Journal: Frontiers in Oncology

Article Title: Downregulated ARID1A by miR-185 Is Associated With Poor Prognosis and Adverse Outcomes in Colon Adenocarcinoma

doi: 10.3389/fonc.2021.679334

Figure Lengend Snippet: Differential expression of ARID1A. (A) Differential ARID1A expression analysis across several cancer types (significant differences by the Mann-Whitney U test are marked with red*). Left, normal; right, tumor); (B) ARID1A expression include paired tumor and adjacent normal tissues from Gene chip data; (C) ARID1A expression include paired tumor and adjacent normal tissues from RNA-Seq data; (D) Significant different expression of ARID1A through metastases, normal, and tumors; (E–F) Experimental verification of ARID1A mRNA and protein levels in colon cancer cell line using qPCR and western blot, respectively.

Article Snippet: After blocking with 5% non-fat milk in Tris-buffered saline (1× TBS) containing 0.05% Tween-20, the membrane was incubated overnight at 4°C with rabbit antibodies against ARID1A (1:300, CUSABIO TECHNOLOGY), βactin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd).

Techniques: Quantitative Proteomics, Expressing, MANN-WHITNEY, RNA Sequencing, Western Blot

Journal: Frontiers in Oncology

Article Title: Downregulated ARID1A by miR-185 Is Associated With Poor Prognosis and Adverse Outcomes in Colon Adenocarcinoma

doi: 10.3389/fonc.2021.679334

Figure Lengend Snippet: COAD patients with low ARID1A mRNA levels had a poorer prognosis and predictive value in the pathological stages of COAD. (A) Prognostic value of ARID1A in primary colon adenocarcinoma using Kaplan-Meier plotter from GEPIA2, OS, Overall survival, DFS, Disease free survival; (B) Prognostic value of ARID1A in metastases using Kaplan-Meier plotter from CanEvolve: M-OS, Metastases overall survival, M-DSS, disease-specific survival, and M-DFS, Metastases disease-free survival; (C) Pathologic M, pathologic N, and pathologic T, respectively; (D) Lymphatic invasion, microsatellite instability, and Vital status, respectively. * p < 0.05 and *** p < 0.001.

Article Snippet: After blocking with 5% non-fat milk in Tris-buffered saline (1× TBS) containing 0.05% Tween-20, the membrane was incubated overnight at 4°C with rabbit antibodies against ARID1A (1:300, CUSABIO TECHNOLOGY), βactin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd).

Techniques:

Journal: Frontiers in Oncology

Article Title: Downregulated ARID1A by miR-185 Is Associated With Poor Prognosis and Adverse Outcomes in Colon Adenocarcinoma

doi: 10.3389/fonc.2021.679334

Figure Lengend Snippet: Mir-185 downregulates ARID1A in colon cancer. (A) ARID1A can be controlled by mir-185-5p; (B) Transcription factors that regulate ARID1A expression from Cistrome (Chip-Seq data); (C) Mir-185 is overexpressed in COAD; (D) ARID1A is negatively correlated with mir-185-5p in COAD; (E, F) Mir185 mimics and inhibitors results detected by qPCR; (G) Mir185 mimics and inhibitors results detected by western blot.

Article Snippet: After blocking with 5% non-fat milk in Tris-buffered saline (1× TBS) containing 0.05% Tween-20, the membrane was incubated overnight at 4°C with rabbit antibodies against ARID1A (1:300, CUSABIO TECHNOLOGY), βactin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd).

Techniques: Expressing, ChIP-sequencing, Western Blot

Journal: Frontiers in Oncology

Article Title: Downregulated ARID1A by miR-185 Is Associated With Poor Prognosis and Adverse Outcomes in Colon Adenocarcinoma

doi: 10.3389/fonc.2021.679334

Figure Lengend Snippet: The correlation between ARID1A and immune cell infiltration. (A) The significant positive correlation between ARID1A and subtypes of immune cells (TIMER); (B) Kaplan-Meier curves for the immune infiltrates and ARID1A Expression. The correlation between ARID1A expression and the abundance of CD4+ T cells, B cells, and natural killer cells, respectively (TIMER).

Article Snippet: After blocking with 5% non-fat milk in Tris-buffered saline (1× TBS) containing 0.05% Tween-20, the membrane was incubated overnight at 4°C with rabbit antibodies against ARID1A (1:300, CUSABIO TECHNOLOGY), βactin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd).

