Screening of 38 Genes Identifies Mutations in 62% of Families with Nonsyndromic Deafness in Turkey

More than 60% of prelingual deafness is genetic in origin, and of these up to 95% are monogenic autosomal recessive traits. Causal mutations have been identified in 1 of 38 different genes in a subset of patients with nonsyndromic autosomal recessive deafness. In this study, we screened 49 unrelated Turkish families with at least three affected children born to consanguineous parents. Probands from all families were negative for mutations in the GJB2 gene, two large deletions in the GJB6 gene, and the 1555A>G substitution in the mitochondrial DNA MTRNR1 gene. Each family was subsequently screened via autozygosity mapping with genomewide single-nucleotide polymorphism arrays. If the phenotype cosegregated with a haplotype flanking one of the 38 genes, mutation analysis of the gene was performed. We identified 22 different autozygous mutations in 11 genes, other than GJB2 , in 26 of 49 families, which overall explains deafness in 62% of families. Relative frequencies of genes following GJB2 were MYO15A (9.9%), TMIE (6.6%), TMC1 (6.6%), OTOF (5.0%), CDH23 (3.3%), MYO7A (3.3%), SLC26A4 (1.7%), PCDH15 (1.7%), LRTOMT (1.7%), SERPINB6 (1.7%), and TMPRSS3 (1.7%). Nineteen of 22 mutations are reported for the first time in this study. Unknown rare genes for deafness appear to be present in the remaining 23 families

Investigation of polymorphic variants of SLC6A4, TPH-1, and TPH-2 genes in cases of completed suicide

Background and objective: Serotonin plays an important role in the pathophysiology of aggressive behavior. Low serotonin levels and altered functions of serotonin receptors affect suicidal behavior. TPH-1, TPH-2 and SLC6A4 genes have important roles in serotonin production and degradation pathways. In this study, polymorphic variants of the TPH-1, TPH-2 and SLC6A4 genes, rs1800532, rs7305115, rs6355 and rs1386494, were investigated in 100 completed suicides and 100 healthy individuals. Materials and methods: After DNA isolation, a new polymerase chain reaction technology KASP TM (Competitive allele-specific polymerase chain reaction method), was used in the genotyping of the selected gene variants. Results: No statistically significant difference was found for the genotype and individual allele frequencies of the polymorphic variants between suicide and control groups, as well as between men and women in suicide cases. However, we observed non-significant tendencies of increased minor alleles in suicidal men for all TPH SNPs. Conclusions: More molecular genetic research studies are needed to understand the pathophysiology of suicide and to reveal its relationship with gender

Behcet's: A Disease or a Syndrome? Answer from an Expression Profiling Study

Behcet's disease (BD) is a chronic, relapsing, multisystemic inflammatory disorder with unanswered questions regarding its etiology/pathogenesis and classification. Distinct manifestation based subsets, pronounced geographical variations in expression, and discrepant immunological abnormalities raised the question whether Behcet's is "a disease or a syndrome". To answer the preceding question we aimed to display and compare the molecular mechanisms underlying distinct subsets of BD. For this purpose, the expression data of the gene expression profiling and association study on BD by Xavier et al (2013) was retrieved from GEO database and reanalysed by gene expression data analysis/visualization and bioinformatics enrichment tools. There were 15 BD patients (B) and 14 controls (C). Three subsets of BD patients were generated: MB (isolated mucocutaneous manifestations, n = 7), OB (ocular involvement, n = 4), and VB (large vein thrombosis, n = 4). Class comparison analyses yielded the following numbers of differentially expressed genes (DEGs); B vs C: 4, MB vs C: 5, OB vs C: 151, VB vs C: 274, MB vs OB: 215, MB vs VB: 760, OB vs VB: 984. Venn diagram analysis showed that there were no common DEGs in the intersection "MB vs C" boolean AND "OB vs C" boolean AND "VB vs C". Cluster analyses successfully clustered distinct expressions of BD. During gene ontology term enrichment analyses, categories with relevance to IL-8 production (MB vs C) and immune response to microorganisms (OB vs C) were differentially enriched. Distinct subsets of BD display distinct expression profiles and different disease associated pathways. Based on these clear discrepancies, the designation as "Behcet's syndrome" (BS) should be encouraged and future research should take into consideration the immunogenetic heterogeneity of BS subsets. Four gene groups, namely, negative regulators of inflammation (CD69, CLEC12A, CLEC12B, TNFAIP3), neutrophil granule proteins (LTF, OLFM4, AZU1, MMP8, DEFA4, CAMP), antigen processing and presentation proteins (CTSS, ERAP1), and regulators of immune response (LGALS2, BCL10, ITCH, CEACAM8, CD36, IL8, CCL4, EREG, NFKBIZ, CCR2, CD180, KLRC4, NFAT5) appear to be instrumental in BS immunopathogenesis

