Journal: Cancers

Article Title: ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

doi: 10.3390/cancers15225377

Figure Lengend Snippet: ARID1A mutations display increased tumor-infiltrating CD8 + T cells and IFN signaling pathways in EAC. ( A , B ) The statistical difference in tumor-infiltrating CD8 + T cells between mutated ARID1A and unmutated ARID1A in pan− cancer by ( A ) CIBERSORT− ABS and ( B ) XCELL. ( C ) The GSEA plot shows the positive enrichment of IFN-α and IFN-γ responses in the ARID1A knockdown cells compared to controls by shRNA in FLO1. ( D ) Volcano plots show GSEA results of the enriched IFN pathways in ARID1A-mutated compared to unmutated samples from OCCAMS and TCGA. Abbreviations: STAD: stomach adenocarcinoma, COAD: colon adenocarcinoma, READ: rectum adenocarcinoma, CHOL: cholangiocarcinoma, KIRC: kidney renal clear cell carcinoma, TGCT: testicular germ cell tumors, ACC: adrenocortical carcinoma, LUSC: lung squamous cell carcinoma, LUAD: lung adenocarcinoma, THCA: thyroid carcinoma, LAML: acute myeloid leukemia, BRCA: breast invasive carcinoma, OV: ovarian serous cystadenocarcinoma, PAAD: pancreatic adenocarcinoma, KIRP: kidney renal papillary cell carcinoma, GBM: glioblastoma multiforme, CESC: cervical squamous cell carcinoma and endocervical adenocarcinoma, LIHC: liver hepatocellular carcinoma, BLCA: bladder urothelial carcinoma, HNSC: head and neck squamous cell carcinoma, PRAD: prostate adenocarcinoma, SARC: sarcoma, SKCM: skin cutaneous melanoma, LGG: brain lower-grade glioma, DLBC: lymphoid neoplasm diffuse large B cell lymphoma, UCS: uterine carcinosarcoma, MESO: mesothelioma.

Article Snippet: The blots were probed with antibodies against ARID1A (12354S, Cell Signaling, Danvers, MA, USA) and β-actin (Cell Signaling, 4970), followed by incubation with alkaline phosphatase-conjugated secondary antibodies (A3687, Sigma-Aldrich, St Louis, MO, USA) for 1 h at room temperature.

Techniques: Protein-Protein interactions, Knockdown, shRNA

Journal: Cancers

Article Title: ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

doi: 10.3390/cancers15225377

Figure Lengend Snippet: ARID1A knockdown induces IFN signaling response in EAC. ( A ) Western blot and ( B ) real-time PCR of ARID1A in FLO1 and SKGT4 ARID1A knockdown cells by shRNA. Representative blots are shown with the mean relative quantitation indicated normalized to ß-actin expression. ( C ) The expression of IFN signaling response-related genes in FLO1 and SKGT4 ARID1A knockdown cells by shRNA. n = 3. Paired, 2-tailed t test: *** p < 0.001, **** p < 0.0001. p values for ( C , D ) were determined by one-way ANOVA.

Article Snippet: The blots were probed with antibodies against ARID1A (12354S, Cell Signaling, Danvers, MA, USA) and β-actin (Cell Signaling, 4970), followed by incubation with alkaline phosphatase-conjugated secondary antibodies (A3687, Sigma-Aldrich, St Louis, MO, USA) for 1 h at room temperature.

Techniques: Knockdown, Western Blot, Real-time Polymerase Chain Reaction, shRNA, Quantitation Assay, Expressing

Journal: Cancers

Article Title: ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

doi: 10.3390/cancers15225377

Figure Lengend Snippet: ARID1A knockdown induces IFN signaling response in murine EAC. ( A – C ) The mRNA expression level of ARID1A in ARID1A knockdown by siRNA in ( A ) YTN5, ( B ) YTN16 and ( C ) YTN2. ( D , F ) The expression of IFN signaling response-related genes in ( D ) YTN5, ( E ) YTN16 and ( F ) YTN2 transfected with ARID1A siRNA. n = 3. Paired, 2-tailed t test: ** p < 0.01, **** p < 0.0001. p values for ( D , F ) were determined by one-way ANOVA.

Article Snippet: The blots were probed with antibodies against ARID1A (12354S, Cell Signaling, Danvers, MA, USA) and β-actin (Cell Signaling, 4970), followed by incubation with alkaline phosphatase-conjugated secondary antibodies (A3687, Sigma-Aldrich, St Louis, MO, USA) for 1 h at room temperature.

Techniques: Knockdown, Expressing, Transfection

Journal: Cancers

Article Title: ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

doi: 10.3390/cancers15225377

Figure Lengend Snippet: ARID1A knockdown inhibits de novo lipogenesis in EAC. ( A , B ) The expression of de novo lipogenesis-related genes in ( A ) SKGT4 and ( B ) FLO1 under ARID1A knockdown by shRNA. ( C ) The mRNA expression under ARID1A knockdown by siRNA in SKGT4. ( D ) The expression levels of FASN and SCD1 in SKGT4 transfected with ARID1A siRNA. ( E , F ) The mRNA expression of FASN and SCD1 in ( E ) FLO1 and ( F ) YTN5 control isogenic cells generated for ARID1A knockdown EAC treated with palmitate for 48 h. n = 3. Paired, 2-tailed t test: * p < 0.05, ** p < 0.01, **** p < 0.0001. p values for ( A , B ) were determined by one-way ANOVA.

Article Snippet: The blots were probed with antibodies against ARID1A (12354S, Cell Signaling, Danvers, MA, USA) and β-actin (Cell Signaling, 4970), followed by incubation with alkaline phosphatase-conjugated secondary antibodies (A3687, Sigma-Aldrich, St Louis, MO, USA) for 1 h at room temperature.

Techniques: Knockdown, Expressing, shRNA, Transfection, Control, Generated

Journal: Cancers

Article Title: ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

doi: 10.3390/cancers15225377

Figure Lengend Snippet: ARID1A knockdown promotes CD8 + T cell recruitment and cytotoxicity in mouse EAC. ( A , B ) The absorbance at 595 nm for the viable cells of ( A ) YTN5 and ( B ) YTN16 with and without ARID1A knockdown by siRNA after CD8 + T cell cytotoxic killing for 24 h. ( C , D ) The number of CD8 + T cells migrated into the culture medium from ( C ) YTN5 and ( D ) YTN16 with and without ARID1A knockdown by siRNA. n ≥ 3. Paired, 2-tailed t test: * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: The blots were probed with antibodies against ARID1A (12354S, Cell Signaling, Danvers, MA, USA) and β-actin (Cell Signaling, 4970), followed by incubation with alkaline phosphatase-conjugated secondary antibodies (A3687, Sigma-Aldrich, St Louis, MO, USA) for 1 h at room temperature.

Techniques: Knockdown