Profiling rogue B cell clones in autoimmune disease using single-cell RNA-sequencing
Mandeep Singh1, J.H. Reed1, S. Rizzetto2, A.A. Eltahla2, C. Cai2, F. Luciani2, C.C. Goodnow1
1Department of Immunology, Garvan Institute of Medical Research, Australia;
2Kirby Institute for Infection and Immunity, Australia
The B cell receptor (BCR) is crucial for B cell development, survival, and activation. Multiple immune tolerance mechanisms ensure that B cells carrying self-reactive BCRs are either purged during development or inactivated in the periphery. How these self-reactive “rogue” B cell clones break tolerance mechanisms and drive disease in autoimmune disorders is poorly understood. The recent emergence of single-cell technologies offers a powerful way to profile rogue cells within highly dynamic and heterogeneous immune populations. In particular, single-cell RNA-sequencing (scRNA-seq) of B or T lymphocytes allows for both the measurement of gene expression and immune repertoire information at single-cell resolution. We developed a novel computation pipeline to assemble full-length heavy and light chain BCR sequences from scRNA-seq using an updated version of the tool VDJPuzzle. We applied our approach to an Sjögren’s syndrome patient presenting IGHV1-69 IgM Rheumatoid Factor autoantibodies and an expanded IGHV1-69+ memory B cell population that persisted longitudinally. Sc-RNA-seq followed by BCR assembly of IGHV1-69+ memory B cells revealed identical V, J and D segments and two extremely similar CDR3 sequences within each heavy and light chain. In contrast, IGHV1-69- memory B cells sorted from the same patient were found to express a polyclonal repertoire. Transcriptome profiling coupled with surface phenotype markers additionally revealed that IGHV1-69+ memory B cells have a distinct phenotype when compared to clonally unrelated cells. These results show that scRNA-seq can be used to characterise a pathogenic B cell clone in an autoimmune disease patient. Profiling rogue B cells and understanding the pathways that are deregulated will help understand the complexity of autoimmune disease pathogenesis and may led to new approaches for targeted therapy.