Techniques: Expressing

Journal: Frontiers in Oncology

Article Title: Downregulated ARID1A by miR-185 Is Associated With Poor Prognosis and Adverse Outcomes in Colon Adenocarcinoma

doi: 10.3389/fonc.2021.679334

Figure Lengend Snippet: Correlation analysis between ARID1A and gene biomarkers of immune cells in COAD (TIMER).

Article Snippet: After blocking with 5% non-fat milk in Tris-buffered saline (1× TBS) containing 0.05% Tween-20, the membrane was incubated overnight at 4°C with rabbit antibodies against ARID1A (1:300, CUSABIO TECHNOLOGY), βactin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd).

Techniques:

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: Primer lists and their sequences used in the study

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Sequencing, Negative Control

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: Identified differentially expressed genes (DEGs)in HCT116‐ARID1A‐wild‐type vs. HCT116‐ARID1A‐knockout (A) Volcano plot of differentially expressed genes (B) Heat map of DEGs in control and knockout groups (C) upper part,KEGG and GO enrichment analysis of differentially upregulated genes. (C) lower part ,KEGG and GO enrichment analysis of differentially downregulated genes

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Knock-Out, Control

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: Expression of EMT‐related markers (VIM) and correlation with ARID1A (A) Vimentin (VIM) overexpression was found in KO cell lines (B) VIM high expression is associated with a poor prognosis in COAD (C) VIM displays high expression in cells with lower ARID1A expression (SW620&RKO) and low expression in cells with a high ARID1A expression (HCT116&LoVo) (D) colon cancer samples were examined for co‐expression of Vimentin and ARID1A (E) GEPIA2 database visualization of the co‐expression of Vimentin and ARID1A in colon cancer tissue.

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Expressing, Over Expression

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: Expression of EMT‐related marker (CDH1) and correlation with ARID1A (A) CDH1 is downregulated in ARID1A deficient cells (B) shows a Kaplan–Maier result of CDH1 in COAD (C and D) E‐cadherin expression correlates positively with ARID1A expression in COAD

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Expressing, Marker

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: ARID1A sequence and mutation profiles in CRC cells used in the research

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Sequencing, Mutagenesis, Variant Assay

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: ARID1A knockdown in HCT116 cell line (A) At 50 nM, 4 μl siRNA‐ARID1A, qPCR demonstrates no change of vimentin and E‐cadherin expression levels in HCT116 after 24 h transfection (B) ARID1A deficiency at 75 nM, 6 μl siRNA‐ARID1A for 24 h activates VIM and suppress CDH1 in HCT116 (C) qPCR results of ARID1A downregulation using 75 nM, 6‐μl siRNA for 48 h showed VIM and CDH1 expression in HCT116. ARID1A silencing altered VIM and E‐cadherin expression (D and E) VIM and CDH1 expression were altered in qPCR results of LS174‐T‐ARID1A knocked down for 24 and 48 h, respectively. ns, Non‐significant; *p < 0.05, **p < 0.001, and ***p < 0.0001

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Knockdown, Expressing, Transfection

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: ARID1A silencing alters VIM and E‐cadherin expression (A and B) VIM and CDH1 expression were altered in WB results after ARID1A knocked down for 24 and 48 h.

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Expressing

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: ARID1A knockdown promotes colon cell line migration and proliferation (A and B) The effect of ARID1A depletion on HCT116 and LS174T cell migration (C) The effect of ARID1A depletion on LS174T cell invasion (D) The proliferation of HCT116 cells was assessed at specified times following ARID1A siRNA transfection (E) Immunoprecipitated DNA from ChIP experiments with anti‐ARID1A antibody was examined by real‐time qPCR using E‐cadherin and Vimentin‐specific promoter primers. IP stands for Immunoprecipitated. *p < 0.05, **p < 0.001, and ***p < 0.0001. Statistical differences were calculated using an imageJ software.

