B cell tolerance and autoimmunity: Lessons from repertoires

Abstract

Adaptive immune cell function is regulated by a highly diverse receptor recombined from variable germline-encoded segments that can recognize an almost unlimited array of epitopes. While this diversity enables the recognition of any pathogen, it also poses a risk of self-recognition, leading to autoimmunity. Many layers of regulation are present during both the generation and activation of B cells to prevent this phenomenon, although they are evidently imperfect. In recent years, our ability to analyze immune repertoires at scale has drastically increased, both through advances in sequencing and single-cell analyses. Here, we review the current knowledge on B cell repertoire analyses, focusing on their implication for autoimmunity. These studies demonstrate that a failure of tolerance occurs at multiple independent checkpoints in different autoimmune contexts, particularly during B cell maturation, plasmablast differentiation, and within germinal centers. These failures are marked by distinct repertoire features that may be used to identify disease- or patient-specific therapeutic approaches.

Figure 1.

Rearrangement of germline Ig loci across the lifecycle of B cells. (A) Schematic of the germline configuration of the IGH, IGK, and IGL loci. IGH contains V, D, and J segments followed by the constant segments, here represented by the letter associated with the Ig isotype, e.g., M for the IgM-associated constant chain Cμ. IGK and IGL only contain V and J segments, followed by a single constant segment for IGK, while in IGL each J segment is associated with its own constant segment. (B) Overview of B cell development and activation with key modifications of the IG loci. At the pro-B cell stage, developing B cells rearrange the IGH locus to yield a functional heavy chain and cells that successfully express a pre-BCR pass a first checkpoint to the pre-BCR stage. At this stage, the light chain loci are rearranged to yield a functional light chain. Finally, during or around the GC reaction, AID can lead to somatic hypermutation (red stars in the VDJ/VJ regions represent mutations) or to class-switching among IGH constant segments (here, depicting a locus that has switched to IgG1, where downstream segments including IgA remain available). Created with BioRender.com.

Figure 2.

Antibody characterization through sequencing approaches. Left: Schematic of the locus (DNA), transcript (RNA with poly-A tail represented by AAA), and resulting antibody (protein) for the heavy and light chain of a representative IgG1 antibody. Constant chain regions are depicted in blue, while antibody-binding fragments are derived from V, D, and J segments (green, yellow, and red, respectively; additional nucleotides inserted during recombination are not pictured). Note that the constant chain segment is separated from the V(D)J portion in the DNA and unspliced mRNA, but contiguous in the mature mRNA. Right: Broad characterization of approaches used for BCR sequencing are shown here for mRNA capture. Bulk approaches focus primarily on the deep sequencing of amplified heavy/light chain regions in an unpaired state. Paired-chain sequencing joins these products in a sequestered PCR reaction (e.g., in an emulsion). Single-cell RNA sequencing relies on separate sequencing on heavy and light chains in the presence of a cell identifier (either a cell barcode in emulsions or a well ID for plate-based approaches). Created with BioRender.com.