De novo variants in H3-3A and H3-3B are associated with neurodevelopmental delay, dysmorphic features, and structural brain abnormalities

Abstract

The histone H3 variant H3.3, encoded by two genes H3-3A and H3-3B, can replace canonical isoforms H3.1 and H3.2. H3.3 is important in chromatin compaction, early embryonic development, and lineage commitment. The role of H3.3 in somatic cancers has been studied extensively, but its association with a congenital disorder has emerged just recently. Here we report eleven de novo missense variants and one de novo stop-loss variant in H3-3A (n = 6) and H3-3B (n = 6) from Baylor Genetics exome cohort (n = 11) and Matchmaker Exchange (n = 1), of which detailed phenotyping was conducted for 10 individuals (H3-3A = 4 and H3-3B = 6) that showed major phenotypes including global developmental delay, short stature, failure to thrive, dysmorphic facial features, structural brain abnormalities, hypotonia, and visual impairment. Three variant constructs (p.R129H, p.M121I, and p.I52N) showed significant decrease in protein expression, while one variant (p.R41C) accumulated at greater levels than wild-type control. One H3.3 variant construct (p.R129H) was found to have stronger interaction with the chaperone death domain-associated protein 6.

Histones: coming of age in Mendelian genetic disorders

“…(A) Frameshift mutations (black) located within the C-terminal tail of H1.4 all result in a mutant H1.4 protein with an identical acidic 38 aa C-terminal tail (red dashed line), with a significantly reduced protein net charge 5 10. (B) Missense mutation sites (purple) located in the N-terminal tail and globular domain of H3.3, and a single nonsense mutation (red) located within an alternative H3F3B gene transcript 23–25. (C) Missense mutation sites (purple) located in the globular domain and C-terminal tail of H4 48 53 54.…”

“…To date, germline mutations in humans have only been reported in the H3.3 genes, H3F3A and H3F3B (MIM 619720, 619721) 23–25. These genes are independently regulated but encode an identical protein product.…”

“…While several H3 variants do affect PTM sites, the majority of H3 and H4 variants are located within the core globular domain of each histone (figure 3). Modelling suggests that these residues are important for intranucleosome stability or histone-chaperone interactions 23 25 53. Thus, rather than simply alterations to PTM sites impacting gene expression, the disease mechanism is more nuanced and must involve disruption of nucleosome dynamics on chromatin, impacting potential multiple processes including transcription and DNA replication.…”

The cell-cycle choreography of H3 variants shapes the genome

“… 101 Not enough or too much proves deleterious. Furthermore, germline mutations in both human H3.3 genes, H3F3A and H3F3B , are linked with neurodegenerative disorders, without detection of cancer in these patients, 102 , 103 including changes of key residues S31, G34, and G90 ( Table 1 ). A case of a newly identified mutation in H3.3, L62R ( Table 1 ), may act as a driver in microcephaly, 104 another disease characterized by chromatin instability.…”

“… 110 Diffuse hemispheric glioma (DHG) 16 years H3.3G34R/V (15%) Giant cell tumors of bone (GCTB) 35 years H3.3G34W/L (92%) Chondroblastoma 21 years H3.3K36M (95%) Cancer (breast, liver, ovarian, colon, bone, gastric, prostate) adult CENP-A overexpression (44%) Renaud-Pageot et al., 100 Sharma et al., 111 and Jeffery et al. 112 These include microcephaly, 102 , 103 , 104 oncohistone cancers: diffuse intrinsic pontine glioma (DIPG), diffuse hemispheric glioma (DHG), giant cell tumors of bone (GCTB), chondroblastoma, 105 , 106 , 107 , 108 , 109 , 110 and cancers with CENP-A overexpression. 100 , 111 , 112 …”