A CD4 T cell population expand and reshape autoreactive B cells, contributing to autoimmune lung pathology and post-infection autoimmunity in children

Community acquired pneumonia (CAP) is a significant risk factor for autoimmune disease development. However, mechanisms underlying infection and autoimmunity remain elusive. Here, we report selective expansion of autoantibody producing CD21-CD19+ B cells by bronchoalveolar PD-1+CCR2+GZMA+RUNX3+ T helper 1 like (aTh1) cells in children with CAP. In bronchoalveolar lavage, the numbers of aTh1, CD21-B cells and the concentrations of IgG-specific autoantibodies correlated with CAP severity. Unexpectedly, PD-1 decreased the ability of CD21- B cells to produce autoantibodies and reshaped their specificity in the course of pathogen invasion. Nevertheless, respiratory infection induced aTh1 and CD21-B cell persistence may trigger autoimmune disease development in susceptible individuals; e.g. they were prevalent in cerebrospinal fluid of children with post-infection Guillain-Barre Syndrome. Thus, we reveal dual roles of aTh1 and CD21-B cells in infection immunity and autoimmune pathology, and demonstrate that PD-1 is a critical checkpoint inhibitor for autoimmune disease development. Overall design: The bronchoalveolar lavage fluid (BALF) samples from five patients were mixed and FACS-sorted as the following strategy. Briefly, the CD45+ fraction was retrieved and followed by depletion of CD14+ and CD16+ cells. The fractions of CD3E+ and CD3E- of the remaining cells were isolated for single-cell RNA sequencing. Human V(D)J+5' Gene Expression product from 10X GENOMICS was used to measure paired gene expression and immune repertoire information (paired TCR or BCR) within single cells. By using Gel Beads-in-emulsion code (GEM-Code) technology, transcripts within each cell were indexed with unique barcode. After reverse transcription, the full-length cDNA was amplified via PCR with primers against common 5' and 3' ends added during GEM-RT. With sufficient starting material, the double stranded cDNA library was split into two subsamples for the construction of Single Cell 5' expression and TCR- or BCR-enriched library, separately. The Single Cell V(D)J and 5' Gene Expression libraries were sequenced at certain depth and running parameters. **The approval process for the data release is pending from the Chinese Government***