Journal: BMC Cancer

Article Title: Bioinformatics identification and validation of m6A/m1A/m5C/m7G/ac4 C-modified genes in oral squamous cell carcinoma

doi: 10.1186/s12885-025-14216-7

Figure Lengend Snippet: Clinical characteristics of risk scores. A OncoPrint of I GF2BP2, HNRNPC, TRMT61B , and NAT10 using the cBioPortal database. Each column represents one patient sample, and each row corresponds to a gene. Different colors or bars indicate various genetic alterations (e.g., mutation, amplification, deep deletion). The bottom legend summarizes the frequency of each alteration type across the cohort. B , C Unpaired ( B ) and paired ( C ) differential analyses for the 4 genes between paraneoplastic and tumor tissues. The expression level of the 4 genes was higher in tumor tissues than in normal tissues. D Immunohistochemistry (IHC) of IGF2BP2, HNRNPC, TRMT61B, and NAT10 in normal versus tumor tissues. Representative tissue microarray images (from the Human Protein Atlas or in-house staining) show the protein localization and intensity. Brown staining indicates positive protein expression, while blue (hematoxylin) represents the nuclear counterstain. The upper panels depict normal oral mucosa, and the lower panels show corresponding OSCC tissues, confirming higher protein expression in tumor samples for most genes. Scale bars (if included) indicate the magnification used

Article Snippet: Representative tissue microarray images (from the Human Protein Atlas or in-house staining) show the protein localization and intensity.

Techniques: Mutagenesis, Amplification, Expressing, Immunohistochemistry, Microarray, Staining

Journal: Journal of Cancer

Article Title: Construction and validation of a comprehensive metabolism-associated prognostic model for predicting survival and immunotherapy benefits in ovarian cancer

doi: 10.7150/jca.100796

Figure Lengend Snippet: The comparison of levels of signature genes expression in tumor and normal controls. (A) Differences of expression levels of the four signature genes among the normal ovarian tissues and Ovarian cancer tissues (TCGA and GTEx database). (B) The relative mRNA levels of the four signature genes between normal ovarian cell lines and OV cell lines. (C) The prognostic value of a 4 sigurenaure gene for patients in TCGA has been confirmed through Kaplan-Meier analysis. (D) The immunohistochemical staining of tissue microarray shows 4 signature genes expressions on protein level between OV and normal control tissues.

Article Snippet: OV and normal ovarian tissue microarray (ZL-OVA961) were bought from ShangHai Zhuoli Biotech Company (China).

Techniques: Comparison, Expressing, Immunohistochemical staining, Staining, Microarray, Control

Journal: EBioMedicine

Article Title: Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer

doi: 10.1016/j.ebiom.2019.05.015

Figure Lengend Snippet: High PIPKIγ expression level predicts a poor clinical outcome in colorectal cancer. (A) Real-time qPCR analysis of the mRNA level of PIPKIγ in colorectal cancer cell lines and the normal colonic epithelial cell NCM460. (B) Cell lysates of indicated cells were collected for immunoblotting analyses using PIPKIγ antibody; β-actin was loaded as a control. (C) IHC analysis was performed in a tissue microarray containing 76 matched tumor and non-tumor colorectal cancer tissues. Representative images of PIPKIγ and its expression intensity in non-tumor and tumor tissues were shown. Scale bar: 100 μm. (D) Kaplan-Meier analyses of overall survival of individuals with colorectal cancer based on PIPKIγ protein expression level. (E) Kaplan-Meier analyses of overall survival in colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ) patients in the Cancer Genome Atlas (TCGA) cohort. The patients were dichotomously categorized on the basis of median PIPKIγ value into 2 groups. Subgroups were compared with the use of the log-rank test. * P < .05; ** P < .01; *** P < .001.

Article Snippet: The colorectal cancer tissue microarray used in this study was purchased from Zhuoli Biotech (#COC1504, http://www.zhuolibiotech.com/ , Shanghai, China).

