B-cell lymphocytosis and reprogramming due to biallelic CARD11 mutations

Background: Adaptive immune responses are tightly controlled by proteins including CARD11 that regulate signaling events downstream of the T- and B-cell receptors. Germline mutations in CARD11 cause several distinct monogenic inborn errors of immunity with early childhood onset and potentially fatal prognoses. Somatic CARD11 gain-of-function mutations are associated with B-cell malignancies. Precisely how various CARD11 mutations culminate in unique clinical entities, and the mechanisms of CARD11-driven B-cell proliferation, is not fully understood. Objective: We sought to identify the genetic basis of disease and characterize immune-cell phenotypes and functions in a patient with apparent BENTA (B-cell expansion with nuclear factor-κB [NF-κB] and T-cell anergy) disease and a history of sibling death in early childhood. Methods: We used whole-exome sequencing, flow and mass cytometry, whole blood mRNA analyses, in vitro T-cell proliferation and B-cell differentiation assays, and single-cell RNA sequencing of patient-derived samples to identify the genetic basis of disease and define its molecular and cellular mechanisms. We also ectopically expressed wild-type and mutant forms of CARD11 in T and B cells and assessed their functional impacts on NF-κB–dependent responses. Results: We report a surprising new genetic basis of BENTA caused by homozygosity for the novel CARD11 mutation R331P and characterized by massive expansion of B cells with a naive surface phenotype and aberrant transcriptional program. This autosomal-recessive form of BENTA features exaggerated B-cell lymphocytosis relative to monoallelic BENTA. Furthermore, we have identified patterns of gene expression that distinguish B cells of patients with the autosomal-recessive form of BENTA from those of healthy controls and from monoallelic BENTA. We found that ectopic CARD11 R331P expression induced constitutive NF-κB activity in T and B cells. These data suggest that R331P is a gain-of-function mutation and causes BENTA in homozygosity. Conclusions: These results define a novel autosomal-recessive form of BENTA disease. Additional analysis of mutation-driven changes in B-cell function may shed light on the mechanisms of B lymphomagenesis in patients with germline or somatic CARD11 variants.