Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC
Integrated high-throughput analysis identifies super enhancers associated with chemoresistance in SCLC
复制标题
综合高通量分析识别与 SCLC 化疗耐药相关的超级增强子
DOI：
10.1186/s12920-019-0520-9
复制
发表时间：
2019-05-22
影响因子：
2.7
通讯作者：
Guo, Linlang
中科院分区：
文献类型：
--
作者：
Bao, Jiarong;Li, Man;Guo, Linlang
背景
化疗耐药是小细胞肺癌治疗面临的主要临床挑战。此外，超级增强子（SE）的转录调控在肿瘤演变中具有重要作用。SE作为一类关键的非编码DNA顺式调控元件，其功能已成为癌症研究领域众多近期研究的主题。
方法
在本研究中，我们利用染色质免疫沉淀测序和RNA测序（RNA - seq），旨在从H69AR细胞中鉴定与化疗耐药相关的SE。通过对MEME芯片进行综合生物信息学分析，我们预测了与SE位点结合的主要转录因子（TF），并通过RNA干扰、细胞计数试剂盒8检测、实时定量逆转录聚合酶链反应验证了SE的TF与耐药性之间的关系。
结果
从H69AR细胞中总共筛选出108个SE。当将此分析与RNA - seq数据相结合时，有45个SE被认为与耐药密切相关。然后，预测有12个主要TF定位于这些SE区域。随后，我们选择叉头框P1（FOXP1）、干扰素调节因子1（IRF1）和特异性蛋白1（SP1），通过SE来验证主要TF与化疗耐药的功能关系。
结论
我们筛选出了与耐药相关的SE，并评估了FOXP1、IRF1和SP1在化疗耐药中的功能。我们的研究结果确定了一大批与小细胞肺癌耐药相关的SE，揭示了SE的耐药机制，并为SE的临床应用提供了见解。
BackgroundChemoresistance is a primary clinical challenge for the management of small cell lung cancer. Additionally, transcriptional regulation by super enhancer (SE) has an important role in tumor evolution. The functions of SEs, a key class of noncoding DNAcis-regulatory elements, have been the subject of many recent studies in the field of cancer research.MethodsIn this study, using chromatin immunoprecipitation-sequencing and RNA-sequencing (RNA-seq), we aimed to identify SEs associated with chemoresistance from H69AR cells. Through integrated bioinformatics analysis of the MEME chip, we predicted the master transcriptional factors (TFs) binding to SE sites and verified the relationships between TFs of SEs and drug resistance by RNA interference, cell counting kit 8 assays, quantitative real-time reverse transcription polymerase chain reaction.ResultsIn total, 108 SEs were screened from H69AR cells. When combining this analysis with RNA-seq data, 45 SEs were suggested to be closely related to drug resistance. Then, 12 master TFs were predicted to localize to regions of those SEs. Subsequently, we selected forkhead box P1 (FOXP1), interferon regulatory factor 1 (IRF1), and specificity protein 1 (SP1) to authenticate the functional relationships of master TFs with chemoresistance via SEs.ConclusionsWe screened out SEs involved with drug resistance and evaluated the functions of FOXP1, IRF1, and SP1 in chemoresistance. Our findings established a large group of SEs associated with drug resistance in small cell lung cancer, revealed the drug resistance mechanisms of SEs, and provided insights into the clinical applications of SEs.