Journal: Journal of Inflammation Research

Article Title: Involvement of ICAM5 in Carcinostasis Effects on LUAD Based on the ROS1-Related Prognostic Model

doi: 10.2147/JIR.S475088

Figure Lengend Snippet: ( A ) Expression of ICAM5 in normal and tumor tissues of pan-cancer cohorts. ( B ) IHC staining images of ICAM5 in normal lung tissue and LUAD. ( C ) Differences in HLA genes expression in LUAD cohort. ( D ) Differences in immunostimulatory factors expression in LUAD cohort. ( E ) Differences in the results of the ESTIMATE algorithm in pan-cancer cohort. ( F ) Forest plot demonstrating the effect of ICAM5 expression in LUAD on OS, DSS, PFI and DFI. ( G ) KM survival analysis of OS in LUAD. ( H, I ) Enrichment plots from GSEA in the high- ICAM5 expression group and low- ICAM5 expression group. *0.01< p <0.05; **0.001< p <0.01; ***0.0001< p <0.001; **** p <0.0001; ns, not significant.

Article Snippet: Immunohistochemistry (IHC) staining images of ICAM5 from LUAD and healthy lung tissue were obtained from the Human Protein Atlas database ( https://www.proteinatlas.org/ ).

Techniques: Expressing, Immunohistochemistry

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: High OPN expression in HCC. ( a ) The mRNA level of SPP1 in different types of tumor tissues and normal tissues in TIMER database. ( b ) Representative images of OPN protein level in HCC detected by IHC staining in HPA database (×400 magnification). ( c ) Comparison of OPN protein expression between HCC and normal tissues in CPTAC database. A two-sided p value was calculated using a Student’s t -test. The box plot indicates the median (center), 25th and 75th percentiles (box boundaries), and the minimum and maximum (whiskers). ( d ) Single-cell RNA sequencing localization analysis of SPP1. (Left) t-SNE plot of three main cell types (Macrophages, dendritic cells, and B cells) in hepatic monocyte-derived macrophages. (Right) SPP1 was enriched in macrophages clusters.

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques: Expressing, Immunohistochemistry, Comparison, RNA Sequencing, Derivative Assay

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: Diagnostic value of serum OPN for HCC. ( a – d ) Violin plots of serum OPN levels in healthy participants, CLD patients, and HCC patients ( a ), in early-stage HCC patients and advanced-stage HCC patients ( b ), in CLD patients and early-stage HCC patients ( c ), in CLD patients and AFP-negative HCC patients ( d ). ( e – g ) ROC curve analysis reveals the diagnostic potential of serum OPN in 178 HCC patients and 138 controls ( e ), in 98 early-stage HCC patients and 53 chronic liver disease patients ( f ), in 101 AFP-negative HCC patients and 53 chronic liver disease patients ( g ). ( h–j ) The waterfall plot illustrates the risk probability distribution between serum samples of patients with HCC (n = 178) and the controls (n = 138) in the whole cohort ( h ), patients with early-stage HCC (n = 98) and the chronic liver disease (n = 53) ( i ), patients with AFP-negative HCC (n = 101) and the chronic liver disease (n = 53) ( j ). ( k ) The rate of positive results for AFP, OPN, or both, in all patients with HCC, for OPN in AFP-negative HCC, and for OPN in early-stage HCC, respectively. ( l ) Comparison of ROC of four diagnostic models for distinguishing HCC from whole controls.

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques: Diagnostic Assay, Comparison

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: Serum OPN as an independent predictor for HCC survival. ( a ) The inter-relationship between each clinical parameters in HCC patients. Values denote the Pearson correlation coefficients; values closer to 1 indicate a better correlation (* p < 0.05; ** p < 0.001). ( b ) Optimal cutoff value of serum OPN was determined by the “surv_cutpoint” function. ( c ) Forest plot of multivariate Cox regression analysis showing serum OPN level, hepatectomy, tumor size, Child-Pugh grade, and BCLC stage as independent prognostic factors for OS. ( d ) Forest plot of multivariate Cox regression analysis showing serum OPN level, Child-Pugh grade, and BCLC stage as independent prognostic factors for DFS. ( e ) Alluvial diagram showing the interrelationship between AFP status, OPN groups, and OS status in HCC. ( f ) Alluvial diagram showing the interrelationship between OPN groups, BCLC stage, and recurrence status in HCC patients.

