Identification of De Novo Radio-Tartaglia Syndrome and Comparison of Clinical and Molecular Characteristics with Those of 1p36 Deletion Syndrome
Article information
Abstract
Purpose
Radio-Tartaglia syndrome (RTS; Mendelian Inheritance in Man [MIM]: 619312) is a rare neurodevelopmental disorder with few reported cases and limited research. It has recently been reported that the clinical features of RTS overlap with those of 1p36 deletion syndrome (1p36DS), a common chromosomal deletion characterized by clinical and molecular heterogeneity. This study aims to report on a Korean patient with RTS and compare the clinical and molecular features with those of patients with 1p36DS.
Methods
A 3-year-old boy was brought to the hospital and underwent whole genome sequencing to evaluate developmental delay and multiple anomalies. This led to the identification of a de novo truncating variant in SPEN. We retrospectively investigated cases of 1p36DS that were either newly diagnosed at our institution or previously reported in the literature and databases.
Results
The clinical profile of RTS includes developmental delay/intellectual disability, hypotonia, feeding difficulties, congenital heart defects, and facial dysmorphisms. SPEN is frequently found within the deleted region associated with 1p36DS. However, in all reported Korean cases of 1p36DS, the deletions were distal and did not involve SPEN; despite this, the clinical features of the disorder overlap considerably with those of RTS.
Conclusion
SPEN is a newly identified gene that plays a role in various developmental processes. Therefore, it is essential to include SPEN in genetic testing when diagnosing patients suspected of having a neurodevelopmental disorder. Additional research is required to explore the molecular and clinical features, as well as the prognosis, of patients with either an isolated SPEN mutation or one that co-occurs with 1p36DS.
Introduction
SPEN haploinsufficiency, also known as Radio-Tartaglia syndrome (RTS; Mendelian Inheritance in Man [MIM]: 619312), is a recently reported neurodevelopmental disorder characterized by developmental delay/intellectual disability and multiple congenital anomalies, including brain anomalies, congenital heart defects, and facial dysmorphisms [1]. The SPEN gene is located on chromosome 1p36.21–p36.13 and encodes a protein involved in chromatin remodeling that plays an important role during human development [2,3]. The function of SPEN and the molecular mechanism of disease development remain to be elucidated. No cases of RTS have been reported in Asian populations to date. SPEN is located proximal to critical regions of the gene involved in 1p36 deletion syndrome (1p36DS) (MIM: 607862). A prior study of 34 patients with RTS reported overlap with clinical features of patients with proximal 1p36DS [1], including neurodevelopmental delay/intellectual disability, autism spectrum disorder, behavioral problems (such as anxiety or aggression), hypotonia, brain/spine anomalies, congenital heart defects, and facial dysmorphisms.
1p36DS is one of the most common chromosomal deletions, with an incidence ranging from 1/5,000 to 1/10,000 live births [4-6]. This syndrome is characterized by both clinical and molecular heterogeneity. Its clinical manifestations include developmental delays, hypotonia, seizures, brain anomalies, vision impairments, hearing loss, and congenital heart defects [7,8]. Two critical regions on the chromosomes, referred to as the distal (telomeric) and proximal (centrometric) critical regions, are associated with overlapping clinical features and distinctive facial characteristics [7]. Diagnosis of 1p36DS can be achieved through conventional cytogenetic analysis, fluorescence in situ hybridization analysis, and chromosomal microarray (CMA) analysis [8].
The aim of our study was to report a novel de novo truncating variant in SPEN, identified in a Korean patient with neurodevelopmental phenotypes and congenital anomalies through trio-based whole genome sequencing (WGS). Additionally, we aimed to investigate patients with 1p36DS to explore the genetic spectrum and compare their clinical and molecular features with those of RTS.
Materials and Methods
1. Radio-Tartaglia syndrome
A 3-year-old boy was brought to the hospital in December 2021 for an evaluation of developmental delay and multiple anomalies. He had no known family history of genetic diseases. His parents, who were nonconsanguineous and healthy, provided informed consent for trio-based WGS and the research use of biological and related clinical data (Institutional Review Board [IRB] No.: SMC 2020-10-042).
