Exome Sequencing Reveals a Phenotype Modifying Variant in ZNF528 in Primary Osteoporosis With a COL1A2 Deletion

Abstract

We studied a family with severe primary osteoporosis carrying a heterozygous p.Arg8Phefs*14 deletion in COL1A2, leading to haploinsufficiency. Three affected individuals carried the mutation and presented nearly identical spinal fractures but lacked other typical features of either osteogenesis imperfecta or Ehlers‐Danlos syndrome. Although mutations leading to haploinsufficiency in COL1A2 are rare, mutations in COL1A1 that lead to less protein typically result in a milder phenotype. We hypothesized that other genetic factors may contribute to the severe phenotype in this family. We performed whole‐exome sequencing in five family members and identified in all three affected individuals a rare nonsense variant (c.1282C > T/p.Arg428*, rs150257846) in ZNF528. We studied the effect of the variant using qPCR and Western blot and its subcellular localization with immunofluorescence. Our results indicate production of a truncated ZNF528 protein that locates in the cell nucleus as per the wild‐type protein. ChIP and RNA sequencing analyses on ZNF528 and ZNF528‐c.1282C > T indicated that ZNF528 binding sites are linked to pathways and genes regulating bone morphology. Compared with the wild type, ZNF528‐c.1282C > T showed a global shift in genomic binding profile and pathway enrichment, possibly contributing to the pathophysiology of primary osteoporosis. We identified five putative target genes for ZNF528 and showed that the expression of these genes is altered in patient cells. In conclusion, the variant leads to expression of truncated ZNF528 and a global change of its genomic occupancy, which in turn may lead to altered expression of target genes. ZNF528 is a novel candidate gene for bone disorders and may function as a transcriptional regulator in pathways affecting bone morphology and contribute to the phenotype of primary osteoporosis in this family together with the COL1A2 deletion. © 2020 The Authors. Journal of Bone and Mineral Research published by Wiley Periodicals LLC on behalf of American Society for Bone and Mineral Research (ASBMR).

CEMIG: prediction of the cis-regulatory motif using the de Bruijn graph from ATAC-seq

“…While no direct evidence links ZNF418 with propanoate metabolism in these cells, ZNF proteins regulate genes in lipid metabolism and hypoxia response [ 45 , 46 ]. Finally, ZN528, or ZNF protein 528, is implicated in gene expression regulation, cell proliferation and differentiation [ 47 ]. Its role in activating Rap1 signaling in K562 cells is crucial for their proliferation and survival [ 48 , 49 ].…”

New Structural and Single Nucleotide Mutations in Type I and Type II Collagens in Taiwanese Children With Type I and Type II Collagenopathies

“…In our case, the deleted COL1A2 allele is likely to produce no COL1A2. While mutations in COL1A2 rendering premature stop codon usually have no phenotypes in heterozygote, modifying variant may contribute to the phenotypes of primary osteoporosis ( Marini et al, 2007 ; Skarp et al, 2020 ). We also observed variable expressivity of the COL1A2 deletion within the family.…”