Journal: iScience

Article Title: FAM65A, as a potential predictor of prognosis, promotes colorectal cancer progression via activating Ras/ERK/RSK signaling

doi: 10.1016/j.isci.2026.114662

Figure Lengend Snippet: FAM65A binds to Ras and activates the Ras/ERK signaling to mediate RSK activation (A) The volcano plot analysis results for the FAM65A high-expression and low-expression groups from the TCGA database were shown. (B) The KEGG and GO results were shown. (C) The GSEA results were shown. (D) GSEA on DEGs between the FAM65A high-expression group and low-expression group in the Reactome database were shown. (E) IP was performed to detect the binding of FAM65A and Ras/p-RSK. (F) IP was performed to detect the binding of Ras and FAM65A/p-RSK. (G) Immunofluorescence was performed to detect the co-localization of FAM65A and Ras. Scale bars, 20 μm. (H) Western blot analysis the Ras and p -ERK expression in FAM65A knockdown or overexpression cells. Data are presented as mean ± SEM of biologically independent experiments.

Article Snippet: p -ERK , Proteintech , Cat# 28733-1-AP; RRID: AB_2881202.

Techniques: Activation Assay, Expressing, Binding Assay, Immunofluorescence, Western Blot, Knockdown, Over Expression

Journal: iScience

Article Title: FAM65A, as a potential predictor of prognosis, promotes colorectal cancer progression via activating Ras/ERK/RSK signaling

doi: 10.1016/j.isci.2026.114662

Figure Lengend Snippet: Ras/ERK signaling activation was indispensable for FAM65A-mediated RSK activation and CRC progression (A) Western blot analysis of Ras and p -ERK expression in HCT116-FAM65A cells treated with 10 μM Abd-7, or without treatment. (B) Results from the CCK8 cell proliferation assay conducted on HCT116-FAM65A cells with and without the application of Abd-7, n = 3, ∗∗∗ p < 0.001. (C) Colony formation assay performed on HCT116-FAM65A cells treated with Abd-7 or not. (D) Quantitative analysis of the colony formation assay results, n = 3, ∗∗∗ p < 0.001. (E) Results from the EdU assay conducted on HCT116-FAM65A cells with and without the application of Abd-7. Scale bars, 100 μm. (F) Quantitative analysis of the EdU assay results, n = 3, ∗∗∗ p < 0.001. (G) Western blot analysis of Ki-67, cleaved Caspase 3, Bcl-2, and Bax expression in HCT116-FAM65A cells treated with Abd-7 or not. (H) Results from the apoptosis assay conducted on HCT116-FAM65A cells treated with Abd-7 or not. Scale bars, 50 μm. (I) Quantitative analysis of the apoptosis experiments, n = 3, ∗∗∗ p < 0.001. (J) Results from the Transwell migration assay conducted on HCT116-FAM65A cells with and without the application of Abd-7. Scale bars, 50 μm. (K) Quantitative analysis of the Transwell migration assay results, n = 3, ∗∗∗ p < 0.001. (L) Results from the wound healing assay performed on HCT116-FAM65A cells treated with Abd-7 or not. Scale bars, 50 μm. (M) Quantitative analysis of the wound healing assay results, n = 3, ∗∗∗ p < 0.001. (N) Western blot analysis the expression of EMT markers in HCT116-FAM65A cells treated with Abd-7 or not. (O) Proposed model of FAM65A in CRC progression. Data are presented as mean ± SEM of biologically independent experiments.

Article Snippet: p -ERK , Proteintech , Cat# 28733-1-AP; RRID: AB_2881202.

Techniques: Activation Assay, Western Blot, Expressing, Proliferation Assay, Colony Assay, EdU Assay, Apoptosis Assay, Transwell Migration Assay, Wound Healing Assay

Journal: iScience

Article Title: FAM65A, as a potential predictor of prognosis, promotes colorectal cancer progression via activating Ras/ERK/RSK signaling

doi: 10.1016/j.isci.2026.114662

Figure Lengend Snippet: Knockdown of FAM65A inhibits tumor progression in vivo (A) LOVO-shCtrl and LOVO-shFAM65A cells were administered into the fourth fat pad of nude mice, and the resulting tumor growth curves were subsequently generated, n = 5, ∗ p < 0.05. (B) The tumors excised from mice across various experimental groups are presented. (C) Hematoxylin and Eosin (HE) staining results of lung tissue from the different groups is displayed. (D) A quantitative analysis of metastatic lung nodules is provided, n = 5, ∗∗ p < 0.01. (E) IHC results for FAM65A, Ki-67, p -RSK, p -ERK, Ras, N-cadherin, vimentin, cleaved Caspase 3, ZO-1, and E-cadherin in tumor tissues are illustrated. (F) A quantitative analysis of the IHC results is included. Data are presented as mean ± SEM of biologically independent experiments, n = 5, ∗∗∗ p < 0.001.

