Integrated single-cell transcriptomics and epigenomics reveals strong germinal center-associated etiology of autoimmune risk loci

Sci Immunol. 2021 Oct 15;6(64):eabh3768. doi: 10.1126/sciimmunol.abh3768. Epub 2021 Oct 8.


The germinal center (GC) response is critical for both effective adaptive immunity and establishing peripheral tolerance by limiting autoreactive B cells. Dysfunction in these processes can lead to defective immune responses to infection or contribute to autoimmune disease. To understand the gene regulatory principles underlying the GC response, we generated a single-cell transcriptomic and epigenomic atlas of the human tonsil, a widely studied and representative lymphoid tissue. We characterize diverse immune cell subsets and build a trajectory of dynamic gene expression and transcription factor activity during B cell activation, GC formation, and plasma cell differentiation. We subsequently leverage cell type–specific transcriptomic and epigenomic maps to interpret potential regulatory impact of genetic variants implicated in autoimmunity, revealing that many exhibit their greatest regulatory potential in GC-associated cellular populations. These included gene loci linked with known roles in GC biology (IL21, IL21R, IL4R, and BCL6) and transcription factors regulating B cell differentiation (POU2AF1 and HHEX). Together, these analyses provide a powerful new cell type–resolved resource for the interpretation of cellular and genetic causes underpinning autoimmune disease.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Autoimmunity / immunology*
  • Cell Differentiation / immunology
  • Epigenomics
  • Germinal Center / immunology*
  • Homeodomain Proteins / genetics
  • Homeodomain Proteins / immunology*
  • Humans
  • Interleukins / genetics
  • Interleukins / immunology*
  • Palatine Tonsil / immunology
  • Sequence Analysis, RNA
  • Single-Cell Analysis*
  • Trans-Activators / genetics
  • Trans-Activators / immunology*
  • Transcription Factors / genetics
  • Transcription Factors / immunology*
  • Transcriptome


  • HHEX protein, human
  • Homeodomain Proteins
  • Interleukins
  • POU2AF1 protein, human
  • Trans-Activators
  • Transcription Factors