CD4+ follicular regulatory T cells (Tfr cells) suppress B cell responses through modulation of follicular helper T cells (Tfh cells) and germinal center (GC) development. We found that Tfr cells also can promote the GC response through provision of IL-10 following acute infection with lymphocytic choriomeningitis virus (LCMV). Sensing of IL-10 by B cells was necessary for optimal development of the GC response. GC B cells formed in the absence of Treg-cell derived IL-10 displayed an altered dark zone state and decreased expression of the transcription factor FOXO1. IL-10 promoted nuclear translocation of FOXO1 in activated B cells. These data indicate that Tfr cells play a multifaceted role in the fine-tuning of the GC response and identify IL-10 as an important mediator by which Tfr cells support the GC reaction.

Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19.

Analyses of somatic hypermutation (SHM) patterns in B-cell immunoglobulin (Ig) sequences have important basic science and clinical applications, but are often confounded by the intrinsic biases of SHM targeting on specific DNA motifs (i.e., hot- and cold-spots). Modeling these biases has been hindered by the difficulty in identifying mutated Ig sequences in vivo in the absence of selection pressures, which skew the observed mutation patterns. To generate a large number of unselected mutations, we immunized B1-8 heavy-chain transgenic mice with nitrophenyl (NP) to stimulate NP-specific λ+ germinal center B cells, and sequenced the unexpressed κ light chains using next-generation methods. Most of these κ sequences had out-of-frame junctions and were presumably uninfluenced by selection. Despite being non-functionally rearranged, they were targeted by SHM and displayed a higher mutation frequency than functional sequences. We used 39,173 mutations to construct a quantitative SHM targeting model. The model showed targeting biases that were consistent with classic hot- and cold-spots, yet revealed additional highly mutable motifs. We observed comparable targeting for functional and non-functional sequences, suggesting similar biological processes operate at both loci. However, we observed species-specific and chain-specific targeting patterns, demonstrating the need for multiple SHM targeting models. Interestingly, the targeting of C/G bases and the frequency of transition mutations at C/G bases was higher in mice compared with humans, suggesting lower levels of DNA repair activity in mice. Our models of SHM targeting provide insights into the SHM process and support future analyses of mutation patterns.

A heterogeneous population of cells secreting mucosal IgA confers protection against influenza virus infection.

of treatment and relapse. To this end, we integrated data from multiple profiling methods on the same patients, including (a) adaptive immune receptor repertoire sequencing (AIRR-Seq) to generate highdepth B cell receptor (BCR) libraries from unselected PBMCs collected at pre-RTX treatment time points and during episodes of post-RTX relapse; (b) previously published sequences of human monoclonal autoantibodies, with known specificity for the MuSK autoantigen, that emerged during post-RTX relapses; and (c) single-cell gene expression analysis with paired BCR repertoire sequencing, to trace B cell populations temporally and to identify the phenotype of B cells that emerge during post-RTX relapse. In comparison with the examination of clonal overlap between bulk BCR repertoires alone, this approach, which we refer to as Single-cell Tracing of Adaptive Immune Receptor (STAIR) repertoires, allows for the unbiased characterization of the gene expression profile of persistent, disease-relevant B cells (including those specific for the autoantigen) at single-cell resolution. By using this approach, we offer new insights into the mechanism of post-RTX relapse in patients with MuSK MG and potential avenues for improving the treatment of MG and other autoantibody-driven autoimmune diseases. ResultsExperimental design. We used the following experimental approach (Figure 1A) to identify and characterize B cell clones that resist RTX depletion in 3 patients with MuSK MG who experienced relapses. We first tested whether B cell clones persisted across pre-and post-RTX repertoires by sequencing the BCR repertoire of unselected PBMCs at high depth using a bulk approach to capture a large number of sequences for identifying persistent clones. Second, we tested whether MuSK autoantibody-producing B cells were among these persistent clones. In previous studies of these same patients, we produced MuSK-specific recombinant human monoclonal antibodies (15, 16) from single B cells isolated during post-RTX relapses.Here, though, we sought to determine whether those specific BCR clones were present in pre-RTX repertoires. Third, we identified the phenotype of both persistent and nonpersistent B cell clones. This was achieved through paired transcriptional profiling and BCR sequencing of single cells. These BCR sequences were traced to high-depth bulk sequencing repertoires derived from pre-RTX time points. The transcriptional profiles of persistent and nonpersistent B cell clones were then compared.A subset of B cell clones are refractory to depletion. We first sought to identify clones that escape RTX depletion and contribute to relapses when the B cell compartment repopulates after treatment. To that end, we sequenced the B cell repertoire, using our high-depth bulk approach, from 3 patients with MG before and after treatment (Figure 1B, Supplemental Table 1, and Supplemental Table 2; supplemental material available online with this article; https://doi.org/10.1172/jci.insight.136471DS1). The number of V(D)J sequences isolated for patien...