Flebbe Hannah, Hamdan Feda H, Kari Vijayalakshmi, Kitz Julia, Gaedcke Jochen, Ghadimi B Michael, Johnsen Steven A, Grade Marian
Department of General, Visceral and Pediatric Surgery, University Medical Center Goettingen, 37075 Goettingen, Germany.
Gene Regulatory Mechanisms and Molecular Epigenetics Laboratory, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA.
Cancers (Basel). 2019 Aug 9;11(8):1142. doi: 10.3390/cancers11081142.
Epigenetic alterations play a central role in cancer development and progression. The acetylation of histone 3 at lysine 27 (H3K27ac) specifically marks active genes. While chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (ChIP-seq) analyses are commonly performed in cell lines, only limited data are available from primary tumors. We therefore examined whether cancer-specific alterations in H3K27ac occupancy can be identified in primary rectal cancer. Tissue samples from primary rectal cancer and matched mucosa were obtained. ChIP-seq for H3K27ac was performed and differentially occupied regions were identified. The expression of selected genes displaying differential occupancy between tumor and mucosa were examined in gene expression data from an independent patient cohort. Differential expression of four proteins was further examined by immunohistochemistry. ChIP-seq for H3K27ac in primary rectal cancer and matched mucosa was successfully performed and revealed differential binding on 44 regions. This led to the identification of genes with increased H3K27ac, i.e., , , , and , which were also highly upregulated in primary rectal cancer in an independent dataset. The increased expression of these four proteins was confirmed by immunohistochemistry. This study demonstrates the feasibility of ChIP-seq-based epigenome mapping of primary rectal cancer and confirms the value of H3K27ac occupancy to predict gene expression differences.
表观遗传改变在癌症的发生和发展中起着核心作用。组蛋白3赖氨酸27位点（H3K27ac）的乙酰化特异性标记活跃基因。虽然染色质免疫沉淀（ChIP）结合下一代测序（ChIP-seq）分析通常在细胞系中进行，但来自原发性肿瘤的相关数据有限。因此，我们研究了原发性直肠癌中是否能识别出H3K27ac占据情况的癌症特异性改变。获取了原发性直肠癌组织样本和匹配的黏膜样本。进行了H3K27ac的ChIP-seq分析并确定了差异占据区域。在来自独立患者队列的基因表达数据中检测了肿瘤和黏膜之间显示出差异占据的选定基因的表达。通过免疫组织化学进一步检测了四种蛋白质的差异表达。成功地对原发性直肠癌和匹配的黏膜进行了H3K27ac的ChIP-seq分析，结果显示在44个区域存在差异结合。这导致了H3K27ac增加的基因的鉴定，即 、 、 和 ，在一个独立数据集中这些基因在原发性直肠癌中也高度上调。免疫组织化学证实了这四种蛋白质的表达增加。本研究证明了基于ChIP-seq的原发性直肠癌表观基因组图谱绘制的可行性，并证实了H3K27ac占据情况对预测基因表达差异的价值。
