Detection and analysis of EBV DNA integration in NK/T cell lymphoma genome
10.3969/j.issn.1000-8179.2018.23.175
- VernacularTitle:NK/T细胞淋巴瘤基因组中EBV DNA整合检测及分析
- Author:
Xin WANG
1
,
2
;
Xudong ZHANG
;
Qingjiang CHEN
;
Guannan WANG
;
Junxia HU
;
Shaoxuan WU
;
Mijing MA
;
Meifeng YIN
;
Wanqiu YANG
;
Meng DONG
;
Mengjie DING
;
Mingzhi ZHANG
;
Linan ZHU
Author Information
1. 郑州大学第一附属医院肿瘤科(郑州市450052)
2. 郑州大学第一附属医院淋巴瘤诊疗中心(郑州市450052)
- Keywords:
NK/T cell lymphoma (NKTCL);
EBV DNA integration;
bioinformatics analysis;
gene expression
- From:
Chinese Journal of Clinical Oncology
2018;45(23):1194-1200
- CountryChina
- Language:Chinese
-
Abstract:
To investigate the presence of integrated Epstein-Barr virus (EBV) DNA in the NK/T cell lymphoma (NKTCL) ge-nome and analyze the integration information in the genome of NKTCL cell lines. Methods: PCR and in situ hybridization were used to detect EBV infection in five EBV (+) NK/T samples and four EBV (-) NK/T samples provided by the biobanks of the First Affiliated Hospi-tal of Zhengzhou University. Whole-genome DNA of the samples was sequenced and subjected to bioinformatics analysis. Whole-ge-nome sequence alignment was used to identify the EBV integration sequence. BLAST analysis was used to compare EBV fasta files of the samples and EBV fasta library. CREST software was used to extract softclip reads, filter all paired reads, and enumerate their distri-bution on chromosomes. The integrated genomics viewer (IGV) was used to compare the distribution of reads in partial regions of chromosome. PCR was used to amplify the high-frequency integration region of the EBV DNA. The amplified fragments were sanger se-quenced. Results: EBV DNA and EBER expression were detected in five EBV (+) NK/T samples but not in the four EBV (-) NK/T samples. Sequencing depth, coverage depth, proportion of coverage, and proportion of alignment all met the requirements for subsequent re-search. Sequence alignment revealed that the captured sequences were viral sequences. Filtered reads were most numerous in EBV (+) NKTCL cell line SNK, YTS, and EBV (+) nasal NKTCL tissue. The reads were non-randomly enriched in chromosome 2. EBV DNA inte-gration in the 400 bp region of chr2:30234084-30234483 caused insertion or deletion in the chr2p23.1 site. Conclusions: EBV DNA is highly integrated in the chr2p23.1 site of EBV (+) NKTCL cells and may affect the expression of related genes.