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques: Knockdown, Migration, Transfection, Immunoprecipitation, Software

Journal: Journal of Cellular and Molecular Medicine

Article Title: ARID1A downregulation promotes cell proliferation and migration of colon cancer via VIM activation and CDH1 suppression

doi: 10.1111/jcmm.17590

Figure Lengend Snippet: List of 87 ARID1A interaction proteins in HCT116

Article Snippet: The membrane was incubated overnight at 4°C with rabbit antibodies against β‐actin (1:1000, Beijing Zhongshan Biotechnology Co., Ltd); ARID1A (1:300, CUSABIO TECHNOLOGY LLC); E‐cadherin Polyclonal antibody, cat on: 20874‐1‐AP; and Vimentin Polyclonal antibody, cat no: 10366‐1‐AP after blocking with 5% non‐fat milk in Tris‐buffered saline containing 0.05%Tween‐20 (1–1000).

Techniques:

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Arid1a deletion and Pik3ca mutation synergistically induces mucosal hyperplasia and gastric cancer in mice (A and B) Analysis of TCGA database according to the molecular GC subtypes. (A) PCA plot (B) gene mutation map. (C) Construction schema of Tff1 cre, Arid1a flox/flox , Cdkn2a (p16) flox/flox , and Loxp-STOP-Loxp Pik3ca H1047R mice. (D) ARID1A staining in WT and Tff1 cre, Arid1a flox/flox mice ( n = 4 mice/group). (E) HE and Ki67/CD45/Alcian blue staining in WT/Arid/Ap16/Apik/APP mice. Numbers of positive cells are quantified ( n = 4 mice/group). The p value was calculated using a t test. (F) Gross findings and HE staining in representative APP mice (aged 6 months) (independent repeats, n = 3). (G) Outline mapping of the dysplasia and adenocarcinoma development according to the combination of the Arid1a , Pik3ca , and p16 mutations. (H) Cumulative incidence of mortality comparing APP and Apik mice ( n = 9 and 5 mice/group respectively). The p value was calculated using a log rank test. Scale bars, 100 μm. Mean ± standard error of the mean (SEM). ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Mutagenesis, Staining

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Aberrant type 2 immunity is involved in Arid1a -mutated tumorigenesis in mice (A–H) Bulk RNA-seq comparing WT and Arid/Ap16/Apik/APP antrum ( n = 2 mice/group). (A) PCA plot. (B) Heatmap showing the expression similarity between samples. The distance between samples is measured by calculating the single-parameter quality control and sample comparison for RNA-seq (SERE) coefficient between each pair of samples. (C) Heatmap of the gene expression. (D) Volcano plot. (E) Venn diagram of the upregulated DEGs of Arid/Ap16/Apik/APP mice compared with WT mice. (F) GSEA analysis with Hallmark gene sets shown as heatmap. (G) GSEA analysis with KEGG (Kyoto Encyclopedia of Genes and Genomes) gene sets shown as heatmap. (H) Gene expressions of ILC2, eosinophil, and mast cells shown as heatmap.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: RNA Sequencing, Expressing, Control, Comparison, Gene Expression

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Arid1a depletion expands epithelial IL-33 expression in pit cell lineage (A) Schematic representation of the single-cell RNA-seq analysis conducted on gastric specimens from Arid and WT mice. (B) UMAP plot displaying 5,880 cells from the gastric antrum across 15 clusters (left) with cells from Arid and WT mice separately visualized (right). (C) Heatmap showing the top five differentially expressed genes across the 15 clusters. (D) Il33 expression across the 15 clusters in Arid and WT mice, depicted in a violin plot. (E) Feature plot illustrating Il33 expression in Arid and WT mice. (F) UMAP plot of gastric epithelial cells in Arid and WT mice. (G) Il33 expression in gastric epithelial cells from Arid and WT mice, depicted in a violin plot. (H) Distribution of cells across the eight gastric epithelial cell clusters in Arid and WT mice. (I) IL-33 (green)/Ki67 (red) and IL-33 (green)/MUC5AC (red) staining in Arid1a -mutated mice. Numbers of positive cells are quantified ( n = 4 mice/group). The p value was calculated using a t test. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Expressing, RNA Sequencing, Staining

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Arid1a mutation disrupts normal differentiation but expands IL-33-expressing pit and metaplastic lineage (A) Trajectory analysis as visualized in the UMAP plot depicting gastric pit/pit progenitor/progenitor cells in WT and Arid mice. (B) Calculation of CytoTRACE2 scores according to the cell clusters presented in a violin plot. (C) Ordering of cell clusters based on Monocle3 pseudotime analysis. (D) Pseudotime calculation visualized in the UMAP plot. (E) Pseudotime calculation in the UMAP plot, separated by WT and Arid mice. (F) Expression of Il33 , Muc5ac , Cblif , Tff2 , Cd44 , and Clu according to the cell clusters as visualized in violin plot. (G) The scheme illustrating alterations in cell differentiation induced by the Arid1a mutation. (H) CD44v6, TFF2, and CLU staining in Arid1a -mutated mice. Numbers of positive cells are quantified ( n = 4 mice/group). The p value was calculated using a t test. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Mutagenesis, Expressing, Cell Differentiation, Staining