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques:

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: Correlation Between Serum OPN and Clinicopathologic Factors in HCC Patients

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques:

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: Prognostic value of OPN in patients with HCC. ( a and b ) In the whole HCC cohort, patients with low levels of serum OPN had longer overall survival ( a ) and disease-free survival (b). ( c – i ) The prognostic value of serum OPN in different subgroups regarding overall survival, including early-stage ( c ), AFP-negative ( d ), Child-Pugh grade A ( e ), hepatectomy ( f ), tumor size ≤ 5 cm ( g ), MVI absent ( h ), ALBI grade 1 ( i ).

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques:

Journal: Journal of Hepatocellular Carcinoma

Article Title: Serum Osteopontin Enhances Hepatocellular Carcinoma Diagnosis and Predicts Anti-PD-L1 Immunotherapy Benefit

doi: 10.2147/JHC.S514144

Figure Lengend Snippet: Serum OPN is a predictor of anti-PD-L1 immunotherapy benefit in patients with HCC. ( a and b ) Immunotherapy significantly prolonged the OS ( a ) and DFS ( b ) of HCC patients with high OPN levels. ( c and d ) HCC patients with low OPN levels did not derived a significant survival benefit from immunotherapy. ( e and f) OS ( e ) and DFS ( f ) of OPN high and OPN low patients in the immunotherapy group were not significantly different. ( g and h ) OPN high patients exhibited a significantly shorter OS ( g ) and DFS ( h ) than OPN low patients in the group without immunotherapy.

Article Snippet: Immunohistochemistry (IHC) staining images of OPN in HCC and normal liver tissues were retrieved from the Human Protein Atlas (HPA; www.proteinatlas.org ) online database.

Techniques: Derivative Assay

Journal: Frontiers in Immunology

Article Title: A multifactorial analysis of FAP to regulate gastrointestinal cancers progression

doi: 10.3389/fimmu.2023.1183440

Figure Lengend Snippet: FAP up-regulation by DNA methylation in gastrointestinal cancers. (A) Expression of FAP mRNA in gastrointestinal cancers. (B, C) Expression of FAP protein in gastrointestinal cancers versus normal tissues (left side), and IHC staining for normal tissue (middle) and tumors (right side) from HPA database. (D) Differential expression of FAP promotor methylation in gastrointestinal tumors versus normal tissues. *** p < 0.001.

Article Snippet: The IHC staining images of FAP in different tumor tissues and normal tissues were obtained from HPA (Human Protein Atlas) dataset.

Techniques: DNA Methylation Assay, Expressing, Immunohistochemistry, Quantitative Proteomics, Methylation

Journal: Frontiers in Immunology

Article Title: A multifactorial analysis of FAP to regulate gastrointestinal cancers progression

doi: 10.3389/fimmu.2023.1183440

Figure Lengend Snippet: Experimental validation of relationship between FAP expression and M2 macrophage polarization. (A) IHC staining of FAP, CD206 and iNOS in LIHC tissues. (B) Experimental diagram. (C, D) Transwell assay investigating the effect of FAP on macrophage invasion. (E) Transwell co-culturing system investigating the effect of FAP on M2 macrophage polarization. * p < 0.05, ** p < 0.01, *** p < 0.001. Scale bar = 1 mm.

Article Snippet: The IHC staining images of FAP in different tumor tissues and normal tissues were obtained from HPA (Human Protein Atlas) dataset.

Techniques: Biomarker Discovery, Expressing, Immunohistochemistry, Transwell Assay

Journal: Journal of Inflammation Research

Article Title: C-Type Lectin Receptors-Triggered Antifungal Immunity May Synergize with and Optimize the Effects of Immunotherapy in Hepatocellular Carcinoma

doi: 10.2147/JIR.S394503

Figure Lengend Snippet: Expression and prognostic analyses of CLRs in HCC tissue and normal tissue data from TCGA. ( A ) Comparative analysis of mRNA expression of CLRs between HCC tissue and normal tissues. ( B ) IHC results from the HPA database showing the protein expression of Dectin-3 and Mincle in normal tissues and HCC tissues. ( C ) CLR promoter methylation levels in normal tissue and HCC tissue. ( D ) Kaplan‒Meier curves for overall survival according to the expression of CLRs. ****p < 0.0001.