The effect of biological heterogeneity on R-CHOP treatment outcome in diffuse large B-cell lymphoma across five international regions

Addressing the global burden of cancer, understanding its diverse biology, and promoting appropriate prevention and treatment strategies around the world has become a priority for the United Nations and International Atomic Energy Agency (IAEA), the WHO, and International Agency for Research on Cancer (IARC). The IAEA sponsored an international prospective cohort study to better understand biology, treatment response, and outcomes of diffuse large B-cell lymphoma (DLBCL) in low and middle-income countries across five UN-defined geographical regions. We report an analysis of biological variation in DLBCL across seven ethnic and environmentally diverse populations. In this cohort of 136 patients treated to a common protocol, we demonstrate significant biological differences between countries, characterized by a validated prognostic gene expression score (p < .0001), but International Prognostic Index (IPI)-adjusted survivals in all participating countries were similar. We conclude that DLBCL treatment outcomes in these populations can be benchmarked to international standards, despite biological heterogeneity

Identification of a patient cohort with relapsing diffuse large b-cell lymphoma with a low international prognostic index in pet/ct using a 2-gene (lmo2/tnfrsf9) scoring system

Treating patients with diffuse large Bcell lymphoma (DLBCL) remains a challenge, with a remission rate of 75% at 2 years from diagnosis. The International Prognostic Index (IPI) [1] and molecularcharacterization [2] are employed in the stratification and relapse prediction. Additionally, 18F-fluorodeoxyglucose positron emission tomography (PET) and computed tomography (CT) have now become part of standard care in differentiating metabolic activity of the disease from fibrosisor necrosis [3]. Early optimism that the speed of response to treatment, as indicated by an interim-PET (iPET) scan after 2?3 cycles of chemotherapy, might reliably predict cure has not been fulfilled [4].To investigate the role of both an interim and an end-treatment-PET (ePET) scan for the management of DLBCL in an international setting, at a time when PET centers were becoming established globally, the International Atomic Energy Agency (IAEA) sponsored a study across 7 countries in Europe, South Asia, Southeast Asia, and South America [5]. This study, the largest study to date, found that 34% of cases were iPET+ after 2 or 3 cycles of standard chemotherapy (R-CHOP), but 54% of the iPET+ cases became ePET?; and that these ?slow responders? had relatively good outcomes at 2 years (event-free survival, EFS: 86%). Notably, the study found that by combining a negative iPET scan with 2 clinical components of the IPI (normal LDH and good performance status), it was possible to identify a population, 35% of all cases, 98% of whom were disease free 2 years after diagnosis. By contrast, iPET+ cases that remained PET+ at the end of treatment had dismal outcomes. These findings raisethe important question of how to separate slow-responding iPET+ cases who are PET? at the end treatment, who are destined for good survival, from those who will fail to achieve a complete or stable remission by continuing standard therapy.Fil: Omidvar, Nader. Cardiff University; Reino UnidoFil: Tekin, Nilgun. Ankara Üniversitesi; TurquíaFil: Conget, Paulette. Universidad del Desarrollo; ChileFil: Bruna, Flavia Alejandra. Universidad del Desarrollo; Chile. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Timar, Botond. Semmelweis Egyetem; HungríaFil: Gagyi, Eva. Semmelweis Egyetem; HungríaFil: Basak, Ranjan. Tata Memorial Hospital; IndiaFil: Auewarakul, Chirayu. Mahidol University; TailandiaFil: Sritana, Narongrit. Mahidol University; TailandiaFil: Cerci, Juliano Julio. Department of Nuclear Medicine, Quanta Diagnóstico e Terapia; BrasilFil: DImamay, Mark Pierre. St Luke's Medical Centre; FilipinasFil: Gyorke, Tamas. Semmelweis University; HungríaFil: Redondo, Francisca. Fundación Arturo López Pérez; ChileFil: Nair, Reena. Tata Memorial Hospital; IndiaFil: Gorospe, Charity. St Luke's Medical Centre; FilipinasFil: Paez, DIana. International Atomic Energy Agency; AustriaFil: Fanti, Stefano. Universidad de Bologna; ItaliaFil: Ozdag, Hilal. Ankara Üniversitesi; TurquíaFil: Padua, Rose Ann. Université Paris Diderot - Paris 7; FranciaFil: Carr, Robert. Guy’s and St. Thomas’ Hospital; Reino Unid

