Novel HIVEP2 Variants in Patients with Intellectual Disability (2025)

Abstract

Intellectual disability (ID) occurs in approximately 1% of the population. Over the last years, broad sequencing approaches such as whole exome sequencing (WES) substantially contributed to the definition of the molecular defects underlying nonsyndromic ID. Pathogenic variants in HIVEP2, which encodes the human immunodeficiency virus type I enhancer binding protein 2, have recently been reported as a cause of ID, developmental delay, behavioral disorders, and dysmorphic features. HIVEP2 serves as a transcriptional factor regulating NF-ĸB and diverse genes that are essential in neural development. To date, only 8 patients with pathogenic de novo nonsense or frameshift variants and 1 patient with a pathogenic missense variant in HIVEP2 have been reported. By WES, we identified 2 novel truncating HIVEP2 variants, c.6609_6616delTGAGGGTC (p.Glu2204*) and c.6667C>T (p.Arg2223*), in 2 young adults presenting with developmental delay and mild ID without any dysmorphic features, systemic malformations, or behavioral issues.

Clinical Reports

Patient 1 is the first child of healthy unrelated German parents. The girl was born after a normal pregnancy at 40 weeks of gestation by spontaneous vaginal delivery with normal length (53 cm; 72nd centile) and weight (3,570 g; 59th centile). The first clinical presentation was orofacial hypotonia with an open mouth posture in infancy. Considerable global developmental delay became apparent approximately at the age of 2 years. Motor development was slightly delayed, but she walked independently at 18 months of age. Some neurological signs such as general muscular hypotonia, poor posture, and notable difficulties in gross and fine motor coordination were noted. Language development was severely affected as she spoke first words at the age of 4 years. A nonverbal intelligence test at 9 years of age revealed mild ID with an IQ of 58. Her behavior has generally been friendly, amiable, and cooperative. Her medical history is unremarkable; there were neither organic malformations, complicated hospitalizations nor any evidence of seizures. She does not show any distinctive dysmorphic features, but a marginally broader nose, narrow chin, and thin upper lip could be conceived (Fig. 1). Her height, weight, and head circumference have always been within the normal range. Currently, at the age of 27 years, she works at a sheltered workshop and does not have any difficulties socializing with other workmates. Prior to WES, conventional chromosomal and SNP array analyses revealed normal results, and Fragile X syndrome was excluded via trinucleotide repeat expansion analysis. Screening for congenital metabolic diseases and congenital disorders of glycosylation yielded negative results.

Patient 2, a female, was the only child of a healthy 29-year-old woman. There is no family medical history regarding ID or any other neurological disorders. Pregnancy was unremarkable and prenatal sonographic scans were normal. She was born at 37 weeks of gestation by uncomplicated vaginal delivery with a birthweight of 2,450 g (19th centile), birth length of 49 cm (72nd centile), and head circumference of 31 cm (9th centile). The patient demonstrated mild motor developmental delay: she started rolling over at 7 months, could sit up and stand with support at 11 months, and learned to walk independently at approximately 20-24 months. She spoke first words at the age of 24 months. She has an elongated and mildly narrow face as well as small ears, but no specific dysmorphic features. Neurological examination was unremarkable without signs of muscular hypotonia, seizures, or autism. EEG was normal. She was diagnosed with mild ID with an IQ of 52. Until the age of 16 years, she attended special schools for ID students. Now, she is 23 years old and has slow speech and limited vocabulary. She tends to use short and repetitive sentences and is often difficult to understand for others, with the exception of her parents. Although she presents irritability and impulsivity, she rarely shows aggressive behavior. Repetitive interests and limited food preference were seen as characteristic features within normal range for a patient with ID. Predominant autistic features were excluded. Regarding medical problems, the patient frequently suffered from upper airway infections, constipation, and oligomenorrhea. Otherwise, no other complicated medical issues have occurred so far. Chromosomal abnormalities, including microdeletions, microduplications, and other copy-number variants (CNVs) have been excluded by conventional karyotyping and array CGH.

Methods and Results

For patient 1, diagnostic WES was performed on genomic DNA extracted from peripheral blood. Coding regions were enriched using a SureSelect XT Human All Exon kit v6 (Agilent Technologies, Santa Clara, CA, USA) for subsequent sequencing as 2 × 125-bp paired-end reads on a HiSeq2500 system (Illumina, San Diego, CA, USA) as published previously [Fritzen et al., 2018]. Generated sequences were analyzed using the megSAP pipeline (https://github.com/imgag/megSAP). Clinical variant prioritization included different filtering steps including a search for rare (MAF <0.1% in ExAC, gnomAD, 3,000 in-house exome datasets) variants in genes that have been associated with the patient's phenotype according to an in-house standard operating procedure.

For patient 2, WES was performed on genomic DNA isolated from the proband's EDTA blood using a TruSeq Exome Enrichment kit (Illumina) on an Illumina HiSeq 2500 sequencer. Approximately 100 million paired reads per sample were generated. The average sequencing depth was 70.2× with over 80% of the target sequence covered at ≥20×. Genomic variants were filtered and prioritized according to the following criteria: the gene reported is to be involved in neurological or mental disorders, its frequency in publicly available variant databases <0.01%, and in silico predicted pathogenic effect of the variant. Bidirectional Sanger sequencing was performed to confirm the variants in both patients and their de novo status.

