Discovery of a novel CHD7 CHARGE syndrome variant by integrated omics analyses.

Chromodomain helicase DNA-binding protein 7 (CHD7) pathogenic variants are identified in more than 90% of infants and children with CHARGE (Coloboma of the iris, retina, and/or optic disk; congenital Heart defects, choanal Atresia, Retardation of growth and development, Genital hypoplasia, and characteristic outer and inner Ear anomalies and deafness) syndrome. Approximately, 10% of cases have no known genetic cause identified. We report a male child with clinical features of CHARGE syndrome and nondiagnostic genetic testing that included chromosomal microarray, CHD7 sequencing and deletion/duplication analysis, SEMA3E sequencing, and trio exome and whole-genome sequencing (WGS). We used a comprehensive clinical assessment, genome-wide methylation analysis (GMA), reanalysis of WGS data, and CHD7 RNA studies to discover a novel variant that causes CHD7 haploinsufficiency. The 7-year-old Hispanic male proband has typical phenotypic features of CHARGE syndrome. GMA revealed a CHD7-associated epigenetic signature. Reanalysis of the WGS data with focused bioinformatic analysis of CHD7 detected a novel, de novo 15 base pair deletion in Intron 4 of CHD7 (c.2239-20_2239-6delGTCTTGGGTTTTTGT [NM_017780.3]). Using proband RNA, we confirmed that this novel deletion causes CHD7 haploinsufficiency by disrupting the canonical 3' splice site and introducing a premature stop codon. Integrated genomic, epigenomic, and transcriptome analyses discovered a novel CHD7 variant that causes CHARGE syndrome.

Modelling the developmental spliceosomal craniofacial disorder Burn-McKeown syndrome using induced pluripotent stem cells.

The craniofacial developmental disorder Burn-McKeown Syndrome (BMKS) is caused by biallelic variants in the pre-messenger RNA splicing factor gene TXNL4A/DIB1. The majority of affected individuals with BMKS have a 34 base pair deletion in the promoter region of one allele of TXNL4A combined with a loss-of-function variant on the other allele, resulting in reduced TXNL4A expression. However, it is unclear how reduced expression of this ubiquitously expressed spliceosome protein results in craniofacial defects during development. Here we reprogrammed peripheral mononuclear blood cells from a BMKS patient and her unaffected mother into induced pluripotent stem cells (iPSCs) and differentiated the iPSCs into induced neural crest cells (iNCCs), the key cell type required for correct craniofacial development. BMKS patient-derived iPSCs proliferated more slowly than both mother- and unrelated control-derived iPSCs, and RNA-Seq analysis revealed significant differences in gene expression and alternative splicing. Patient iPSCs displayed defective differentiation into iNCCs compared to maternal and unrelated control iPSCs, in particular a delay in undergoing an epithelial-to-mesenchymal transition (EMT). RNA-Seq analysis of differentiated iNCCs revealed widespread gene expression changes and mis-splicing in genes relevant to craniofacial and embryonic development that highlight a dampened response to WNT signalling, the key pathway activated during iNCC differentiation. Furthermore, we identified the mis-splicing of TCF7L2 exon 4, a key gene in the WNT pathway, as a potential cause of the downregulated WNT response in patient cells. Additionally, mis-spliced genes shared common sequence properties such as length, branch point to 3' splice site (BPS-3'SS) distance and splice site strengths, suggesting that splicing of particular subsets of genes is particularly sensitive to changes in TXNL4A expression. Together, these data provide the first insight into how reduced TXNL4A expression in BMKS patients might compromise splicing and NCC function, resulting in defective craniofacial development in the embryo.

Ectrodactyly-ectodermal dysplasia-clefting syndrome presenting with bilateral choanal atresia and rectal stenosis.

We present the case of a male who shortly after birth developed acute respiratory distress due to bilateral choanal atresia, following which he was found to have rectal stenosis. Genetic testing for CHARGE syndrome was negative, but whole genome sequencing identified heterozygosity for a pathogenic missense variant in TP63 (c.727C > T, p.(Arg243Trp). He also has partial cutaneous syndactyly of the third and fourth fingers of the right hand, and bilateral lacrimal duct stenosis/aplasia. A later maxillofacial review identified a palpable submucousal cleft and his scalp hair is blond and slightly sparse. Choanal atresia and rectal stenosis are recognized features of ectrodactyly-ectodermal dysplasia-clefting syndrome, but we believe this is the first report of a case presenting with these features in the absence of the cardinal features.