Article Snippet: To observe the protein expression levels of CLRs, the Human Protein Atlas (HPA) platform ( www.proteinatlas.org ) was used to acquire immunohistochemistry (IHC) images of CLRs (Dectin-3 and Mincle) staining in normal liver tissues and liver cancer tissues.

Techniques: Expressing, Methylation

Journal: Journal of Inflammation Research

Article Title: C-Type Lectin Receptors-Triggered Antifungal Immunity May Synergize with and Optimize the Effects of Immunotherapy in Hepatocellular Carcinoma

doi: 10.2147/JIR.S394503

Figure Lengend Snippet: Enrichment analysis revealed the potential biological mechanisms of CLRs. ( A ) Volcano map of the DEGs and the results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the DEGs of the high and low Dectin-1 expression groups based on TCGA data. ( B ) Volcano map of the DEGs and the results of GO and KEGG analyses of the DEGs of the high and low Dectin-3 expression groups based on TCGA data. ( C ) Volcano map of the DEGs and the results of GO and KEGG analyses of the DEGs of the high and low Mincle expression groups based on TCGA data.

Article Snippet: To observe the protein expression levels of CLRs, the Human Protein Atlas (HPA) platform ( www.proteinatlas.org ) was used to acquire immunohistochemistry (IHC) images of CLRs (Dectin-3 and Mincle) staining in normal liver tissues and liver cancer tissues.

Techniques: Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Differential expression of PLIN3 and its prognostic potential across various cancers. ( A ) Comparison of PLIN3 levels in tumor versus normal tissue samples from GTEx and TCGA databases. ( B ) PLIN3 mRNA expression in paired tumor and normal samples from TCGA. ( C ) PLIN3 expression profiles across various organs comparing tumor and normal tissues. ( D ) Diagnostic ROC curves evaluating PLIN3 as a biomarker across multiple cancers. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Quantitative Proteomics, Comparison, Expressing, Diagnostic Assay, Biomarker Discovery

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Expressing, Staining

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Survival analysis correlating PLIN3 expression with patient outcomes in pan-cancer. ( A–D ) Forest plots displaying the prognostic significance of PLIN3 for OS, DSS, DFI, and PFI via univariate Cox regression analysis. ( E ) Kaplan-Meier plots for OS, with the red and blue lines representing high and low PLIN3 expression groups, respectively. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Genetic alterations of PLIN3 across various cancers. ( A ) Overview of PLIN3 mutation types using data from the COSMIC database. ( B ) Mutation frequency of PLIN3 across different cancer types. ( C ) Detailed mapping of PLIN3 genetic alterations, including sites and numbers, sourced from cBioPortal. ( D ) Histogram depicting the frequency of somatic copy number alterations of PLIN3 in each cancer type. ( E ) Analysis of differential PLIN3 expression across various CNV types in pan-cancer. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Mutagenesis, Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Associations of PLIN3 with DNA repair, stemness, and epigenetic modifications. ( A ) Heatmap illustrating correlations between PLIN3 and five MMR-related genes. ( B ) Lollipop chart detailing the correlation of PLIN3 levels with DNA methylation-based stem scores. ( C ) Bar chart showing the correlation of PLIN3 levels with RNA methylation-based stem scores. ( D ) Heatmap of the relationships between PLIN3 levels and RNA modifications. ( E ) Heatmap displaying associations of PLIN3 with four methyltransferases. ( F ) Radar chart presenting the Spearman correlation between PLIN3 expression levels and TMB across pan-cancer. ( G ) Radar chart showing the Spearman correlation between PLIN3 expression levels and MSI across pan-cancer. ( H ) Heatmap displaying relationships between PLIN3 expression and ESTIMATE, Immune, and Stromal scores, with statistical significance indicated as *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: DNA Methylation Assay, Methylation, Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Functional analysis of PLIN3 in human cancers using GSEA. Bubble plot illustrating differential enrichment of hallmark gene sets between PLIN3-high and -low tumor patients. Circle size corresponds to the magnitude of the P-value, while color transitions from red to white to blue indicate the strength of NES. The red boxes highlight key pathways that are significantly enriched in PLIN3-high tumor patients, emphasizing their potential biological importance in cancer progression. Abbreviation list of tumor cohorts from TCGA is given in Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Functional Assay