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Expansion of IL-33-expressing lineage is driven by WNT inactivation mediated through Arid1a mutation (A) Schematic representation of tumor organoid generation. Organoids generated from Arid1a flox/flox , Cdkn2a (p16) flox/flox , and Loxp-STOP-Loxp Pik3ca H1047R mice were infected with GFP-Cre lentivirus (hereafter APP [Cre] organoids). (B) HE and Alcian blue staining in WT and APP (Cre) organoids ( n = 20/group). (C) GSEA with gene sets of WNT/β-catenin pathway in WT and APP (Cre) organoids. (D) Venn diagram of the upregulated DEGs of APP (Cre) organoids and Arid1a- mutated mice. (E) IL-33 staining in WT and APP (Cre) organoids ( n = 20/group). (F) GSEA with gene sets of WNT/β-catenin pathway in Arid, Ap16, and APP mice compared with WT mice. (G) WT organoids were treated with shRNA- Arid1a or a control adenovirus. Western blots for ARID1A, IL-33, CTNNB1, AXIN2, and β-actin are shown (independent repeats: n = 3). (H) WT organoids were cultured in a medium without WNT/R-spondin. HE, Alcian blue, MUC5AC (red)/IL-33 (green), and β-catenin (red) staining are shown ( n = 20/group). (I) RNA-ISH using Lgr4 (red)/Lgr5 (blue) probes in WT, Arid, and APP mice ( n = 4/group). The p value was calculated using a t test. (J–L) Lineage tracing experiments. (J) Gene construction schema of Lgr5 -CreERT; Rosa26 -Lox-Stop-Lox- tdTomato ; Arid1a flox/flox mice. (K) Schematic of the experimental protocol and representative image of tdTomato and GFP expression in the antrum gland following tamoxifen induction. (L) RFP (red)/ARID1A (green) (top) and RFP (red)/IL-33 (green) (bottom) staining of Lgr5 -CreERT; Rosa26 -Lox-Stop-Lox- tdTomato ; Arid1a flox/flox mice (days 8, 15, and 22). Numbers of ARID1A and IL-33-positive cells in the RFP-positive cells and RFP-negative cells are quantified ( n = 4/group). The p value was calculated using a t test. (M and N) GSEA with gene sets of WNT/β-catenin pathway in human gastric cancers with and without ARID1A mutation. (M) Sigmoid curve. (N) Heatmap of representative WNT target genes. (O) Schema of the relationship between ARID1A mutation, WNT/β-catenin pathway, and IL-33 upregulation. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Expressing, Mutagenesis, Generated, Infection, Staining, shRNA, Control, Western Blot, Cell Culture

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Activated IL-33/IL-13 axis could be a therapeutic target in Arid1a -mutated gastric cancers (A) Re-PCA, UMAP, and the clustering of inflammatory cells are shown. (B) Feature plots of Gata3 , Icos , and Kit shown as UMAP plots. (C) Heatmap showing the top 10 differentially expressed genes across the five clusters. (D) Five clusters split by WT and Arid mice shown as UMAP plots. (E) Distribution of cells across the five inflammatory cell clusters in Arid and WT mice. (F) ICOS (green), ST2 (red), and tryptase (red)/DCLK1 (green) staining of WT and Arid/Ap16/Apik/APP mice. Numbers of positive cells per field are quantified ( n = 4/group). The p value was calculated using a t test. (G) FACS gating strategy of ILC2s. CD45 + Lin − CD90.2 + ICOS + cells were defined as ILC2s and the numbers in WT and APP mice were quantified ( n = 3/group). The p value was calculated using a t test. (H) Treatment with adeno-associated virus vectors expressing type 1 cytokines (IL-12a/-12b/-23a and TNF), type 2 cytokines (IL-25/-33/-5/-13), and IL-13 in WT mice. Ki67 (red)/GSII (green) staining is shown. Numbers of positive cells are quantified ( n = 4 mice/group). The p value was calculated using a t test. (I) H&E staining of APP mice treated with control antibody or neutralizing antibody against IL-33. Average gland heights were quantified ( n = 4/group). The p value was calculated using a t test. (J) H&E staining of APP mice treated with control antibody or neutralizing antibodies against ICOS. Average gland heights were quantified ( n = 4/group). The p value was calculated using a t test. (K) H&E staining of APP mice treated with control antibody or neutralizing antibody against IL-13. Average gland heights were quantified ( n = 3/group). The p value was calculated using a t test. (L) Scheme of the type 2 immunity-dependent tumorigenesis in APP mice. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Staining, Virus, Expressing, Control