Burn-McKeown syndrome with biallelic promoter type 2 deletion in TXNL4A in two siblings.

Burn-McKeown syndrome (BMKS) (MIM# 608572) is a rare condition caused by biallelic variants in TXNL4A. BMKS is characterized by craniofacial dysmorphism, choanal atresia, and normal intellect in affected individuals. BMKS has overlapping clinical features with Treacher Collins syndrome. Till date, 15 families have been described with BMKS. Homozygosity or compound heterozygosity of promoter deletions and null variants in TXNL4A are known to cause most cases of BMKS. We describe the first Indian family with two siblings with BMKS and promoter type 2 deletion in homozygous state.

Does DNA Methylation Matter in FSHD?

Facioscapulohumeral muscular dystrophy (FSHD) has been associated with the genetic and epigenetic molecular features of the CpG-rich D4Z4 repeat tandem array at 4q35. Reduced DNA methylation of D4Z4 repeats is considered part of the FSHD mechanism and has been proposed as a reliable marker in the FSHD diagnostic procedure. We considered the assessment of D4Z4 DNA methylation status conducted on distinct cohorts using different methodologies. On the basis of the reported results we conclude that the percentage of DNA methylation detected at D4Z4 does not correlate with the disease status. Overall, data suggest that in the case of FSHD1, D4Z4 hypomethylation is a consequence of the chromatin structure present in the contracted allele, rather than a proxy of its function. Besides, CpG methylation at D4Z4 DNA is reduced in patients presenting diseases unrelated to muscle progressive wasting, like Bosma Arhinia and Microphthalmia syndrome, a developmental disorder, as well as ICF syndrome. Consistent with these observations, the analysis of epigenetic reprogramming at the D4Z4 locus in human embryonic and induced pluripotent stem cells indicate that other mechanisms, independent from the repeat number, are involved in the control of the epigenetic structure at D4Z4.

CHARGE syndrome in nine patients from China.

CHARGE syndrome (CS) is a multiple congenital anomalies condition with the majority of cases caused by dominant loss-of-function mutations of the CHD7 gene. It is clinically characterized by coloboma of the eyes, heart defects, choanal atresia, retardation of growth and/or development, genital and/or urinary anomalies and ear malformations associated with deafness and vestibular disorder(s). This case series reported nine molecularly confirmed Chinese CS patients from nine unrelated families in Hong Kong. Clinical phenotype and facial features of these nine Chinese CS patients together with four previously reported Chinese patients were reviewed. Typical presentations like coloboma and choanal atresia were not universally present. The prevalence of choanal atresia in these Chinese CS patients was found to be significantly lower than that in previous cohorts of other ethnic groups. This report highlighted the existence of phenotypic variation of CS among different ethnicities and suggested that a high index of suspicion is necessary for diagnosis of CS in Chinese patients.

Role of the Chromosome Architectural Factor SMCHD1 in X-Chromosome Inactivation, Gene Regulation, and Disease in Humans.

Structural maintenance of chromosomes flexible hinge domain-containing 1 (SMCHD1) is an architectural factor critical for X-chromosome inactivation (XCI) and the repression of select autosomal gene clusters. In mice, homozygous nonsense mutations in Smchd1 cause female-specific embryonic lethality due to an XCI defect. However, although human mutations in SMCHD1 are associated with congenital arhinia and facioscapulohumeral muscular dystrophy type 2 (FSHD2), the diseases do not show a sex-specific bias, despite the essential nature of XCI in humans. To investigate whether there is a dosage imbalance for the sex chromosomes, we here analyze transcriptomic data from arhinia and FSHD2 patient blood and muscle cells. We find that X-linked dosage compensation is maintained in these patients. In mice, SMCHD1 controls not only protocadherin (Pcdh) gene clusters, but also Hox genes critical for craniofacial development. Ablating Smchd1 results in aberrant expression of these genes, coinciding with altered chromatin states and three-dimensional (3D) topological organization. In a subset of FSHD2 and arhinia patients, we also found dysregulation of clustered PCDH, but not HOX genes. Overall, our study demonstrates preservation of XCI in arhinia and FSHD2, and implicates SMCHD1 in the regulation of the 3D organization of select autosomal gene clusters.

