ARID1A Deficiency Regulates Anti-Tumor Immune Response in Esophageal Adenocarcinoma

Abstract

ARID1A, a member of the chromatin remodeling SWI/SNF complex, is frequently lost in many cancer types, including esophageal adenocarcinoma (EAC). Here, we study the impact of ARID1A deficiency on the anti-tumor immune response in EAC. We find that EAC tumors with ARID1A mutations are associated with enhanced tumor-infiltrating CD8⁺ T cell levels. ARID1A-deficient EAC cells exhibit heightened IFN response signaling and promote CD8⁺ T cell recruitment and cytolytic activity. Moreover, we demonstrate that ARID1A regulates fatty acid metabolism genes in EAC, showing that fatty acid metabolism could also regulate CD8⁺ T cell recruitment and CD8⁺ T cell cytolytic activity in EAC cells. These results suggest that ARID1A deficiency shapes both tumor immunity and lipid metabolism in EAC, with significant implications for immune checkpoint blockade therapy in EAC.

Keywords: ARID1A; CD8+ T cells; IFN response; esophageal adenocarcinoma; lipid metabolism; tumor immunity.

Figure 1

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.

Figure 1

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.

Figure 2

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.

Figure 3

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.

Figure 4

Palmitate potentiates CD8⁺ T cell recruitment and cytotoxicity in mouse EAC. (A) A diagram of CD8⁺ T cell migration assay. (B) A diagram of CD8⁺ T cell cytotoxicity co-culture assay. (C,D) The number of CD8⁺ T cells migrated into the culture medium from siControl of (C) YTN5 and (D) YTN16 with and without 48 h palmitate treatment. (E,F) The mRNA expression of CXCL9 and CXCL10 in siControl of (E) YTN5 and (F) YTN16 with and without 48 h palmitate treatment. (G,H) The cell viability of (G) YTN5 and (H) YTN16 siControl with and without palmitate treatment after CD8⁺ T cell cytotoxic killing for 24 h. n ≥ 3. Paired, 2-tailed t test: ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Figure 5

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.

Figure 6

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.