Transcriptomic analysis of B cells suggests that CD70 and LY9 may be novel features in patients with systemic lupus erythematosus

Qun Liu; Yiyao Deng; Xiaomin Liu; Ying Zheng; Qinggang Li; Guangyan Cai; Zhe Feng; Xiangmei Chen

doi:10.1016/j.heliyon.2023.e15684

Transcriptomic analysis of B cells suggests that CD70 and LY9 may be novel features in patients with systemic lupus erythematosus

Heliyon. 2023 Apr 23;9(5):e15684. doi: 10.1016/j.heliyon.2023.e15684. eCollection 2023 May.

Authors

Qun Liu^{1

2

3}, Yiyao Deng⁴, Xiaomin Liu^{2

3}, Ying Zheng^{2

3}, Qinggang Li^{2

3}, Guangyan Cai², Zhe Feng², Xiangmei Chen^{1

2

3}

Affiliations

¹ School of Medicine, Nankai University, Tianjin, 300071, China.
² Department of Nephrology, The First Medical Center, Chinese PLA General Hospital, Medical School of Chinese PLA, Chinese PLA Institute of Nephrology, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing, 100853, China.
³ Haihe Laboratory of Cell Ecosystem, Tianjin, 300020, China.
⁴ Department of Nephrology, Guizhou Provincial People's Hospital, 83, Zhongshan Road, Nanming District, Guiyang, 550002, Guizhou, China.

Abstract

Dysfunction of B-cell subsets is critical in the development of systemic lupus erythematosus (SLE). There is a great diversity of B-lineage cells, and their features and functions in SLE need to be clarified. In this study, we analyzed single-cell RNA sequencing (scRNA-seq) data from peripheral blood mononuclear cells (PBMCs) and bulk transcriptomic data of isolated B-cell subsets from patients with SLE and healthy controls (HCs). We preformed scRNA-seq analysis focused on the diversity of B-cell subsets and identified a subset of antigen-presenting B cells in SLE patients that highly expressed ITGAX. A list of marker genes of each B-cell subset in patients with SLE was also identified. Comparison of bulk transcriptomic data of isolated B-cell subpopulations between SLE patients and HCs revealed the upregulated differentially expressed genes (DEGs) for each B-cell subpopulation in SLE. Common genes identified using these two methods were considered to be upregulated marker genes of B cells in SLE. The scRNA-seq data of SLE patients and HCs revealed that CD70 and LY9 were overexpressed in B cells vs. other cell types from SLE patients, and this pattern was validated by RT‒qPCR. Because CD70 is the cellular ligand of CD27, previous studies on CD70 have focused mainly on T cells from SLE patients. LY9 appears to have different functions in mice and humans: its expression is decreased in lupus-prone mice but is increased in T cells and some B-cell subpopulations in SLE patients. Here, we describe the overexpression of two costimulatory molecules, CD70 and LY9, which may be a novel feature of B cells in SLE patients.

Keywords: B cells; CD70; LY9; Systemic lupus erythematosus; Transcriptomic analysis.