A novel approach for small sample size family-based association studies: sequential tests

In this paper, we propose a sequential probability ratio test (SPRT) to overcome the problem of limited samples in studies related to complex genetic diseases. The results of this novel approach are compared with the ones obtained from the traditional transmission disequilibrium test (TDT) on simulated data. Although TDT classifies single-nucleotide polymorphisms (SNPs) to only two groups (SNPs associated with the disease and the others), SPRT has the flexibility of assigning SNPs to a third group, that is, those for which we do not have enough evidence and should keep sampling. It is shown that SPRT results in smaller ratios of false positives and negatives, as well as better accuracy and sensitivity values for classifying SNPs when compared with TDT. By using SPRT, data with small sample size become usable for an accurate association analysis

Protocol for qRT-PCR analysis from formalin fixed paraffin embedded tissue sections from diffuse large b-cell lymphoma: Validation of the six-gene predictor score

As a part of an international study on the molecular analysis of Diffuse Large B-cell Lymphoma (DLBCL), a robust protocol for gene expression analysis from RNA extraction to qRT-PCR using Formalin Fixed Paraffin Embedded tissues was developed. Here a study was conducted to define a strategy to validate the previously reported 6-gene (LMO2, BCL6, FN1, CCND2, SCYA3 and BCL2) model as predictor of prognosis in DLBCL. To avoid variation, all samples were tested in a single centre and single platform. This study comprised 8 countries (Brazil, Chile, Hungary, India, Philippines, S. Korea, Thailand and Turkey). Using the Kaplan-Meier and log rank test on patients (n=162) and two mortality risk groups (with those above and below the mean representing high and low risk groups) confirmed that the 6-gene predictor score correlates significantly with overall survival (OS, p < 0.01) but not with event free survival (EFS, p=0.18). Adding the International Prognostic Index (IPI) shows that the 6-gene predictor score correlates significantly with high IPI scores for OS (p < 0.05), whereas those with low IPI scores show a trend not reaching significance (p=0.08). This study defined an effective and economical qRT-PCR strategy and validated the 6-gene score as a predictor of OS in an international setting.Fil: Tekin, Nilgun. Ankara University. Biotechology Institute; TurquíaFil: Omidvar, Nader. Cardiff University; Reino UnidoFil: Morris, Tim Peter. Clinical Trials Unit at University College. Medical Research Council; Reino UnidoFil: Conget, Paulette. Universidad del Desarrollo; ChileFil: Bruna, Flavia Alejandra. Universidad del Desarrollo; Chile. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Medicina y Biología Experimental de Cuyo; ArgentinaFil: Timar, Botond. Semmelweis University. Department of Pathology and Experimental Cancer Research; HungríaFil: Gagyi, Eva. Semmelweis University. Department of Pathology and Experimental Cancer Research; HungríaFil: Basak, Ranjan. Tata Memorial Hospital. Departments of Medical Oncology & Pathology; IndiaFil: Naik, Omkar. Tata Memorial Hospital. Departments of Medical Oncology & Pathology; IndiaFil: Auewarakul, Chirayu. Faculty of Medicine Sirira; Tailandia. Chulabhorn Cancer Centre; TailandiaFil: Sritana, Narongrit. Faculty of Medicine Sirira; Tailandia. Chulabhorn Cancer Centre; TailandiaFil: Levy, Debora. Chulabhorn Cancer Centre; Tailandia. Faculty of Medicine Sirira; TailandiaFil: Cerci, Juliano Julio. Department of Nuclear Medicine. Quanta - Diagnóstico e Terapia; BrasilFil: Bydlowski, Sergio Paulo. Universidade de Sao Paulo; BrasilFil: Pereira, Juliana. Universidade de Sao Paulo; BrasilFil: Dimamay, Mark Pierre. St. Lukes Medical. Research and Biotechnology Division; FilipinasFil: Natividad, Filipinas. St. Lukes Medical. Research and Biotechnology Division; FilipinasFil: Chung, June-Key. Seoul National University Hospital. Department of Nuclear Medicine; Corea del SurFil: Belder, Nevin. Ankara University. Biotechology Institute; TurquíaFil: Kuzu, Isinsu. Ankara University. Faculty of Medicina; TurquíaFil: Paez, Diana. International Atomic Energy Agency; AustriaFil: Dondi, Maurizio. International Atomic Energy Agency; AustriaFil: Carr, Robert. King’s College. Guy’s & St Thomas’ Hospital; Reino UnidoFil: Ozdag, Hilal. Ankara University. Faculty of Medicina; TurquíaFil: Padua, Rose Ann. Institut National de la Sante Et de la Recherche Médica; Francia. Université Paris-Diderot; Francia. Institut Universitaire d'Hématologie; Franci