FSHD2- and BAMS-associated mutations confer opposing effects on SMCHD1 function.

Structural maintenance of chromosomes flexible hinge domain-containing 1 (Smchd1) plays important roles in epigenetic silencing and normal mammalian development. Recently, heterozygous mutations in SMCHD1 have been reported in two disparate disorders: facioscapulohumeral muscular dystrophy type 2 (FSHD2) and Bosma arhinia microphthalmia syndrome (BAMS). FSHD2-associated mutations lead to loss of function; however, whether BAMS is associated with loss- or gain-of-function mutations in SMCHD1 is unclear. Here, we have assessed the effect of SMCHD1 missense mutations from FSHD2 and BAMS patients on ATP hydrolysis activity and protein conformation and the effect of BAMS mutations on craniofacial development in a Xenopus model. These data demonstrated that FSHD2 mutations only result in decreased ATP hydrolysis, whereas many BAMS mutations can result in elevated ATPase activity and decreased eye size in Xenopus Interestingly, a mutation reported in both an FSHD2 patient and a BAMS patient results in increased ATPase activity and a smaller Xenopus eye size. Mutations in the extended ATPase domain increased catalytic activity, suggesting critical regulatory intramolecular interactions and the possibility of targeting this region therapeutically to boost SMCHD1's activity to counter FSHD.

Many faces of SMCHD1.

The chromatin scaffolding protein SMCHD1 (structural maintenance of chromosomes flexible hinge domain containing 1) was previously shown to have diverse roles in X-chromosome inactivation, imprinting and double-strand break repair, and mutations in SMCHD1 contribute to a type of muscular dystrophy. Now, development of the nose and eyes is added to its list of functions.

[Advances in treatment of congenital posterior choanal atresia].

Congenital posterior choanal atresia is a rare congenital deformity. Due to the influence of nose and face and intellectual development, its preferred surgical treatment. But surgical treatment methods and technology are in dispute. The using of high resolution display systems combine with micro tools can effectively reduce postoperative scarring and adhesion formation which is the key point to prevent restenosis. There is also the focus of controversy whether should place an expansive tube after operation. Currently nasal endoscopic approach has become the first choice for otolaryngologist treating congenital posterior choanal atresia.

Interstitial 1p32.1p32.3 deletion in a patient with multiple congenital anomalies.

Interstitial deletions encompassing chromosome bands 1p32.1p32.3 are rare. Only nine unrelated patients with partially overlapping 1p32.1p32.3 deletions of variable size and position have been reported to date. We report on a 17-month-old boy with choanal atresia, hearing loss, urogenital anomalies, and microcephaly in whom an interstitial de novo deletion of 6.4 Mb was detected in 1p32.1p32.3 (genomic position chr1:54,668,618-61,113,264 according to GRCh37/hg19). The deleted region harbors 31 RefSeq genes. Notable genes in the region are PCSK9, haploinsufficiency of which caused low LDL cholesterol plasma levels in the patient, and DAB1, which is a candidate gene for cognitive deficits, microcephaly, and cerebral abnormalities such as ventriculomegaly and agenesis of the corpus callosum. Choanal atresia, microcephaly, and severe hearing loss were previously not known to be associated with 1p32 deletions. Our reported patient thus broadens the spectrum of clinical findings in this chromosome region and further facilitates genotype-phenotype correlations. Additional patients with overlapping deletions and/or point mutations in genes of this region need to be identified to elucidate the role of individual genes for the complex clinical manifestations.

Choanal atresia: histochemical, immunohistochemical and ultrastructure study of the nasal mucosa.

OBJECTIVES: To study the nasal mucosal changes in cases with choanal atresia at the light and electron microscope and to compare the results with the normal side in unilateral cases. STUDY DESIGN: Cross sectional study. SETTING: Tertiary University hospital, departments of Otolaryngology and pathology. METHODS: Sixteen patients diagnosed to have choanal atresia (seven bilateral and nine unilateral); ranging in age from 3 days to 9 years; were included in this study. During surgical repair, a biopsy of the inferior turbinate mucosa was taken. Biopsy from patent side in unilateral choanal atresia was also taken (as a control). Then biopsies were subjected to histopathological, histochemical, immunohistochemical and ultrastructure studies. RESULTS: The nasal mucosa in choanal atresia side (weather unilateral or bilateral) showed distorted cilia, marked increase of mucous submucosal glands associated with marked reduction of goblet cell density and lymphocytic cellular infiltration. The patent side (control) showed normal respiratory epithelium with obviously noted intra-epithelial goblet cells. Submucosal glands were less in number and activity than in the atretic side. CONCLUSIONS: Choanal atresia showed a condition of the nasal mucous membrane with characteristic excessive nasal tenacious secretion; mostly actively secreted besides some effect of lack of drainage due to interrupted cilia. Further studies are required to evaluate the impact of atresia repair on detected features.

