A case report of a novel HIST1H1E mutation and a review of the bibliography to evaluate the genotype–phenotype correlations

Abstract Background HIST1H1E is a member of the H1 gene family. Excess de novo likely gene‐disruptive variants involving the C‐terminal tail of HIST1H1E have been reported in neurodevelopmental disorders. Although clinical phenotypes in some patients have been described in single studies, few studies have reviewed the genotype and phenotype relationships using a relatively large cohort of patients with HIST1H1E variants. Methods Whole‐exome sequencing (WES) was performed on the proband. The variant was validated using Sanger sequencing in both proband and parents. Published HIST1H1E variants in neuropsychiatric disorders were reviewed. Results Herein, we reported a new de novo frameshift mutation in HIST1H1E (NM_005321.2, c.416_419dupAGAA, p.Ala141GlufsTer56) in an individual with Rahman syndrome. To explore the genotype–phenotype correlations for HIST1H1E variants in neurodevelopmental disorders, we comprehensively curated and summarized 23 variants and the clinical features from 52 patients. Our findings revealed that likely gene‐disrupting variants in HIST1H1E contribute to a wide range of neurodevelopmental phenotypes. We observed the common phenotypes including craniofacial features, ID, hypotonia, and autism/behavior problem in patients with HIST1H1E variants. While the different genotypes corresponding to different phenotypes or the same phenotype were also observed. Conclusion These data provide scientific evidence for the genetic diagnosis and precision clinical management.


| INTRODUCTION
HIST1H1E (MIM:142220), encoded by HIST1H1E, is a globular domain-containing factor.HIST1H1E binds to linker DNA between nucleosomes forming the chromatin fiber to modulate gene expression and DNA replication, recombination, and repair (Bayona-Feliu et al., 2017;Fan et al., 2005;Happel et al., 2009;Hendzel et al., 2004;Hergeth & Schneider, 2015;Izzo et al., 2013).With the rapid development of next-generation sequencing technologies, HIST1H1E, a member of the H1 gene family, was first reported as a causative gene of schizophrenia (Xu et al., 2012).Variants within HIST1H1E have been frequently reported in neurodevelopmental disorders characterized by mild to severe intellectual disability (ID), overgrowth which may appear in early infancy but become progressively closer to average in adults, and facial deformity, such as high hairline, prominent forehead, bitemporal narrowing, downward slant palpebral fissures, deepset eyes, hypertelorism, and so on, indicating a complex phenotypic outcome.Despite the advent of next-generation sequencing has accelerated to elucidate the genetic causes of neurodevelopmental disorders, many individuals with neurodevelopmental disorders remain without a genetic diagnosis because of the fuzzy correlations between genotype and phenotype.Importantly the GeneReviews, as they already show data from 47 cases, which is critical in the understanding of genotype-phenotype relationships.
Here, we report a new de novo frameshift mutation within the HIST1H1E gene in a patient with Rahman syndrome.In addition, we comprehensively curated 23 variants from 52 individuals with neurodevelopmental disorders from the published literature and online databases and this study to investigate the genotype and phenotype relationships.We thoroughly evaluate more detailed phenotypic aspects of all published cases harboring HIST1H1E mutations.The phenotypic similarities and diversity between different types of variants were analyzed and discussed.The results will be beneficial for the genetic diagnosis and clinical management of patients with HIST1H1E variants, and promote the selection of treatment targets in the future.

| Review of the HIST1H1E genotype and phenotype data
To comprehensively identify previously published patients with HIST1H1E variants, we checked Clinvar and Human Gene Mutation Database (Online Professional Version) to identify any potential HIST1H1E pathogenic variants.We then carefully curated the previous individual case reports as well as large-scale cohort studies.The curated variants were subsequently classified following the standards and guidelines for the interpretation of sequence variants from the American College of Medical Genetics and Genomics (ACMG) (Richards et al., 2015).The detailed molecular and phenotypic information was curated from corresponding studies if available (Table S1).

