通过H3K27ac染色质免疫沉淀测序进行活性增强子评估揭示紧密连接蛋白-1作为结直肠癌放射抗性的生物标志物

Active Enhancer Assessment by H3K27ac ChIP-seq Reveals Claudin-1 as a Biomarker for Radiation Resistance in Colorectal Cancer.

作者信息

Chen Zu-Xuan, Huang He-Qing, Wen Jia-Ying, Qin Li-Sha, Song Yao-Dong, Fang Ye-Ying, Zeng Da-Tong, Huang Wei-Jian, Qin Xin-Gan, Gan Ting-Qing, Luo Jie, Li Jian-Jun

机构信息

Department of Medical Oncology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China.

Department of Radiotherapy, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P.R. China.

出版信息

Dose Response. 2021 Dec 8;19(4):15593258211058981. doi: 10.1177/15593258211058981. eCollection 2021 Oct-Dec.

DOI:10.1177/15593258211058981

PMID:34987334

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8669133/

Abstract

BACKGROUND

Colorectal cancer (CRC) represents the third most common malignant tumor in the worldwide. Radiotherapy is the common therapeutic treatment for CRC, but radiation resistance is often encountered. ChIP-seq of Histone H3K27 acetylation (H3K27ac) has revealed enhancers that play an important role in CRC. This study examined the relationship between an active CRC enhancer and claudin-1 (CLDN1), and its effect on CRC radiation resistance.

METHODS

The target CRC genes of active enhancers were obtained from public H3K27ac ChIP-seq, and the genes highly expressed in radio-resistant CRC were screened and intersected with enhancer-driven genes. The clinical roles of CLDN1 in radiation resistance were examined using the t-test, standard mean deviation (SMD), summary receiver operating characteristic curve and Kaplan-Meier curves. The co-expressed genes of CLDN1 were calculated using Pearson Correlation analysis, and Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes and Gene Set Variation Analysis (GSVA) analyses were used to examine the molecular mechanisms of CLDN1.

RESULTS

Total 13 703 CRC genes were regulated by enhancers using 58 H3K27ac ChIP-seq. Claudin-1 (CLDN1) was enhancer-driven and notably up-regulated in CRC tissues compared to non-CRC controls, with a SMD of 3.45 (95 CI % = .56-4.35). CLDN1 expression was increased in radiation-resistant CRC with a SMD of .42 (95% CI = .16-.68) and an area under the curve of .74 (95% CI = .70-.77). The cell cycle and immune macrophage levels were the most significant pathways associated with CLDN1.

CONCLUSION

CLDN1 as an enhancer-regulated gene that can boost radiation resistance in patients with CRC.

摘要

背景

结直肠癌（CRC）是全球第三大常见恶性肿瘤。放射治疗是CRC的常见治疗方法，但常出现放射抗性。组蛋白H3K27乙酰化（H3K27ac）的ChIP-seq揭示了在CRC中起重要作用的增强子。本研究探讨了活性CRC增强子与紧密连接蛋白1（CLDN1）之间的关系及其对CRC放射抗性的影响。

方法

从公共的H3K27ac ChIP-seq中获取活性增强子的目标CRC基因，筛选在放射抗性CRC中高表达的基因并与增强子驱动的基因进行交集分析。使用t检验、标准平均偏差（SMD）、汇总受试者工作特征曲线和Kaplan-Meier曲线来研究CLDN1在放射抗性中的临床作用。使用Pearson相关分析计算CLDN1的共表达基因，并使用基因本体（GO）、京都基因与基因组百科全书和基因集变异分析（GSVA）分析来研究CLDN1的分子机制。

结果

使用58个H3K27ac ChIP-seq，共有13703个CRC基因受增强子调控。紧密连接蛋白1（CLDN1）由增强子驱动，与非CRC对照相比，在CRC组织中显著上调，SMD为3.45（95%置信区间=.56-4.35）。CLDN1在放射抗性CRC中的表达增加，SMD为.42（95%置信区间=.16-.68），曲线下面积为.74（95%置信区间=.70-.77）。细胞周期和免疫巨噬细胞水平是与CLDN1相关的最显著途径。