Article Snippet: p -ERK , Proteintech , Cat# 28733-1-AP; RRID: AB_2881202.

Techniques: Knockdown, In Vivo, Generated, Staining

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Copper metabolism related genes DLD and UBE2D3 act as protective factors in KIRC. (A) The OS Kaplan-Meier curve of DLD genes. (B) The ROC curve of DLD gene. (C) The Kaplan-Meier curve (OS) of UBE2D3 gene. The ROC curve of UBE2D3 gene (D) shows the differential expression of UBE2D3 gene at different T stages (E). (F) The expression differences of gene UBE2D3 in different G stages. (G) The calibration curve of the Norman plot is used to predict 1-, 3-, and 5-year survival rates. (H) By drawing a line graph, we predicted the OS period over a time range of 1-, 3-, and 5-year. Each risk factor corresponds to a point axis by drawing a line on the graph. *, P<0.05; **, P<0.01; ***, P<0.001. AUC, area under the curve; CI, confidence interval; G, grade; H, high; HR, hazard ratio; KIRC, kidney renal clear cell carcinoma; L, low; OS, overall survival; ROC, receiver operating characteristic; T, tumor.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Quantitative Proteomics, Expressing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 functional analysis. (A) UBE2D3 gene expression risk prognostic model. (B) UBE2D3 protein interaction network diagram. (C) Volcano plot based on UBE2D3. (D) GO analysis of differential genes between high and low UBE2D3 groups. (E) KEGG enrichment analysis between high and low UBE2D3 groups. (F) GSEA signal pathway enrichment analysis based on UBE2D3 expression. BP, biological process; CC, cellular component; ES, Enrichment Score; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; MF, molecular function; NP, nominal P value.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Functional Assay, Gene Expression, Expressing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Correlation analysis between UBE2D3 expression and immune cells. (A) Using CIBERSORT method to explore the differences in expression levels of 22 immune cells at different levels of UBE2D3. (B) Correlation analysis between 22 different immune cells. (C) Correlation analysis between UBE2D3 expression levels and biological markers between B cell, Th cell, CD8 + T cell, and DC. (D) Correlation analysis between UBE2D3 expression levels and biological markers between M2 macrophages. (E) Correlation analysis between UBE2D3 expression levels and biological markers between CAF, MDSC, and TAM. (F) Expression of UBE2D3 Correlation analysis chart between levels and biological markers of T exhausted cell, Treg T cell, and macrophages. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. CAF, cancer-associated fibroblast; CIBERSORT, Cell-Identification By Estimating Relative Subsets Of RNA Transcripts; MDSC, myeloid-derived suppressor cells; TAM, tumor-associated macrophages.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Expressing, Derivative Assay

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 affects the tumor immune microenvironment. (A) Using TIMER database to evaluate the correlation between UBE2D3 and immune cells. (B) Box plot shows the distribution of each immune subgroup in KIRC at each copy number state, comparing the infiltration levels of each SCNA category with normal levels. *, P<0.05; **, P<0.01; ***, P<0.001; ****, P<0.0001. KIRC, kidney renal clear cell carcinoma; SCNA, Somatic Copy-number Alteration; TCGA, The Cancer Genome Atlas; TIMER, Tumor Immune Estimation Resource.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques:

