Kristen L. Sund

Mutations in SLC25A46, encoding a UGO1-like protein, cause an optic atrophy spectrum disorder

Dominant optic atrophy (DOA) and axonal peripheral neuropathy (Charcot-Marie-Tooth type 2, or CMT2) are hereditary neurodegenerative disorders most commonly caused by mutations in the canonical mitochondrial fusion genes OPA1 and MFN2, respectively. In yeast, homologs of OPA1 (Mgm1) and MFN2 (Fzo1) work in concert with Ugo1, for which no human equivalent has been identified thus far. By whole-exome sequencing of patients with optic atrophy and CMT2, we identified four families with recessive mutations in SLC25A46. We demonstrate that SLC25A46, like Ugo1, is a modified carrier protein that has been recruited to the outer mitochondrial membrane and interacts with the inner membrane remodeling protein mitofilin (Fcj1). Loss of function in cultured cells and in zebrafish unexpectedly leads to increased mitochondrial connectivity, while severely affecting the development and maintenance of neurons in the fish. The discovery of SLC25A46 strengthens the genetic overlap between optic atrophy and CMT2 while exemplifying a new class of modified solute transporters linked to mitochondrial dynamics.

Regions of homozygosity identified by SNP microarray analysis aid in the diagnosis of autosomal recessive disease and incidentally detect parental blood relationships

Purpose:The purpose of this study was to document the ability of single-nucleotide polymorphism microarray to identify copy-neutral regions of homozygosity, demonstrate clinical utility of regions of homozygosity, and discuss ethical/legal implications when regions of homozygosity are associated with a parental blood relationship.Methods:Study data were compiled from consecutive samples sent to our clinical laboratory over a 3-year period. A cytogenetics database identified patients with at least two regions of homozygosity >10 Mb on two separate chromosomes. A chart review was conducted on patients who met the criteria.Results:Of 3,217 single-nucleotide polymorphism microarrays, 59 (1.8%) patients met inclusion criteria. The percentage of homozygosity ranged from 0.9 to 30.1%, indicating parental relationships from distant to first-degree relatives. First-degree kinship was suspected in the parents of at least 11 patients with regions of homozygosity covering >21.3% of their autosome. In four patients from two families, homozygosity mapping discovered a candidate gene that was sequenced to identify a clinically significant mutation.Conclusion:This study demonstrates clinical utility in the identification of regions of homozygosity, as these regions may aid in diagnosis of the patient. This study establishes the need for careful reporting, thorough pretest counseling, and careful electronic documentation, as microarray has the capability of detecting previously unknown/unreported relationships.Genet Med 2013:15(1):70–78

Analysis of Ellis van Creveld syndrome gene products: implications for cardiovascular development and disease

Mutations identified in a cohort of patients with atrioventricular septal defects as a part of Ellis van Creveld syndrome (EvC syndrome) led us to study the role of two non-homologous genes, EVC and LBN, in heart development and disease pathogenesis. To address the cause of locus heterogeneity resulting in an indistinguishable heart-hand phenotype, we carried out in situ hybridization and immunofluorescence and identified co-localization of Evc and Lbn mRNA and protein. In the heart, expression was identified to be strongest in the secondary heart field, including both the outflow tract and the dorsal mesenchymal protrusion, but was also found in mesenchymal structures of the atrial septum and the atrioventricular cushions. Finally, we studied the transcriptional hierarchy of EVC and LBN but did not find any evidence of direct transcriptional interregulation between the two. Due to the locus heterogeneity of human mutations predicted to result in a loss of protein function, a bidirectional genomic organization and overlapping expression patterns, we speculate that these proteins function coordinately in cardiac development and that loss of this coordinate function results in the characteristics of EvC syndrome.

