通过转录组谱分析鉴定系统性红斑狼疮的免疫相关基因。

Immune-relevant genes of systemic lupus erythematosus by transcriptome profiling analysis.

机构信息

Department of Critical Care Medicine, The First Hospital of Jilin University, No.71, Xinmin Street, Changchun 130021, China.

Department of Rheumatology, The First Hospital of Jilin University, No. 71, Xinmin Street, Changchun 130021, China.

出版信息

Cytokine. 2022 Oct;158:155975. doi: 10.1016/j.cyto.2022.155975. Epub 2022 Aug 11.

DOI:10.1016/j.cyto.2022.155975

PMID:35964416

Abstract

OBJECTIVE

Our study aimed to reveal the roles of long noncoding RNA (lncRNA) and immune-relevant genes in systemic lupus erythematosus (SLE).

METHODS

Expression profiling dataset GSE65391 consisted of 72 healthy blood samples and 924 SLE blood samples was downloaded from the Gene Expression Omnibus. Differentially expressed RNAs (DERs) in SLE samples were identified using the Limma package. Immune-relevant DERs were uncovered after assessing the immune cell infiltration types of different samples. Modules significantly related to the disease were extracted via weighted gene co-expression network analysis (WGCNA), followed by module-trait analysis. LncRNA-mRNA co-expression network was constructed for DERs in immune-relevant modules. Genes related to SLE were further revealed via the Comparative Toxicogenomics Database (CTD). Validation assay was conducted by another independent expression profiling dataset, GSE46907 (consisted of 5 healthy blood samples and 5 SLE blood samples) and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis of 15 healthy blood samples and 15 SLE blood samples.

RESULTS

A total of 606 DERs, including 19 lncRNAs and 587 mRNAs, were identified. Obvious differences were observed in the proportions of 20 immune cell types, and 378 immune-relevant DERs were revealed. Genes in the lncRNA-mRNA co-expression network were significantly enriched in primary immunodeficiency, hematopoietic cell lineage, B cell receptor signaling pathway, SLE (up-regulated FCGR3A, down-regulated CD40LG, up-regulated HIST1H2BE, down-regulated human leukocyte antigen [HLA]-DOA, down-regulated HLA-DOB, up-regulated HIST1H3D, and up-regulated HIST1H2BC), and intestinal immune network for IgA production. SLE-related gene, CD40LG, retrieved from CTD has co-expression interactions with seven differentially expressed lncRNAs (HCG27, LINC02555, LINC02210, DHRS4-AS1, MIR600HG, DANCR, and LINC01278). CD40LG and HLA-DOA, were observed down-regulated, and FCGR3A, and HIST1H2BE were up-regulated in validation dataset GES46907. Moreover, CD40LG was validated to be down-regulated using qRT-PCR.

CONCLUSIONS

Our results provide new insight in understanding the pathogenesis of SLE and might be helpful for developing new therapeutic approaches of SLE by modulating immune response.

摘要

目的

本研究旨在揭示长链非编码 RNA（lncRNA）和免疫相关基因在系统性红斑狼疮（SLE）中的作用。

方法

从基因表达综合数据库中下载了包含 72 个健康血液样本和 924 个 SLE 血液样本的表达谱数据集 GSE65391。使用 Limma 软件包鉴定 SLE 样本中的差异表达 RNA（DER）。评估不同样本的免疫细胞浸润类型后，发现免疫相关 DER。通过加权基因共表达网络分析（WGCNA）提取与疾病显著相关的模块，然后进行模块特征分析。为免疫相关模块中的 DER 构建 lncRNA-mRNA 共表达网络。通过比较毒理学基因组数据库（CTD）进一步揭示与 SLE 相关的基因。使用另一个独立的表达谱数据集 GES46907（包含 5 个健康血液样本和 5 个 SLE 血液样本）进行验证实验，并通过定量逆转录-聚合酶链反应（qRT-PCR）分析 15 个健康血液样本和 15 个 SLE 血液样本进行验证。

结果

共鉴定出 606 个 DER，包括 19 个 lncRNA 和 587 个 mRNA。20 种免疫细胞类型的比例差异明显，发现 378 个免疫相关 DER。lncRNA-mRNA 共表达网络中的基因在原发性免疫缺陷、造血细胞谱系、B 细胞受体信号通路、SLE（上调 FCGR3A、下调 CD40LG、上调 HIST1H2BE、下调人类白细胞抗原 [HLA]-DOA、下调 HLA-DOB、上调 HIST1H3D、上调 HIST1H2BC）和肠道免疫网络中 IgA 产生方面显著富集。从 CTD 中检索到的 SLE 相关基因 CD40LG 与七个差异表达 lncRNA（HCG27、LINC02555、LINC02210、DHRS4-AS1、MIR600HG、DANCR 和 LINC01278）具有共表达相互作用。在验证数据集 GES46907 中观察到 CD40LG 和 HLA-DOA 下调，FCGR3A 和 HIST1H2BE 上调。此外，通过 qRT-PCR 验证 CD40LG 下调。