Ferda Ozkinay

A comprehensive molecular study on Coffin–Siris and Nicolaides–Baraitser syndromes identifies a broad molecular and clinical spectrum converging on altered chromatin remodeling

Chromatin remodeling complexes are known to modify chemical marks on histones or to induce conformational changes in the chromatin in order to regulate transcription. De novo dominant mutations in different members of the SWI/SNF chromatin remodeling complex have recently been described in individuals with Coffin-Siris (CSS) and Nicolaides-Baraitser (NCBRS) syndromes. Using a combination of whole-exome sequencing, NGS-based sequencing of 23 SWI/SNF complex genes, and molecular karyotyping in 46 previously undescribed individuals with CSS and NCBRS, we identified a de novo 1-bp deletion (c.677delG, p.Gly226Glufs*53) and a de novo missense mutation (c.914G>T, p.Cys305Phe) in PHF6 in two individuals diagnosed with CSS. PHF6 interacts with the nucleosome remodeling and deacetylation (NuRD) complex implicating dysfunction of a second chromatin remodeling complex in the pathogenesis of CSS-like phenotypes. Altogether, we identified mutations in 60% of the studied individuals (28/46), located in the genes ARID1A, ARID1B, SMARCB1, SMARCE1, SMARCA2, and PHF6. We show that mutations in ARID1B are the main cause of CSS, accounting for 76% of identified mutations. ARID1B and SMARCB1 mutations were also found in individuals with the initial diagnosis of NCBRS. These individuals apparently belong to a small subset who display an intermediate CSS/NCBRS phenotype. Our proposed genotype-phenotype correlations are important for molecular screening strategies.

Loss of the BMP Antagonist, SMOC-1, Causes Ophthalmo-Acromelic (Waardenburg Anophthalmia) Syndrome in Humans and Mice

Ophthalmo-acromelic syndrome (OAS), also known as Waardenburg Anophthalmia syndrome, is defined by the combination of eye malformations, most commonly bilateral anophthalmia, with post-axial oligosyndactyly. Homozygosity mapping and subsequent targeted mutation analysis of a locus on 14q24.2 identified homozygous mutations in SMOC1 (SPARC-related modular calcium binding 1) in eight unrelated families. Four of these mutations are nonsense, two frame-shift, and two missense. The missense mutations are both in the second Thyroglobulin Type-1 (Tg1) domain of the protein. The orthologous gene in the mouse, Smoc1, shows site- and stage-specific expression during eye, limb, craniofacial, and somite development. We also report a targeted pre-conditional gene-trap mutation of Smoc1 (Smoc1tm1a) that reduces mRNA to ∼10% of wild-type levels. This gene-trap results in highly penetrant hindlimb post-axial oligosyndactyly in homozygous mutant animals (Smoc1tm1a/tm1a). Eye malformations, most commonly coloboma, and cleft palate occur in a significant proportion of Smoc1tm1a/tm1a embryos and pups. Thus partial loss of Smoc-1 results in a convincing phenocopy of the human disease. SMOC-1 is one of the two mammalian paralogs of Drosophila Pentagone, an inhibitor of decapentaplegic. The orthologous gene in Xenopus laevis, Smoc-1, also functions as a Bone Morphogenic Protein (BMP) antagonist in early embryogenesis. Loss of BMP antagonism during mammalian development provides a plausible explanation for both the limb and eye phenotype in humans and mice.

Testing the Psychosis Continuum: Differential Impact of Genetic and Nongenetic Risk Factors and Comorbid Psychopathology Across the Entire Spectrum of Psychosis

A growing number of studies demonstrate high rates of subthreshold psychotic experiences, but there is considerable heterogeneity in rates due to study cohort and design factors, obscuring how prevalent psychotic experiences may or may not relate to rare psychotic disorders. In a representative general population sample (n = 4011) in Izmir, Turkey, the full spectrum of expression of psychosis was categorized across 5 groups representing (1) absence of psychosis, (2) subclinical psychotic experiences, (3) low-impact psychotic symptoms, (4) high-impact psychotic symptoms, and (5) full-blown clinical psychotic disorder and analyzed for continuity and discontinuity in relation to (1) other symptom dimensions associated with psychotic disorder and (2) proxies of genetic and nongenetic etiology. Results were tested for linear and extralinear contrasts between clinical and nonclinical and between disorder and nondisorder expression of psychosis. Demographic variables, indexing premorbid social adjustment and socioeconomic status, impacted mostly linearly; proxy variables of genetic loading (more or more severely affected relatives) impacted in a positive extralinear fashion; environmental risk factors sometimes impacted linearly (urbanicity and childhood adversity) and sometimes extralinearly (cannabis), occasioning a disproportional shift in risk at the clinical disorder end of the spectrum. Affective symptoms were associated with a disproportionally higher risk below the disorder threshold, whereas a disproportionally higher risk above the threshold was associated with psychotic symptom load, negative symptoms, disorganization, and visible signs of mental illness. Liability associated with respectively affective and nonaffective symptom domains, in interaction with environmental risks, may operate by impacting differentially over a quasi-continuous extended psychosis phenotype in the population.