Genetic Testing Practices in Infants with Congenital Heart Disease

OBJECTIVE Clinical genetic testing is expanding rapidly, but the application of new testing has not been reported in an unselected, comprehensive congenital heart disease (CHD) patient population. This study aims to identify cytogenetic testing practices and diagnostic yield in infants with CHD as an important first step toward understanding clinical utility of dedicated cytogenetic testing. We hypothesized that chromosome microarray analysis (CMA) would identify genetic abnormalities underlying both syndromic and isolated CHD. DESIGN This is a single institution retrospective study that characterizes cytogenetic testing practices and diagnostic yield for all cytogenetic testing in each infant identified with CHD over a 32-month period. CHD was classified by type, complexity, and presence or absence of extracardiac anomalies. RESULTS Among the 1087 infants identified with CHD by echocardiogram, 277 infants (25%) had some form of cytogenetic testing, including karyotype, fluorescence in situ hybridization, and/or CMA. Forty-one percent of infants who had cytogenetic testing had more than one test. CMA was performed in 121 patients (11%), and abnormalities (both clinically significant and variants of unknown significance) were identified in 35/121 (29%). Forty-nine percent of CMA abnormalities were in patients with apparently isolated nonsyndromic CHD. CONCLUSIONS This single institution study identified that only 25% of infants with CHD underwent cytogenetic testing, indicating possible underutilization of testing in this age group. The high multiple testing rate indicates a need for improved guidelines for cost effective testing approaches. The diagnostic yield in this study suggests that CMA is a particularly useful first screening test when a specific syndrome is not clinically identifiable. Larger studies investigating cardiac lesion-specific diagnostic yield in isolated CHD are warranted.

Acrofacial Dysostosis, Cincinnati Type, a Mandibulofacial Dysostosis Syndrome with Limb Anomalies, Is Caused by POLR1A Dysfunction

We report three individuals with a cranioskeletal malformation syndrome that we define as acrofacial dysostosis, Cincinnati type. Each individual has a heterozygous mutation in POLR1A, which encodes a core component of RNA polymerase 1. All three individuals exhibit varying degrees of mandibulofacial dysostosis, and two additionally have limb anomalies. Consistent with this observation, we discovered that polr1a mutant zebrafish exhibited cranioskeletal anomalies mimicking the human phenotype. polr1a loss of function led to perturbed ribosome biogenesis and p53-dependent cell death, resulting in a deficiency of neural-crest-derived skeletal precursor cells and consequently craniofacial anomalies. Our findings expand the genotypic and phenotypic heterogeneity of congenital acrofacial disorders caused by disruption of ribosome biogenesis.

Keutel syndrome: Report of two novel MGP mutations and discussion of clinical overlap with arylsulfatase E deficiency and relapsing polychondritis

Keutel syndrome is a rare, autosomal recessive disorder characterized by diffuse cartilage calcification, peripheral pulmonary artery stenosis, midface retrusion, and short distal phalanges. To date, 28 patients from 18 families have been reported, and five mutations in the matrix Gla protein gene (MGP) have been identified. The matrix Gla protein (MGP) is a vitamin K‐dependent extracellular protein that functions as a calcification inhibitor through incompletely understood mechanisms. We present the clinical manifestations of three affected siblings from a consanguineous Turkish family, in whom we detected the sixth MGP mutation (c.79G>T, which predicts p.E27X) and a fourth unrelated patient in whom we detected the seventh MGP mutation, a partial deletion of exon 4. Both mutations predict complete loss of MGP function. One of the patients presented initially with a working diagnosis of relapsing polychondritis. Clinical features suggestive of Keutel syndrome were also observed in one additional unrelated patient who was later found to have a deletion of arylsulfatase E, consistent with a diagnosis of X‐linked recessive chondrodysplasia punctata. Through a discussion of these cases, we highlight the clinical overlap of Keutel syndrome, X‐linked chondrodysplasia punctata, and the inflammatory disease relapsing polychondritis.

Variability in laboratory reporting practices for regions of homozygosity indicating parental relatedness as identified by SNP microarray testing.

Purpose:Single-nucleotide polymorphism (SNP) microarrays are capable of detecting regions of homozygosity (ROH) that can suggest parental consanguinity or incest. This study was designed to describe the variable reporting practices of clinical laboratories in the United States regarding ROH found on SNP microarray tests, to discuss the follow-up practices of laboratory personnel when findings of ROH indicate consanguinity or incest, and to highlight the legal and ethical dilemmas faced by workers who have discovered these incidental findings.Methods:A 20-question survey was administered to microarray experts at 18 laboratories offering clinical SNP microarray tests. The results are presented using descriptive statistics.Results:There was variability in laboratory SNP microarray reporting practices with respect to information and interpretation of ROH findings. All the laboratories agreed that they have a duty to inform the ordering physician about results suggesting consanguinity or incest, but the follow-through practices varied among laboratories.Conclusions:This study discovered variability in reporting practices and follow-up procedures for microarray results that suggest parental consanguinity or incest. Our findings highlight the need for laboratory guidelines to standardize reporting practices for SNP microarray and other tests that are capable of detecting ROH.Genet Med 2012:14(12):971–976

