Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of the 5-gene signature. (A) Forest plot of univariate Cox regression analysis in The Cancer Genome Atlas dataset. Cox results for the top five and bottom five genes. (B) Least absolute shrinkage and selection operator regression analysis. (C) λ curves show the least absolute shrinkage and the best λ was selected based on the minimum criteria. (D) The protein-protein interaction network between FOXO3 and 294 genes. FOXO3, DDX55, RAB10, RAB7A, TAF1B and TAF3 are highlighted by red dots and the remaining genes are represented by green dots. The color of the edges was determined by the combined score obtained from STRING. FOXO3, Forkhead box O3; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; SLC4A1AP, solute carrier family 4 member 1 adaptor protein; ZNF765, zinc finger protein 765; MORC3, MORC family CW-type zinc finger 3; WWC2, WW and C2 domain containing 2; UBE3A, ubiquitin protein ligase E3A; SECISBP2L, SECIS binding protein 2 like; FAN1, FANCD2 And FANCI associated nuclease 1.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Selection, Binding Assay, Ubiquitin Proteomics

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Construction and validation of a 5-gene prognostic model. (A) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in TCGA dataset. (B) Overall survival of patients with HCC in the high- and low- RS groups in TCGA dataset. (C) Time-dependent ROC curve of RS in TCGA dataset. (D) The distribution of RS, survival status and expression of the 5-gene signature between the high- and low-risk groups in the ICGC dataset. (E) Overall survival of patients with HCC in the high- and low-RS groups in the ICGC dataset. (F) Time-dependent ROC curve of RS in the ICGC dataset. RS, risk score; TCGA, The Cancer Genome Atlas; ICGC, International Cancer Genome Consortium; ROC, receiver operating characteristic; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; AUC, area under the curve.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Biomarker Discovery, Expressing, Binding Assay

Journal: Oncology Letters

Article Title: Identification of a novel FOXO3‑associated prognostic model in hepatocellular carcinoma

doi: 10.3892/ol.2025.14976

Figure Lengend Snippet: Identification of five biomarkers in HCC. (A) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and normal tissues from TCGA. Overall survival curves in patients with HCC with high or low expression of (B) DDX55, (C) RAB10, (D) RAB7A, (E) TAF1B and (F) TAF3 from TCGA dataset. The best cut-off value for each gene was obtained using the X-tile software. (G) mRNA expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, assessed using reverse transcription-quantitative PCR. (H) Immunohistochemical images of DDX55, RAB10 and RAB7A in HCC and normal tissues obtained from the HPA. (I) Protein expression of DDX55, RAB10, RAB7A, TAF1B and TAF3 in HCC and paired paracancerous tissues from 10 patients with HCC, evaluated using western blot analysis. The figure on the right is a relative semi-quantitative histogram of protein expression. The gray values were obtained by ImageJ and analyzed using GraphPad Prism. (J) Cell Counting Kit-8 curves after knockdown of RAB10, RAB7A and TAF3 in Huh7 cells by siRNA. *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001. T, tumor; NT, not-tumor; HCC, hepatocellular carcinoma; TCGA, The Cancer Genome Atlas; DDX55, DEAD-box helicase 55; RAB10, RAB10, member RAS oncogene family; RAB7A, RAB7A, member RAS oncogene family; TAF1B, TATA-box binding protein associated factor, RNA polymerase I subunit B; TAF3, TATA-box binding protein associated factor 3; HPA, The Human Protein Atlas; NC, negative control.

Article Snippet: The following antibodies were used: β-actin (1:1,000; cat. no. ET1702-52; HUABIO), DDX55 (1:1,000; cat. no. ER63225; HUABIO), RAB10 (1:1,000; cat. no. 11808-1-AP; Proteintech Group, Inc.), RAB7A (1:1,500; cat. no. 55469-1-AP; Proteintech Group, Inc.), TAF1B (1:500; cat. no. 12818-1-AP; Proteintech Group, Inc.), FOXO3 (1:1,000; cat. no. A9270; ABclonal Biotech Co., Ltd.) and TAF3 (1:500; cat. no. 18901-1-AP; Proteintech Group, Inc.), HRP conjugated goat anti-rabbit IgG polyclonal antibody (1:30000, HA1001, HUABIO), HRP conjugated goat anti-mouse IgG polyclonal antibody (1:30,000, HA1006, HUABIO).

