Table 1 Summary of recent transcriptome studies in SLE
From: Transcriptomic studies of systemic lupus erythematosus
Groups | Authors | Year | SLE samples and patients | Material | Method | Summary of findings |
|---|---|---|---|---|---|---|
Pascual and colleagues | Chiche et al. [17] | 2014 | 157 samples/ 62 adults | Whole blood | Microarray | Modular repertoire analysis identified three distinct IFN signatures in SLE, which involved the previous IFNα signature as well as IFNβ and IFNγ signatures. |
Banchereau et al. [33] | 2016 | 924 samples/ 158 children | Whole blood | Microarray | Longitudinal immunomonitoring stratified SLE patients into seven groups based on five modules correlated with SLEDAI (erythropoiesis, IFN, myeloid lineage/neutrophils, plasmablasts and lymphoid lineage modules). | |
Hong et al. [34] | 2019 | 92 pregnant women | Whole blood | Microarray | Sustained IFN response and plasma cell signatures were observed in pregnant SLE patients with fetal complications. Patients with preeclampsia showed remarkable upregulation of the neutrophil signature. | |
Nehar-Belaid et al. [22] | 2020 | 33 children and 8 adults | PBMCs | scRNA-seq | The high IFN signature was limited to a small number of cells within each major cell type. Subpopulations enriched in ISGs and/or monogenic lupus-associated genes were expanded, especially in active SLE. | |
Other groups | McKinney et al. [39] | 2015 | 23 adults | CD4+ T cells, CD8+ T cells | Microarray | The exhaustion signature in CD8+ T cells, which was associated with poor outcomes in patients with viral infections, was correlated with a lower risk of disease relapse in AAV and SLE patients. |
Chong et al. [40] | 2015 | 9 adults with DLE | Skin | Microarray | CD163+ macrophages were polarized in DLE skin. M1 macrophage-associated genes such as CXCL10 and CCL5 were upregulated in DLE skin. | |
Sherbiny et al. [18] | 2018 | 114 adults | PBMCs and sorted monocytes, T, NK and three B cell subsets | qRT-PCR | IFN score A was increased in SLE only, whereas IFN score B was increased in both SLE and RA. Both scores were correlated with mucocutaneous and hematological, but not musculoskeletal, activity in SLE. | |
Petri et al. [16] | 2019 | 243 adults | Whole blood | Microarray | IFN, BAFF, plasma cell and LDG signatures were relatively stable in patients over time. The changes in IFN and BAFF signatures did not coincide with changes in disease activity. | |
Panousis et al. [35] | 2019 | 142 samples/ 142 adults | Whole blood | RNA-seq | The SLE “activity signature” included genes related to immune cell metabolism, protein synthesis and proliferation. Active nephritis was characterized by neutrophil and humoral response signatures. | |
Catalina et al. [20] | 2019 | More than 1000 patients from multiple publicly available datasets | PBMCs, whole blood, skin, synovium, kidney, monocytes, B cells and CD4+ T cells | Microarray | The IFN signature was enriched in SLE skin and synovium and, to a lesser extent, in LN kidneys. The lack of correlation between the IFN signature in PBMCs and SLEDAI is due to its persistent overexpression in inactive SLE monocytes. | |
Minstry et al. [37] | 2019 | 11 adults | PBMCs | RNA-seq, scRNA-seq | The highest ISG expression was observed in LDGs among various cell subpopulations. CD10+ LDGs showed the strongest proinflammatory phenotype and the most significant association with organ damage. | |
Accelerating Medicine Partnership in SLE Network | Der et al. [43] | 2017 | 16 adults (kidney) and 12 adults (skin) with LN | Kidney and skin | scRNA-seq | IFN scores in renal tubular cells were positively correlated with the chronicity index, urinary protein levels and glomerular IgG deposition. Patients with higher IFN scores were less likely to respond to treatment. |
Der et al. [44] | 2019 | 21 adults (kidney) and 17 adults (skin) with LN | Kidney and skin | scRNA-seq | The fibrotic gene signatures related to ECM pathways in tubular cells predicted a poor treatment response. Comparisons among histological subclasses revealed distinct inflammation and fibrosis pathways in each subclass. | |
Arazi et al. [45] | 2019 | 21 adults with LN | Kidney | scRNA-seq | CD16+ monocytes acquired phagocytic function and differentiated into M2-like macrophages in the kidney of LN patients. Twenty-one cell subpopulations including cytotoxic CD8+ T cells and DN2-like B cells infiltrated the kidney. | |
Fava et al. [46] | 2020 | 30 adults with LN | Kidney and urine | scRNA-seq + proteomics | A chemokine gradient induced by IFNγ distinguished proliferative LN from membranous LN. Urinary chemokines were predominantly produced by infiltrating CD8+ T cells, followed by NK and myeloid cells. |