De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay

Abstract

Chromatin remodeling through histone acetyltransferase (HAT) and histone deactylase (HDAC) enzymes affects fundamental cellular processes including the cell-cycle, cell differentiation, metabolism, and apoptosis. Nonsense mutations in genes that are involved in histone acetylation and deacetylation result in multiple congenital anomalies with most individuals displaying significant developmental delay, microcephaly and dysmorphism. Here, we report a syndrome caused by de novo heterozygous nonsense mutations in KAT6A (a.k.a., MOZ, MYST3) identified by clinical exome sequencing (CES) in four independent families. The same de novo nonsense mutation (c.3385C>T [p.Arg1129∗]) was observed in three individuals, and the fourth individual had a nearby de novo nonsense mutation (c.3070C>T [p.Arg1024∗]). Neither of these variants was present in 1,815 in-house exomes or in public databases. Common features among all four probands include primary microcephaly, global developmental delay including profound speech delay, and craniofacial dysmorphism, as well as more varied features such as feeding difficulties, cardiac defects, and ocular anomalies. We further demonstrate that KAT6A mutations result in dysregulation of H3K9 and H3K18 acetylation and altered P53 signaling. Through histone and non-histone acetylation, KAT6A affects multiple cellular processes and illustrates the complex role of acetylation in regulating development and disease.

Figure 1

Location of Mutations in KAT6A (A) Pedigrees of families 1–4. (B) Photos of probands 1-II-1, 2-II-2, and 4-II-1 depict the characteristic eye and nasal features observed in KAT6A syndrome. (C) KAT6A is located at 8p11.2. All four de novo mutations are located in exons 16 and 17 (arrows) that are predicted to lead to a truncated protein (red arrowheads) that is missing most of the acidic (orange) and the Serine- and Methionine-rich domains (yellow); NEMM, N-terminal part of Enok, MOZ, or MORF; PHD, Plant homeodomain-linked zinc finger; HAT, Histone Acetyltransferase. (D) Sequence traces of KAT6A from genomic DNA of Proband 1-II-1 demonstrates the p.Arg1129^∗ variant and Proband 3-II-1 demonstrates the p.Arg1024^∗ variant.

Figure 2

KAT6A Mutations Do Not Undergo Nonsense-Mediated Decay (A) RNA from control (ATCC), proband 1-II-1 and proband 3-II-1 dermal fibroblasts were amplified and sequenced by capillary electrophoresis. The mutation in proband 1-II-1 in the last exon of KAT6A showed equal presence of the WT and mutant transcript. The mutation in proband 3-II-1 showed allelic preference for the reference allele. (B) Quantitative real-time PCR in fibroblasts from proband 1-II-1 and 3-II-1 showed no significant decrease in KAT6A mRNA compared to control fibroblast samples. All samples were run triplicate and normalized against GAPDH. All samples were compared to biological controls and the (2^(-ddCt)) method was used for statistical analysis.

Figure 3

KAT6A Nonsense Mutations Result in Global Changes in Histone Acetylation and p53 Signaling Pathways (A) H3K9 acetylation was decreased in histone extracts from proband 1-II-1 dermal fibroblasts relative to control. H3K18 acetylation was increased in proband 1-II-1 dermal fibroblasts compared to control. All experiments were performed in duplicate. (B) Genes in the P53 signaling pathway that show significant differences between experimental (Proband 1-II-1 or Proband 3-II-1) and control fibroblasts growing in culture were assessed using RNaseq. All genes shown were significantly increased or decreased if the q value was less than the FDR-adjusted p value of the test statistic.