Patients with Common Variable Immunodeficiency Disorders (CVID) present with antibody deficiency and increased risk of malignancy, both of which involve DNA damage and repair (DDR) pathways. The aim of this study was to interrogate DDR in CVID patients.
A custom panel of 285 genes involved in DDR designed using Agilent’s HaloPlexHS Target Enrichment System was analysed in 39 CVID patients. Potentially pathogenic variants were identified by filtering based on quality, functional consequences and allele frequency <1% in public repositories. PBMCs from healthy controls (n=11) and patients (n=34) were exposed to γ-irradiation and viability, γH2AX, phosphorylated (p)ATM and 53BP1 measured by flow cytometry after 1 and 24 hours (h).
From a total of 89,003 variants, we identified 226 rare variants, including 64 novel variants, with a median of 6 variants per individual (range 1-14). EP400, TP53BP1 and POLR2B were the most variable genes. CVID CD4+T cells had higher endogenous levels of γH2AX than controls at 1 and 24h (1h p=0.006; 24h p=0.03). Following γ-irradiation, T cells had a higher γH2AX than controls at 1h (CD4+p<=0.001; CD8+ p=0.002) and 24h (CD4+p<=0.001; CD8+p=0.001), while B cells had higher γH2AX at 24h (p=0.03). A subset of patients’ B cells had lower pATM than controls at 24h (p=0.04). These pATMlo B cells had increased γH2AX, decreased 53BP1 and increased apoptosis (r=-0.91, p<=0.001).
We identified rare variants in genes involved in DNA damage and repair in CVID patients. Our functional analyses have demonstrated evidence of dysregulated DDR and apoptosis in a subgroup of CVID patients.