SOX17 initiates an immune evasion program in early colorectal cancers [RNAseq_230707Yil]

In addition to accumulation of step-wise genetic mutations, epigenetic alterations play critical roles in the evolution of colon cancers. However, distinct mutational patterns and patient backgrounds render it challenging to distinguish driver epigenetic alterations from passenger epigenetic alterations. To address this, we combined the colon cancer organoid orthotopic transplantation approach with comprehensive epigenomic and transcriptomic analyses. We found that an in vivo environment induces epigenetic alterations with fetal intestinal features that converge on SOX17, a transcription factor that is required for endoderm development. Surprisingly, SOX17 knockout leads to tumour rejection in immunocompetent mice, but not in immunodeficient mice, by turning immune cold tumours into hot with robust infiltration of activated CD8+ T cells. Mechanistically, SOX17 suppresses Ifngr1-mediated MHC-I expression to evade CD8+ T cell-mediated tumour cell killing. At the tumour initiation, SOX17 expression is induced by APC loss, and SOX17 facilitates the production of LGR5- cells with low MHC-I expression to evade immune surveillance. Together, our result reveals that SOX17 is a master transcriptional factor that induces in vivo epigenetic reprograming of tumours, which provides fundamental understanding of how an immune evasion program is initiated at the early stages of colon cancer development. We performed RNA-seq in naïve AKP organoids, bulk primary tumours, and flow cytometry-sorted tdTomato+ tumour cells from primary tumours. Furthermore, we employed Villin-CreERT2; Apc f/f; Kras LSL-G12D; P53 f/f; Rosa LSL-tdTomato (AKPVT) mice to generate autochthonous tumours by colonoscopy-guided 4-OH-Tamoxifen injection into the colonic mucosa. We perfomed RNA-seq in these endogenous AKPVT tumours and normal colonic crypts.

除逐步累积的基因突变外，表观遗传改变在结肠癌的演化进程中发挥关键作用。然而，独特的突变谱与患者个体背景使得区分驱动型表观遗传改变与乘客型表观遗传改变颇具挑战。为解决这一难题，我们将结肠癌类器官（colon cancer organoid）原位移植技术与全面的表观基因组分析与转录组分析相结合。研究发现，体内环境可诱导带有胎儿肠道特征的表观遗传改变，且这类改变最终汇聚于转录因子SOX17——该因子对内胚层（endoderm）发育不可或缺。令人意外的是，SOX17基因敲除可在免疫健全小鼠中引发肿瘤排斥，而在免疫缺陷小鼠中则无此效果，其机制是将免疫“冷”肿瘤转化为免疫“热”肿瘤，伴随活化CD8阳性T细胞（CD8+ T cell）的大量浸润。从机制层面而言，SOX17通过抑制干扰素γ受体1（Ifngr1）介导的主要组织相容性复合体I型（MHC-I）表达，从而逃逸CD8阳性T细胞介导的肿瘤细胞杀伤。在肿瘤发生起始阶段，SOX17的表达由腺瘤性结肠息肉病蛋白（APC）缺失所诱导，且SOX17可促进低表达MHC-I的LGR5阴性细胞（LGR5- cells）产生，以逃逸免疫监视。综上，我们的研究揭示SOX17是介导肿瘤体内表观遗传重编程的核心转录因子，这为理解结肠癌发生早期阶段免疫逃逸程序的启动机制提供了基础性认识。我们对未处理的AKP类器官、实体原发肿瘤以及从原发肿瘤中经流式细胞术（flow cytometry）分选得到的tdTomato阳性肿瘤细胞进行了RNA测序（RNA-seq）。此外，我们使用Villin-CreERT2; Apc f/f; Kras LSL-G12D; P53 f/f; Rosa LSL-tdTomato（AKPVT）小鼠，在结肠镜引导下向结肠黏膜注射4-羟基他莫昔芬（4-OH-Tamoxifen）来构建自发性肿瘤模型。我们对这些内源AKPVT肿瘤与正常结肠隐窝进行了RNA测序（RNA-seq）。