2. Case collection and literature selection for 1p36DS
We analyzed data from three Korean patients newly diagnosed with 1p36DS who underwent CMA at Samsung Medical Center between 2020 and 2021. Our goal was to compare and analyze their clinical features with those associated with RTS. These patients were evaluated through a review of medical records, which included various parameters such as growth, craniofacial features, cognition and behavior, neurological features, brain anomalies, cardiac features, gastrointestinal features, ocular involvement, and musculoskeletal anomalies. A retrospective analysis of these 1p36DS cases received approval from the IRB of Samsung Medical Center and was exempted from the requirement of informed consent (IRB No.: SMC 2024-02-087).
We further investigated the clinical and molecular features of 1p36DS cases as reported in previous publications. A literature search was conducted in March 2024 using the keyword ‘chromosome 1p36 deletion’ on PubMed (https://scholar.google.com/) and KoreaMed (https://koreamed.org/). We included studies that met the following criteria: (1) research involving Korean patients, and (2) studies that provided a clear description of the 1p36 deletion breakpoint. Additionally, we gathered data on copy number variants, including SPEN, from the public repository Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources (DECIPHER) v.11.23 (https://www.deciphergenomics.org/) [9], and analyzed the clinical features documented in the database.
3. Whole genome sequencing
Genomic DNA was extracted from peripheral blood for WGS. The DNA was fragmented and then used to prepare a library without amplification. This library underwent paired-end sequencing on the NovaSeq 6000 platform (Illumina, San Diego, CA, USA) achieving a mean depth of 35×. Sequence reads were aligned to the human reference genome GRCh38 (hg38) using the Burrows-Wheeler Alignment software (BWA-MEM) version 0.7.17. Preprocessing and variant calling were subsequently carried out using the Genome Analysis Toolkit (GATK) version 4.2.0. Variant annotation was conducted using ANNOtate VARiation (ANNOVAR) and SnpEff across all genomic sequences, including introns. Information on the pathogenicity of the variants was sourced from disease databases such as Online Mendelian Inheritance in Man (OMIM) (http://omim.org), ClinVar (https://ncbi.nlm.nih.gov/clinvar), and various in silico tools that predict the functional effects of each variant. The pathogenicity of each identified variant was assessed based on the 2015 American College of Medical Genetics and Genomics (ACMG) sequence variant interpretation guidelines [10].
4. Chromosomal microarray
DNA was analyzed using the Affymetrix CytoScan Dx platform (Affymetrix, Santa Clara, CA, USA), following the manufacturer’s recommendations. This platform features approximately 1,950,000 copy number variation (CNV) markers and 750,000 single nucleotide polymorphism markers, achieving a resolution between 25 and 50 kB. Data analysis was conducted using the Chromosome Analysis Suite Dx software package from Affymetrix. The reference sequence used was the human reference genome GRCh37 (hg19). All detected CNVs were categorized as pathogenic, likely pathogenic, variant of uncertain significance, likely benign, or benign, in accordance with the ACMG’s CNV interpretation guidelines [11].
