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Abstract
Background The phenotypic, signaling and metabolic diversities of leucocytes of systemic lupus erythematosus (SLE) impede comprehensive identification of immunopathologically-relevant alterations in leucocytes associated with active SLE. We aimed to identify these alteration signatures in leucocytes from patients with active SLE by an integrated platform comprising high-dimensional flow cytometry, cytometry by time of flight (CyTOF) and RNA sequencing (RNA-seq).
Methods Peripheral blood mononuclear cells (PBMCs) of SLE patients and healthy subjects were subjected to high-dimensional flow cytometry and CyTOF for studying alterations of myeloid cells and lymphocytes. Bulk RNA-seq was conducted for 8 sorted cell populations. Data were subjected to integrative analyses with Cytozoom that identified cellular signatures of active SLE. Differences in T-cell and B-cell receptor clonalities, cellular signaling and metabolic reaction pathways were studied based on SLE activity.
Results SLE patients with active disease had significantly lower CD14+CD16highCD86+HLA-DR+ and higher circulating CD3+CCR4+CXC3CR1+CD45RO+CD27+cells in their PBMCs (See figures 1A to 1Y), and higher TCR diversity in inactive CD8+ T cells compared to those with inactive disease, coupled with downregulated Sirtuin and upregulated oxidative phosphorylation and EIF2 signaling pathways in CD8+ T cells and B cells. Upregulated keratin sulphate synthesis reaction was observed in activated B cells, monocytes and plasmacytoid dendritic cells while the reaction was downregulated in inactive CD8+ T cells in active SLE patients
Conclusions An integrated analytical platform comprising high-dimensional cytometric analyses and RNA-seq demonstrated signatures that highlight the concerted and complex pathogenic signatures of non-classical monocytes, tissue-homing memory T cells and altered signaling/metabolic pathways of lymphocytes and myeloid cells in patients with active SLE.
The paradigms in searching for flare-related cell types in Myeloid (A-L) and T/NK (M-Y) lineages, presented with UMAP and PAGA plots, and Leiden clustering
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