Generation of a novel iPSC-based model to explore the molecular and functional phenotype of a rare genetic immunodeficiency, the ICF syndrome type 2.

ICF syndrome (Immunodeficiency, Centromeric instability and Facial anomalies) is a rare genetic disorder characterized by severe immunodeficiency that leads to lethal infections in early childhood. In addition, more than half of affected individuals show mild to severe intellectual disability at very early onset. Two genes explain the majority of the ICF cases, DNMT3B and ZBTB24, defining ICF1 and ICF2 subtypes. Despite unifying clinical features, ICF patients display variability in molecular and phenotypic defects with no clear genotype/phenotype correlation. Aberrant DNA methylation is the main molecular hallmark of ICF syndrome. Among the disease models, patient-derived iPSCs were acknowledged as a powerful tool enabling the study of ICF syndrome etiology during early development. Here, we show the generation of a novel ICF2 disease model by reprogramming CD34+ cells derived from patient peripheral whole blood into iPSCs. We provide the molecular and phenotypical characterization of the disease model. In particular, we examined the DNA methylation profiles at genome-wide level, demonstrating that iPSCs recapitulate the methylation defects specifically associated with ZBTB24 deficiency. We discuss these results and compare them with the molecular features identified in ICF1-patient derived iPSCs caused by DNMT3B loss of function. DNA samples extracted from ICF2 pYM_patient and Control iPSCs, as well as pYM_patient peripheral blood were subjected to methylation analysis using Infinium MethylationEPIC 850K Bead Chip Array. We assessed the methylation levels at both genome-wide and satellite repetitive elements. 4 Controls from the same batch were downloaded from GSE237676 (GSM7635690 to GSM7635693). The GSM is also reported as colname in the Matrix_processed_blood file.