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: ARID1A and PIK3CA cooperatively orchestrate AKT phosphorylation and cell proliferation in gastric epithelial cells (A) Representative image and proliferation assay of WT and APP (Cre) organoids. Organoid diameters were quantified at the indicated points ( n = 20/group). The p value was calculated using a t test. (B) Gross findings in APP (Cre) xenografts. The success rate of xenograft generation was 9/12 (75%). A representative HE image is shown. (C) GSEA of hallmark gene sets with bulk RNA-seq for WT and APP (Cre) organoids is shown as a bubble plot. (D) Treatment with AKT inhibitor (MK-2206) in WT and APP (Cre) organoids. Organoid diameters were quantified ( n = 20/group). The p value was calculated using a t test. (E) Western blotting of p -AKT (S473), p -AKT (T308), and total-AKT in WT and APP (Cre) organoids is shown (independent repeats: n = 3). (F) WT organoids were treated with shRNA- Arid1a or a control adenovirus. Western blots of p -AKT (S473), p -AKT (T308), and total-AKT are shown (independent repeats: n = 3). (G) p -AKT (Ser473) staining in WT and Arid mice. Numbers of positive cells are quantified ( n = 4/per group). The p value was calculated using a t test. (H) GES1 and AGS cell lines were treated with control or shRNA- ARID1A adenovirus. Western blots of ARID1A, p -AKT (S473), p -AKT (T308), total-AKT, IL-33 and β-actin are shown (independent repeats: n = 2). (I) GES1 and AGS cell lines were treated with the control or shRNA- ARID1A adenovirus, with or without PS48. Western blots of ARID1A, p -AKT (S473), p -AKT (T308), total-AKT, IL-33 and β-actin are shown (independent repeats: n = 2). (J) GES1 cells were treated with the control, shRNA- ARID1A adenovirus, or PS48. The cell proliferation assay is shown ( n = 5/group). The p value was calculated using a t test. (K) AGS cells were treated with the control, shRNA- ARID1A adenovirus, or PS48. The cell proliferation assay is shown ( n = 5/group). The p value was calculated using a t test. (L) GES1 cells were treated with control, shRNA- ARID1A adenovirus, PS48, or AKT inhibitors (MK-2206). The cell proliferation assay is shown ( n = 5/group). The p value was calculated using a t test. (M) AGS cells were treated with control, shRNA- ARID1A adenovirus, PS48, or AKT inhibitors (MK-2206). The cell proliferation assay is shown ( n = 5/group). The p value was calculated using a t test. (N) Schema of the relationship among ARID1A, PIK3CA, and AKT phosphorylation. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Phospho-proteomics, Proliferation Assay, RNA Sequencing, Western Blot, shRNA, Control, Staining

Journal: iScience

Article Title: ARID1A mutation drives gastric tumorigenesis via activating type 2 immune dominant microenvironment

