Jacob Hogue

Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia

Background Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified. Objective To identify genomic alterations that contribute to the development of diaphragmatic defects. Methods A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis. Results Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype. Conclusions Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.

Phenotypic expansion and further characterisation of the 17q21.31 microdeletion syndrome

Background: The recognition of the 17q21.31 microdeletion syndrome has been facilitated by high resolution microarray technology. Recent clinical delineation of this condition emphasises a typical facial appearance, cardiac and renal defects, and speech delay in addition to intellectual disability, hypotonia and seizures. Methods and results: We describe 11 previously unreported patients expanding the phenotypic spectrum to include aortic root dilatation, recurrent joint subluxation, conductive hearing loss due to chronic otitis media, dental anomalies, and persistence of fetal fingertip pads. Molecular analysis of the deletions demonstrates a critical region spanning 440 kb involving either partially or wholly five genes, CRHR1, IMP5, MAPT, STH, and KIAA1267. Conclusion: These data have significant implications for the clinical diagnosis and management of other individuals with 17q21.31 deletions.

De novo mutations in beta-catenin (CTNNB1) appear to be a frequent cause of intellectual disability: expanding the mutational and clinical spectrum.

Recently, de novo heterozygous loss-of-function mutations in beta-catenin (CTNNB1) were described for the first time in four individuals with intellectual disability (ID), microcephaly, limited speech and (progressive) spasticity, and functional consequences of CTNNB1 deficiency were characterized in a mouse model. Beta-catenin is a key downstream component of the canonical Wnt signaling pathway. Somatic gain-of-function mutations have already been found in various tumor types, whereas germline loss-of-function mutations in animal models have been shown to influence neuronal development and maturation. We report on 16 additional individuals from 15 families in whom we newly identified de novo loss-of-function CTNNB1 mutations (six nonsense, five frameshift, one missense, two splice mutation, and one whole gene deletion). All patients have ID, motor delay and speech impairment (both mostly severe) and abnormal muscle tone (truncal hypotonia and distal hypertonia/spasticity). The craniofacial phenotype comprised microcephaly (typically −2 to −4 SD) in 12 of 16 and some overlapping facial features in all individuals (broad nasal tip, small alae nasi, long and/or flat philtrum, thin upper lip vermillion). With this detailed phenotypic characterization of 16 additional individuals, we expand and further establish the clinical and mutational spectrum of inactivating CTNNB1 mutations and thereby clinically delineate this new CTNNB1 haploinsufficiency syndrome.

Expanding the Clinical Spectrum Associated With GLIS3 Mutations

Context: GLIS3 (GLI-similar 3) is a member of the GLI-similar zinc finger protein family encoding for a nuclear protein with 5 C2H2-type zinc finger domains. The protein is expressed early in embryogenesis and plays a critical role as both a repressor and activator of transcription. Human GLIS3 mutations are extremely rare. Objective: The purpose of this article was determine the phenotypic presentation of 12 patients with a variety of GLIS3 mutations. Methods: GLIS3 gene mutations were sought by PCR amplification and sequence analysis of exons 1 to 11. Clinical information was provided by the referring clinicians and subsequently using a questionnaire circulated to gain further information. Results: We report the first case of a patient with a compound heterozygous mutation in GLIS3 who did not present with congenital hypothyroidism. All patients presented with neonatal diabetes with a range of insulin sensitivities. Thyroid disease varied among patients. Hepatic and renal disease was common with liver dysfunction ranging from hepatitis to cirrhosis; cystic dysplasia was the most common renal manifestation. We describe new presenting features in patients with GLIS3 mutations, including craniosynostosis, hiatus hernia, atrial septal defect, splenic cyst, and choanal atresia and confirm further cases with sensorineural deafness and exocrine pancreatic insufficiency. Conclusion: We report new findings within the GLIS3 phenotype, further extending the spectrum of abnormalities associated with GLIS3 mutations and providing novel insights into the role of GLIS3 in human physiological development. All but 2 of the patients within our cohort are still alive, and we describe the first patient to live to adulthood with a GLIS3 mutation, suggesting that even patients with a severe GLIS3 phenotype may have a longer life expectancy than originally described.

