Genomic analysis of Tet2 knockout macrophages. Mus musculus

Ten-Eleven-Translocation-2 (Tet2) is a DNA methylcytosine dioxygenase that functions as a tumor suppressor in hematopoietic malignancies. In this study, we revealed a role for Tet2 in sustaining the immunosuppressive function of tumor-tissue myeloid cells. We found that Tet2 expression is increased in intratumoral myeloid cells both in mouse models of melanoma and in melanoma patients, and that this increased expression is dependent on an IL-1R-MyD88 pathway. Ablation of Tet2 in myeloid cells suppressed melanoma growth in vivo, and shifted the immunosuppressive gene expression program in tumor-associated macrophages to a proinflammatory one, with a concomitant reduction of the immunosuppressive function. This resulted in increased numbers of effector T cells in the tumor, and T cell depletion abolished the reduced tumor growth observed upon myeloid-specific deletion of Tet2. Our findings reveal a non-cell-intrinsic, tumor-promoting function for Tet2, and suggest that Tet2 may present a therapeutic target for the treatment of non-hematologic malignancies. Overall design: [BMDM] This dataset contains RNAseq experiments of in vitro polarized bone marrow derived macrophages (BMDMs), with wildtype (WT) or Tet2 knockout (KO) genotype. For BMDM experiments, BMDMs were differentiated from WT or Tet2 KO mice, and were treated with IL4 (20 ng/ml) for 0, 10 or 24 hours. Cells were harvested for RNA for RNAseq with two biological replicates. [5hmC] This dataset contains DNA-immunoprecipitation sequencing (DIP-seq) experiments of genome-wide 5-hydroxymethylcytosine (5hmC) levels in wildtype (WT) or Tet2 knockout (KO) bone marrow derived macrophages (BMDMs). For 5hmC experiments, BMDMs were differentiated from WT or Tet2 KO mice, and were treated with IL4 (20 ng/ml) for 24 hours. Genomic DNA was harvested and 5hmc binding DNA segments was pulled down by 5hmc specific antibody for DIP-seq. [TAM] This dataset contains RNAseq experiments of tumor associated macrophages (TAMs) isolated from wildtype (WT) or Myeloid-specific Tet2 knockout (KO) mice . For TAM experiments, YUMM1.7 cell line was injected into WT (LysMcre wt/wt, Tet2 fl/fl) or Tet2 KO mice (LysMcre +/wt, Tet2 fl/fl). TAMs were harvested from the resultant tumors for RNAseq analysis.

十-十一易位酶2（Ten-Eleven Translocation 2, TET2）是一种DNA甲基胞嘧啶双加氧酶，在造血系统恶性肿瘤中发挥肿瘤抑制因子的作用。本研究揭示了TET2在维持肿瘤组织髓系细胞免疫抑制功能中的作用。我们发现，在黑色素瘤小鼠模型与黑色素瘤患者体内，瘤内髓系细胞中的TET2表达均会上调，且该上调过程依赖于IL-1R-MyD88信号通路。髓系细胞中TET2的敲除可在体内抑制黑色素瘤的生长，并将肿瘤相关巨噬细胞（tumor-associated macrophages, TAMs）中的免疫抑制性基因表达程序转换为促炎型程序，同时伴随免疫抑制功能的减弱。这一变化会导致肿瘤内效应T细胞数量增多，而T细胞耗竭则会抵消髓系特异性TET2敲除所带来的肿瘤生长抑制效应。本研究发现TET2具有非细胞自主性的促肿瘤功能，提示TET2或可作为非造血系统恶性肿瘤的治疗靶点。
整体设计：
[BMDM] 本数据集包含体外极化的野生型（Wildtype, WT）或TET2敲除（Knockout, KO）骨髓来源巨噬细胞（Bone Marrow Derived Macrophages, BMDMs）的RNA测序（RNAseq）实验数据。该组实验中，我们从野生型或TET2敲除小鼠体内分离并诱导分化得到骨髓来源巨噬细胞，随后用浓度为20 ng/ml的IL4分别处理0、10或24小时，收集细胞并提取RNA进行RNA测序，每组设置2次生物学重复。
[5hmC] 本数据集包含野生型或TET2敲除骨髓来源巨噬细胞全基因组范围内5-羟甲基胞嘧啶（5-hydroxymethylcytosine, 5hmC）水平的DNA免疫沉淀测序（DNA-immunoprecipitation sequencing, DIP-seq）实验数据。该组实验中，我们从野生型或TET2敲除小鼠体内诱导分化得到骨髓来源巨噬细胞，用浓度为20 ng/ml的IL4处理24小时后收集基因组DNA，通过5hmC特异性抗体富集与5hmC结合的DNA片段，随后进行DIP-seq测序。
[TAM] 本数据集包含从野生型或髓系特异性TET2敲除小鼠体内分离得到的肿瘤相关巨噬细胞（Tumor Associated Macrophages, TAMs）的RNA测序（RNAseq）实验数据。该组实验中，我们将YUMM1.7细胞系接种至野生型小鼠（基因型为LysMcre wt/wt, Tet2 fl/fl）或髓系特异性TET2敲除小鼠（基因型为LysMcre +/wt, Tet2 fl/fl）体内，从形成的肿瘤中分离肿瘤相关巨噬细胞并提取RNA进行RNA测序分析。