Results
1. Radio-Tartaglia syndrome
The presenting boy was born at a gestational age of 39 weeks and 3 days, weighing 2,760 g. At 2 months old, he exhibited congenital stridor due to epiglottic malacia and demonstrated poor sucking power. During infancy, he presented with axial hypotonia and primary microcephaly, with a head circumference of 35.3 cm at 2 months (3rd to 5th percentile) and 45.1 cm at 2 years (<3rd percentile). There was no history of delayed development or genetic disorders in his immediate family, including his older brother and parents. He displayed distinct facial dysmorphisms, including a small anterior fontanelle, prominent vertex, retrognathia, and hypertelorism. An echocardiogram revealed a moderate secondum atrial septal defect measuring 7.3×5.4×6.1 mm. In addition, horseshoe kidney and communicating hydrocele were found on abdominal ultrasonography (Fig. 1A). Due to poor weight gain and recurrent aspiration, he underwent fundoplication and gastrostomy at 4 months of age and continued tube feeding until the age of 3. He achieved head control at 10 months, rolled over at 13 months, and sat with support at 28 months. He showed global developmental delays according to the Korean Bayley Scales of Infant Development-III. At 28 months, his scores were as follows: cognitive scale, 7 months; receptive communication scale, 14 months; expressive communication scale, 13 months; fine motor scale, 9 months; and gross motor scale, 6 months. By the age of 5, he was able to walk with support and combine two words when speaking. Currently, at 6 years old, he exhibits no abnormal behaviors or psychiatric features. His brain magnetic resonance imaging showed ventriculomegaly and a dysmorphic cranium (brachycephaly) without any brain parenchymal abnormalities (Fig. 1B). Cytogenetic analysis confirmed a normal karyotype (46,XY). WGS identified a heterozygous variant in SPEN, NM_015001.3:c.5806C>T (Fig. 1C), predicted to cause premature termination of the SPEN protein (p.Arg1936*). This SPEN variant was classified as pathogenic based on the following evidence: (1) absence in the gnomAD dataset, (2) prediction of a stop-gained variant leading to loss of normal protein function through nonsense-mediated decay, and (3) previous pathogenic classification in ClinVar. Furthermore, the SPEN variant was not found in his parents, confirming its de novo occurrence (Fig. 1C). No other significant candidate variants were identified in the WGS results.
Clinical features and pathogenic SPEN truncating variant in a patient with Radio-Tartaglia syndrome. (A) A transverse ultrasonogram displays the connecting isthmus crossing anterior to the retroperitoneal great vessels, along with the renal parenchyma of each limb of the horseshoe kidney. (B) Brain magnetic resonance imaging reveals ventriculomegaly accompanied by non-specific cerebrospinal fluid space widening and a dysmorphic cranium. (C) An Integrative Genomics Viewer snapshot of the pathogenic variant in c.5806C>T (p.Arg1936Ter) identified through whole genome sequencing.
2. 1p36DS and their CMA results
The molecular and clinical characteristics of cases with 1p36DS are summarized in Table 1 and Fig. 2. We retrieved a total of 159 publications using the search term ‘chromosome 1p36 deletion’ from PubMed and KoreaMed, covering the period from 2015 to March 2024. Out of these, three publications were selected based on specific criteria [12-14]. Among them, the study by Shim et al. [12] explored the detailed phenotypes of 15 patients with 1p36DS. This study was utilized to compare the clinical features of patients identified at our institution with those reported in the DECIPHER database, as illustrated in Table 1.
Genotype-phenotype correlation analysis of patients with 1p36 deletions
Schematic representation of known critical regions of 1p36 and deletions with or without SPEN. Distal and proximal critical regions (CRs) of 1p36 deletion (orange boxes). The deletions reported by Shim et al. [12] and Lee and Song [13] are associated in the present study with the distal 1p36 CR and are indicated by gray bars. One Korean case by Park et al. [14] showed an interstitial deletion (1 Mb) at 1p36.11–p35.3 (green bar). Deletions overlapping with SPEN that have previously been reported in Database of Genomic Variation and Phenotype in Humans Using Ensembl Resources (DECIPHER) are shown as blue bars (DECIPHER v11.23, https://www.deciphergenomics.org/).
All three Korean patients with 1p36DS at our institution exhibited pathogenic or likely pathogenic CNVs located in the distal critical region, none of which included SPEN. The patients fell into different age categories at diagnosis: one was a neonate, another was an infant aged 10 months, and the third was a preschool-aged child of 6 years. The neonate, who underwent CMA due to neonatal seizures and distinct facial features, had a 1.3 MB deletion at 1p36.33, affecting approximately 50 genes. Among these, the deletion of gamma-aminobutyric acid type A receptor subunit delta (GABRD) was believed to be responsible for his seizures. In the cases of the infant and the preschooler, both of whom exhibited delayed development, deletions measured 900 kB and 5.2 MB at 1p36.33, respectively. All patients displayed consistent phenotypes associated with 1p36DS, including delayed development, impaired cognition, and distinctive facial features.