Truncating mutations in the last exon of NOTCH3 cause lateral meningocele syndrome

Lateral meningocele syndrome (LMS, OMIM%130720), also known as Lehman syndrome, is a very rare skeletal disorder with facial anomalies, hypotonia and meningocele‐related neurologic dysfunction. The characteristic lateral meningoceles represent the severe end of the dural ectasia spectrum and are typically most severe in the lower spine. Facial features of LMS include hypertelorism and telecanthus, high arched eyebrows, ptosis, midfacial hypoplasia, micrognathia, high and narrow palate, low‐set ears and a hypotonic appearance. Hyperextensibility, hernias and scoliosis reflect a connective tissue abnormality, and aortic dilation, a high‐pitched nasal voice, wormian bones and osteolysis may be present. Lateral meningocele syndrome has phenotypic overlap with Hajdu–Cheney syndrome. We performed exome resequencing in five unrelated individuals with LMS and identified heterozygous truncating NOTCH3 mutations. In an additional unrelated individual Sanger sequencing revealed a deleterious variant in the same exon 33. In total, five novel de novo NOTCH3 mutations were identified in six unrelated patients. One had a 26 bp deletion (c.6461_6486del, p.G2154fsTer78), two carried the same single base pair insertion (c.6692_93insC, p.P2231fsTer11), and three individuals had a nonsense point mutation at c.6247A > T (pK2083*), c.6663C > G (p.Y2221*) or c.6732C > A, (p.Y2244*). All mutations cluster into the last coding exon, resulting in premature termination of the protein and truncation of the negative regulatory proline‐glutamate‐serine‐threonine rich PEST domain. Our results suggest that mutant mRNA products escape nonsense mediated decay. The truncated NOTCH3 may cause gain‐of‐function through decreased clearance of the active intracellular product, resembling NOTCH2 mutations in the clinically related Hajdu–Cheney syndrome and contrasting the NOTCH3 missense mutations causing CADASIL.

A novel EFNB1 mutation (c.712delG) in a family with craniofrontonasal syndrome and diaphragmatic hernia.

We report on the occurrence of congenital diaphragmatic hernia in a family with craniofrontonasal syndrome found to have a previously unreported mutation in EFNB1. The female proband presented with hypertelorism, telecanthus, bifid nasal tip, widows peak, frontal bossing, and a widened metopic suture. Her father was noted to have hypertelorism, telecanthus, widows peak, and a history of pectus carinatum. He was found to have a previously unreported mutation in exon 5 of EFNB1 predicted to cause premature protein truncation. The parents of the proband previously had a female fetus with congenital diaphragmatic hernia. The occurrence of congenital diaphragmatic hernia, phenotypic differences between males and females, and utility of molecular testing in craniofrontonasal syndrome are demonstrated.

Homozygosity for a FBN1 missense mutation causes a severe Marfan syndrome phenotype.

To the Editor : Marfan syndrome (OMIM 154700) is a connective tissue disorder involving the cardiovascular, ocular, and skeletal systems caused by heterozygous mutations in FBN1 . It is autosomal dominant with clinical variability partially explained by allelic heterogeneity (1). Individuals with biallelic FBN1 mutations provide insight into molecular mechanisms and clinical care of Marfan syndrome. We report a woman with severe Marfan syndrome homozygous for a previously unreported FBN1 missense mutation. The proband is a Mexican-American woman born from a consanguineous union (F = 0.25). She was thin with a pectus carinatum, scoliosis, arachnodactyly, dislocated lenses, mitral valve prolapse, aortic dilatation, dural ectasias, and anterior sacral meningocele. Brain imaging revealed low lying cerebellar tonsils and moderate hydrocephalus. Her scoliosis worsened, her ocular lenses were extracted, she developed urethral prolapse and neurogenic bladder, and an eye was enucleated for glaucoma. She had mild cognitive impairment. At 18 years of age, her height was 155 cm (10th percentile), span to height ratio was 1.05, and she had a narrow, asymmetric face, dolichocephaly, hypertelorism with an interpupillary distance of 6.4 cm (97th percentile), down-slanting palpebral fissures, kyphoscoliosis, narrow palate, positive wrist and thumb signs, arachnodactyly with middle finger length of 8.4 cm (97th percentile), and mild joint contractures (Fig. 1). Clinical sequencing of FBN1 revealed homozygosity for a single base pair substitution, c.7726C>T, predicting p.Arg2576Cys (transcript NM_000138.4). She became pregnant at 20 years of age. Her aortic root was 4.3 cm at 14 weeks gestation. At 30 weeks she developed chest pain and dyspnea. Computerized tomography scan revealed new aortic insufficiency and dilatation. Cesarean section and aortic root repair of a type A dissection were performed. Her son was small for gestational age but healthy. He had dolichocephaly, down-slanting palpebral fissures, midface hypoplasia, high narrow palate, and mild right knee contracture. Ophthalmology exam and echocardiogram were normal. Mutation testing has not been performed, but heterozygosity has been assumed. The proband’s mother lacks examination findings of Marfan syndrome and had a normal optometry examination. Mutation analysis confirmed her to be heterozygous for c.7726C>T. The proband’s father had a cardiac event attributed to drug abuse although aortic dissection cannot be excluded. He reportedly had no other features of Marfan syndrome, but was unavailable for the examination. Patients from five families have been reported with confirmed homozygosity or compound heterozygosity for FBN1 mutations (Table 1) (2–5). In each case, the individual with two FBN1 mutations exhibited more severe manifestations than their heterozygous family members. In addition, heterozygous parents in several families lacked or had only mild Marfan syndrome manifestations. The proband’s mutation has not been reported in the medical literature but was seen in another patient tested at the same clinical laboratory. It is predicted to be disease causing by Mutation Taster (p = 0.999) and probably damaging by Polyphen-2

