Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability and facial anomalies syndrome with distinctive genome-wide DNA hypomethylation

Abstract

Immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome is in most cases–caused by mutations in either DNMT3B, ZBTB24, CDCA7, or HELLS. However, the causative genes of a few ICF patients remain unknown. We, herein, identified UHRF1 as a novel causative gene of one such patient with atypical symptoms. This patient is a compound heterozygote for two previously unreported mutations in UHRF1: c.886C > T (p.R296W) and c.1852C > T (p.R618X). The R618X mutation plausibly caused nonsense-mediated decay, while the R296W mutation changed the higher order structure of UHRF1, which is indispensable for the maintenance of CG methylation along with DNMT1. Genome-wide methylation analysis revealed that the patient had a centromeric/pericentromeric hypomethylation, which is the main ICF signature, but also had a distinctive hypomethylation pattern compared to patients with the other ICF syndrome subtypes. Structural and biochemical analyses revealed that the R296W mutation disrupted the protein conformation and strengthened the binding affinity of UHRF1 with its partner LIG1, and reduced ubiquitylation activity of UHRF1 towards its ubiquitylation substrates, histone H3 and PAF15. We confirmed that the R296W mutation causes hypomethylation at pericentromeric repeats by generating the HEK293 cell-lines that mimic the patient’s UHRF1 molecular context. Since proper interactions of the UHRF1 with LIG1, PAF15, and histone H3 are essential for the maintenance of CG methylation, the mutation could disturb the maintenance process. Evidence for the importance of the UHRF1 conformation for CG methylation in humans is, herein, provided for the first time, and deepens our understanding of its role in regulation of CG methylation.

Exploring the intersection of epigenetics, DNA repair, and immunology from studies of ICF syndrome, an inborn error of immunity

“…To date, five genes have been reported to be mutated in ICF patients: DNA methyltransferase 3B (DNMT3B), zinc finger and BTB domain containing 24 (ZBTB24), cell division cycle associated 7 (CDCA7), helicase lymphoid specific (HELLS, also known as LSH), and Ubiquitin-like containing PHD and RING finger domains 1 (UHRF1, also known as ICBP90 or Np95) in type-1 (ICF1), -2 (ICF2), -3 (ICF3), -4 (ICF4), and atypical ICF patients, respectively (3,4). Briefly, DNMT3B functions as a de novo DNA methyltransferase, ZBTB24 serves as a transcriptional factor whose targets include CDCA7, and CDCA7 and HELLS proteins constitute a chromatin remodeling complex.…”

CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses

“…ICF syndrome is a genetically heterogeneous disease and can be caused by mutations in DNMT3B ( 49 , 51 , 52 ), ZF and BTB domain containing 24 ( ZBTB24 ) ( 78 , 79 ), CDCA7 ( 3 ), HELLS ( 3 ), or UHRF1 ( 80 ). Our data suggest that CDCA7 functionally overlaps in the regulation of clustered Pcdh gene expression with at least two other ICF syndrome–causing factors, the de novo DNA methyltransferase DNMT3B and the chromatin remodeler HELLS, such that their disruption leads to aberrant hypomethylation and increased expression of Pcdh isoforms in neuronal tissue ( 35 ) or mouse embryonic fibroblasts (MEFs) ( 63 ), respectively.…”

“…Our data suggest that CDCA7 functionally overlaps in the regulation of clustered Pcdh gene expression with at least two other ICF syndrome–causing factors, the de novo DNA methyltransferase DNMT3B and the chromatin remodeler HELLS, such that their disruption leads to aberrant hypomethylation and increased expression of Pcdh isoforms in neuronal tissue ( 35 ) or mouse embryonic fibroblasts (MEFs) ( 63 ), respectively. This is intriguing since the PCDHA promoters are among the few loci found to be aberrantly hypomethylated in the blood of patients with ICF carrying DNMT3B , ZBTB24 , CDCA7 , HELLS , or UHRF1 mutations ( 5 , 80 ). Considering that the clustered PCDH genes are critical for generating neuronal diversity ( 81 , 82 ) and their suggested links to neurological disease ( 83 , 84 ), clustered PCDH dysregulation could be a potential contributor to the neurodevelopmental symptoms including intellectual disability that have been described in patients with ICF ( 3 ).…”

The ICF2 gene Zbtb24 specifically regulates the differentiation of B1 cellsviapromoting heme synthesis

“…Approximately 50% of ICF cases (ICF1) have mutations in the DNA methyltransferase 3B ( DNMT3B, OMIM 602900), and about 30% of patients (ICF2) carry nonsense or missense mutations in the zinc finger and BTB domain containing 24 ( ZBTB24, OMIM 614064) (de Greef et al, 2011; Weemaes et al, 2013; Xu et al, 1999). Although mutations in the cell division cycle associated 7 ( CDCA7 , OMIM 609937), helicase, lymphoid-specific ( HELLS , OMIM 603946), and ubiquitin-like with plant homeodomain and ring finger domains 1 ( UHRF1 , OMIM 607990) have been recently shown to the associated with ICF3, ICF4 and an atypical ICF case, respectively, there are still few ICF cases (ICFX) left with unidentified disease genes (Thijssen et al, 2015; Unoki et al, 2023). In line with the similar molecular and clinical characteristics across different ICF subtypes, these disease genes act sequentially/corporately to modulate chromatin accessibilities and DNA methylations (Funabiki et al, 2023; Hardikar et al, 2020; Jenness et al, 2018; Ren et al, 2019; Thompson et al, 2018; Unoki et al, 2023; Wu et al, 2016).…”