Single-cell multi-omics analysis reveals IFN-driven alterations in T lymphocytes and natural killer cells in systemic lupus erythematosus

Wellcome Open Res. 2022 May 12;6:149. doi: 10.12688/wellcomeopenres.16883.2. eCollection 2021.


Background: The characterisation of the peripheral immune system in the autoimmune disease systemic lupus erythematosus (SLE) at the single-cell level has been limited by the reduced sensitivity of current whole-transcriptomic technologies. Here we employ a targeted single-cell multi-omics approach, combining protein and mRNA quantification, to generate a high-resolution map of the T lymphocyte and natural killer (NK) cell populations in blood from SLE patients. Methods: We designed a custom panel to quantify the transcription of 534 genes in parallel with the expression of 51 surface protein targets using the BD Rhapsody AbSeq single-cell system. We applied this technology to profile 20,656 T and NK cells isolated from peripheral blood from an SLE patient with a type I interferon (IFN)-induced gene expression signature (IFN hi), and an age- and sex- matched IFN low SLE patient and healthy donor. Results: We confirmed the presence of a rare cytotoxic CD4 + T cell (CTL) subset, which was exclusively present in the IFN hi patient. Furthermore, we identified additional alterations consistent with increased immune activation in this patient, most notably a shift towards terminally differentiated CD57 + CD8 + T cell and CD16 + NK dim phenotypes, and the presence of a subset of recently-activated naïve CD4 + T cells. Conclusions: Our results identify IFN-driven changes in the composition and phenotype of T and NK cells that are consistent with a systemic immune activation within the IFN hi patient, and underscore the added resolving power of this multi-omics approach to identify rare immune subsets. Consequently, we were able to find evidence for novel cellular peripheral biomarkers of SLE disease activity, including a subpopulation of CD57 + CD4 + CTLs.

Keywords: AbSeq; BD Rhapsody; Single-cell RNA-sequencing (scRNA-seq); biomarker; cytotoxic CD4+ T cells (CTLs); multi-omics; systemic lupus erythematosus (SLE); type I interferon (IFN).

Grant support

This work was supported by a strategic award to the Diabetes and Inflammation Laboratory from the JDRF (4-SRA-2017-473-A-A) and the Wellcome (107212/A/15/Z), and a grant from the JDRF (1-SRA-2019-657-A-N) to JAT and LSW.