Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Examination of NEDD1 expression levels in hepatocellular carcinoma tissues. ( A ) The mRNA expression levels of NEDD1 across various cancers were obtained from the TCGA-GTEx database; ( B – F ) NEDD1 expression in the TCGA-LIHC, GSE76427 , GSE144269 , GSE39791 , and GSE112790 datasets; P < 0.05; P < 0.01; * P < 0.001.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Correlation between NEDD1 expression and prognosis in primary HCC. ( A – C ) Overall survival, Disease-specific survival, and Progression-free interval associated with NEDD1 expression in TCGA-LIHC; ( D – H ) Overall survival associated with NEDD1 expression in various subgroups of TCGA-LIHC (age > 60 years, male, Asian, BMI > 25, fibrosis Ishak score 6).

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Diagnostic and prognostic analysis of NEDD1. ( A – C ) Diagnostic ROC curves for NEDD1 in TCGA-LIHC, GSE76427 , and GSE144269 ; ( D – F ) Time-dependent ROC curves for NEDD1 in TCGA-LIHC, GSE76427 , and GSE144269 ; ( G ) Univariate and multivariate Cox regression analysis of NEDD1 expression levels; ( H , I ) Prognostic histograms and calibration curves showing the correlation between NEDD1 expression and multiple clinical variables.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Diagnostic Assay, Expressing

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Enrichment analysis of NEDD1. ( A ) Volcano plot of differentially expressed genes in the high NEDD1 expression group; ( B , C )GO enrichment analysis of differentially expressed genes in the high NEDD1 expression group; ( D ) Signaling pathways positively correlated with high NEDD1 expression; ( E ) Signaling pathways negatively correlated with high NEDD1 expression.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing, Protein-Protein interactions

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Methylation of the NEDD1 gene. ( A ) DNA methylation level of the NEDD1 promoter region in TCGA-LIHC; ( B – D ) OS, DSS, and PFI analyses for four subgroups based on NEDD1 gene expression and promoter methylation levels in TCGA-LIHC; ( E , F ) Methylation levels at nine sites in the NEDD1 promoter region in HCC tissues versus normal liver tissues in TCGA-LIHC; ( G – K ) Methylation levels at five specific sites in the NEDD1 promoter region in HCC and normal liver tissues.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Methylation, DNA Methylation Assay, Gene Expression

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Phosphorylation of the NEDD1 protein. ( A – G ) Phosphorylation levels of seven NEDD1 sites (s403, s404, s412, s430, s517, t522, s523) in the PDC000199 dataset; ( H ) Single-factor Cox survival analysis for each phosphorylation site.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Phospho-proteomics

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Drug prediction related to NEDD1. ( A , B ) CTRP and GDSC2 drug databases predicting the correlation between NEDD1 expression levels and drug response; ( C ) Number of overlapping drugs predicted by CTRP and GDSC2; (D, E ) Scatter plot showing the correlation between NEDD1 expression levels and PD-1 or CTLA4; ( F – I ) Immunotherapy analysis of PD-1 or CTLA4 expression in relation to NEDD1 expression in TCIA.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Expression profiles of NEDD1 and its associated genes in a single-cell dataset. ( A ) The gene most significantly interacting with NEDD1 in the STRING database was MZT2B; ( B , C ) Analysis of MZT2B expression in the TCGA-LIHC dataset and its association with prognosis. ( D ) UMAP distribution of cell subtypes in the GSE140228 -HCC dataset; ( E ) Correlation scatter plot showing the relationship between NEDD1 and MZT2B gene expression levels across various cell subtypes in the GSE140228 -HCC dataset, with the top 10 cell subtypes identified based on their correlation coefficient (R). ( F – H ) Survival analysis of infiltrating NK cells, monocytes, and macrophages in the TCGA-LIHC dataset.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing, Single Cell, Gene Expression

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Validation of NEDD1 expression and its effect on the biological behavior of HCC cells. ( A – D ) Immunohistochemical and RT-qPCR evaluation of NEDD1 expression in HCC tissue and adjacent normal liver tissue; ( E ) CRISPR-Cas9 screens using the DepMap database to identify the top 200 cell lines based on CERES scores; ( F ) Comparative analysis of NEDD1 gene expression in normal liver cells, 97 H, and HUH7 cells; ( G , H ) Western blot and RT-qPCR experiments to validate NEDD1 knockdown efficiency; ( I , J ) Viability and colony-forming ability of 97 H and HUH7 cells post-transfection (CCK8 assay and clonal formation assay); ( K ) Transwell assay to analyze the effect of NEDD1 on the migration of 97 H and HUH7 cells; ( L ) Representative tumor images showing differences in tumor mass and size at the end of the experiment between si-NC and si-1 experimental groups in the HUH7 cell line. P < 0.05; * P < 0.01; ** P < 0.001.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Biomarker Discovery, Expressing, Immunohistochemical staining, Quantitative RT-PCR, CRISPR, Gene Expression, Western Blot, Knockdown, Transfection, CCK-8 Assay, Tube Formation Assay, Transwell Assay, Migration

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Expression of NEDD1 and MZT2B in the spatial transcriptome. ( A , F , K , P ) Spatial maps showing malignant and non-malignant regions in the HRA000437-L-HCC dataset; ( B , C , G , H , L , M , Q , R ) Expression of NEDD1 and MZT2B genes in the four slice datasets. ( D , I , N , S ) Histograms of the expression of NEDD1 in each slice dataset; ( E , J , O , T ) Histograms of the expression of MZT2B in each slice dataset.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Expressing

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: Evaluation of Spatial Features for the NEDD1, MZT2B, and APOE Gene Sets in HCC Sections. ( A , D , G , J ) Spatial maps showing detailed cellular component regions in the HRA000437-L-HCC dataset; ( B , E , H , K ) Specific gene sets (NEDD1, MZT2B, and APOE) score active landscapes in microregions; ( C , F , I , L ) The correlation between AUC scores of specific gene sets (NEDD1, MZT2B, and APOE) and various cellular components.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques:

Journal: Scientific Reports

Article Title: Multi-omics analysis of NEDD1 in hepatocellular carcinoma: biological function, prognostic value, and clinical significance

doi: 10.1038/s41598-026-42505-z

Figure Lengend Snippet: A Model of NEDD1 Regulatory Network and Function in HCC. This schematic summarizes an integrated mechanism: NEDD1 overexpression, potentially regulated by promoter hypomethylation, drives tumor malignancy via key pathways and correlates with poor prognosis. The NEDD1-MZT2B module shows context-specific expression in tumor cells and APOE+ macrophages, linking to immune checkpoint upregulation and therapy resistance, thereby contributing to an immunosuppressive microenvironment.

Article Snippet: The membrane was blocked with 5% skim milk powder for 50 min, then incubated overnight at 4 °C with primary antibodies: NEDD1 (1:1000, Proteintech, 13993-1-AP) and Beta Actin (1:20000, Proteintech, 66009-1-Ig).

Techniques: Over Expression, Expressing