Impaired CpG Demethylation in Common Variable Immunodeficiency Associates With B Cell Phenotype and Proliferation Rate

Abstract

Common Variable Immunodeficiency (CVID) is characterized by impaired antibody production and poor terminal differentiation of the B cell compartment, yet its pathogenesis is still poorly understood. We first reported the occurrence of epigenetic alterations in CVID by high-throughput methylation analysis in CVID-discordant monozygotic twins. Data from a recent whole DNA methylome analysis throughout different stages of normal B cell differentiation allowed us to design a new experimental approach. We selected CpG sites for analysis based on two criteria: one, CpGs with potential association with the transcriptional status of relevant genes for B cell activation and differentiation; and two, CpGs that undergo significant demethylation from naïve to memory B cells in healthy individuals. DNA methylation was analyzed by bisulfite pyrosequencing of specific CpG sites in sorted naïve and memory B cell subsets from CVID patients and healthy donors. We observed impaired demethylation in two thirds of the selected CpGs in CVID memory B cells, in genes that govern B cell-specific processes or participate in B cell signaling. The degree of demethylation impairment associated with the extent of the memory B cell reduction. The impaired demethylation in such functionally relevant genes as AICDA in switched memory B cells correlated with a lower proliferative rate. Our new results reinforce the hypothesis of altered demethylation during B cell differentiation as a contributing pathogenic mechanism to the impairment of B cell function and maturation in CVID. In particular, deregulated epigenetic control of AICDA could play a role in the defective establishment of a post-germinal center B cell compartment in CVID.

Monozygotic Twins Concordant for Common Variable Immunodeficiency: Strikingly Similar Clinical and Immune Profile Associated With a Polygenic Burden

“…In line with this, a pair of MZ twins discordant for CVID was previously reported (3), with a significant increase in DNA methylation of B cells in the affected sister (3, 65). Consistent with this finding, a recent study showed that impaired demethylation in B-cell key genes is associated with the reduction of memory B cells in CVID patients (66). In our context, it will be interesting to explore the epigenetic landscape of the MZ concordant twins in order to confirm its contribution to the disease and add a new layer of insight to our clinical, immunological, and genomic data.…”

Defective Bcl-2 expression in memory B cells from common variable immunodeficiency patients

“…Activated naive B cells from CVID patients and controls could increase AICDA expression, but the expression was dampened in CVID patients, particularly in those with reduced numbers of Sm B cells. Diminished AICDA induction together with low Sm B cells reveal the blockage in CSR and SHM present in CVID patients, with the reduced SHM rate observed in our CVID cohort [23].…”

“…CVID is a complex disease with high variability in its clinical presentation and different penetrance, even when monogenic defects are present [21], which suggests that a polygenic heterogeneous predisposing genetic background [6], the involvement of epigenetic alterations [23,53] and multiple cumulative defects could lead to the B cell deregulation present in CVID patients.…”

“…The recent general consensus is that the pathogenesis of CVID is complex and multi-factorial in most patients, rather than the consequence of a monogenic defect [6]. A plausible hypothesis for the pathogenesis of CVID is that of a polygenic or even epigenetic heterogeneous predisposing genetic background [6,23], inducing several cumulative defects and leading to the deregulation of B cell differentiation.…”

The impact of rare and low-frequency genetic variants in common variable immunodeficiency (CVID)

“…More complex genetic scenarios are in consideration for the disease’s possible oligogenic background 4 . Some studies also showed that epigenetic factors such as altered demethylation and hypermethylation play a significant role in pathogenic mechanism and clinical manifestations of the disease 5 , 6 .…”