3. Comparison of clinical and molecular features
The clinical features of the patient with RTS identified in this study were compared with those of previously reported cases involving truncating mutations of SPEN, as detailed in Table 2. Although the neurodevelopmental characteristics of our patient closely resembled those reported previously, no behavioral or psychiatric disorders have been observed to date (Table 2). Notably, the presence of genitourinary anomalies, such as a horseshoe kidney and a communicating hydrocele, sets our findings apart from previous reports [1]. To assess the genotype-phenotype correlation in patients with 1p36DS based on the presence of SPEN, we analyzed the clinical features of the patients in this study and compared them with those documented in earlier cases, as presented in Table 1. The analysis revealed common clinical features between RTS and 1p36DS, including developmental delay/intellectual disability, facial dysmorphisms, and cardiac anomalies.
Clinical findings of the present patient with a SPEN-related disease phenotype
Discussion
Developmental delays and intellectual disabilities affect 1%–3% of the general population [15]. Recent advances in genetic testing, along with a deeper understanding of genetic disorders, now enable genetic diagnoses for some children whose developmental delays or intellectual disabilities were previously unexplained [16,17]. In 2021, Radio et al. [1] analyzed data from 34 individuals with truncating variants in the SPEN gene and concluded that SPEN haploinsufficiency is the primary causative gene for disorders associated with 1p36 deletion. In our current study, we identified RTS as the sole molecular cause in a patient with developmental delay and multiple anomalies. We also found that this patient's clinical features were consistent with those reported in previous studies of patients with 1p36DS [12-14], aligning with the findings of Radio et al. [1].
The main features of RTS include developmental delay/intellectual disability, behavioral and/or psychiatric disorders, brain anomalies, congenital heart defects, and facial dysmorphisms [1]. Behavioral and psychiatric features such as autism spectrum disorder, anxiety, aggressive behavior, and attention deficit disorder are reported at a high rate of 81% in the literature [1]. Therefore, it is essential to closely monitor these symptoms in patients with detected truncating mutations in the SPEN gene. Additionally, the structural genitourinary anomaly observed in the current study, such as horseshoe kidney, has not been previously reported in the literature on RTS. Given the limited research in this area, further studies on the function of the SPEN gene and associated disease phenotypes are necessary. To address the genotype-phenotype correlation in patients with RTS and 1p36DS, we compared the clinical features of the patient with RTS from this study with those of previously reported patients with 1p36DS (Tables 1 and 2) [12]. The phenotype of our patient included facial dysmorphisms, developmental delays, intellectual disabilities, and cardiac anomalies, which are also observed in 1p36DS, but there were no instances of hearing loss or endocrinologic abnormalities.
SPEN is located on chromosome 1p36.21–p36.13 and comprises 15 exons that span nearly 92.7 kb. To date, the Human Gene Mutation Database (HGMD) professional version 2023.4 has reported only 30 disease-causing mutations in SPEN. Most of these mutations are of the truncating type and are distributed throughout the coding region. SPEN is expressed in the brain during human development [18] and is thought to play a role in X chromosome inactivation and X-linked gene silencing [1]. Further research is necessary to elucidate the gene's function and the mechanisms underlying disease development.
In conclusion, we identified a p.Arg1936Ter truncating pathogenic variant in the SPEN gene. To our knowledge, this is the first genetically confirmed case of RTS in an Asian population. This case underscores the importance of including genetic testing for the SPEN gene in patients suspected of having a neurodevelopmental disorder.
Notes
Conflicts of interest
Jeehun Lee is an editorial board member of the journal, but he was not involved in the peer reviewer selection, evaluation, or decision process of this article. No other potential conflicts of interest relevant to this article were reported.
Author contribution
Conceptualization: HYK and MAJ. Data curation: JL (Jeehun Lee), JHJ, and JWK. Formal analysis: HYK, JL (Jiwon Lee), and MAJ. Funding acquisition: MAJ. Methodology: HYK and MAJ. Project administration: JL (Jiwon Lee) and MAJ. Visualization: MAJ. Writing-original draft: HYK, JL (Jiwon Lee), and MAJ. Writing-review & editing: JL (Jiwon Lee) and MAJ.
Acknowledgments
This work was supported by the Basic Science Research Program through a National Research Foundation of Korea (NRF) grant funded by the Ministry of Education, Science and Technology (2017R1C1B5018081 and 2021R1C1C1005725).