Differentially expressed genes between benign lymphoepithelial lesions of lacrimal gland and mucosa-associated lymphoid tissue lymphoma

Authors: Liu Rui,  Wu Hao,  Zhao Pengxiang,  Ge Xin,  Zhang Jingxue,  Ma Jianmin
DOI: 10.3760/cma.j.cn115989-20200329-00221
Published 2020-11-10
Cite as Chin J Exp Ophthalmol, 2020,38(11): 973-978.

Abstract

Objective

To screen and analyze the differentially expressed genes between lacrimal gland benign lymphoepithelial lesions (LGBLEL) and mucosa-associated lymphoid tissue (MALT) lymphoma.

Methods

A cross-sectional study was performed.Ten consecutive patients were included in Beijing Tongren Hospital Affiliated to Capital Medical University from January 2015 to November 2017, including five patients with LGBLEL and five patients with MALT lymphoma.Clinical data and peripheral blood sample were collected from each patient.DNA was extracted from peripheral blood.The whole-exome sequencing (WES) was employed for gene sequencing.The BWA software was used for the screen of differentially expressed gene; GATK software was used to detect genomic variation; ANNOVAR software was used to annotate and predict the effects of the variation; Varscan software was used to analyze single nucleotide polymorphisms (SNPs) and insertion-deletions (InDels), and ExomeCNV software was used to identify copy number variations (CNVs). The mutated hub gene with the maximal clique centrality was screened out by the analysis of protein interaction network and construction of functional module network.This study was approved by an Ethics Committee of Beijing Tongren Hospital Affiliated to Capital Medical University.Written informed consent was obtained from each patient prior to any medical examination.

Results

There was 16.63 Gb sequencing data per sample on average.Synonymous mutation and missense mutation were the most common SNPs mutation types in the LGBLEL group and MALT lymphoma group, and no significant difference was found in gene mumber of synonymous mutation and missense mutation between the two groups.The number of terminating codon missing mutation genes in the LGBLEL group was more than that in the MALT lymphoma group (P<0.05). The most common InDels types were frameshift mutation, non-frameshift insertion and non-frameshift deletion, and there was no significant difference in gene number of InDels between the LGBLEL group and MALT lymphoma group.The number of exon CNVs was few in both two groups and showed no significant influence in final result.Six differentially expressed hub genes were found, including IGFN1, TCP10, SLC45A4, BTBD7, PHGR1 and PIEZ02.

Conclusions

IGFN1, TCP10, SLC45A4, BTBD7, PHGR1 and PIEZ02 genes may participate in the development of LGBLEL into MALT lymphoma.

Key words:

Benign lymphoepithelial lesion; Lacrimal gland; Mucosa-associated lymphoid tissue lymphoma; Whole-exome sequencing; Gene expression

Contributor Information

Liu Rui
Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Being Ophthalmology&Vision Science Key Lab, Beijing 100730, China
Wu Hao
College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing 100124, China
Zhao Pengxiang
College of Life Science and Bio-Engineering, Beijing University of Technology, Beijing 100124, China
Ge Xin
Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Being Ophthalmology&Vision Science Key Lab, Beijing 100730, China
Zhang Jingxue
Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Being Ophthalmology&Vision Science Key Lab, Beijing 100730, China
Ma Jianmin
Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Institute of Ophthalmology, Being Ophthalmology&Vision Science Key Lab, Beijing 100730, China
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Updated: November 19, 2020 — 3:29 am