De novo partial trisomy distal 4q: a case report.

We present a case of de novo distal partial trisomy 4q with firstly described chronic cholecystitis, rarely seen hypothyroidism, and bilateral membranous choanal atresia. The patient, a 10-month-old baby girl had dysmorphic facial features as well as neuromotor retardation, congenital hypothyroidism, atrial septal defect (ASD), white matter atrophy in cranial MRI, grade 2 dilatation in pelvicalyceal system of the left kidney, and bilateral ureteral reflux. In peripheral blood chromosome analysis 46, XX, dup(4) (q21q35) karyotype was detected. In FISH analysis using 4p/4q subtelomeric probe; 3 signals for 4 q region and 2 signals for 4p region were observed. In chromosome analyses of her healthy parents, no anomaly was detected. Herein we present a case of de novo partial distal trisomy 4q syndrome to contribute to the literature since it is rarely seen and this is the first patient with partial trisomy distal 4q syndrome presented with chronic cholecystitis and the second patient with hypothyroidism.

Evaluation of CHD7 as a candidate gene for choanal atresia in alpacas (Vicugna pacos).

Choanal atresia (CA) is a craniofacial malformation characterized by obstruction of the posterior nasal aperture, resulting in laborious respiratory inspiration and exhalation. Alpaca crias with CA typically develop fatal pneumonia, frequently as the result of milk aspiration during nursing, and euthanasia is usually inevitable. Nonsense or missense mutations in the CHD7 gene cause a comparable condition (CHARGE syndrome) in humans. In this study, the coding region of CHD7 was sequenced in six CA-affected alpacas. Forty-nine sequence variants were identified, of which 10 would result in amino acid changes (non-synonymous), some with potentially deleterious effects. However, none of the observed variants would result in the obvious deleterious effects caused by nonsense or missense mutations. Although a role for CHD7 mutations in CA cannot be definitively dismissed, these do not appear to be the primary cause of CA in alpacas.

[Unilateral choanal atresia: a missed diagnosis].

Bilateral choanal atresia is a congenital anomaly usually diagnosed at birth. In contrast, unilateral atresia causes variable degrees of nasal stuffiness and discharge that might mask the diagnosis and delay the proper treatment. We present five cases of unilateral atresia in which the correct diagnosis was delayed and erroneous treatments were instituted--two adults who had undergone unnecessary septal and turbinate surgery, two older children who were treated medically and one patient who was treated for epiphora. Insufficient awareness of this entity occurring in adults and older children and other possible causes of diagnostic error are discussed. A unilateral mucoid or watery rhinorrhea and obstruction, that lasts from early childhood without evidence of sinusitis and not responding to any medical treatment, should alert the physician to consider unilateral atresia and to perform endoscopic and computed tomography examinations at an early age. Careful interpretation of the computed tomography scan including the axial planes is required.

Atresia de coanas, tratamiento quirúrgico endoscópico, 5 años de experiencia / Choanal atresia, endoscopic surgical repair, a 5 year experience

Atresia de coanas es la obstrucción congénita de la región posterior de las fosas nasales. Múltiples técnicas quirúrgicas han sido empleadas para su reparación. En el presente estudio se recopiló la información de 5 años de trabajo en el Hospital Universitario del Valle en la ciudad Santiago de Cali - Colombia, entre los años 2003 y 2008. Se obtuvo un total de 16 casos.La información demográfica documentada incluyó datos como edad, sexo, síntomas iniciales, método diagnóstico, lateralidad, tipo de atresia de coanas, comorbilidades, tratamiento inicial, edad de intervención quirúrgica, técnica quirúrgica usada. La técnica quirúrgica consistió en el fresado y apertura de la placa atrésica vía endoscópica transnasal utilizando taladro, previa realización de colgajos mucosos en cruz y resecando parcialmente paredes del vómer.La experiencia observada en estos 5 años de trabajo demuestra que el abordaje endoscópico transnasal presenta grandes ventajas, entre ellas la baja tasa de reestenosis.

