Effect of depletion of CBX1 on gene expression of SUNE1 cells [RNA-seq]

Nasopharyngeal carcinoma (NPC), which arises from the nasopharyngeal pharynx, is a metastasis-prone malignancy highly prevalent in East and Southeast Asia, especially southern China. Despite progress in chemo-radiotherapeutic strategies, about 20% of NPC patients still suffer from distant metastasis, thus developing new therapeutic strategies for NPC is of vital importance. N6-methyladenosine (m6A) RNA modification, the most abundant epitranscriptomic modification in eukaryotic mRNA, has attracted great attention in cancer research because of its vital biological functions. However, little is known about the underlying molecular mechanisms between m6A modification and NPC progression. We aimed to identified differential m6A peaks by analyzing the m6A modification profile in NPC with paired tissues with or without metastasis using m6A-seq. For RNA-seq and ChIP-seq, we aimed to identified the downstream targets of CBX1 in NPC. Overall design: Comparative gene expression profiling analysis of RNA-seq data for SUNE1 cells (sgCBX1 and sgNC). To investigate the CBX1 in the progression of nasopharyngeal carcinoma, we established SUNE1 cell lines in which CBX1 has been knocked out by sgRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of sgNC and sgCBX1.

鼻咽癌（Nasopharyngeal carcinoma, NPC）是起源于鼻咽部的易转移性恶性肿瘤，在东亚及东南亚地区高发，尤以中国南方为甚。尽管放化疗策略已取得一定进展，但仍有约20%的鼻咽癌患者会发生远处转移，因此开发鼻咽癌新型治疗策略至关重要。N6-甲基腺苷酸（N6-methyladenosine, m6A）RNA修饰是真核生物mRNA中最丰富的表观转录组修饰，因其关键的生物学功能而在癌症研究领域受到广泛关注。然而，目前对于m6A修饰与鼻咽癌进展之间的潜在分子机制仍知之甚少。本研究旨在通过m6A测序（m6A-seq）分析伴或不伴转移的配对鼻咽癌组织的m6A修饰谱，以鉴定差异m6A峰。针对RNA测序（RNA-seq）与染色质免疫沉淀测序（ChIP-seq），本研究旨在鉴定鼻咽癌中CBX1的下游靶基因。整体实验设计：对SUNE1细胞（sgCBX1组与sgNC组）的RNA-seq数据开展比较基因表达谱分析。为探究CBX1在鼻咽癌进展中的作用，本研究通过单引导RNA（sgRNA）构建了CBX1敲除的SUNE1细胞系。随后，本研究利用sgNC与sgCBX1组的RNA-seq数据完成了基因表达谱分析。