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Integrated bulk and single-cell RNA-sequencing identified disease-relevant monocytes and a gene network module underlying systemic sclerosis
Journal of Autoimmunity ( IF 12.8 ) Pub Date : 2020-10-08 , DOI: 10.1016/j.jaut.2020.102547
Satomi Kobayashi 1 , Yasuo Nagafuchi 2 , Mai Okubo 1 , Yusuke Sugimori 1 , Harumi Shirai 1 , Hiroaki Hatano 1 , Maeda Junko 1 , Haruyuki Yanaoka 3 , Yusuke Takeshima 2 , Mineto Ota 2 , Yukiko Iwasaki 1 , Shuji Sumitomo 1 , Tomohisa Okamura 2 , Kazuhiko Yamamoto 4 , Hirofumi Shoda 1 , Keishi Fujio 1
Affiliation  

Objective

Immunological disturbances have been reported in systemic sclerosis (SSc). This study assessed the transcriptome disturbances in immune cell subsets in SSc and characterized a disease-related gene network module and immune cell cluster at single cell resolution.

Methods

Twenty-one Japanese SSc patients were enrolled and compared with 13 age- and sex-matched healthy controls (HC). Nineteen peripheral blood immune cell subsets were sorted by flow cytometry and bulk RNA-seq analysis was performed for each. Differential expression and pathway analyses were conducted. Iterative weighted gene correlation network analysis (iWGCNA) of each subset revealed clustered co-expressed gene network modules. Random forest analysis prioritized a disease-related gene module. Single cell RNA-seq analysis of 878 monocytes was integrated with bulk RNA-seq analysis and with a public database for single cell RNA-seq analysis of SSc patients.

Results

Inflammatory pathway genes were differentially expressed in widespread immune cell subsets of SSc. An inflammatory gene module from CD16+ monocytes, which included KLF10, PLAUR, JUNB and JUND, showed the greatest discrimination between SSc and HC. One of the clusters of SSc monocytes identified by single-cell RNA-seq analysis characteristically expressed these inflammatory co-expressed genes and was similar to lung infiltrating FCN1hi monocytes expressing IL1B.

Conclusions

Our integrated analysis of bulk and single cell RNA-seq analysis identified an inflammatory gene module and a cluster of monocytes that are relevant to SSc pathophysiology. They could serve as candidate novel therapeutic targets in SSc.



中文翻译:

集成的批量和单细胞 RNA 测序确定了与疾病相关的单核细胞和系统性硬化症背后的基因网络模块

客观的

系统性硬化症 (SSc) 中已有免疫紊乱的报道。本研究评估了 SSc 中免疫细胞亚群的转录组紊乱,并以单细胞分辨率表征了疾病相关基因网络模块和免疫细胞簇。

方法

招募了 21 名日本 SSc 患者,并与 13 名年龄和性别匹配的健康对照 (HC) 进行了比较。通过流式细胞术对 19 个外周血免疫细胞亚群进行分类,并对每个亚群进行大量 RNA-seq 分析。进行了差异表达和途径分析。每个子集的迭代加权基因相关网络分析 (iWGCNA) 揭示了聚集的共表达基因网络模块。随机森林分析优先考虑与疾病相关的基因模块。878 个单核细胞的单细胞 RNA-seq 分析与批量 RNA-seq 分析和公共数据库相结合,用于 SSc 患者的单细胞 RNA-seq 分析。

结果

炎症通路基因在广泛分布的 SSc 免疫细胞亚群中差异表达。来自 CD16 +单核细胞的炎症基因模块,包括KLF10、PLAURJUNBJUND,显示出 SSc 和 HC 之间的最大区别。通过单细胞 RNA-seq 分析鉴定的 SSc 单核细胞簇中的一个特征性地表达了这些炎症共表达基因,并且类似于肺浸润的 FCN1 hi单核细胞表达IL1B

结论

我们对大量和单细胞 RNA-seq 分析的综合分析确定了一个炎症基因模块和一组与 SSc 病理生理学相关的单核细胞。它们可以作为 SSc 的候选新治疗靶点。

更新日期:2020-10-08
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