Journal: Frontiers in Immunology

Article Title: Exploratory transcriptomic analysis of mouse articular cartilage in response to tissue inhibitor of metalloproteinase 3 identifies inflammation-associated gene expression changes

doi: 10.3389/fimmu.2026.1794078

Figure Lengend Snippet: RNA-seq analysis of TIMP-3–treated cartilage under hypoxia. (A) MA plot showing differential expression between TIMP-3–treated and control articular cartilage, with log 2 FC plotted against average log 2 CPM expression (n = 4). Grey: no change, red: upregulated, blue: downregulated (P < 0.01, |log 2 FC| > 0.58). The 10 most highly expressed regulated genes are labelled. G1 and G2 correspond to E430024I08Rik and AC127578.1 respectively. Complete gene lists are in . (B) Heatmap of differentially expressed genes (log 2 FC versus the mean of the controls). Genes are ordered by hierarchical clustering. Sample labels: HC1-4: hypoxia controls; HT1-4: hypoxia TIMP-3-treated. (C) Protein–protein interaction (PPI) network corresponding to genes downregulated by TIMP-3 under hypoxia (P <0.01 by quasi-likelihood F-test in edgeR, |log 2 FC| > 0.58), generated using STRING (default interaction score ≥ 0.400). All nodes represent the initially filtered gene list and are included to show the network context and highlight that only Pbk and Racgap1 display a documented interaction. Line colors indicate evidence type: green, text mining; pink, experimental; black, co-expression. Combined interaction score: 0.711. (D) RT-qPCR validation. RNA-seq (left) and RT-qPCR (right) data shown as log 2 FC versus the mean of the controls (mean ± SD, n = 4). RNA-seq: log 2 FC were calculated from normalized CPM values; § FDR < 0.05 (hypoxia effect), # P < 0.01 (TIMP-3 effect) by quasi-likelihood F-test applied to raw counts (edgeR); RT-qPCR: *P < 0.05, **P < 0.01 by unpaired two-sided Welch’s t-test on log 2 FC values (-ΔΔCq). CPM, counts per million; Ctrl, control.

Article Snippet: TaqMan assays used included Saa3 (Mm00441203_m1), Il17b (Mm01258783_m1), Mmp3 (Mm00440295_m1), Lcn2 (Mm01324470_m1), Pbk (Mm01313789_g1), Racgap1 (Mm00488845_m1), Hprt (Mm00446968_m1).

Techniques: RNA Sequencing, Quantitative Proteomics, Control, Expressing, Generated, Quantitative RT-PCR, Biomarker Discovery

Journal: Cells

Article Title: RacGAP1 Plays an Oncogenic Role in Lung Adenocarcinoma by Regulating the Wnt/β-Catenin Pathway

doi: 10.3390/cells14110773

Figure Lengend Snippet: RacGAP1 expression in lung adenocarcinoma tissues and normal tissues. RacGAP1 mRNA levels in lung adenocarcinoma (T) and non-tumoral (NT) samples from ( a ) GSE31210 , ( b ) GSE10072 , ( c ) GSE33532 , ( d ) GSE19188 and ( e ) TCGA-LUAD datasets from the R2 platform ( https://r2.amc.nl accessed on 10 October 2023). ( f ) Box plot reporting RacGAP1 protein levels (Z-value) in tumoral (T) and non-tumoral (NT) samples from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset using the UALCAN database ( https://ualcan.path.uab.edu/index.html accessed on 10 October 2023). **** p < 0.0001 for Mann-Whitney test ( a , b , e , f ) and Unpaired t -test ( c , d ).

Article Snippet: At 80–90% confluence, the cells were transfected with 50 nM of Mission ® esiRNA RacGAP1 (EHU081301, Merck, Darmstadt, Germany), a heterogeneous pool of siRNAs effectively targeting the transcript, or Mission siRNA Universal Negative Control #1 (SIC001, Merck, Darmstadt, Germany), using 2 μL Lipofectamine 2000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) per 1 μg of nucleic acids.

