Distinctive Genome-Wide DNA Methylation Profiling in a Cohort of Patients with Known Pathogenic STAT1 Gain-of-Function Variants

Background High throughput sequencing techniques are very effective tools to achieve a timely genetic definition of inborn errors of immunity (IEIs). However, they often reveal variants of uncertain significance (VUS), and in some cases, the identification of a causative genetic alteration may be hampered by technical issues. Recent studies suggest that genome-wide DNA methylation profiling on blood samples may represent an effective tool for reassessing the pathogenic role of VUS in a defined set of disease-causing genes and to increase the diagnostic yield in unresolved cases. Aim The aim of the study is to define the genome-wide DNA methylation profiling in a cohort of patients with known pathogenic STAT1 gain-of-function (GOF) variants. Methods As proof of principle, genome-wide DNA methylation profiling was evaluated on 11 patients carrying 7 different known pathogenic STAT1 GOF variants. Results We compared the DNA methylation profile (β-values) between all cases with GOF variants in STAT1 and age- and sex-matched controls. Through hierarchical clustering, we were able to differentiate the patients’ and controls’ groups. In total, 2356 differentially methylated CpG probes (DMPs) were identified. Among these, 75 DMPs (64% hypomethylated and 36% hypermethylated) were in genes regulated by STAT1 and 58 DMPs (60% hypomethylated and 40% hypermethylated) were in genes regulated by STAT3. Using the genes covered by the 2356 DMPs, we performed KEGG pathway enrichment analysis revealing genes implicated in antiviral response to CMV and HPV but also genes implicated in cancer, cellular senescence, and thyroid hormone signaling. Conclusions These preliminary data suggest that patients with different STAT1 GOF variants display a distinctive genome-wide DNA methylation profile. Further data on a larger cohort of patients are necessary to validate these results and to define whether this technique is effective in assessing the pathogenicity of VUS. If confirmed, this study may be extended to other different IEIs.