doi: 10.1016/j.isci.2025.113117

Figure Lengend Snippet: Type 2 immunity activation is conserved in human Epstein-Barr virus-associated or ARID1A -mutated gastric cancer (A) Analyzing human tissue array with ARID1A-positive ( n = 17) and -negative ( n = 55) GC. Representative ARID1A (green)/IL-33 (red) staining is shown. The grade of IL-33 staining was scored. (B and C) Comparison GCs between Epstein-Barr virus (EBV)-associated and non-associated cases ( n = 24 vs. 241), as well as mutated and non-mutated ARID1A cases in total GCs ( n = 84 vs. 176) and mutated and non-mutated PIK3CA cases with ARID1A mutation ( n = 37 vs. 47), from The Cancer Genome Atlas data. (B) A Venn diagram shows the common upregulated DEGs in EBV-associated, ARID1A -mutated, and ARID1A/PIK3CA -mutated GCs. (C) Immunogram analysis results are presented as a radar diagram. (D and E) Values of mast cells (left), M2 macrophages (middle), and absolute scores (right) analyzed with CIBERSORTx comparing GCs between (D) EBV-associated and non-associated cases in total GCs ( n = 24 vs. 241) and (E) ARID1A -mutated (AM[+]) and non-mutated (AM[−]) cases in total GCs (top) ( n = 84 vs. 176), EBV-associated (middle) ( n = 14 vs. 10), and non EBV-associated GCs (bottom) ( n = 70 vs. 166), shown as a violin plot. The p value was calculated using a t test. (F–I) The analysis of public single-cell RNA-seq data for GC ( GSE183904 ) comparing tumor epithelial samples with high ARID1A expression to those with low ARID1A expression. (F) UMAP plot colored by GC patient IDs. UMAP plot (G) and PCA plot (H) stratified on the bases of ARID1A expression. (I) GSEA with upregulated and downregulated DEGs in ARID mice and gene sets of PI3K/AKT pathway and asthma. Scale bars, 100 μm. Mean ± SEM. ∗ p < 0.05.

Article Snippet: The following primary antibodies were used: ARID1A (Cell Signaling Technology; 1:200), Ki67 (Cell Signaling Technology; 1:200), CD45 (Cell Signaling Technology; 1:200), IL33 (RD Bioscience; 1:200), MUC5AC (Abcam; 1:200), ICOS (Cell Signaling Technology; 1:200), ST2 (Abcam; 1:200), IL13 (Abcam; 1:200), CD206 (Cell Signaling Technology; 1:200), Tryptase (Abcam; 1:200), DCLK1 (Abcam; 1:200), β-catenin (Cell Signaling Technology; 1:200), F4/80 (Cell Signaling Technology; 1:200), p -AKT at Ser473 (Cell Signaling Technology; 1:200), H/K-ATPase (Santa Cruz Biotechnology, Santa Cruz, CA, USA; 1:200), GIF (Columbia University, New York, NY, USA; 1:200), CD44v6 (Bio-RAD, Hercules, CA, USA; 1:200), GSII (Vector Laboratories, Newark, CA, USA; 1:200), Clusterin (RD bioscience; 1:200), TFF2 (Sino Biological, Beijing, China; 1:200), RFP (Rockland; 1:200), GFP (Abcam; 1:200) and αSMA (Cell signaling Technology; 1:200).

Techniques: Activation Assay, Virus, Staining, Comparison, Mutagenesis, RNA Sequencing, Expressing

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: Characterization of mutation rate and expression of ARID1A in SCLC. (A) Oncoprint of ARID1A and ARID1B mutations in human primary SCLC. (B to F) Scatterplots of ARID1A expression in SCLC cell lines relative to LUAD cell lines (B; CCLE dataset), in primary SCLC relative to normal lung tissues (C; GEO60052 dataset), in SCLC tissues relative to adjacent normal tissues (paraSCLC) (D; GEO149507 dataset), in 107 paired SCLC and paraSCLC retrieved from the GSA database (E; HRA003419 dataset), and in SCLC blood relative to healthy and benign blood from exoRBase database 2.0 (F). (G) Protein expression of ARID1A in 112 paired SCLC and paraSCLC, retrieved from the OMIX database (OMIX002489). (H and I) Kaplan–Meier survival analysis of the correlations between ARID1A expression and OS (H) and PFS (I) in 41 (H) or 33 (I) patients with SCLC by log-rank tests, respectively. Statistical analysis was performed using 2-tailed unpaired Student’s t tests for (B) to (E), and 2-tailed paired Student’s t tests for (F) and (G).

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Mutagenesis, Expressing

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A suppresses cell viability and clonogenicity in SCLC. (A) RT-qPCR analysis of ARID1A expression in 8 SCLC cell lines and 2 LUAD cell lines. A549 was used as the control for standardization. (B) Detection of ARID1A expression by Western blot across a panel of lung cancer cell lines. β-Actin was used as a loading control. (C) RT-qPCR analysis of ARID1A in DMS273 and DMS53 cells with ARID1A KD and overexpression (OE). (D) Western blot analysis of ARID1A expression following ARID1A KD and OE in DMS273 and DMS53 cells. (E) Representative images of EdU staining in SCLC cells following ARID1A KD and OE (left). Quantitative analysis of the results is shown on the right. (F to I) Cell viability (F and G) and colony formation (H and I) assay after ARID1A KD (F and H)/OE (G and I). The quantitative analysis of the colonies was performed using ImageJ software. Data are shown as the mean ± SEM, n ≥ 3 independent experiments. Statistical analysis was performed using 2-tailed unpaired Student’s t tests. ns, no significance; ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Quantitative RT-PCR, Expressing, Control, Western Blot, Over Expression, Staining, Software