Techniques: Expressing, Software, Reverse Transcription, Real-time Polymerase Chain Reaction, Immunohistochemical staining, Western Blot, Cell Counting, Knockdown, Binding Assay, Negative Control

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Article Title: CCN1 Enhances Tumor Immunosuppression through Collagen-Mediated Chemokine Secretion in Pancreatic Cancer.

doi: 10.1002/advs.202500589

Figure Lengend Snippet: Figure 2. Ccn1 expression in PDAC correlates with immunosuppression. A) Tumor growth curves of sgCtrl and sgCcn1 KPC cells subcutaneously in- oculated in C57B/L6 mouse. n = 6 mice per group. B) Representative images of tumors (left) and quantification of tumor weight (right) in sgCtrl and sgCcn1 KPC cell-inoculated mice. C) Representative images of H&E, and immunohistochemistry analysis for Ki67, CCN1, CD45, F4/80, CD4, CD8, and

Article Snippet: The sections were then stained with antibodies against CCN1 (26689-1-AP, Proteintech), AACT (RAB-0011, MXB), AAT (RAB-0012, MXB), CA199 (MAB-0778, MXB), CD3 (MAB-0740, MXB), CD20 (Kit-0001, MXB), CD34 (Kit-0004, MXB), CD68 (Kit-0026, MXB), CD163 (MAB-0869, MXB), CD3 (MAB-0740, MXB), Ki-67 (MAB-0672, MXB), F4/80 (SC-377009, Santa Cruz), CD8 (SC-7970, Santa Cruz), CD3 (SC-20047, Santa Cruz), CD45 (SC-1178, Santa Cruz), CD86 (SC-28347, Santa Cruz), Gr (SC-393232, Santa Cruz), and GranzymeB (SC-8022, Santa Cruz) followed by incubation with secondary antibodies (SD3100, Celnovte) for 20 min at 37 °C in the dark.

Techniques: Expressing, Immunohistochemistry

Journal: Advanced science (Weinheim, Baden-Wurttemberg, Germany)

Article Title: CCN1 Enhances Tumor Immunosuppression through Collagen-Mediated Chemokine Secretion in Pancreatic Cancer.

doi: 10.1002/advs.202500589

Figure Lengend Snippet: Figure 6. Targeting Ccn1 enhances the efficacy of gemcitabine and anti-PD-1 in PDAC. A) Cell viability of sgCtrl and sgCcn1 KPC cells after treatment with indicated concentrations of gemcitabine for 48 h. B) ROS levels in sgCtrl and sgCcn1 KPC cells with gemcitabine for 48 h by Fluorescence-activated cell sorting (FACS) analysis. C) Representative images (left) and quantification (right) of ROS level in sgCtrl and sgCcn1 KPC cells treated with gemcitabine for 48 h. D,E) C57B/L6 mice were inoculated subcutaneously with sgCtrl and sgCcn1 KPC cells. Tumor-bearing mice were treated with isotype control, anti-PD1 mAb, gemcitabine, or a combination of both treatments (n = 5 mice per group). Tumor volume was monitored (D), and representative tumor images (left) were acquired with final tumor weights (right) shown (E). F) C57BL/6 mice were orthotopically implanted with sgCtrl or sgCcn1 KPC cells. Tumor-bearing mice were treated with isotype control, anti-PD1 monoclonal antibody, gemcitabine, or a combination of both (n = 5 mice per group). Representative tumor images (top) and final tumor weights (bottom) are shown. G) Representative images of Masson’s trichrome staining and immunohistochemical analysis for F4/80, CD8, CD45, GranzymeB (GrzB), and Gr in sgCtrl and sgCcn1 KPC orthotopic tumors.

Article Snippet: The sections were then stained with antibodies against CCN1 (26689-1-AP, Proteintech), AACT (RAB-0011, MXB), AAT (RAB-0012, MXB), CA199 (MAB-0778, MXB), CD3 (MAB-0740, MXB), CD20 (Kit-0001, MXB), CD34 (Kit-0004, MXB), CD68 (Kit-0026, MXB), CD163 (MAB-0869, MXB), CD3 (MAB-0740, MXB), Ki-67 (MAB-0672, MXB), F4/80 (SC-377009, Santa Cruz), CD8 (SC-7970, Santa Cruz), CD3 (SC-20047, Santa Cruz), CD45 (SC-1178, Santa Cruz), CD86 (SC-28347, Santa Cruz), Gr (SC-393232, Santa Cruz), and GranzymeB (SC-8022, Santa Cruz) followed by incubation with secondary antibodies (SD3100, Celnovte) for 20 min at 37 °C in the dark.

Techniques: Fluorescence, FACS, Control, Staining, Immunohistochemical staining