Choanal atresia is a congenital disorder where the back of the nasal passage is blocked. Many surgical techniques have been used to repair this disorder. In this study we collected information from 5 years of work at the Hospital Universitario del Valle in the city of Santiago de Cali - Colombia, between 2003 and 2008. A total of 16 cases were obtained. The documented data included demographic information like age, sex, initial symptoms, diagnostic methods, laterality, type of atresia, comorbilities, initial treatment and surgical technique used. The surgical technique consisted in endoscopic opening of the atretic plate using drill. Mucosal flaps and resection of partial plate of vomer were made previously.The experience observed in these 5 years of work shows that the endoscopic transnasal approach has major advantages, including low restenosis rate.

Tbx22null mice have a submucous cleft palate due to reduced palatal bone formation and also display ankyloglossia and choanal atresia phenotypes.

Craniofacial defects involving the lip and/or palate are among the most common human birth defects. X-linked cleft palate and ankyloglossia results from loss-of-function mutations in the gene encoding the T-box transcription factor TBX22. Further studies show that TBX22 mutations are also found in around 5% of non-syndromic cleft palate patients. Although palate defects are obvious at birth, the underlying developmental pathogenesis remains unclear. Here, we report a Tbx22(null) mouse, which has a submucous cleft palate (SMCP) and ankyloglossia, similar to the human phenotype, with a small minority showing overt clefts. We also find persistent oro-nasal membranes or, in some mice a partial rupture, resulting in choanal atresia. Each of these defects can cause severe breathing and/or feeding difficulties in the newborn pups, which results in approximately 50% post-natal lethality. Analysis of the craniofacial skeleton demonstrates a marked reduction in bone formation in the posterior hard palate, resulting in the classic notch associated with SMCP. Our results suggest that Tbx22 plays an important role in the osteogenic patterning of the posterior hard palate. Ossification is severely reduced after condensation of the palatal mesenchyme, resulting from a delay in the maturation of osteoblasts. Rather than having a major role in palatal shelf closure, we show that Tbx22 is an important determinant for intramembranous bone formation in the posterior hard palate, which underpins normal palate development and function. These findings could have important implications for the molecular diagnosis in patients with isolated SMCP and/or unexplained choanal atresia.

Nasal, septal, and turbinate anatomy and embryology.

This article discusses the development and anatomy of the nasal septum and structures of the lateral nasal wall. Emphasis is placed on anatomic variations associated with surgically correctable nasal obstruction. Common variations, such as deviated nasal septum, inferior turbinate hypertrophy, paradoxic middle turbinate, and concha bullosa, are discussed. Rare developmental causes of nasal obstruction are briefly outlined.

Abnormal basiocciput development in CHARGE syndrome.

BACKGROUND AND PURPOSE: The causative gene of the common congenital malformation referred to as CHARGE syndrome is CHD7. Affected individuals often undergo head and neck imaging to assess abnormalities of the olfactory structures, hypothalamus-pituitary axis, and inner ear. We encountered a few children with severe hypoplasia of the basiocciput during a radiologic assessment of patients with CHARGE syndrome. To our knowledge, this anomaly has not been reported. Our purpose was to evaluate the incidence and severity of this anomaly in this syndrome. MATERIALS AND METHODS: Sagittal MR images of 8 patients with CHARGE syndrome were retrospectively reviewed by 2 radiologists who consensually evaluated the status of the basiocciput of the patients with CHARGE syndrome, as either normal or hypoplastic; and associated anomalies, which include basilar invagination, Chiari type I malformation, and syringomyelia, as either present or absent. The length between the basion (Ba) and the endo-sphenobasion (Es) and between the basion and the exo-sphenobasion (Xs) was measured on midsagittal MR images of the 8 patients and 70 age-matched controls. We searched for trends related to age in the length of Ba-Es and Ba-Xs of the control children by using a matched t test. RESULTS: Basioccipital hypoplasia was identified in 7 of the 8 patients with CHARGE syndrome and was severe in 6. Of those, 5 had associated basilar invagination and 1 had Chiari type I malformation with syringomyelia. CONCLUSIONS: Basioccipital hypoplasia and basilar invagination are prevalent in patients with CHARGE syndrome.