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Expression and infiltration of UBE2D3 among different cell populations in the single-cell sequencing dataset. (A) The expression of UBE2D3 in different cells in different datasets. (B) The distribution of GSE139555 cells in the scRNA seq dataset. (C) The distribution of 11 annotation groups in the scRNA seq dataset. (D) The distribution of UBE2D3 in different cells in the scRNA seq dataset. (E) The expression differences of UBE2D3 in different cells between KIRC patients and normal individuals. (F) The expression differences of UBE2D3 in different tumor stages and cells. GSE, GEO Series Accession Number; KIRC, kidney renal clear cell carcinoma; N.S., not significant; NAT, normal adjacent tissue; PBMC, peripheral blood mononuclear cells; scRNA seq, single-cell RNA sequencing; TNM, tumor-node-metastasis; TPM, transcripts per million.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Expressing, Single Cell, Sequencing, RNA Sequencing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: UBE2D3 mutation and methylation analysis. (A) Methylation level analysis of UBE2D3 between tumor and normal groups. (B) Methylation level analysis of UBE2D3 in normal group and different stage. (C) Methylation level analysis of UBE2D3 in normal group and different grade stages. (D) Methylation level analysis of UBE2D3 in normal group and different N-stage. (E) Heat map analysis of DNA methylation in the MethSurv database. (F) Correlation between CNV and expression level of UBE2D3. (G) Correlation between CNV level of UBE2D3 and survival. *, P<0.05; **, P<0.01; ***, P<0.001. CNV, copy number variation; Cor, correlation; DFI, disease-free interval; DSS, disease-specific survival; FDR, false discovery rate; KIRC, kidney renal clear cell carcinoma; mRNA, messenger RNA; N, node; OS, overall survival; PFS, progression-free survival; RSEM, RNA-seq by expectation-maximization; TCGA, The Cancer Genome Atlas.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Mutagenesis, Methylation, DNA Methylation Assay, Expressing, RNA Sequencing

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Analyze the drug sensitivity of UBE2D3 in KIRC and predict the IC 50 of the drug. (A) Vincristine. (B) Bosutinib. (C) Ambazone. (D) Finefloxacin. (E) Anagrelide. (F) Meclizine. (G) Dabrafenib. (H) Navitoclax. (I) Propranolol. ***, P<0.001. IC 50 , median inhibitory concentration; KIRC, kidney renal clear cell carcinoma.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Concentration Assay

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Molecular docking patterns of key drugs and core targets. (A) Vincristine binding to P113 isosite. (B) Bosutinib binding to S100 isosite. (C) Ambazone binding to L89 isosite. (D) Finefloxacin binding to P95 isosite. (E) Anagrelide binding to T98 isosite. (F) Meclizine binding to P57 isosite. (G) Dabrafenib binding to K63 isosite. (H) Navitoclax binding to A68 isosite. (I) Propanol binding to E9 isosite. (J) Different small molecule drugs binding to target UBE2D3 Vina score comparison.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Binding Assay, Comparison

Journal: Translational Andrology and Urology

Article Title: Systematic analysis of UBE2D3 and its association with prognosis, tumor microenvironment, and drug sensitivity in renal clear cell carcinoma

doi: 10.21037/tau-2025-427

Figure Lengend Snippet: Immunostaining image of UBE2D3 . (A) Expression of UBE2D3 in Para cancer (100×). (B) Expression of UBE2D3 in Para cancer (200×). (C) Expression of UBE2D3 in KIRC (100×). (D) Expression of UBE2D3 in KIRC (200×). (E) IHC staining statistics of UBE2D3 in KIRC and adjacent tissues. **, P<0.01. AOD, average optical density; IHC, immunohistochemistry; KIRC, kidney renal clear cell carcinoma.

Article Snippet: The paraffin-embedded tissue sections were deparaffinized overnight at 4 °C with rabbit anti UBE2D3 (15475-1-AP, Protein, (15475-1-AP, Proteintech, Wuhan, China) at a dilution ratio of 1:400.

Techniques: Immunostaining, Expressing, Immunohistochemistry

Journal: Molecules

Article Title: Vincamine Ameliorates Epithelial-Mesenchymal Transition in Bleomycin-Induced Pulmonary Fibrosis in Rats; Targeting TGF-β/MAPK/Snai1 Pathway

doi: 10.3390/molecules28124665

Figure Lengend Snippet: Effect of vincamine on fibronectin ( A ), N-cadherin ( B ), and collagen ( C ) levels in lung tissues. Bars represent mean ± SD. Significant difference was analyzed by one-way ANOVA test followed by post hoc Dunnett test, where * p < 0.001, compared to sham group, and # p < 0.001, compared to BLM-induced group.

Article Snippet: In lung tissue homogenates, levels of fibronectin, N-cadherin, and collagen were also assessed, according to the manufacturer’s instructions, utilizing rat fibronectin ELISA kit (#MBS761397, MyBioSource, CA, USA), N-cadherin ELISA kit (#KOA0665, Rockland immunochemical Inc., Royersford, PA, USA), and collagen type I ELISA kit (#MBS262647, MyBioSource, CA, USA), respectively.

Techniques: