts with YAP1 and promotes YAP1 expression and nuclear translocation. A WB analysis examining the effects of NCAPH overexpression or knockdown on Hippo-YAP1 signaling (Full-length gels are presented in Supplementary Fig. 6). B WB analysis assessing the effect of NCAPH overexpression on YAP1 nuclear translocation (Full-length gels are presented in Supplementary Fig. 7). C IF showing co-localization of NCAPH and YAP1 proteins within cells. D Co-IP assay demonstrating the interaction between NCAPH and YAP1 (Full-length gels are presented in Supplementary Fig. 7)

Article Snippet: The primary antibodies used were against NCAPH (1:5000, Cat# 67,655–1-Ig), CD133 (1:5000, Cat#18,470–1-AP), CD44 (1:5000, Cat#60,224–1-Ig), YAP1 (1:5000, Cat# 13,584–1-AP), phospho-YAP1 (Ser127, 1:5000, Cat#29,018–1-AP), OCT4 (1:5000, Cat#60,242–1-Ig), SOX2 (1:2000, Cat#66,411–1-Ig), Nanog (1:2000, Cat#67,255–1-Ig), Cyclin D1 (1:5000, Cat#26,939–1-AP), CDK1 (1:5000, Cat#67,575–1-Ig), CDK2 (1:5000, Cat#10,122–1-AP), CDK4 (1:5000, Cat#66,950–1-Ig), β-actin (1:5000, Cat#66,009–1-Ig), Flag (1:5000, Cat#66,008–4-Ig), α-Tubulin (1:5000, Cat#66,031–1-Ig), and GAPDH (1:5000, Cat#10,494–1-AP), all sourced from Proteintech (Rosemont, IL, USA).

Techniques: Expressing, Translocation Assay, Over Expression, Knockdown, Co-Immunoprecipitation Assay

Journal: Stem Cell Research & Therapy

Article Title: NCAPH-YAP1 interaction promotes breast cancer stemness and tumor progression

doi: 10.1186/s13287-025-04648-0

Figure Lengend Snippet: The YAP1 inhibitor Verteporfin reverses NCAPH overexpression-induced enhancement of CSC properties, proliferation, migration, and invasion in BC cells. A Verteporfin inhibits YAP1 expression and also reverses the increase in tumorsphere formation induced by NCAPH overexpression (Full-length gels are presented in Supplementary Fig. 8). B WB experiments show that Verteporfin reverses CSC marker protein expression induced by NCAPH overexpression (Full-length gels are presented in Supplementary Fig. 8). C The CCK-8 assay shows that Verteporfin reverses the enhanced proliferative capacity in BC cell lines induced by NCAPH overexpression. D ​The wound healing assay indicates that Verteporfin reverses the increase in migratory capacity of BC cell lines induced by NCAPH overexpression. E The Transwell assay reveals that Verteporfin markedly reverses the enhancement of migratory and invasive capabilities in BC cell lines induced by NCAPH overexpression. Data are presented as mean ± SD (*P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001)

Article Snippet: The primary antibodies used were against NCAPH (1:5000, Cat# 67,655–1-Ig), CD133 (1:5000, Cat#18,470–1-AP), CD44 (1:5000, Cat#60,224–1-Ig), YAP1 (1:5000, Cat# 13,584–1-AP), phospho-YAP1 (Ser127, 1:5000, Cat#29,018–1-AP), OCT4 (1:5000, Cat#60,242–1-Ig), SOX2 (1:2000, Cat#66,411–1-Ig), Nanog (1:2000, Cat#67,255–1-Ig), Cyclin D1 (1:5000, Cat#26,939–1-AP), CDK1 (1:5000, Cat#67,575–1-Ig), CDK2 (1:5000, Cat#10,122–1-AP), CDK4 (1:5000, Cat#66,950–1-Ig), β-actin (1:5000, Cat#66,009–1-Ig), Flag (1:5000, Cat#66,008–4-Ig), α-Tubulin (1:5000, Cat#66,031–1-Ig), and GAPDH (1:5000, Cat#10,494–1-AP), all sourced from Proteintech (Rosemont, IL, USA).

Techniques: Over Expression, Migration, Expressing, Marker, CCK-8 Assay, Wound Healing Assay, Transwell Assay