Disruption of ALX1 Causes Extreme Microphthalmia and Severe Facial Clefting: Expanding the Spectrum of Autosomal-Recessive ALX-Related Frontonasal Dysplasia

We present an autosomal-recessive frontonasal dysplasia (FND) characterized by bilateral extreme microphthalmia, bilateral oblique facial cleft, complete cleft palate, hypertelorism, wide nasal bridge with hypoplasia of the ala nasi, and low-set, posteriorly rotated ears in two distinct families. Using Affymetrix 250K SNP array genotyping and homozygosity mapping, we mapped this clinical entity to chromosome 12q21. In one of the families, three siblings were affected, and CNV analysis of the critical region showed a homozygous 3.7 Mb deletion containing the ALX1 (CART1) gene, which encodes the aristaless-like homeobox 1 transcription factor. In the second family we identified a homozygous donor-splice-site mutation (c.531+1G > A) in the ALX1 gene, providing evidence that complete loss of function of ALX1 protein causes severe disruption of early craniofacial development. Unlike loss of its murine ortholog, loss of human ALX1 does not result in neural-tube defects; however, it does severely affect the orchestrated fusion between frontonasal, nasomedial, nasolateral, and maxillary processes during early-stage embryogenesis. This study further expands the spectrum of the recently recognized autosomal-recessive ALX-related FND phenotype in humans

Functionally Conserved Effects of Rapamycin Exposure on Zebrafish

Mechanistic target of rapamycin (mTOR) is a conserved serine/threonine kinase important in cell proliferation, growth and protein translation. Rapamycin, a well‑known anti‑cancer agent and immunosuppressant drug, inhibits mTOR activity in different taxa including zebrafish. In the present study, the effect of rapamycin exposure on the transcriptome of a zebrafish fibroblast cell line, ZF4, was investigated. Microarray analysis demonstrated that rapamycin treatment modulated a large set of genes with varying functions including protein synthesis, assembly of mitochondrial and proteasomal machinery, cell cycle, metabolism and oxidative phosphorylation in ZF4 cells. A mild however, coordinated reduction in the expression of proteasomal and mitochondrial ribosomal subunits was detected, while the expression of numerous ribosomal subunits increased. Meta‑analysis of heterogeneous mouse rapamycin microarray datasets enabled the comparison of zebrafish and mouse pathways modulated by rapamycin, using Kyoto Encyclopedia of Genes and Genomes and Gene Ontology pathway analysis. The analyses demonstrated a high degree of functional conservation between zebrafish and mice in response to rapamycin. In addition, rapamycin treatment resulted in a marked dose‑dependent reduction in body size and pigmentation in zebrafish embryos. The present study is the first, to the best of our knowledge, to evaluate the conservation of rapamycin‑modulated functional pathways between zebrafish and mice, in addition to the dose‑dependent growth curves of zebrafish embryos upon rapamycin exposure.Scopu