肿瘤特异性MHC II类（tsMHC-II）表达影响肿瘤微环境的免疫。tsMHC-II阳性的癌细胞可能充当替代性抗原呈递细胞和CD4+T细胞介导的溶解靶。在结直肠癌中，由于CIITA启动子甲基化，tsMHC-II阴性很常见。为了阐明结直肠癌中tsMHC-II抑制的机制，我们分析了与来源组织表观遗传保真的结直肠癌器官样体。将15个原发性结直肠癌器官样体分别用IFNγ ±表观遗传修饰剂处理，采用流式细胞术检测tsMHC-II表达。利用qRT-PCR、总RNA测序、纳米孔测序、亚硫酸盐转化/焦磷酸测序和Western印迹法定量CIITA、STAT1、IRF1和JAK1的表达，突变和启动子甲基化，并采用染色质免疫沉淀法定量CIITA上的H3K9ac、H3K9Me2和EZH2的占位。我们将结直肠癌的对IFNγ的反应定义为三种类型：强、弱和不可诱导性。即使经过长时间的IFNγ暴露，表达也会出现延迟和局限性，这是由于IFNγ介导的EZH2占位CIITA。在非可诱导的器官样体中，EZH2和组蛋白去乙酰化酶抑制剂促进了tsMHC-II的表达。非可诱导性在三个共识分子亚型1（CMS1）器官样体中由于JAK1突变而出现。没有器官样体表现CIITA启动子甲基化。只要IFNγ信号传导完好，大多数结直肠癌器官样体都可诱导II类。在15个器官样体中，通过靶向表观遗传治疗提高了tsMHC-II的表达。我们的方法可以作为一个蓝图，用来研究其他癌症中特定表观遗传机制的异质性免疫抑制机制在患者个体间的差异，并且如何有针对性地应用于未来的表观遗传治疗为免疫辅助剂在癌症中提供更加战略性的指导。肿瘤细胞的MHC II类表达对肿瘤微环境的免疫有显著影响。以往研究利用细胞系调查调控IFNγ诱导的类II表达的抑制机制显示通过表观遗传沉默IFN信号通路基因作为常见的免疫逃避策略。与细胞系不同，患者来源的器官样体保持与组织起源的表观遗传保真性。在首次进行的研究中，我们分析了一系列结直肠癌器官样体中IFNγ诱导的类II表达的模式、动态和表观遗传控制。© 2023 The Authors; Published by the American Association for Cancer Research.

Tumor-specific MHC class II (tsMHC-II) expression impacts tumor microenvironmental immunity. tsMHC-II positive cancer cells may act as surrogate antigen-presenting cells and targets for CD4+ T cell-mediated lysis. In colorectal cancer, tsMHC-II negativity is common, in cell lines due to CIITA promoter methylation. To clarify mechanisms of tsMHC-II repression in colorectal cancer, we analyzed colorectal cancer organoids which are epigenetically faithful to tissue of origin. 15 primary colorectal cancer organoids were treated with IFNγ ± epigenetic modifiers: flow cytometry was used for tsMHC-II expression. qRT-PCR, total RNA sequencing, nanopore sequencing, bisulfite conversion/pyrosequencing, and Western blotting was used to quantitate CIITA, STAT1, IRF1, and JAK1 expression, mutations and promoter methylation and chromatin immunoprecipitation to quantitate H3K9ac, H3K9Me2, and EZH2 occupancy at CIITA. We define three types of response to IFNγ in colorectal cancer: strong, weak, and noninducibility. Delayed and restricted expression even with prolonged IFNγ exposure was due to IFNγ-mediated EZH2 occupancy at CIITA. tsMHC-II expression was enhanced by EZH2 and histone deacetylase inhibition in the weakly inducible organoids. Noninducibility is seen in three consensus molecular subtype 1 (CMS1) organoids due to JAK1 mutation. No organoid demonstrates CIITA promoter methylation. Providing IFNγ signaling is intact, most colorectal cancer organoids are class II inducible. Upregulation of tsMHC-II through targeted epigenetic therapy is seen in one of fifteen organoids. Our approach can serve as a blueprint for investigating the heterogeneity of specific epigenetic mechanisms of immune suppression across individual patients in other cancers and how these might be targeted to inform the conduct of future trials of epigenetic therapies as immune adjuvants more strategically in cancer.Cancer cell expression of MHC class II significantly impacts tumor microenvironmental immunity. Previous studies investigating mechanisms of repression of IFNγ-inducible class II expression using cell lines demonstrate epigenetic silencing of IFN pathway genes as a frequent immune evasion strategy. Unlike cell lines, patient-derived organoids maintain epigenetic fidelity to tissue of origin. In the first such study, we analyze patterns, dynamics, and epigenetic control of IFNγ-induced class II expression in a series of colorectal cancer organoids.© 2023 The Authors; Published by the American Association for Cancer Research.