Techniques: Expressing, Western Blot, Control, Microarray

Journal: EBioMedicine

Article Title: Type Iγ phosphatidylinositol phosphate kinase promotes tumor growth by facilitating Warburg effect in colorectal cancer

doi: 10.1016/j.ebiom.2019.05.015

Figure Lengend Snippet: PIPKIγ promotes colorectal cancer cell proliferation in vitro and tumor growth in vivo. (A) COAD samples derived from TCGA cohort was categorized into 2 groups (high versus low) based on median PIPKIγ value. Gene set enrichment analysis (GSEA) was performed to discover the difference between 2 groups. False discovery rate (FDR) was set at 0.25. NES represents normalized enrichment score. (B) Validation of pan-PIPKIγ knockdown and ectopic expression of mutant-PIPKIγ_i2 (resistant to PIPKIγ shRNA) in SW480 and LOVO cells using Western blotting. (C, D) The influence of PIPKIγ on colorectal cancer in vitro cell proliferation was determined by CCK-8 (C) and colony formation (D) assays, respectively. (E) sh-Ctrl, sh-PIPKIγ-1, and sh-PIPKIγ-1 + mPIPKIγ1_i2 SW480 cells were injected subcutaneously into the left forelimb of nude mice ( n = 6 per group). Four weeks later, mice were sacrificed and tumor weights in each group were shown. (F) IHC analysis of PIPKIγ and PCNA expression from indicated subcutaneous xenograft. * P < .05 and ** P < .01.

Article Snippet: The colorectal cancer tissue microarray used in this study was purchased from Zhuoli Biotech (#COC1504, http://www.zhuolibiotech.com/ , Shanghai, China).

Techniques: In Vitro, In Vivo, Derivative Assay, Biomarker Discovery, Knockdown, Expressing, Mutagenesis, shRNA, Western Blot, CCK-8 Assay, Injection

Journal: NPJ Precision Oncology

Article Title: Vertical pathway inhibition of receptor tyrosine kinases and BAD with synergistic efficacy in triple negative breast cancer

doi: 10.1038/s41698-023-00489-3

Figure Lengend Snippet: a pBADSer99 levels and BAD expression were determined using immunohistochemistry (IHC) in adjacent normal (AD) and TNBC tissue specimens. Representative IHC images of pBADSer99 in TNBC and AD tissues (up). Scale bar, 20 μm. Analysis of the pBADSer99/BAD ratio and pBADSer99 staining (%) in AD and TNBC tissue specimens (down). For pBADSer99, the immunoreactive score (IRS) 0 to 4 was categorized as negative and IRS 5 to 12 as positive. For the pBADSer99/BAD ratio, the IRS ratio higher than 0.75 was regarded as positive . Cell survival of MDA-MB-231 ( b ) and BT549 ( c ) cells after transfection with pBADS99A knock in plasmid or vector control. Data represent means ± SD ( n = 3). * P < 0.05, ** P < 0.01, and *** P < 0.001. Corresponding immunoblots displaying levels of pBADSer99 and BAD. The sizes of detected bands in kDa are shown on the left. d Transwell analysis was performed to determine the effect of pBADS99A knock in on cell migration of MDA-MB-231 and BT549 cells. The TNBC cells were transfected with pBADS99A plasmid or vector control. Scale bar, 50 μm. Data represent means ± SD ( n = 5). * P < 0.05, ** P < 0.01, and *** P < 0.001.

Article Snippet: The TNBC tissue microarray (ZL-Brc3N961) was obtained from Zhuoli Biotech Co., Ltd. (Shanghai, China).

Techniques: Expressing, Immunohistochemistry, Staining, Transfection, Knock-In, Plasmid Preparation, Control, Western Blot, Migration

Journal: NPJ Precision Oncology

Article Title: Vertical pathway inhibition of receptor tyrosine kinases and BAD with synergistic efficacy in triple negative breast cancer

doi: 10.1038/s41698-023-00489-3

Figure Lengend Snippet: a Petasis reaction, a three component boronic Mannich-type reaction which utilizes boronic acids as a potential nucleophilic species, salicylaldehyde, and substituted piperazines to form the new C–C bond of the formula I compound, was utilized to synthesize NCK (C 22 H 21 Cl 2 N 3 O). b 3D surface and enlarged view of the docked compounds NPB (red) & NCK (black) with the BAD protein (dim grey). The yellow color indicates the site of the Serine 99 residue. c 2D structure representation of NCK interacting with BAD protein residues. d Sensorgrams obtained by SPR analysis of NCK with the BAD protein. BAD protein was immobilized on the surface of a CM5 sensor chip. A solution of NCK at variable concentrations (1.25–160 μM) was injected to generate the binding responses (RU) recorded as a function of time (s). The results were analyzed using BIA evaluation 4.1. e Western Blot analysis was used to assess the level of BAD phosphorylation at Ser99, Ser75 and Ser118 in TNBC cells after treatment with NCK and NPB. β-ACTIN was used as input control for cell lysate. The sizes of detected bands in kDa are shown on the left. f Dose-dependent effect of NCK and NPB in 2D and 3D culture on MDA-MB-231 and BT549 TNBC cells measured by using total cell number and AlamarBlue assay respectively ( n = 3). g Western Blot analysis was used to assess the level of BAD phosphorylation at Ser99 in TNBC cells after transfection with siRNA-BAD. β-ACTIN was used as input control for cell lysate. The sizes of detected bands in kDa are shown on the left. h CASPASE3/7 activities of MDA-MB-231 cells after transfecting with siRNA targeting BAD transcript or scrambled control and treated with 5 μM NCK were evaluated using the Biovision Caspase 3/7 DEVD Assay Kit. Data represent means ± SD ( n = 3). * P < 0.05, ** P < 0.01, and *** P < 0.001. i Cell survival of MDA-MB-231 cells after transfecting with siRNA targeting BAD transcript or scrambled control and treated with 5 μM NCK. Data represent means ± SD ( n = 3). * P < 0.05, ** P < 0.01, and *** P < 0.001.