Techniques: Expressing, MANN-WHITNEY

Journal: Cells

Article Title: RacGAP1 Plays an Oncogenic Role in Lung Adenocarcinoma by Regulating the Wnt/β-Catenin Pathway

doi: 10.3390/cells14110773

Figure Lengend Snippet: Correlation between RacGAP1 expression and clinical features in lung adenocarcinoma patients. Box plots showing RacGAP1 expression related to ( a ) race, ( b ) age, ( c ) sex, ( d ) tumor stage from TCGA dataset. Stacked bar graphs showing RacGAP1 expression related to ( e ) tumor size or ( f ) lymph node metastasis, referred to the number of patients (Y axis) in the two groups characterized by RacGAP1 expression < median RNAseq and ≥ median RNAseq (X axis); analyses were performed on LUAD patients from TCGA dataset by chi-square test. RacGAP1 expression in non-tumoral (NT) samples and tumoral sample from patients with different smoking habits in ( g ) GSE31210 and ( h ) GSE10072 datasets from the R2 platform. The number of patients is reported for each group ( n =). ns: not significant, * p < 0.05, ** p < 0.01, **** p < 0.0001 for one-way ANOVA ( a – d , g , h ) and chi-square test ( e , f ).

Article Snippet: At 80–90% confluence, the cells were transfected with 50 nM of Mission ® esiRNA RacGAP1 (EHU081301, Merck, Darmstadt, Germany), a heterogeneous pool of siRNAs effectively targeting the transcript, or Mission siRNA Universal Negative Control #1 (SIC001, Merck, Darmstadt, Germany), using 2 μL Lipofectamine 2000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) per 1 μg of nucleic acids.

Techniques: Expressing

Journal: Cells

Article Title: RacGAP1 Plays an Oncogenic Role in Lung Adenocarcinoma by Regulating the Wnt/β-Catenin Pathway

doi: 10.3390/cells14110773

Figure Lengend Snippet: Correlation between RacGAP1 expression and survival in lung adenocarcinoma patients. The correlation between RacGAP1 expression (red line: high expression; blue line: low expression according to median value) and overall survival (reported as follow-up months) was analyzed through the Kaplan–Meier plotter on ( a ) TCGA-LUAD and ( b ) GSE31210 datasets using the R2 platform. ( c ) Correlation analysis between RacGAP1 expression and relapse-free survival performed on GSE31210 dataset. p -values were calculated by two-tailed chi-square test and are reported on the graphs.

Article Snippet: At 80–90% confluence, the cells were transfected with 50 nM of Mission ® esiRNA RacGAP1 (EHU081301, Merck, Darmstadt, Germany), a heterogeneous pool of siRNAs effectively targeting the transcript, or Mission siRNA Universal Negative Control #1 (SIC001, Merck, Darmstadt, Germany), using 2 μL Lipofectamine 2000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) per 1 μg of nucleic acids.

Techniques: Expressing, Two Tailed Test

Journal: Cells

Article Title: RacGAP1 Plays an Oncogenic Role in Lung Adenocarcinoma by Regulating the Wnt/β-Catenin Pathway

doi: 10.3390/cells14110773

Figure Lengend Snippet: Effect of RacGAP1 silencing on cell proliferation, migration and invasion. Cells were transfected with the indicated molecules, control siRNA molecule (siCTRL) and siRNA against RacGAP1 (siRacGAP1). ( a ) RacGAP1 silencing efficiency was evaluated by determining its expression in the different samples through RT-qPCR (left panel) and Western blot (right panel) after 48 h from transfections. RacGAP1 expression values are reported as fold mean (2 −ΔΔCt ) relative to control (siCTRL) set as 1. ( b ) Cell growth was evaluated by MTT assay 48 h after transfections; the values are reported as percentage from transfection control experiment (siCTRL), which was set to 100. ( c ) Cell migration was assessed by wound-healing assay. Left panel: representative images of migrating cells; Right panel: bar graph showing percentage of wound closure relative to transfection control experiments at 24h and 48h after transfection compared to T0. ( d ) Cell invasion was measured by transwell assay. Left panel: four representative crystal violet-stained fields of invading cells; Right panel: bar graph showing cell counting percentage of invading siRacGAP1 transfected cells relative to siCTRL transfected cells set at 100. Data are the mean ± SD of three independent experiments. * p < 0.05, ** p < 0.01, **** p < 0.0001 for Student’s t -test.

Article Snippet: At 80–90% confluence, the cells were transfected with 50 nM of Mission ® esiRNA RacGAP1 (EHU081301, Merck, Darmstadt, Germany), a heterogeneous pool of siRNAs effectively targeting the transcript, or Mission siRNA Universal Negative Control #1 (SIC001, Merck, Darmstadt, Germany), using 2 μL Lipofectamine 2000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) per 1 μg of nucleic acids.

