Synergistic use of glycomics and single-molecule molecular inversion probes for identification of congenital disorders of glycosylation type-1.

Congenital disorders of glycosylation type 1 (CDG-I) comprise a group of 27 genetic defects with heterogeneous multisystem phenotype, mostly presenting with nonspecific neurological symptoms. The biochemical hallmark of CDG-I is a partial absence of complete N-glycans on transferrin. However, recent findings of a diagnostic N-tetrasaccharide for ALG1-CDG and increased high-mannose N-glycans for a few other CDG suggested the potential of glycan structural analysis for CDG-I gene discovery. We analyzed the relative abundance of total plasma N-glycans by high resolution quadrupole time-of-flight mass spectrometry in a large cohort of 111 CDG-I patients with known (n = 75) or unsolved (n = 36) genetic cause. We designed single-molecule molecular inversion probes (smMIPs) for sequencing of CDG-I candidate genes on the basis of specific N-glycan signatures. Glycomics profiling in patients with known defects revealed novel features such as the N-tetrasaccharide in ALG2-CDG patients and a novel fucosylated N-pentasaccharide as specific glycomarker for ALG1-CDG. Moreover, group-specific high-mannose N-glycan signatures were found in ALG3-, ALG9-, ALG11-, ALG12-, RFT1-, SRD5A3-, DOLK-, DPM1-, DPM3-, MPDU1-, ALG13-CDG, and hereditary fructose intolerance. Further differential analysis revealed high-mannose profiles, characteristic for ALG12- and ALG9-CDG. Prediction of candidate genes by glycomics profiling in 36 patients with thus far unsolved CDG-I and subsequent smMIPs sequencing led to a yield of solved cases of 78% (28/36). Combined plasma glycomics profiling and targeted smMIPs sequencing of candidate genes is a powerful approach to identify causative mutations in CDG-I patient cohorts.

Severe neurologic manifestations from cervical spine instability in spondylo-megaepiphyseal-metaphyseal dysplasia.

Spondylo-megaepiphyseal-metaphyseal dysplasia (SMMD; OMIM 613330) is a dysostosis/dysplasia caused by recessive mutations in the homeobox-containing gene, NKX3-2 (formerly known as BAPX1). Because of the rarity of the condition, its diagnostic features and natural course are not well known. We describe clinical and radiographic findings in six patients (five of which with homozygous mutations in the NKX3-2 gene) and highlight the unusual and severe changes in the cervical spine and the neurologic complications. In individuals with SMMD, the trunk and the neck are short, while the limbs, fingers and toes are disproportionately long. Radiographs show a severe ossification delay of the vertebral bodies with sagittal and coronal clefts, missing ossification of the pubic bones, large round "balloon-like" epiphyses of the long bones, and presence of multiple pseudoepiphyses at all metacarpals and phalanges. Reduced or absent ossification of the cervical vertebrae leads to cervical instability with anterior or posterior kinking of the cervical spine (swan neck-like deformity, kyknodysostosis). As a result of the cervical spine instability or deformation, five of six patients in our series suffered cervical cord injury that manifested clinically as limb spasticity. Although the number of individuals observed is small, the high incidence of cervical spine deformation in SMMD is unique among skeletal dysplasias. Early diagnosis of SMMD by recognition of the radiographic pattern might prevent of the neurologic complications via prophylactic cervical spine stabilization.

Additional features of unique Primrose syndrome phenotype.

Primrose syndrome is a unique condition of intellectual disability, dysmorphic facial features, and specific minor abnormalities including large calcified ear auricles. Only six patients have been previously reported. We describe a Brazilian boy with the striking similar facies and the main clinical findings that reinforced the singular phenotype of this rare disorder. The key features of all patients already published were compared. Our young patient has abnormalities that were not observed in preceding reports: nail dysplasia and hyperuricemia.

Tibial hemimelia in Langer-Giedion syndrome with 8q23.1-q24.12 interstitial deletion.

Langer-Giedion syndrome (LGS) (OMIM 150230) is defined as a contiguous gene syndrome caused by loss of functional copies of the TRPS1 and EXT1 genes usually secondary to 8q microdeletion. Tibial hemimelia (TH) is the least common lower limb deficiency characterized by hypoplasia of the tibia with relatively intact fibula. We describe the third report of LGS with bilateral TH and an 8q23.1-q24.12 interstitial deletion. It is not possible to exclude that this association is fortuitous, but our report reinforces the suggestion of a putative gene involved in limb development in this chromosomal region interval.

Regulatory variants of FOXG1 in the context of its topological domain organisation.

FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD. Herein we map three de novo translocation breakpoints to the proximal regulatory domain of FOXG1. The classical FOXG1 syndrome in these and in other translocation patients, and in a patient with an intergenic deletion that removes the hESC-specific TAD boundary, do not support the hypothesised enhancer adoption as a main contributor to the FOXG1 syndrome. Also, virtual 4 C and HiC-interaction data suggest that the hESC-specific TAD boundary may not be critical for FOXG1 regulation in a majority of human cells and tissues, including brain tissues and a neuronal progenitor cell line. Our data support the importance of a critical regulatory region (SRO) proximal to the hESC-specific TAD boundary. We further narrow this critical region by a deletion distal to the hESC-specific boundary, associated with a milder clinical phenotype. The distance from FOXG1 to the SRO ( > 500 kb) highlight a limitation of ENCODE DNase hypersensitivity data for functional prediction of LRPE. Moreover, the SRO has little overlap with a cluster of frequently associating regions (FIREs) located in the proximal hESC-TAD.

Analysis of novel ARG1 mutations causing hyperargininemia and correlation with arginase I activity in erythrocytes.

Hyperargininemia (HA) is an autosomal recessive disease that typically has a clinical presentation that is distinct from other urea cycle disorders. It is caused by the deficient activity of the enzyme arginase I, encoded by the gene ARG1. We screened for ARG1 mutations and measured erythrocyte enzyme activity in a series of 16 Brazilian HA patients. Novel mutations, in addition to previously described missense mutations, were analysed for their effect on the structure, stability and/or function of arginase I (ARG1) using bioinformatics tools. Three previously reported mutations were found (p.R21X; p.I11T and p.W122X), and five novel mutations were identified (p.G27D; p.G74V; p.T134I; p.R308Q; p.I174fs179). The p.T134I mutation was the most frequent in the Brazilian population. Patients carrying the p.R308Q mutation had higher residual ARG1 decreased activity, but presented no distinguishable phenotype compared to the other patients. Bioinformatics analyses revealed that missense mutations (1) affect the ARG1 active site, (2) interfere with the stability of the ARG1 folded conformation or (3) alter the quaternary structure of the ARG1. Our study reinforced the role of Arg308 residue for assembly of the ARG1 homotrimer. The panel of heterogeneous ARG1 mutations that cause HA was expanded, nevertheless a clear genotype-phenotype correlation was not observed in our series.

Craniofacial findings in fibrodysplasia ossificans progressiva: computerized tomography evaluation.

OBJECTIVE: The aim of this study was the evaluation by using computerized tomography (CT) of craniofacial abnormalities in fibrodysplasia ossificans progressiva (FOP) patients regarding jaw restriction and retrognathia. STUDY DESIGN: Seven FOP patients were evaluated retrospectively in this observational study. Inclusion criteria were detection of ACVR1 gene mutation and complete craniofacial CT examination. The age of jaw restriction and presence of retrognathia were clinically determined. The features analyzed were skull base structures and heterotopic ossification (HO). RESULTS: Of this group (age range 4-23 years), the 3 oldest patients presented with jaw restriction and retrognathia as well as displayed elongation of the lateral pterygoid plate with HO of the pterygoid muscles that reached the medial surface of the right mandibular ramus. They had significant history of trauma or surgery. The other 4 patients did not have retrognathia or HO involving the facial or masticatory muscles, and the mouth opening was normal. CONCLUSIONS: CT evaluation can reveal HO of the pterygoid muscles that probably may cause jaw restriction and retrognathia in older FOP patients.

3T MR with diffusion tensor imaging and single-voxel spectroscopy in giant axonal neuropathy.

Magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), and MR spectroscopy (MRS) data were obtained in a patient with giant axonal neuropathy (GAN) and compared to a control group. Fractional anisotropy (FA) and apparent coefficient diffusion (ADC) data were obtained from specific white matter tracts including the corticospinal tracts (CST), corpus callosum (CC), optic radiations (OR), and middle cerebellar peduncle (MCP). Analysis of the MRS was performed. DTI parameters and MRS results were correlated with the neuropathological findings described for GAN. No significant difference between the FA of the CC of the patient and the control group was found. However, there was a significant difference between the FA of the CST, OR, and MCP of the patient and the control group. The ADC values for all tracts of the patient were significantly increased. N-acetylaspartate to creatine (NAA/Cr) and N-acetylaspartate to choline (NAA-Cho) (choline) metabolite ratios were slightly decreased and choline to creatine (Cho/Cr) and myo-inositol to creatine (Ins/Cr) metabolite ratios were increased in the parietal gray and white matter of the patient as compared to the control group. Cerebellar involvement was less evident. The DTI and MRS findings suggest myelin and axonal damage.