| A new HIST1H1E frameshift mutation and the clinical characterizations
The male proband is the first child of his healthy, nonconsanguineous Chinese parents.He was born prematurely at 33 weeks with the weight of 2.55 kg and height of 44 cm.In the neonatal period, he cried rarely and had pneumonia.No asphyxia nor jaundice.On examination at 4 years of age, his weight was 24 kg (+3 SD), height 113 cm (+2 SD), and head circumference 52.5 cm (+1 SD).Developmental milestones were delayed.He was able to crawl at the age of 2.5 years.He was able to sit without support at the age of 1 year.He was able to walk without support at the age of 3 years.Speech development was more delayed.After the age of 2 years, he started to speak his first phrases.At the age of 4 years, he could only speak a few words.His behavior was characterized by stereotypic movements and sleeping problems.Developmental regression was reported.He presents a severe ID and autism.Brain MRI performed at the age of 5 months showed mild bilateral ventricular enlargement, slightly wide cavum septum pellucidum, the left temporal extracerebral space slightly wider, thin corpus callosum, delayed myelination, and pituitary gland with nodular protrusion of superior margin.A moderate hearing deficit was noted in only the left ear.He has no hypotonia or scoliosis.Craniofacial features characterized by a high hairline, prominent forehead, bitemporal narrowing, epicanthus, telecanthus, hypertelorism, a low and broad nasal bridge, upturned and full nasal tip, short philtrum, and low set ears.His hair is sparse and delayed growth at the temples.Abnormal dentition including widely spaced teeth, pointed teeth, and dental caries was presented.Other physical features included myopia, astigmatism, flat feet, simple syndactyly of the toes, thin nails, multiple nevi, atrial septum defect, bilateral cryptorchidism, and hypothyroidism.He had advanced bone age (Figure 1b).Medical concerns included hypothyroidism.G-banded karyotyping revealed a normal karyotype (46, XY) for the proband.WES identified a de novo frameshift mutation in HIST1H1E (NM_005321.2, c.416_419dupAGAA:p.Ala141GlufsTer56) (Figure 1b).Sanger sequencing confirmed this variant in the proband but not in the parents (Figure 1a,c).
Interestingly, all variants are located in the C terminus.The HIST1H1E variants escape nonsense-mediated RNA decay since HIST1H1E is a single exon, intronless gene.Stable proteins have a reduced net positive charge, which disrupts the normal binding between the positively charged H1.4 linker histone and negatively charged DNA (Tatton-Brown et al., 2017).Because the resultant abnormal stable proteins disrupt the normal proliferation rate and competence of cells, the cells hardly enter into the S phase, and undergo accelerated senescence (Flex et al., 2019).In addition, proteintruncating variants disrupt proper compaction of DNA, which are associated with abnormally methylation of genes encoding proteins involved in synaptic transmission and neuronal function (Ciolfi et al., 2020;Flex et al., 2019).
Fourteen patients were reported with the frameshift variant (Ala144Glyfs*52).The frameshift variant at the Ala144 locus might represent a particular subtype of neurodevelopmental disorders.We attempted to compare the phenotypes between patients with Ala144 frameshift variants and other than Ala144 in order to get divergent phenotypic patterns.We found that hypotonia (12/14 vs. 20/38), autism/behavior problem (10/14 vs. 14/38), brain MRI (9/14 vs. 15/38), ocular deformity (7/14 vs. 12/38), and cardiac abnormalities (7/14 vs. 12/38) occurred with F I G U R E 2 Protein model of HIST1H1E with all reported variants indicated.The novel de novo frameshift variant identified in this study is marked with red color.× arabic numerals represent the number of independent cases indicated in the present study.
F I G U R E 3 Genotype-phenotype correlations for HIST1H1E (GenBank accession number: NM_005321.2).(a) The key clinical presentations of patients with all reported HIST1H1E variants.Events in dark gray are de novo, blue are male, yellow are female, red are present, light gray are absent, and white are unreported.MRI, magnetic resonance imaging.(b) Comparison results of clinical presentations between patients with variants at c.430dupG:p.Ala144Glyfs*52 site and patients with variants other than Ala144Glyfs*52 site.The blue bars represent patients with variants at c.430dupG:p.Ala144Glyfs*52 site and the orange bars represent patients with variants other than the Ala144Glyfs*52 site.Summary 1 (%) represents the number of individuals reported to have the specific phenotype divided by the number of individuals only evaluated for this specific phenotype ("+" and "−").Summary 2 (%) represents the number of individuals reported to have the specific phenotype divided by the number of individuals who were analyzed for genotype-phenotype correlation regardless of whether they were evaluated for this specific phenotype ("+," "−," and "na").a higher prevalence in patients with Ala144 frameshift variants other than Ala144.Interestingly, patients with variants other than the Ala144 site had a higher prevalence of speech delay (15/38 vs. 3/14), motor delay (16/38 vs. 2/14), cryptorchidism (11/38 vs. 3/14), skin (12/38 vs. 1/14), nail anomalies (9/38 vs. 1/14), and skull abnormalities (7/38 vs. 1/14) than those with frameshift variants Ala144 (Figure 3a,b).Finally, we observe remarkable phenotypic differences between patients with Ala144 frameshift variants and other than Ala144 sites.This phenotype difference showed that the function of the Ala144 locus is different from that of other Ala144 locus.Further studies to explore the biological mechanisms of such frameshift variants of HIST1H1E are needed.