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Correlation analysis between PLIN3 expression and immune cell infiltration. ( A ) Heatmap showing correlations between PLIN3 mRNA expression and the expression of chemokines, chemokine receptors, immune-inhibitors, immune-stimulatory, and MHC genes. ( B ) Heatmaps displaying correlations between PLIN3 expression and infiltration levels of various immune cells. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: PLIN3 as a Potential Marker of M2 Macrophage Infiltration. ( A ) Heatmap showing PLIN3 gene expression across various microdomains in pan-cancer spatial transcriptomic sections. Rows represent different datasets, each labeled in a color specific to the disease type. Columns represent different cell types, with the color intensity on the right scale indicating data values—darker red signifies higher values, and lighter colors indicate lower values. Gray indicates that the cell type is absent in the microregion. The red boxes highlight PLIN3’s widespread expression in macrophage and malignant cell types. ( B ) Spearman correlation analysis used to calculate the correlation between cell content across all spots and between cell content and gene expression levels. Red lines indicate positive correlations, green lines indicate negative correlations, and gray lines indicate non-significant correlations. Line thickness represents the magnitude of the correlation coefficient ( C ) Spatial transcriptomics exploring co-localization patterns of PLIN3 with CD68 and CD163, color-coded by expression levels. Each dot represents a microdomain (spot) with deeper red indicating higher gene expression. ( D ) Expression of PLIN3 in cancer-specific single-cell clusters analyzed using the TISCH database. The red boxes highlight PLIN3’s widespread expression in monocyte, macrophage and malignant cell types. ( E-F ) UMAP plots detailing cell type distributions and PLIN3 intensity in KIRC ( E ) and NSCLC ( F ). Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Marker, Gene Expression, Labeling, Expressing

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Investigation of PLIN3’s role in regulating malignancy in LUAD tumor cells. ( A ) Fluorescent staining of tumor tissues showing CD68 (red) and PLIN3 (green), with DAPI (blue) for counterstaining. ( B ) Fluorescent images of tumor tissues with CD163 (red) and PLIN3 (green), counterstained with DAPI (blue). ( C ) PLIN3 mRNA expression levels in transfected cells. ( D ) Colony formation assay to evaluate the impact of PLIN3 on tumor cell proliferation. ( E ) Wound healing assay assessing the effect of PLIN3 knockdown on tumor cell migration.

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: Staining, Expressing, Transfection, Colony Assay, Wound Healing Assay, Knockdown, Migration

Journal: Journal of Inflammation Research

Article Title: The Role of PLIN3 in Prognosis and Tumor-Associated Macrophage Infiltration: A Pan-Cancer Analysis

doi: 10.2147/JIR.S509245

Figure Lengend Snippet: Drug Sensitivity Analysis. ( A ) Bubble plot illustrating correlations between PLIN3 expressions and drug sensitivity across various databases. A p-value < 0.05 was considered statistically significant. ( B ) The heatmap illustrates potential compounds that target PLIN3, identified using CMap analysis across various cancers. ( C ) Identification of PLIN3-targeting compounds through CMap analysis for LUAD. ( D ) 3D molecular docking illustrations showing interactions between PLIN3 and compound clofibrate. Abbreviation list of tumor cohorts from TCGA is given in. Supplementary Table 1 .

Article Snippet: Figure 3 Differential analysis of PLIN3 protein levels. ( A ) Wilcoxon Rank Sum Tests to compare the statistical differences in expression levels between the tumor and normal groups from the CPTAC dataset. ( B ) IHC images of PLIN3 staining sourced from the Human Protein Atlas.

Techniques: