Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability

Abstract

To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated. Functional network analyses demonstrated that epigenetic regulation is a prominent biological process dysregulated in individuals with OGID. Mutations in six epigenetic regulation genes-NSD1, EZH2, DNMT3A, CHD8, HIST1H1E, and EED-accounted for 44% of individuals (311/710). There was significant overlap between the 14 genes involved in OGID and 611 genes in regions identified in GWASs to be associated with height (p = 6.84 × 10^-8), suggesting that a common variation impacting function of genes involved in OGID influences height at a population level. Increased cellular growth is a hallmark of cancer and there was striking overlap between the genes involved in OGID and 260 somatically mutated cancer driver genes (p = 1.75 × 10^-14). However, the mutation spectra of genes involved in OGID and cancer differ, suggesting complex genotype-phenotype relationships. These data reveal insights into the genetic control of human growth and demonstrate that exome sequencing in OGID has a high diagnostic yield.

Keywords: EZH2; HIST1H1E; NSD1; epigenetic regulation; exome sequencing; intellectual disability; overgrowth syndrome; sotos syndrome; weaver syndrome.

Figure 1

Causal Mutation Identified in 50% of OGID Probands Proportion of pathogenic mutations identified in 710 individuals with OGID. Epigenetic regulation genes (red), including NSD1 which is the predominant gene, constitute the major gene set. PI3K/AKT pathway genes (blue) also significantly contribute to OGID.

Figure 2

HIST1H1E Mutations Cause OGID (A) HIST1H1E mutations cluster within 12 bp region in the carboxy-terminal domain (CTD) and have a similar predicted impact on protein function. The three different frameshift mutations generate the same open reading frame (frame 2), which is predicted to reduce the length and net charge (at pH 7) of the CTD compared to the wild-type (frame 1). The other possible alternate reading frame (frame 3) increases the protein length and net charge. Abbreviations: CTD, carboxy-terminal domain; NTD, amino-terminal domain. (B–D) Facial images of three individuals with HIST1H1E mutations showing full cheeks and high hairline.

Figure 3

Schematic of Key Biological Processes Impacted in OGID (A) Epigenetic regulation. NSD1, EED, and EZH2 directly methylate specific histone tail lysine residues. DNMT3A is a de novo DNA methyltransferase and CHD8 is a chromatin remodeling complex protein that binds methylated lysine 4 of histone H3. H1.4 (encoded by HIST1H1E) stabilizes higher-order chromatin structures. (B) All OGID mutations are predicted to lead to reduced function PI3K/AKT pathway. The PI3K/AKT pathway positively regulates growth. AKT3, MTOR, and p110α (encoded by PIK3CA) are pathway activators. PTEN and B56δ (encoded by PPP2R5D) are pathway suppressors. OGID mutations in AKT3, MTOR, and PIK3CA are activating, whereas OGID mutations in PTEN and PPP2R5D are inactivating.

Figure 4

Phenotypic Differences between OGID due to Mutations in Epigenetic Regulation Genes Compared to PI3K/AKT Pathway Genes Comparison of the distribution of (A) overgrowth categories and (B) degree of intellectual disability in case subjects with epigenetic regulation gene mutations (red) compared with PI3K/AKT pathway gene mutations (blue).

Figure 5

Mutations in Epigenetic Regulation Genes in OGID and Cancers Protein schematics showing the position of mutations in HIST1H1E, EZH2, DNMT3A, NSD1, and CHD8 in OGID (below the gene) and specific cancers (above the gene). The somatic cancer driver mutations are from Lawrence et al. Abbreviations are as follows: AML, acute myeloid leukemia; CLL, chronic lymphocytic leukemia; DLBCL, diffuse large B-cell lymphoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; OGID, overgrowth-intellectual disability.