Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Single-Cell RNA-Seq of Memory B cells in Early Untreated Rheumatoid Arthritis Patients (Gene Expression Data)

ABSTRACT: In recent years, a circulating subset of B cells phenotypically negative for CD21 has been reported to be expanded in chronic infectious and autoimmune inflammatory diseases. While reports on the function of these cells differ by disease origin, their role in rheumatoid arthritis (RA) has remained elusive. Here, we combine clinical data with flow cytometric analyses for patients untreated for and newly diagnosed with RA. We show correlations between the frequency of CD21-Tbet+CD11c+ and destruction of both cartilage and bone in in the joints of patients at the time of diagnosis. Combining single-cell 5’ RNA sequencing with B-cell receptor (VDJ)-enriched sequencing, we are able to identify the Tbet+CD11c+ cells in the scRNA-seq data from untreated newly diagnosed RA patients. Further, we describe a characteristic gene expression pattern, with overrepresentation of upregulated genes involved in antigen processing and presenting processes. The same gene signature is near identically expressed by autoimmune-associated cells infiltrating synovial tissue of RA patients. Our findings suggest that Tbet+CD11c+ B cells may be poised for antigen presentation in the periphery, and could be capable of recirculating between the periphery and joint tissue, thereby promoting autoimmune responses. Overall, we demonstrate a potential pathogenic role of Tbet+CD11c+ B cells in RA, in which they contribute to joint destruction.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Inga-Lill Mårtensson

PROVIDER: E-MTAB-11961 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Memory B cells play a fundamental role in host defenses against viruses. This dataset aimed at understanding the recruitment and remodeling of the memory B cell repertoire in the context of BA.1-breakthrough infection in BNT162b2 mRNA vaccinated individuals. All four donors enrolled in the study had received a booster (3rd dose) of BNT162b2 mRNA vaccine and had no history of prior SARS-CoV-2 infection. All four experienced a documented breakthrough infection between 12/24/2021 and 01/30/2022 when BA.1 was responsible for > 85% of SARS-CoV-2 infections in France. All donors were sampled at Henri Mondor University Hospital (AP-HP, Paris France), and samples used for scRNA-seq were collected shortly after breakthrough infection (PO_M0 samples; between day 7 and day 18) and 5 to 6 months after infection (PO_M6 samples; between day 152 and day 173). Clinical and biological characteristics of these patients are summarized in the Patient_information.csv file. For each sample, an initial pool of 50.000 total peripheral CD3-CD14-CD56- CD19+ IgD- cells was always sorted and afterward, to enrich for cells of interest, only CD19+CD38low antibody secreting cells (ASCs), CD19hi IgD+ cells and SARS-CoV-2 Spike/RBD PE/tetramer positive B cells were sorted, leading to approximately 55000-60000 total sorted cells per sample. Sorted cells were then counted and up to 20 000 cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. The scRNA-seq libraries for gene expression (mRNA), ADT and VDJ BCR libraries were generated using Chromium Next GEM Single Cell V(D)J Reagent Kit v.1.1 with Feature Barcoding (10x Genomics) according to the manufacturer’s protocol. PBMCs were initially isolated from venous blood samples via standard density gradient centrifugation and used after cryopreservation at -150°C. PBMCs were thawed using RPMI-1640 (Gibco) 10% FBS, washed twice and approximately 15x106 cells were then resuspended in 100µL PBS 2%FBS and incubated for 40 minutes at 4°C with a decoy tetramer (biotinylated Bovine Serum albumin coupled with BV785 streptavidin) and Hu-1 Spike, BA.1 Spike, Hu-1 RBD and BA.1 RBD tetramers (constructed using PE-labelled TotalSeqC® streptavidin with different barcodes for each individual antigens (see feature_reference.csv.gz files).). Cells were washed, resuspended in 100µL PBS 2%FBS and stained with a cocktail of fluorochrome conjugated (CD3, CD14 both APC-H7 at 1:100 each; CD15 and CD56 BV785 at 1:100 each, CD19 PECF594 at 1:100, IgD FITC at 1:100, CD38 PercP-Cy5.5 at 1:100) and TotalSeqC® (CD38, CD27, CD71, CD21, CD11c, CD39, FCRL5, CD95 all at 1:40 (all obtained from BioLegend)) antibodies for 40 minutes on ice. Viable cells were identified using a LIVE/DEAD Fixable Aqua Dead Cell Stain Kit (Thermo Fisher Scientific, 1:200) incubated with conjugated antibodies. Two distinct sorts were performed for each donor: one at the early time-point (PO_M0) and one at the 6 months’ time-point (PO_M6).

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Single-Cell RNA-Seq of Memory B cells in Early Untreated Rheumatoid Arthritis Patients (Gene Expression Data)

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