A regulatory role for CD72 expression on B cells and increased soluble CD72 in primary Sjogren’s syndrome

Shi, Yuqi; Ma, Yue; Xie, Jingyuan; Lin, Liang-In; Shi, Yifan; Li, Xiao; Shen, Ping; Pan, Xiaoxia; Ren, Hong

doi:10.1186/s12865-020-00351-2

Cited by 11 publications

(12 citation statements)

References 25 publications

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“…Markers for the activated memory B cells, B_4 (Figure 5D right), match those from a recent single-cell study of healthy individuals (King et al, 2021). The transitional B cell subtype (B_3) was annotated by marker genes, CD72 and TCL1A , identified from previous studies (Shen et al, 2020; Stewart et al, 2020). These findings are also consistent with our observation of TNFSF13B upregulation in these patients (identified in our LR analysis), as BAFF has been shown to enhance survival of these B cell subtypes (Hsu et al, 2002).…”

Section: Resultsmentioning

confidence: 99%

Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals

Mitchel

Gordon

Perez

et al. 2022

Preprint

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Tissue- and organism-level biological processes often involve coordinated action of multiple distinct cell types. Current computational methods for the analysis of single-cell RNA-sequencing (scRNA-seq) data, however, are not designed to capture co-variation of cell states across samples, in part due to the low number of biological samples in most scRNA-seq datasets. Recent advances in sample multiplexing have enabled population-scale scRNA-seq measurements of tens to hundreds of samples. To take advantage of such datasets, here we introduce a computational approach called single-cell Interpretable Tensor Decomposition (scITD). This method extracts multicellular gene expression patterns that vary across different biological samples. These patterns capture how changes in one cell type are connected to changes in other cell types. The multicellular patterns can be further associated with known covariates (e.g., disease, treatment, or technical batch effects) and used to stratify heterogeneous samples. We first validated the performance of scITD using in vitro experimental data and simulations. We then applied scITD to scRNA-seq data on peripheral blood mononuclear cells (PBMCs) from 115 patients with systemic lupus erythematosus and 56 healthy controls. We recapitulated a well-established pan-cell-type signature of interferon-signaling that was associated with the presence of anti-dsDNA autoantibodies and a disease activity index. We further identified a novel multicellular pattern that appears to potentiate renal involvement for patients with anti-dsDNA autoantibodies. This pattern was characterized by an expansion of activated memory B cells along with helper T cell activation and is predicted to be mediated by an increase in ICOSLG-ICOS interaction between monocytes and helper T cells. Finally, we applied scITD to two PBMC datasets from patients with COVID-19 and identified reproducible multicellular patterns that stratify patients by disease severity. Overall, scITD is a flexible method for exploring co-variation of cell states in multi-sample single-cell datasets, which can yield new insights into complex non-cell-autonomous dependencies that define and stratify disease.

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Section: Resultsmentioning

confidence: 99%

Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals

Mitchel

Gordon

Perez

et al. 2022

Preprint

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“…Our GSEA results also suggest that BTK is closely associated with the B-cell receptor signaling pathway. It was shown that BTK may be involved in the radioresistance process of NPC cells ( 27 ). This suggests to us that BTK may be a new key biomarker for NPC.…”

Section: Discussionmentioning

confidence: 99%

Construction of lncRNA and mRNA co-expression network associated with nasopharyngeal carcinoma progression

Chen

Wang

et al. 2022

Front. Oncol.

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Nasopharyngeal carcinoma is a type of head and neck cancer with a high incidence in men. In the past decades, the survival rate of NPC has remained around 70%, but it often leads to treatment failure due to its distant metastasis or recurrence. The lncRNA-mRNA regulatory network has not been fully elucidated. We downloaded the NPC-related gene expression datasets GSE53819 and GSE12452 from the Gene Expression Omnibus database; GSE53819 included 18 NPC tissues and 18 normal tissues, and GSE12452 included 31 NPC tissues and 10 normal tissues. Weighted gene co-expression network analysis was performed on mRNA and lncRNA to screen out modules that were highly correlated with tumor progression. The two datasets were subjected to differential analysis after removing batch effects, and then Venn diagrams were used to screen for overlapping genes in the module genes and differential genes. The lncRNA-mRNA co-expression network was then constructed, and key mRNAs were identified by MCODE analysis and expression analysis. GSEA analysis and qRT-PCR were performed on key mRNAs. Through a series of analyses, we speculated that BTK, CD72, PTPN6, and VAV1 may be independent predictors of the prognosis of NPC patients.Taken together, our study provides potential candidate biomarkers for NPC diagnosis, prognosis, or precise treatment.

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“…Therapeutics that reduce the proliferation of B cells, including TGs (39) and HCQ (40), have been used to treat SS. Indeed, SS is considered an autoimmune disease associated with hyperactivity, a pathologic autoantibody response of B cells (41), and elevated levels of serum IgG (42). Therefore, the levels of immunoglobulins in peripheral blood are considered to be important indicators of SS activity (7).…”

Section: Discussionmentioning

confidence: 99%

Efficacy and safety of Tripterygium glycosides in Sjögren’s syndrome treatment: evidence from 12 randomized controlled trials

Luo¹,

Zhang²,

Kuai³

et al. 2021

Ann Palliat Med

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A regulatory role for CD72 expression on B cells and increased soluble CD72 in primary Sjogren’s syndrome

Cited by 11 publications

References 25 publications

Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals

Tensor decomposition reveals coordinated multicellular patterns of transcriptional variation that distinguish and stratify disease individuals

Construction of lncRNA and mRNA co-expression network associated with nasopharyngeal carcinoma progression

Efficacy and safety of Tripterygium glycosides in Sjögren’s syndrome treatment: evidence from 12 randomized controlled trials

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