SMOC1 is essential for ocular and limb development in humans and mice.

Microphthalmia with limb anomalies (MLA) is a rare autosomal-recessive disorder, presenting with anophthalmia or microphthalmia and hand and/or foot malformation. We mapped the MLA locus to 14q24 and successfully identified three homozygous (one nonsense and two splice site) mutations in the SPARC (secreted protein acidic and rich in cysteine)-related modular calcium binding 1 (SMOC1) in three families. Smoc1 is expressed in the developing optic stalk, ventral optic cup, and limbs of mouse embryos. Smoc1 null mice recapitulated MLA phenotypes, including aplasia or hypoplasia of optic nerves, hypoplastic fibula and bowed tibia, and syndactyly in limbs. A thinned and irregular ganglion cell layer and atrophy of the anteroventral part of the retina were also observed. Soft tissue syndactyly, resulting from inhibited apoptosis, was related to disturbed expression of genes involved in BMP signaling in the interdigital mesenchyme. Our findings indicate that SMOC1/Smoc1 is essential for ocular and limb development in both humans and mice.

Lupus anticoagulant and protein S deficiency in otherwise healthy children with acute varicella infection

Acquired protein S deficiency and lupus anticoagulant have been described in children with varicella who had purpura fulminans, disseminated intravascular coagulation or thrombosis. The aim of this study was to investigate the natural anticoagulants, hypercoagulability markers, other parameters of coagulation and fibrinolytic systems, and the presence of the lupus anticoagulant in otherwise healthy children with acute varicella infection. Blood samples were obtained from 17 children with varicella without thrombosis during acute varicella infection and 1 mo after onset. Coagulation tests included determinations of the prothrombin time, the activated partial thromboplastin time, the thrombin time, the thrombin antithrombin complex, the prothrombin fragment F 1 + 2, the tissue plasminogen activator, the plasminogen activator inhibitor‐1, protein C activity and free protein S antigen. Antiphospholipid antibodies were determined in enzyme‐linked immunosorbent assays. The mean free protein S concentration in the acute phase (0.63 ±0.16U/ml) was significantly lower than that of the concentration determined 1 mo later (0.82 ± 0.17 U/ml). The children with acquired free protein S deficiency also had a lupus anticoagulant. Elevated concentrations of the prothrombin fragment F 1+2, the thrombin antithrombin complex, D‐Dimer, tissue plasminogen activator and plasminogen activator inhibitor‐1 were detected in most of the children.

Triple a Syndrome—Clinical Aspects and Molecular Genetics

The triple A syndrome or Allgrove syndrome (MIM*231550) is characterized by adrenocorticotropic hormone (ACTH) resistant Adrenal insufficiency, Achalasia of the cardia and Alacrima. In addition to the main features, patients frequently suffer from neurological disturbances. Dermatological abnormalities such as palmoplantar hyperkeratosis as well as other signs like short stature, microcephaly and osteoporosis point to the multisystemic character of the disorder. The molecular defect of the autosomal recessively inherited triple A syndrome is not known. We initially performed a systematic genome linkage scan in eight triple A families and were able to map the syndrome to a 6 cM interval on human chromosome 12q13 near the type II keratin gene cluster. A refinement of the triple A critical region was achieved by detailed haplotype analysis in a further 37 families from different ethnic backgrounds. There was no indication of genetic heterogeneity. The achalasia-alacrima (AA) syndrome which has been defined as a distinct clinical entity (MIM 200440) is most likely a variant of the triple A syndrome as shown by haplotype analysis in three AA families. We constructed a high-resolution BAC/PAC-based transcript map of the region which will greatly facilitate the identification of the triple A syndrome gene. The considerable intra- and interfamilial variability of the severity of the disorder implies a variable expression of an impaired pleiotropically acting gene.