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A restrains tumor growth in vivo . (A) Tumor volume curves of DMS273 control cells and ARID1A depletion cells (top) or overexpression (bottom). (B) Scatterplot representing tumor weights of DMS273 control cells and ARID1A depletion cells (top) or overexpression (bottom) at the endpoint of experiments. (C) Imaging of representative tumors from each group. (D) RT-qPCR analysis of mRNA expression of ARID1A , c-MYC , PARP1 , and RAD51 after KD (top)/OE (bottom) of ARID1A in vivo. (E) IHC analysis of the expression of ARID1A, c-MYC, PARP1, RAD51, and γH2AX in subcutaneous tumor tissues of mice. Scale bars, 100 μm. (F) Quantification of the IHC. The signals were quantified by IOD, equal to optical density by area, by using ImageJ software and indicated as mean ± SEM. Statistical analysis was performed using 2-tailed unpaired Student’s t tests. * P < 0.05, ** P < 0.01, **** P < 0.0001.

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: In Vivo, Control, Over Expression, Imaging, Quantitative RT-PCR, Expressing, Software

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A controls SCLC cell survival by inhibiting c-MYC / PARP1 expression. (A and B) Western blot analysis of the indicated proteins in DMS273 and DMS53 cells following ARID1A KD (A) or OE (B). (C) Western blot analysis of the indicated proteins following ARID1A overexpression in ARID1A KD DMS273 and DMS53 cells. (D and E) Clonal formation (D) and cell viability (E) assays following ARID1A overexpression in ARID1A KD DMS273 and DMS53 cells. (F and G) Western blot analysis of the indicated proteins following c-MYC (F) or PARP1 (G) overexpression in ARID1A -overexpressing DMS273 and DMS53 cells. (H to K) Cell viability (H and J) and clonal formation (I and K) assays following c-MYC (H and I) or PARP1 (J and K) overexpression in ARID1A -overexpressing DMS273 and DMS53 cells. Data are shown as the mean ± SEM; n ≥ 3 independent experiments. Statistical analysis was performed using a one-way ANOVA. ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Expressing, Western Blot, Over Expression

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A transcriptionally suppresses the expression of c-MYC and PARP1 . (A and B) RT-qPCR analysis of c-MYC and PARP1 mRNA expression in DMS273 and DMS53 cells following ARID1A KD (A) or OE (B). (C and D) ChIP-PCR analysis of DMS273 cells expressing control or sh ARID1A using antibodies against ARID1A for the promoter regions of PARP1 (C) and c-MYC (D). (E to H) ChIP-PCR analysis of DMS273 cells expressing control or sh ARID1A using antibodies against H3K27Ac (E and F) and H3K27me3 (G and H) for the promoter regions of PARP1 (E and G) and c-MYC (F and H). (I and J) The relative luciferase activities were detected in DMS273 cells with ARID1A KD or OE after transfection with the PARP1 promoter-driven luciferase (I) or the c-MYC promoter-driven luciferase (J) constructs. The firefly luciferase activities were measured and normalized to Renilla luciferase activities (F/R). Data are shown as the mean ± SEM; n ≥ 3 independent experiments. Statistical analysis was performed using 2-tailed unpaired Student’s t tests. * P < 0.05, ** P < 0.01, *** P < 0.001.

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Expressing, Quantitative RT-PCR, Control, Luciferase, Transfection, Construct

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A participates in DDR in SCLC through the c-MYC/PARP axis. (A and B) Western blot analysis of DDR-related gene in DMS273 and DMS53 cells following ARID1A KD (A) or OE (B). (C and D) Representative images of immunofluorescence staining for γ-H2AX (C) and RAD51 (D) in DMS273 and DMS53 cells following ARID1A KD. Cells with more than 5 foci were considered positive. Quantification of γ-H2AX /RAD51 fluorescence intensities from 3 independent experiments was shown as mean ± SD. Statistical analysis was performed using 2-tailed unpaired Student’s t tests. **** P < 0.0001. (E to G) Western blot analysis of the indicated proteins following ARID1A (E), c-MYC (F), or PARP1 (G) overexpression in ARID1A KD DMS273 and DMS53 cells. (H and I) Western blot analysis of PI3K downstream phospho-proteins in DMS273 and DMS53 cells following ARID1A KD (H) or OE (I).