Techniques: Migration, Transfection, Control, Expressing, Quantitative RT-PCR, Western Blot, MTT Assay, Wound Healing Assay, Transwell Assay, Staining, Cell Counting

Journal: Cells

Article Title: RacGAP1 Plays an Oncogenic Role in Lung Adenocarcinoma by Regulating the Wnt/β-Catenin Pathway

doi: 10.3390/cells14110773

Figure Lengend Snippet: Role of RacGAP1 in the Wnt pathway regulation. ( a ) Box plot reporting RacGAP1 protein levels (Z-value) in normal samples, in patients with altered Wnt pathway status and in patients without Wnt alteration (Others) from Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset using the UALCAN database. Number of analyzed patients (n =) is reported in parenthesis; ( b ) Scatter plot representing the positive correlation between RacGAP1 and β-catenin expression in the LUAD dataset from TCGA ( r = 0.164, p = 0.0002). ( c ) β-catenin transcriptional activity was evaluated using the TOP flash assay in A549 cells transfected with the indicated molecules. The Luc/Rl ratio (firefly luciferase activity/Renilla reniformis activity) was determined 48 h after transfections and reported as percentage from transfection control experiment (siCTRL), which was set to 100. ( d ) β-catenin expression levels were evaluated by RT-qPCR on RNA purified from A549 48 h after transfections with the indicated molecules. The values are reported as fold mean (2 −ΔΔCt ) relative to control (siCTRL) set as 1. ( e ) Western blot analysis of cytoplasmic and nuclear protein extracts from A549 cells 48 h after transfections with the indicated molecules. Cropped images of blots for β-catenin and loading controls, i.e., α-tubulin and histone H3 for the cytoplasmic and nuclear fractions, respectively. ( f ) Expression levels of Wnt-related genes were evaluated by RT-qPCR on RNA purified from A549 48 h after transfections with the indicated molecules. The values are reported as fold mean (2 −ΔΔCt ) relative to control (siCTRL) set as 1. Data are the mean ± SD of three independent experiments. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 for one-way ANOVA ( a ), Pearson coefficient analysis ( b ) and t -test ( c , d , f ).

Article Snippet: At 80–90% confluence, the cells were transfected with 50 nM of Mission ® esiRNA RacGAP1 (EHU081301, Merck, Darmstadt, Germany), a heterogeneous pool of siRNAs effectively targeting the transcript, or Mission siRNA Universal Negative Control #1 (SIC001, Merck, Darmstadt, Germany), using 2 μL Lipofectamine 2000 (Invitrogen, Thermo Fisher Scientific, Waltham, MA, USA) per 1 μg of nucleic acids.

Techniques: Expressing, Activity Assay, Transfection, Luciferase, Control, Quantitative RT-PCR, Purification, Western Blot

Journal: Frontiers in Oncology

Article Title: RACGAP1 and MKI67 are potential prognostic biomarker in hepatocellular carcinoma caused by HBV/HCV via lactylation

doi: 10.3389/fonc.2025.1537084

Figure Lengend Snippet: A comprehensive Correlation Analysis Between LRG Expressions Enrichments and Viruses (A, B) Box plots demonstrating the most relevant enrichments of MKI67 and RACGAP1 between high vs low expression in liver cancer (C, D) The box plot showing the significant correlation of these genes with HCV-associated HCC (E, F) The box plot showing the significant correlation of these genes with HBV associated HCC. Statistical significance is indicated as follows: ns (Non-significant) p > 0.05; *p < 0.05; **p < 0.01; ***p < 0.001; ****p < 0.0001.

Article Snippet: The sections were incubated with primary antibodies against MKI67 (1:100 dilution, Ki67 rabbit mAb (A20018) and RACGAP1 (1:100 dilution, RACGAP1 rabbit mAb (A24948), ABclonal) overnight at 4°C.

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: RACGAP1 and MKI67 are potential prognostic biomarker in hepatocellular carcinoma caused by HBV/HCV via lactylation

doi: 10.3389/fonc.2025.1537084

Figure Lengend Snippet: Validation of MKI67 and RACGAP1 expression levels in HCC groups by IHC (A, C, E) The images representing the expression level of MKI67 between HCC, HCC-HBV and HCC-HCV, similarly (B, D, F) images showing the RACGAP1 expression between HCC, HCC-HBV and HCC-HCV (G) The box plots indicating the OD values of these genes across the HCC groups (H, I) The correlation of MKI67 , RACGAP1 expression with pathological grade and bilirubin levels indicating by box plot and scatter plot, respectively. Statistical significance is indicated as follows: ns (non-significant) p > 0.05; *p < 0.05; **p < 0.01; ***p < 0.001.

Article Snippet: The sections were incubated with primary antibodies against MKI67 (1:100 dilution, Ki67 rabbit mAb (A20018) and RACGAP1 (1:100 dilution, RACGAP1 rabbit mAb (A24948), ABclonal) overnight at 4°C.

Techniques: Biomarker Discovery, Expressing