A mutation in FRIZZLED2 impairs Wnt signaling and causes autosomal dominant omodysplasia

Autosomal dominant omodysplasia is a rare skeletal dysplasia characterized by short humeri, radial head dislocation, short first metacarpals, facial dysmorphism and genitourinary anomalies. We performed next-generation whole-exome sequencing and comparative analysis of a proband with omodysplasia, her unaffected parents and her affected daughter. We identified a de novo mutation in FRIZZLED2 (FZD2) in the proband and her daughter that was not found in unaffected family members. The FZD2 mutation (c.1644G>A) changes a tryptophan residue at amino acid 548 to a premature stop (p.Trp548*). This altered protein is still produced in vitro, but we show reduced ability of this mutant form of FZD2 to interact with its downstream target DISHEVELLED. Furthermore, expressing the mutant form of FZD2 in vitro is not able to facilitate the cellular response to canonical Wnt signaling like wild-type FZD2. We therefore conclude that the FRIZZLED2 mutation is a de novo, novel cause for autosomal dominant omodysplasia.

Looking down the atrioventricular canal.

This editorial refers to ‘Downs syndrome-like cardiac developmental defects in embryos of the transchromosomic Tc1 mouse’ by L. Dunlevy et al ., pp. 287–295, this issue. Downs syndrome (DS) is the most common aneuploidy diagnosed in liveborn babies (∼1/700 live births). While DS is typically associated with recognizable dysmorphic features, clinical anomalies exhibit variable expressivity. The DS phenotype includes many organ systems and affects all three embryonic germ layers. DS is the most frequent chromosomal cause of mental retardation, is a recognized genetic aetiology of Alzheimer disease, and is associated with congenital anomalies of the gastrointestinal and cardiac systems.1 It has been over 50 years since trisomy 21 was discovered as the genetic aetiology of DS.2 Despite progress in diagnosis and management of DS-related health problems, the definition of the pathogenetic mechanisms by which these gene dosage errors induce the DS phenotype and elucidation of DS genotype–phenotype correlations remains elusive. One of the barriers to progress in defining the underlying pathogenesis of this common genetic disorder has been the lack of a suitable animal model (reviewed in refs.3,4). This has been especially true for DS-associated cardiovascular malformations. Nearly half of the DS patients have a congenital heart malformation;5 the signature cardiac defect is atrioventricular septal defect (AVSD), also known as atrioventricular (AV) canal defect or endocardial cushion defect.6,7 The paper by Dunlevy et al .8 in the … *Corresponding author. Tel: +1 513 636 0389; fax: +1 513 636 5958, Email: woody.benson{at}cchmc.org

Copb2 is essential for embryogenesis and hypomorphic mutations cause human microcephaly

Primary microcephaly is a congenital brain malformation characterized by a head circumference less than three standard deviations below the mean for age and sex and results in moderate to severe mental deficiencies and decreased lifespan. We recently studied two children with primary microcephaly in an otherwise unaffected family. Exome sequencing identified an autosomal recessive mutation leading to an amino acid substitution in a WD40 domain of the highly conserved Coatomer Protein Complex, Subunit Beta 2 (COPB2). To study the role of Copb2 in neural development, we utilized genome-editing technology to generate an allelic series in the mouse. Two independent null alleles revealed that Copb2 is essential for early stages of embryogenesis. Mice homozygous for the patient variant (Copb2R254C/R254C) appear to have a grossly normal phenotype, likely due to differences in corticogenesis between the two species. Strikingly, mice heterozygous for the patient mutation and a null allele (Copb2R254C/Zfn) show a severe perinatal phenotype including low neonatal weight, significantly increased apoptosis in the brain, and death within the first week of life. Immunostaining of the Copb2R254C/Zfnbrain revealed a reduction in layer V (CTIP2+) neurons, while the overall cell density of the cortex is unchanged. Moreover, neurospheres derived from animals with Copb2 variants grew less than control. These results identify a general requirement for COPB2 in embryogenesis and a specific role in corticogenesis. We further demonstrate the utility of CRISPR-Cas9 generated mouse models in the study of potential pathogenicity of variants of potential clinical interest.