Characterization of X-linked Hypohidrotic Ectodermal Dysplasia (XL-HED) Hair and Sweat Gland Phenotypes Using Phototrichogram Analysis and Live Confocal Imaging

Hypohidrotic ectodermal dysplasia (HED) is the most common type of ectodermal dysplasia (ED), which encompasses a large group of syndromes that share several phenotypic features such as missing or malformed ectodermal structures, including skin, hair, sweat glands, and teeth. X‐linked hypohidrotic ectodermal dysplasia (XL‐HED) is associated with mutations in ectodysplasin (EDA1). Hypohidrosis due to hypoplastic sweat glands and thin, sparse hair are phenotypic features that significantly affect the daily lives of XL‐HED individuals and therefore require systematic analysis. We sought to determine the quality of life of individuals with XL‐HED and to quantify sweat duct and hair phenotypes using confocal imaging, pilocarpine iontophoresis, and phototrichogram analysis. Using these highly sensitive and non‐invasive techniques, we demonstrated that 11/12 XL‐HED individuals presented with a complete absence of sweat ducts and that none produced sweat. We determined that the thin hair phenotype observed in XL‐HED was due to multiple factors, such as fewer terminal hairs with decreased thickness and slower growth rate, as well as fewer follicular units and fewer hairs per unit. The precise characterization of XL‐HED phenotypes using sensitive and non‐invasive techniques presented in our study will improve upon larger genotype–phenotype studies and the assessment of future therapies in XL‐HED.

An emerging, recognizable facial phenotype in association with mutations in GLI‐similar 3 (GLIS3)

Neonatal diabetes and hypothyroidism (NDH) syndrome was first described in 2003 in a consanguineous Saudi Arabian family where two out of four siblings were reported to have presented with proportionate IUGR, neonatal non‐autoimmune diabetes mellitus, severe congenital hypothyroidism, cholestasis, congenital glaucoma, and polycystic kidneys. Liver disease progressed to hepatic fibrosis. The renal disease was characterized by enlarged kidneys and multiple small cysts with deficient cortico‐medullary junction differentiation and normal kidney function. There was minor facial dysmorphism (depressed nasal bridge, large anterior fontanelle, long philtrum) reported but no facial photographs were published. Mutations in the transcription factor GLI‐similar 3 (GLIS3) gene in the original family and two other families were subsequently reported in 2006. All affected individuals had neonatal diabetes, congenital hypothyroidism but glaucoma and liver and kidney involvement were less consistent features. Detailed descriptions of the facial dysmorphism have not been reported previously. In this report, we describe the common facial dysmorphism consisting of bilateral low‐set ears, depressed nasal bridge with overhanging columella, elongated, upslanted palpebral fissures, persistent long philtrum with a thin vermilion border of the upper lip in a cohort of seven patients with GLIS3 mutations and report the emergence of a distinct, probably recognizable facial gestalt in this group which evolves with age.

Clefting in trisomy 9p patients: Genotype-phenotype correlation using microarray comparative genomic hybridization

Duplication 9p syndrome (partial trisomy 9p) is characterized by craniofacial anomalies, mental retardation, and distal phalangeal hypoplasia. Here, we present a female patient with microcephaly and incomplete bilateral cleft lip and palate, whose initial cytogenetic analysis revealed a de novo trisomy 9p. The patient, now 21 years old, has persistent microcephaly, craniofacial and hand anomalies, history of a seizure disorder, and global mental retardation. Oligonucleotide-based array comparative genomic hybridization was performed and revealed partial trisomy 9p21.1->9pter and a deletion of 9p12.1 to 9p11.2. Our case supports the utility of array comparative genomic hybridization for the precise characterization of chromosomal anomalies and for the ascertainment of genotype-phenotype correlation in patients with partial trisomy 9p.