| DISCUSSION
HIST1H1E is an essential gene located on human chromosome 6, encoding Histone H1.4 that is contained a globular domain flanked by N-and C-terminal tails.HIST1H1E is one of a family of linker histones that is responsible for higher order chromatin structure and has an important role in genome stability, DNA replication, and repair (Bayona-Feliu et al., 2017;Fan et al., 2005;Hergeth & Schneider, 2015;Izzo et al., 2013).
Here we present that a de novo frameshift variant (c.416_419dupAGAA) within HIST1H1E in a patient with HIST1H1E syndrome.He had a severe ID and distinctive facial features including a high hairline, prominent forehead, and so on; most characteristics were prominently similar to previously reported in papers on patients with HIST1H1E variants (Burkardt et al., 2019;Duffney et al., 2018;Flex et al., 2019;Takenouchi et al., 2018;Tatton-Brown et al., 2017).Given the molecular nature of the de novo frameshift variant (c.416_419dupAGAA) in HIST1H1E, it is strongly supported that this variant is pathogenicity.Interestingly, the variant of c.416_419dup-AGAA in our patient and another 22 variants are reported in previous studies are all located in the C-terminal domain, which suggests that the domain is a mutation "hotspot."The C-terminal domain of linker histones has a net positive charge, which is necessary to regulate higher order chromatin structure (Subirana, 1990;Tatton-Brown et al., 2017).A net positive charge of the C-terminus is necessary to binding linker DNA (Hendzel et al., 2004;Subirana, 1990;Tatton-Brown et al., 2017).The truncated protein will likely impede the chromatin function and structure.
To explore the relationship between genotype and phenotype for HIST1H1E variants, we comprehensively curated variants-related phenotypes.We identified some common phenotypes, such as craniofacial features, ID (DD), abnormal dentition, hypotonia, autism/behavior problem, brain MRI, ocular deformity, cardiac abnormalities, speech delay, motor delay, hands abnormalities, and RX abnormalities.We observed some shared clinical characteristics but also some diverse phenotypes.For instance, micrognathia, hypotonia, febrile seizures, downward slant palpebral fissures, deepset eyes, ptosis, prominent cheekbones have been observed in patient with the variant p.Thr142Lysfs*54 (Flex et al., 2019), but not observed in our patient with p.Ala141GlufsTer56.Contrarily, our patient had an upturned nasal tip, advanced bone age, atrial septum defect, bilateral, and hypothyroidism, whereas patient with the variant p.Thr142Lysfs*54 did not.Remarkably, although patients with the same variants, diverse phenotype was observed.For example, the frameshift variant (Ala144Glyfs*52) was identified in 14 patients.Co-occurring manifestations, such as ocular deformity, speech delay, motor delay, scoliosis, skull abnormalities, and hands abnormalities were observed in all patients, but some different phenotypes were also identified in patients with the same variant, such as ID (13/14), hypotonia (12/13), autism/behavior problem (10/13), cardiac abnormalities (7/11), cryptorchidism (3/12), and several other features.Taken together, phenotypic heterogeneity indicates that it is a site-specific effect on phenotypes for the variant occurring at different positions.A possible explanation of the diverse phenotype observed in patients with the same variant (Ala144Glyfs*52) is the difference in genetic backgrounds.However, the important phenotype of aging appearance as reported in previous studies was not observed in every subject included in this work, which suggests that aging appearance might represent a feature characterizing elderly.
The outstanding question that remains has not been able to answer in our current study is whether the underlying HIST1H1E gene variant determines the extent and severity of clinical features.Currently, because there are too few patients that have been determined, a strong genotypephenotype analysis cannot be performed.Following the report of patients with the HIST1H1E syndrome is increased, which will be beneficial for a better understanding of genotype-phenotype correlations in the future.
In conclusion, the present findings facilitate current knowledge regarding the spectrum of HIST1H1E variants and related phenotypic features, which is helpful to assist diagnosis and clinical management of disease.The consistency and heterogeneity of phenotypes were observed in patients with different or same variants within HIST1H1E, which emphasizes the importantance of studying the sitespecific functions of variants.Our study will stimulate and facilitate research of HIST1H1E variants, which is important for the development of personalized treatments in the future.

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I G U R E 1 A new de novo frameshift variant in HIST1H1E (NM_005321.2, c.416_419dupAGAA, p.Ala141GlufsTer56) in an individual with Rahman syndrome.(a) The segregation of this variant in the family; (b) A hand radiograph; (c) Sanger sequencing results.GenBank accession number (NCBI Reference Sequence): NM_005321.2.