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Western Blot, Immunofluorescence, Staining, Fluorescence, Over Expression

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: The effects of ARID1A on the response to replication stress and DSB induced by HU. (A and B) Western blot analysis of DDR-related genes following the exposure to 2 mM HU (A) and 4 mM HU (B) for the indicated times in ARID1A KD or OE DMS273 cells. (C to H) Cell viability (C and F) and clonal formation (D, E, G, and H) assays following 2 mM HU (C to E) and 4 mM HU (F to H) in ARID1A KD or OE DMS273 cells. n ≥ 3 independent experiments. Data are shown as the mean ± SEM; n ≥ 3 independent experiments. Statistical analysis was performed using a one-way ANOVA. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Western Blot

Journal: Research

Article Title: ARID1A Governs Genomic Stability and Proliferation in SCLC via c-MYC/PARP1 Suppression Driving Vulnerability to BET Inhibitors

doi: 10.34133/research.0908

Figure Lengend Snippet: ARID1A deficiency enhances JQ1 sensitivity and identifies BRD-K98645985 as a novel therapeutic candidate in SCLC. (A and B) Pearson correlation analysis of IC 50 values of JQ1 from the GDSC1 dataset and the mRNA level of ARID1A (A) and MYC family gene (B). (C) Dose–response analysis of JQ1 treatment on cell viability upon ARID1A KD DMS273 and DMS53 cells. (D) Western blot analysis of DDR-related genes following the exposure to JQ1 at indicated concentrations in ARID1A KD DMS273 and DMS53 cells. (E) Tumor volume curves of DMS273 control cells (SCR) and ARID1A KD cells upon exposure to JQ1 in vivo. KD denotes shARID1A-2#. (F) Scatterplot representing tumor weights of DMS273 control cells (SCR) and ARID1A KD cells upon exposure to JQ1 at the endpoint of experiments in vivo. KD refers to shARID1A-2#. (G) Colony formation assays demonstrating the effect of BRD-K98645985 on the cytotoxicity of JQ1 in DMS273 cells. (H) Drug–response curves of BRD-K98645985 and JQ1 combination in DMS273 cells. Cells were treated with escalating doses for 72 h, with viability measured by CellTiter-Glo. (I) Bliss analysis (Combenefit software) showing synergistic effects. (J) Tumor growth curves in xenograft mice treated with JQ1, BRD-K98645985 (BRD), or their combination (JQ1 + BRD). (K) Scatterplot depicting tumor weights from xenograft mice at the endpoints of the experiments. (L) Representative images of xenograft tumors. Data are mean ± SEM, and statistical analysis was performed using a one-way ANOVA. * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001. (M) Proposed model depicting the function of ARID1A to modulate cell proliferation and genome stability through c-MYC and PARP1 .

Article Snippet: Primary antibodies against the following proteins were used for immunoblotting: ARID1A [Cell Signaling Technology (CST), #12354S, 1:1,000], c-MYC (CST, #5605, 1:1,000), PARP1 (Active Motif, #39559,1:5,000), phospho-Akt (Ser 473 ) (CST, #9271, 1:1,000), phospho-S6 ribosomal protein (Ser 235/236 ) (CST, #4858, 1:1,000), phospho-CHK1 (Ser 317 ) (CST, #12302, 1:1,000), p-RPA2/32 (Ser 4 /Ser 8 ) (Novus, NB100-544, 1:5,000), γ-H2AX (CST, #9718, 1:1,000), RAD51 (Abcam, ab133534, 1:1,000), RPA2/32 (Abcam, ab2175, 1:1,000), CHK1 (CST, 2360S, 1:1,000), β-actin (Transgen, HC201-02, 1:10,000), DNA-PKcs (CST, #4602, 1:1,000), p-DNA-PK (CST, #68716, 1:1,000), and 53BP1 (CST, #4937, 1:1,000).

Techniques: Western Blot, Control, In Vivo, Software