Article Snippet: The TNBC tissue microarray (ZL-Brc3N961) was obtained from Zhuoli Biotech Co., Ltd. (Shanghai, China).

Techniques: Residue, Injection, Binding Assay, Western Blot, Phospho-proteomics, Control, Alamar Blue Assay, Transfection

Journal: NPJ Precision Oncology

Article Title: Vertical pathway inhibition of receptor tyrosine kinases and BAD with synergistic efficacy in triple negative breast cancer

doi: 10.1038/s41698-023-00489-3

Figure Lengend Snippet: a The survival fraction of NCK, OSI-930 (OSI) and Crizotinib (CRI) or combination treatments were evaluated with total cell number assay ( n = 3). b CI was measured with Chou-Talalay, where CI < 1 denotes synergy, CI = 1 denotes additivity, CI > 1 denotes antagonism. Synergy score was measured with HSA and bliss synergy analysis ( www.synergyfinder.com ), where CI > 0 denotes synergy, CI < 0 denotes antagonism. c Dose-response analysis of the shift in IC 50 of OSI-930 (OSI) and Crizotinib (CRI) in TNBC cells after co-treatment with NCK (2 μM) was evaluated with total cell number assay. Fold difference was calculated. Data represent means ± SD ( n = 3).

Article Snippet: The TNBC tissue microarray (ZL-Brc3N961) was obtained from Zhuoli Biotech Co., Ltd. (Shanghai, China).

Techniques:

Journal: NPJ Precision Oncology

Article Title: Vertical pathway inhibition of receptor tyrosine kinases and BAD with synergistic efficacy in triple negative breast cancer

doi: 10.1038/s41698-023-00489-3

Figure Lengend Snippet: a Representative flow cytometry plots using Annexin V FITC/PI staining for apoptotic cell death of MDA-MB-231 and BT549 cells measured after treatment with 5 μM NCK, 5 μM OSI-930 (OSI), 5 μM Crizotinib (CRI) or combinations using flow cytometry analysis at 72 hours as described in materials and methods ( n = 3). b CASPASE 3/7 activities were evaluated in MDA-MB-231 and BT549 cells using the Biovision Caspase 3/7 DEVD Assay Kit after treatment with 5 μM NCK, 5 μM OSI-930 (OSI), 5 μM Crizotinib (CRI) or combinations. Data represent means ± SD ( n = 3). * P < 0.05, ** P < 0.01, and *** P < 0.001. c Crystal violet staining of foci in colonies generated by MDA-MB-231 cells and BT549 cells after exposure to 5 μM NCK, 5 μM OSI-930 (OSI), 5 μM Crizotinib (CRI) or combinations. d Representative images of MDA-MB-231 cells and BT549 cells cultured in 3D Matrigel after exposure to 5 μM NCK, 5 μM OSI-930 (OSI), 5 μM Crizotinib (CRI) or combinations. Scale bar, 100μm. e Western blot analysis was used to assess the level of various apoptotic proteins in TNBC cells after treatment with 1 μM NCK, 1 μM OSI-930 (OSI), 1 μM Crizotinib (CRI) or combinations. β-ACTIN was used as input control for cell lysate. The sizes of detected bands in kDa are shown on the left. f Western blot analysis was used to assess the expression/phosphorylation of various proteins of the PI3K/AKT and MAPK pathways after treatment with 1 μM NCK, 1 μM OSI-930 (OSI), 1 μM Crizotinib (CRI) or combinations. β-ACTIN was used as input control for cell lysate. The sizes of detected bands in kDa are shown on the left.

Article Snippet: The TNBC tissue microarray (ZL-Brc3N961) was obtained from Zhuoli Biotech Co., Ltd. (Shanghai, China).

Techniques: Flow Cytometry, Staining, Generated, Cell Culture, Western Blot, Control, Expressing, Phospho-proteomics