The missing “link”: an autosomal recessive short stature syndrome caused by a hypofunctional XYLT1 mutation

Proteoglycan (PG) synthesis begins with the sequential addition of a “linker chain”, made up of four sugar residues, to a specific region of a core protein. Defects in the enzymes catalyzing steps two to four of the linker chain synthesis have been shown to cause autosomal recessive human phenotypes while no mutation has yet been reported in humans for the xylosyltransferases 1 and 2 (XT1 and XT2), the initiating enzymes in the linker chain formation. Here, we present a consanguineous Turkish family with two affected individuals presenting with short stature, distinct facial features, alterations of fat distribution, and moderate intellectual disability. X-rays showed only mild skeletal changes in the form of a short femoral neck, stocky and plump long bones and thickened ribs. Using a combination of whole-exome sequencing (WES), determination of homozygous stretches by WES variants, and classical linkage analysis, we identified the homozygous missense mutation c.C1441T in XYLT1, encoding XT1, within a large homozygous stretch on chromosome 16p13.12-p12.1. The mutation co-segregated with the phenotype in the family, is not found in over 13,000 alleles in the exome variant server and is predicted to change a highly conserved arginine at position 481 (p.R481W) located in the putative catalytical domain. Immunostaining of primary patient fibroblasts showed a loss of predominance of Golgi localization in mutant cells. Moreover, western blot analysis of decorin in cell culture supernatant demonstrated glycosylation differences between patient and control cells. Our data provide evidence that functional alterations of XT1 cause an autosomal recessive short stature syndrome associated with intellectual disability.

Cytogenetic abnormalities in 179 cases with male infertility in Western Region of Turkey: Report and review

PurposeIn this study we aimed to evaluate the postnatally screened karyotype results in couples who were referred because of primary infertility between 2000 and 2006 in Izmir.MethodsThe records of a total of 179 cases were evaluated retrospectively.ResultsA total of 21 cases (11.74%) showed chromosomal alteration. Thirteen (7.26%) were 47,XXY; three (1.68%) were pericentric inversion of chromosome 9; one (0.56%) 46,XY/45,XO; one (0.56%) 46,XY/47,XXY/48,XXXY; one (0.56%) 46,XY,t(X;1); one (0.56%) 46,XY/46,XY,del(Y)(q11.2) and one (0.56%) 46,XX.ConclusionsThe rate of gonosomal chromosomal abnormalities was nearly three times higher in our region than the rate in the literature. Chromosomal analysis is strongly suggested particularly in those who suffer fertility problems.

Complications of varicella in healthy children in Izmir, Turkey

Abstract Background : The purpose of the paper was to evaluate the indications of hospital admissions and complications of varicella infection in immunologically healthy children.

Febrile Seizures: Interleukin 1β and Interleukin-1 Receptor Antagonist Polymorphisms

In order to investigate the association between IL-1beta -511 C-->T and IL-1 receptor antagonist intron 2 variable tandem repeat polymorphisms, and febrile seizures in children, 90 children (mean age, 19.7 +/- 11.2 months) diagnosed with febrile seizure and 106 healthy controls (mean age, 14.2 +/- 3.6 months) with no seizure or neurologic events were included in the study. The polymorphisms were analyzed using restriction fragment length polymorphism and agarose gel electrophoresis methods. In the patient group, the frequencies of IL-1beta genotypes CC, CT, and TT were 24.4%, 52.2%, and 23.3%, respectively, compared with 38.7%, 50.95%, and 10.4%, respectively, in the control group. The TT genotype was significantly more common in the patient group than in the control group (P = 0.044), and the T allele frequency was significantly higher in the patient group (0.50 vs 0.36, P = 0.040). Among the three genotypes (RN1/1, RN1/2, and RN2/2) of the IL receptor antagonist gene variable tandem repeat polymorphisms, the frequency of both the RN2/2 genotype and the RN2 allele were significantly higher in the patient group (P = 0.007). Also RN2 allele frequency was found higher in patient group than controls (0.29 vs 0.15, P = 0.020). IL-1beta -511 and IL-1 receptor antagonist intron 2 variable tandem repeat polymorphisms may be involved in susceptibility to febrile convulsions in children.