Discussion

Six years ago, in a cohort study of 51 patients, Rauch et al. [2012] reported 1 de novo heterozygous truncating variant in HIVEP2 as a possible cause of nonsyndromic ID in a female patient. Only limited clinical information of the patient was presented. Srivastava et al. [2016] reported further clinical details for this patient who exhibited not only severe ID, but also dysmorphic features, congenital malformations, ataxic gait, and aggressive behavior. In addition, the same authors identified 2 further unrelated children with de novo heterozygous HIVEP2 truncating variants presenting with moderate ID, developmental delay, mild facial dysmorphism, and, in one of them, behavioral problems, suggesting loss of function and haploinsufficiency as the pathomechanism [Rauch et al., 2012]. More recently, Steinfeld et al. [2016] identified 5 de novo truncating variants and 1 de novo missense variant in HIVEP2 in 6 unrelated children with ID. Last, in 2 cohort studies, 1 de novo missense variant and 1 de novo nonsense variant have been identified among patients affected by bipolar disorder and ID, respectively [Kataoka et al., 2016; Hamdan et al., 2017]. However, both publications did not provide any clinical phenotype details.

HIVEP2 variants identified so far in ID patients are shown in Figure 2. Clinical details are given in Table 1. Overall, only 8 patients with pathogenic nonsense or frameshift variants and 1 patient with a pathogenic missense variant in HIVEP2 have been reported together with clinical information. All of them, 5 females and 4 males, showed mild to moderate ID. Motor development was markedly delayed in all. Seven out of 9 patients were able to walk independently at the age of ∼2-3 years and 1 of them needed a walker until the age of 4-5 years. Apart from general muscular hypotonia which was present in 7 out of 9 patients, other overlapping neurological features such as ataxia, dystonia, dyspraxia, dysphagia, gait difficulties, spasticity, and progressive Parkinsonism and quadriplegia have been registered in 7 cases. All of them had remarkable language development delay and 7 showed pronounced behavioral abnormalities, such as hyperactivity, impulsivity, lack of concentration, but also anxiety, aggressive and/or hand flapping behavior. Less frequently reported clinical features include microcephaly (3 cases) or seizures (2 cases). Some of them also presented with nonspecific dysmorphic features, which were not predominant in our patients. The majority of reported cases suffered from minor medical problems, mostly gastrointestinal symptoms, such as abdominal pain, constipation or reflux. Congenital anomalies are uncommon. Brain MRI did not reveal any specific pathological findings. In comparison to the previously reported cases, our 2 patients did not show any complex neurological findings and had an uncomplicated medical history without predominant behavioral abnormalities. The variants identified in our patients are located in the last exon of HIVEP2 and are predicted to result in the generation of a truncated protein. This could possibly lead to some residual function or a dominant-negative effect and might also explain the milder phenotype of these patients.

HIVEP2 operates as a transcription factor for various genes involved in brain development, such as the somatostatin receptor type II (SSTR-2) that is known to show expression in the frontal cortex and hippocampus during embryonic brain and nerve formation [Takagi et al., 2006]. HIVEP2 also binds to nuclear factor-ĸB (NF-ĸB) reducing the transcription of NF-ĸB-dependent genes that play an important role in immune response. Hivep2 knock-out mice displayed chronic inflammation signs in several brain areas due to upregulation of NF-ĸB target gene proposing a paradigm that alterations in immune response can influence neurodevelopmental disorders [Takao et al., 2013; Choi et al., 2015]. RNA expression analysis in hippocampus and amygdala illustrated a downregulation of some early genes that are involved in stress response and neuroplasticity [Takagi et al., 2006]. Hivep2 knock-out mice showed not only severe cognitive impairments but also behavioral abnormalities, which could be compared with those of 7 of the reported patients. No remarkable deficits in health condition, physical appearance, or motor functions were observed in the mutant mice. Administration of haloperidol and anti-inflammatory drugs to murine models reduced inflammation markers in the brain and improved social interactions and memory abilities [Takao et al., 2013]. Although behavioral problems have not been observed in our patients, this type of pharmacological therapy has been suggested as a possible treatment for such symptoms [Takao et al., 2013].

This report supports the growing evidence that WES can be a useful approach to elucidate the underlying molecular cause of ID [Helsmoortel et al., 2015; Vrijenhoek et al., 2018]. Patients with heterozygous pathogenic variants in HIVEP2 share a nonspecific phenotype of developmental delay/ID and other variable clinical features. Our 2 cases are the oldest reported patients with pathogenic HIVEP2 variants that have been clinically characterized so far. Both reached maturity with mild ID but without predominant behavioral difficulties or other serious medical problems. Clinical follow-up of additional patients will outline the development of the mental phenotype and further define the clinical spectrum of HIVEP2-associated ID. Functional studies are needed to shed light on the molecular mechanisms underlying the pathological effect of the variants on the central nervous system.

Statement of Ethics

Informed consent was obtained prior to investigation.

Disclosure Statement

The authors have no conflicts of interest to declare.

Funding Sources

This study was supported by the German Bundesministerium für Bildung und Forschung (BMBF) through the Juniorverbund in der Systemmedizin “mitOmics” (FKZ 01ZX1405C to T.B.H.) and the Intramurale Fortüne program.

Author Contributions

J. Park collected and analyzed the data and drafted the manuscript. R. Colombo and L. Janiri kindly provided the clinical and molecular information of the second patient. In addition, R. Colombo contributed to the conception of the work, reviewed for accurate interpretation of molecular data, and revised the work thoroughly for scientific content. K. Schäferhoff and M. Grimmel were involved in WES data analysis and provided the molecular information. M. Sturm developed and applied the bioinformatics data analysis pipeline. T. Haack reviewed the work critically for appropriate content and supervised execution of the project. M. Kehrer, U. Grasshoff, and A. Dufke contributed as clinicians to the phenotypic analysis and cared for close communication with patient 1. M. Kehrer initiated and supervised the project.

References